pdb id class method authors reference annotation
10mh transferase-DNA X-ray (2.55 Å) Sheikhnejad G, Brank A, Christman JK, Goddard A, Alvarez E, Ford Jr H, Marquez VE, Marasco CJ, Sufrin JR, O'gara M, Cheng X (1999) "Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine." J.Mol.Biol., 285, 2021-2034. doi: 10.1006/jmbi.1998.2426. Ternary structure of hhai methyltransferase with adohcy and hemimethylated DNA containing 5,6-dihydro-5-azacytosine at the target. SNAP output
173d DNA-antibiotic X-ray (3.0 Å) Kamitori S, Takusagawa F (1994) "Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2-Actinomycin D Complexes and its Host DNA." J.Am.Chem.Soc., 116, 4154. doi: 10.1021/JA00089A002. Multiple binding modes of anticancer drug actinomycin d: x-ray, molecular modeling, and spectroscopic studies of d(gaagcttc)2-actinomycin d complexes and its host DNA. SNAP output
185d DNA-antibiotic NMR Addess KJ, Feigon J (1994) "Sequence Specificity of Quinoxaline Antibiotics. 1. Solution Structure of a 1:1 Complex between Triostin a and [D(Gacgtc)]2 and Comparison with the Solution Structure of the [N-Mecys3,N-Mecys7]Tandem-[D(Gatatc)]2 Complex." Biochemistry, 33, 12386. doi: 10.1021/BI00207A005. Sequence specificity of quinoxaline antibiotics. 1. solution structure of a 1:1 complex between triostin a and [d(gacgtc)]2 and comparison with the solution structure of the [n-mecys3, n-mecys7]tandem-[d(gatatc)]2 complex. SNAP output
193d DNA-antibiotic NMR Chen H, Patel DJ (1995) "Solution Structure of a Quinomycin Bisintercalator-DNA Complex." J.Mol.Biol., 246, 164. doi: 10.1006/JMBI.1994.0074. Solution structure of a quinomycin bisintercalator-DNA complex. SNAP output
1a02 transcription-DNA X-ray (2.7 Å) Chen L, Glover JN, Hogan PG, Rao A, Harrison SC (1998) "Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA." Nature, 392, 42-48. doi: 10.1038/32100. Structure of the DNA binding domains of nfat, fos and jun bound to DNA. SNAP output
1a0a transcription-DNA X-ray (2.8 Å) Shimizu T, Toumoto A, Ihara K, Shimizu M, Kyogoku Y, Ogawa N, Oshima Y, Hakoshima T (1997) "Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition." EMBO J., 16, 4689-4697. doi: 10.1093/emboj/16.15.4689. Phosphate system positive regulatory protein pho4-DNA complex. SNAP output
1a1f transcription-DNA X-ray (2.1 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Dsnr (zif268 variant) zinc finger-DNA complex (gacc site). SNAP output
1a1g transcription-DNA X-ray (1.9 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Dsnr (zif268 variant) zinc finger-DNA complex (gcgt site). SNAP output
1a1h transcription-DNA X-ray (1.6 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Qgsr (zif268 variant) zinc finger-DNA complex (gcac site). SNAP output
1a1i transcription-DNA X-ray (1.6 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Radr (zif268 variant) zinc finger-DNA complex (gcac site). SNAP output
1a1j transcription-DNA X-ray (2.0 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Radr (zif268 variant) zinc finger-DNA complex (gcgt site). SNAP output
1a1k transcription-DNA X-ray (1.9 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Radr (zif268 variant) zinc finger-DNA complex (gacc site). SNAP output
1a1l transcription-DNA X-ray (2.3 Å) Elrod-Erickson M, Benson TE, Pabo CO (1998) "High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition." Structure, 6, 451-464. doi: 10.1016/S0969-2126(98)00047-1. Zif268 zinc finger-DNA complex (gcac site). SNAP output
1a1v hydrolase-DNA X-ray (2.2 Å) Kim JL, Morgenstern KA, Griffith JP, Dwyer MD, Thomson JA, Murcko MA, Lin C, Caron PR (1998) "Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding." Structure, 6, 89-100. doi: 10.1016/S0969-2126(98)00010-0. Hepatitis c virus ns3 helicase domain complexed with single stranded sDNA. SNAP output
1a31 isomerase-DNA X-ray (2.1 Å) Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol WG (1998) "Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA." Science, 279, 1504-1513. doi: 10.1126/science.279.5356.1504. Human reconstituted DNA topoisomerase i in covalent complex with a 22 base pair DNA duplex. SNAP output
1a35 isomerase-DNA X-ray (2.5 Å) Redinbo MR, Stewart L, Kuhn P, Champoux JJ, Hol WG (1998) "Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA." Science, 279, 1504-1513. doi: 10.1126/science.279.5356.1504. Human topoisomerase i-DNA complex. SNAP output
1a36 isomerase-DNA X-ray (2.8 Å) Stewart L, Redinbo MR, Qiu X, Hol WG, Champoux JJ (1998) "A model for the mechanism of human topoisomerase I." Science, 279, 1534-1541. doi: 10.1126/science.279.5356.1534. Topoisomerase i-DNA complex. SNAP output
1a3q transcription-DNA X-ray (2.1 Å) Cramer P, Larson CJ, Verdine GL, Muller CW (1997) "Structure of the human NF-kappaB p52 homodimer-DNA complex at 2.1 A resolution." EMBO J., 16, 7078-7090. doi: 10.1093/emboj/16.23.7078. Human nf-kappa-b p52 bound to DNA. SNAP output
1a66 transcription-DNA NMR Zhou P, Sun LJ, Dotsch V, Wagner G, Verdine GL (1998) "Solution structure of the core NFATC1/DNA complex." Cell(Cambridge,Mass.), 92, 687-696. doi: 10.1016/S0092-8674(00)81136-8. Solution NMR structure of the core nfatc1-DNA complex, 18 structures. SNAP output
1a6b viral protein-DNA NMR Schuler W, Dong C, Wecker K, Roques BP (1999) "NMR structure of the complex between the zinc finger protein NCp10 of Moloney murine leukemia virus and the single-stranded pentanucleotide d(ACGCC): comparison with HIV-NCp7 complexes." Biochemistry, 38, 12984-12994. doi: 10.1021/bi990378d. NMR structure of the complex between the zinc finger protein ncp10 of moloney murine leukemia virus and a sequence of the psi-packaging domain of hiv-1, 20 structures. SNAP output
1a6y transcription-DNA X-ray (2.3 Å) Zhao Q, Khorasanizadeh S, Miyoshi Y, Lazar MA, Rastinejad F (1998) "Structural elements of an orphan nuclear receptor-DNA complex." Mol.Cell, 1, 849-861. doi: 10.1016/S1097-2765(00)80084-2. Reverba orphan nuclear receptor-DNA complex. SNAP output
1a73 hydrolase-DNA X-ray (1.8 Å) Flick KE, Jurica MS, Monnat Jr RJ, Stoddard BL (1998) "DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI." Nature, 394, 96-101. doi: 10.1038/27952. Intron-encoded endonuclease i-ppoi complexed with DNA. SNAP output
1a74 hydrolase-DNA X-ray (2.2 Å) Flick KE, Jurica MS, Monnat Jr RJ, Stoddard BL (1998) "DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI." Nature, 394, 96-101. doi: 10.1038/27952. I-ppol homing endonuclease-DNA complex. SNAP output
1aay transcription-DNA X-ray (1.6 Å) Elrod-Erickson M, Rould MA, Nekludova L, Pabo CO (1996) "Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions." Structure, 4, 1171-1180. doi: 10.1016/S0969-2126(96)00125-6. Zif268 zinc finger-DNA complex. SNAP output
1ahd DNA binding protein-DNA NMR Billeter M, Qian YQ, Otting G, Muller M, Gehring W, Wuthrich K (1993) "Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex." J.Mol.Biol., 234, 1084-1097. doi: 10.1006/jmbi.1993.1661. Determination of the NMR solution structure of an antennapedia homeodomain-DNA complex. SNAP output
1ais transcription-DNA X-ray (2.1 Å) Kosa PF, Ghosh G, DeDecker BS, Sigler PB (1997) "The 2.1-A crystal structure of an archaeal preinitiation complex: TATA-box-binding protein/transcription factor (II)B core/TATA-box." Proc.Natl.Acad.Sci.USA, 94, 6042-6047. doi: 10.1073/pnas.94.12.6042. Tata-binding protein-transcription factor (ii)b-tata-box complex from pyrococcus woesei. SNAP output
1akh DNA binding protein-DNA X-ray (2.5 Å) Li T, Jin Y, Vershon AK, Wolberger C (1998) "Crystal structure of the MATa1/MATalpha2 homeodomain heterodimer in complex with DNA containing an A-tract." Nucleic Acids Res., 26, 5707-5718. doi: 10.1093/nar/26.24.5707. Mat a1-alpha2-DNA ternary complex. SNAP output
1am9 transcription-DNA X-ray (2.3 Å) Parraga A, Bellsolell L, Ferre-D'Amare AR, Burley SK (1998) "Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution." Structure, 6, 661-672. doi: 10.1016/S0969-2126(98)00067-7. Human srebp-1a bound to ldl receptor promoter. SNAP output
1an2 transcription-DNA X-ray (2.9 Å) Ferre-D'Amare AR, Prendergast GC, Ziff EB, Burley SK (1993) "Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain." Nature, 363, 38-45. doi: 10.1038/363038a0. Recognition by max of its cognate DNA through a dimeric b-hlh-z domain. SNAP output
1an4 transcription-DNA X-ray (2.9 Å) Ferre-D'Amare AR, Pognonec P, Roeder RG, Burley SK (1994) "Structure and function of the b/HLH/Z domain of USF." EMBO J., 13, 180-189. Structure and function of the b-hlh-z domain of usf. SNAP output
1aoi DNA binding protein-DNA X-ray (2.8 Å) Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) "Crystal structure of the nucleosome core particle at 2.8 A resolution." Nature, 389, 251-260. doi: 10.1038/38444. Complex between nucleosome core particle (h3,h4,h2a,h2b) and 146 bp long DNA fragment. SNAP output
1apl DNA binding protein-DNA X-ray (2.7 Å) Wolberger C, Vershon AK, Liu B, Johnson AD, Pabo CO (1991) "Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions." Cell(Cambridge,Mass.), 67, 517-528. doi: 10.1016/0092-8674(91)90526-5. Crystal structure of a mat-alpha2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. SNAP output
1au7 transcription-DNA X-ray (2.3 Å) Jacobson EM, Li P, Leon-del-Rio A, Rosenfeld MG, Aggarwal AK (1997) "Structure of Pit-1 POU domain bound to DNA as a dimer: unexpected arrangement and flexibility." Genes Dev., 11, 198-212. Pit-1 mutant-DNA complex. SNAP output
1awc transcription-DNA X-ray (2.15 Å) Batchelor AH, Piper DE, de la Brousse FC, McKnight SL, Wolberger C (1998) "The structure of GABPalpha/beta: an ETS domain- ankyrin repeat heterodimer bound to DNA." Science, 279, 1037-1041. doi: 10.1126/science.279.5353.1037. Mouse gabp alpha-beta domain bound to DNA. SNAP output
1az0 hydrolase-DNA X-ray (2.0 Å) Perona JJ, Martin AM (1997) "Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis." J.Mol.Biol., 273, 207-225. doi: 10.1006/jmbi.1997.1315. Ecorv endonuclease-DNA complex. SNAP output
1azp DNA binding protein-DNA X-ray (1.6 Å) Robinson H, Gao YG, McCrary BS, Edmondson SP, Shriver JW, Wang AH (1998) "The hyperthermophile chromosomal protein Sac7d sharply kinks DNA." Nature, 392, 202-205. doi: 10.1038/32455. Hyperthermophile chromosomal protein sac7d bound with kinked DNA duplex. SNAP output
1azq DNA binding protein-DNA X-ray (1.94 Å) Robinson H, Gao YG, McCrary BS, Edmondson SP, Shriver JW, Wang AH (1998) "The hyperthermophile chromosomal protein Sac7d sharply kinks DNA." Nature, 392, 202-205. doi: 10.1038/32455. Hyperthermophile chromosomal protein sac7d bound with kinked DNA duplex. SNAP output
1b01 gene regulation-DNA X-ray (2.56 Å) Gomis-Ruth FX, Sola M, Acebo P, Parraga A, Guasch A, Eritja R, Gonzalez A, Espinosa M, del Solar G, Coll M (1998) "The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator." EMBO J., 17, 7404-7415. doi: 10.1093/emboj/17.24.7404. Transcriptional repressor copg-DNA complex. SNAP output
1b3t protein-DNA X-ray (2.2 Å) Bochkarev A, Bochkareva E, Frappier L, Edwards AM (1998) "The 2.2 A structure of a permanganate-sensitive DNA site bound by the Epstein-Barr virus origin binding protein, EBNA1." J.Mol.Biol., 284, 1273-1278. doi: 10.1006/jmbi.1998.2247. Ebna-1 nuclear protein-DNA complex. SNAP output
1b69 integrase-DNA NMR Wojciak JM, Connolly KM, Clubb RT (1999) "NMR structure of the Tn916 integrase-DNA complex." Nat.Struct.Biol., 6, 366-373. doi: 10.1038/7603. The solution structure of tn916 integrase n-terminal domain-DNA complex. SNAP output
1b72 protein-DNA X-ray (2.35 Å) Piper DE, Batchelor AH, Chang CP, Cleary ML, Wolberger C (1999) "Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation." Cell(Cambridge,Mass.), 96, 587-597. doi: 10.1016/S0092-8674(00)80662-5. Pbx1, homeobox protein hox-b1-DNA ternary complex. SNAP output
1b8i transcription-DNA X-ray (2.4 Å) Passner JM, Ryoo HD, Shen L, Mann RS, Aggarwal AK (1999) "Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex." Nature, 397, 714-719. doi: 10.1038/17833. Structure of the homeotic ubx-exd-DNA ternary complex. SNAP output
1b94 hydrolase-DNA X-ray (1.9 Å) Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin GS (1999) "Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group." Nucleic Acids Res., 27, 3438-3445. doi: 10.1093/nar/27.17.3438. Restriction endonuclease ecorv with calcium. SNAP output
1b95 hydrolase-DNA X-ray (2.05 Å) Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin GS (1999) "Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group." Nucleic Acids Res., 27, 3438-3445. doi: 10.1093/nar/27.17.3438. Analysis of a mutational hot-spot in the ecorv restriction endonuclease: a catalytic role for a main chain carbonyl group. SNAP output
1b96 hydrolase-DNA X-ray (2.3 Å) Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin GS (1999) "Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group." Nucleic Acids Res., 27, 3438-3445. doi: 10.1093/nar/27.17.3438. Analysis of a mutational hot-spot in the ecorv restriction endonuclease: a catalytic role for a main chain carbonyl group. SNAP output
1b97 hydrolase-DNA X-ray (1.9 Å) Thomas MP, Brady RL, Halford SE, Sessions RB, Baldwin GS (1999) "Structural analysis of a mutational hot-spot in the EcoRV restriction endonuclease: a catalytic role for a main chain carbonyl group." Nucleic Acids Res., 27, 3438-3445. doi: 10.1093/nar/27.17.3438. Analysis of a mutational hot-spot in the ecorv restriction endonuclease: a catalytic role for a main chain carbonyl group. SNAP output
1bbx DNA binding protein-DNA NMR Agback P, Baumann H, Knapp S, Ladenstein R, Hard T (1998) "Architecture of Nonspecific Protein-DNA Interactions in the Sso7D-DNA Complex." Nat.Struct.Biol., 5, 579-584. doi: 10.1038/836. Non-specific protein-DNA interactions in the sso7d-DNA complex, NMR, 1 structure. SNAP output
1bc7 transcription-DNA X-ray (2.01 Å) Mo Y, Vaessen B, Johnston K, Marmorstein R (1998) "Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: insights into DNA sequence discrimination by Ets proteins." Mol.Cell, 2, 201-212. doi: 10.1016/S1097-2765(00)80130-6. Serum response factor accessory protein 1a (sap-1)-DNA complex. SNAP output
1bc8 transcription-DNA X-ray (1.93 Å) Mo Y, Vaessen B, Johnston K, Marmorstein R (1998) "Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: insights into DNA sequence discrimination by Ets proteins." Mol.Cell, 2, 201-212. doi: 10.1016/S1097-2765(00)80130-6. Structures of sap-1 bound to DNA sequences from the e74 and c-fos promoters provide insights into how ets proteins discriminate between related DNA targets. SNAP output
1bdh transcription-DNA X-ray (2.7 Å) Glasfeld A, Schumacher MA, Choi KY, Zalkin H, Brennan RG (1996) "A Positively Charged Residue Bound in the Minor Groove Does not Alter the Bending of a DNA Duplex." J.Am.Chem.Soc., 118, 13073-13074. Purine repressor mutant-hypoxanthine-palindromic operator complex. SNAP output
1bdi transcription-DNA X-ray (3.0 Å) Glasfeld A, Schumacher MA, Choi KY, Zalkin H, Brennan RG (1996) "A Positively Charged Residue Bound in the Minor Groove Does not Alter the Bending of a DNA Duplex." J.Am.Chem.Soc., 118, 13073-13074. Purine repressor mutant-hypoxanthine-palindromic operator complex. SNAP output
1bdt gene regulation-DNA X-ray (2.5 Å) Schildbach JF, Karzai AW, Raumann BE, Sauer RT (1999) "Origins of DNA-binding specificity: role of protein contacts with the DNA backbone." Proc.Natl.Acad.Sci.USA, 96, 811-817. doi: 10.1073/pnas.96.3.811. Wild type gene-regulating protein arc-DNA complex. SNAP output
1bdv gene regulation-DNA X-ray (2.8 Å) Schildbach JF, Karzai AW, Raumann BE, Sauer RT (1999) "Origins of DNA-binding specificity: role of protein contacts with the DNA backbone." Proc.Natl.Acad.Sci.USA, 96, 811-817. doi: 10.1073/pnas.96.3.811. Arc fv10 cocrystal. SNAP output
1bf4 DNA-binding protein-DNA X-ray (1.6 Å) Gao YG, Su SY, Robinson H, Padmanabhan S, Lim L, McCrary BS, Edmondson SP, Shriver JW, Wang AH (1998) "The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA." Nat.Struct.Biol., 5, 782-786. doi: 10.1038/1822. Chromosomal DNA-binding protein sso7d-d(gcgaacgc) complex. SNAP output
1bf5 gene regulation-DNA X-ray (2.9 Å) Chen X, Vinkemeier U, Zhao Y, Jeruzalmi D, Darnell Jr JE, Kuriyan J (1998) "Crystal structure of a tyrosine phosphorylated STAT-1 dimer bound to DNA." Cell(Cambridge,Mass.), 93, 827-839. doi: 10.1016/S0092-8674(00)81443-9. Tyrosine phosphorylated stat-1-DNA complex. SNAP output
1bg1 transcription-DNA X-ray (2.25 Å) Becker S, Groner B, Muller CW (1998) "Three-dimensional structure of the Stat3beta homodimer bound to DNA." Nature, 394, 145-151. doi: 10.1038/28101. Transcription factor stat3b-DNA complex. SNAP output
1bgb hydrolase-DNA X-ray (2.0 Å) Horton NC, Perona JJ (1998) "Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts." J.Biol.Chem., 273, 21721-21729. doi: 10.1074/jbc.273.34.21721. Ecorv endonuclease complex with 5'-cgggatatccc DNA. SNAP output
1bhm hydrolase-DNA X-ray (2.2 Å) Newman M, Strzelecka T, Dorner LF, Schildkraut I, Aggarwal AK (1995) "Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding." Science, 269, 656-663. Restriction endonuclease bamhi complex with DNA. SNAP output
1bj6 viral protein-DNA NMR Morellet N, Demene H, Teilleux V, Huynh-Dinh T, de Rocquigny H, Fournie-Zaluski MC, Roques BP (1998) "Structure of the complex between the HIV-1 nucleocapsid protein NCp7 and the single-stranded pentanucleotide d(ACGCC)." J.Mol.Biol., 283, 419-434. doi: 10.1006/jmbi.1998.2098. 1h NMR of (12-53) ncp7-d(acgcc) complex, 10 structures. SNAP output
1bl0 transcription-DNA X-ray (2.3 Å) Rhee S, Martin RG, Rosner JL, Davies DR (1998) "A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator." Proc.Natl.Acad.Sci.USA, 95, 10413-10418. doi: 10.1073/pnas.95.18.10413. Multiple antibiotic resistance protein (mara)-DNA complex. SNAP output
1bnk hydrolase-DNA X-ray (2.7 Å) Lau AY, Scharer OD, Samson L, Verdine GL, Ellenberger T (1998) "Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision." Cell(Cambridge,Mass.), 95, 249-258. doi: 10.1016/S0092-8674(00)81755-9. Human 3-methyladenine DNA glycosylase complexed to DNA. SNAP output
1bnz DNA binding protein-DNA X-ray (2.0 Å) Gao YG, Su SY, Robinson H, Padmanabhan S, Lim L, McCrary BS, Edmondson SP, Shriver JW, Wang AH (1998) "The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA." Nat.Struct.Biol., 5, 782-786. doi: 10.1038/1822. Sso7d hyperthermophile protein-DNA complex. SNAP output
1bp7 transcription-DNA X-ray (3.0 Å) Jurica MS, Monnat Jr RJ, Stoddard BL (1998) "DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI." Mol.Cell, 2, 469-476. doi: 10.1016/S1097-2765(00)80146-X. Group i mobile intron endonuclease i-crei complexed with homing site DNA. SNAP output
1bpx transferase-DNA X-ray (2.4 Å) Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H (1997) "Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism." Biochemistry, 36, 11205-11215. doi: 10.1021/bi9703812. DNA polymerase beta-DNA complex. SNAP output
1bpy transferase-DNA X-ray (2.2 Å) Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H (1997) "Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism." Biochemistry, 36, 11205-11215. doi: 10.1021/bi9703812. Human DNA polymerase beta complexed with gapped DNA and ddctp. SNAP output
1bpz transferase-DNA X-ray (2.6 Å) Sawaya MR, Prasad R, Wilson SH, Kraut J, Pelletier H (1997) "Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism." Biochemistry, 36, 11205-11215. doi: 10.1021/bi9703812. Human DNA polymerase beta complexed with nicked DNA. SNAP output
1brn hydrolase-DNA X-ray (1.76 Å) Buckle AM, Fersht AR (1994) "Subsite binding in an RNase: structure of a barnase-tetranucleotide complex at 1.76-A resolution." Biochemistry, 33, 1644-1653. doi: 10.1021/bi00173a005. Subsite binding in an rnase: structure of a barnase-tetranucleotide complex at 1.76 angstroms resolution. SNAP output
1bss hydrolase-DNA X-ray (2.15 Å) Horton NC, Newberry KJ, Perona JJ (1998) "Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases." Proc.Natl.Acad.Sci.USA, 95, 13489-13494. doi: 10.1073/pnas.95.23.13489. Ecorv-t93a-DNA-ca2+. SNAP output
1bsu hydrolase-DNA X-ray (2.0 Å) Martin AM, Sam MD, Reich NO, Perona JJ (1999) "Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease." Nat.Struct.Biol., 6, 269-277. doi: 10.1038/6707. Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease. SNAP output
1bua hydrolase-DNA X-ray (2.15 Å) Martin AM, Sam MD, Reich NO, Perona JJ (1999) "Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease." Nat.Struct.Biol., 6, 269-276. doi: 10.1038/6707. Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease. SNAP output
1bvo complex (transcription factor-DNA) X-ray (2.7 Å) Cramer P, Varrot A, Barillas-Mury C, Kafatos FC, Muller CW (1999) "Structure of the specificity domain of the Dorsal homologue Gambif1 bound to DNA." Structure Fold.Des., 7, 841-852. doi: 10.1016/S0969-2126(99)80107-5. Dorsal homologue gambif1 bound to DNA. SNAP output
1by4 gene regulation-DNA X-ray (2.1 Å) Zhao Q, Chasse SA, Devarakonda S, Sierk ML, Ahvazi B, Rastinejad F (2000) "Structural basis of RXR-DNA interactions." J.Mol.Biol., 296, 509-520. doi: 10.1006/jmbi.1999.3457. Structure and mechanism of the homodimeric assembly of the rxr on DNA. SNAP output
1c0w gene regulation-DNA X-ray (3.2 Å) Pohl E, Holmes RK, Hol WG (1999) "Crystal structure of a cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal-binding SH3-like domain." J.Mol.Biol., 292, 653-667. doi: 10.1006/jmbi.1999.3073. Crystal structure of the cobalt-activated diphtheria toxin repressor-DNA complex reveals a metal binding sh-like domain. SNAP output
1c7u transcription-DNA NMR Huang K, Louis JM, Donaldson L, Lim FL, Sharrocks AD, Clore GM (2000) "Solution structure of the MEF2A-DNA complex: structural basis for the modulation of DNA bending and specificity by MADS-box transcription factors." Embo J., 19, 2615-2628. doi: 10.1093/emboj/19.11.2615. Complex of the DNA binding core domain of the transcription factor mef2a with a 20mer oligonucleotide. SNAP output
1c7y recombination-DNA X-ray (3.1 Å) Ariyoshi M, Nishino T, Iwasaki H, Shinagawa H, Morikawa K (2000) "Crystal structure of the holliday junction DNA in complex with a single RuvA tetramer." Proc.Natl.Acad.Sci.USA, 97, 8257-8262. doi: 10.1073/pnas.140212997. E.coli ruva-holliday junction complex. SNAP output
1c8c DNA binding protein-DNA X-ray (1.45 Å) Su S, Gao YG, Robinson H, Liaw YC, Edmondson SP, Shriver JW, Wang AH (2000) "Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs." J.Mol.Biol., 303, 395-403. doi: 10.1006/jmbi.2000.4112. Crystal structures of the chromosomal proteins sso7d-sac7d bound to DNA containing t-g mismatched base pairs. SNAP output
1c9b transcription-DNA X-ray (2.65 Å) Tsai FT, Sigler PB (2000) "Structural basis of preinitiation complex assembly on human pol II promoters." EMBO J., 19, 25-36. doi: 10.1093/emboj/19.1.25. Crystal structure of a human tbp core domain-human tfiib core domain complex bound to an extended, modified adenoviral major late promoter (admlp). SNAP output
1ca5 structural protein-DNA X-ray (2.2 Å) Su S, Gao Y-G, Robinson H, Liaw YC, Edmondson SP, Shriver JW, Wang AH-J (2000) "Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs." J.Mol.Biol., 303, 395-403. doi: 10.1006/jmbi.2000.4112. Intercalation site of hyperthermophile chromosomal protein sso7d-sac7d bound to DNA. SNAP output
1ca6 structural protein-DNA X-ray (2.2 Å) Su S, Gao Y-G, Robinson H, Liaw YC, Edmondson SP, Shriver JW, Wang AH-J (2000) "Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs." J.Mol.Biol., 303, 395-403. doi: 10.1006/jmbi.2000.4112. Intercalation site of hyperthermophile chromosomal protein sso7d-sac7d bound to DNA. SNAP output
1cbv immune system-DNA X-ray (2.66 Å) Herron JN, He XM, Ballard DW, Blier PR, Pace PE, Bothwell AL, Voss Jr EW, Edmundson AB (1991) "An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex." Proteins, 11, 159-175. doi: 10.1002/prot.340110302. An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded fab and a deoxynucleotide-fab complex. SNAP output
1cdw transcription-DNA X-ray (1.9 Å) Nikolov DB, Chen H, Halay ED, Hoffman A, Roeder RG, Burley SK (1996) "Crystal structure of a human TATA box-binding protein/TATA element complex." Proc.Natl.Acad.Sci.USA, 93, 4862-4867. doi: 10.1073/pnas.93.10.4862. Human tbp core domain complexed with DNA. SNAP output
1cez transferase-DNA X-ray (2.4 Å) Cheetham GM, Jeruzalmi D, Steitz TA (1999) "Structural basis for initiation of transcription from an RNA polymerase-promoter complex." Nature, 399, 80-83. doi: 10.1038/19999. Crystal structure of a t7 RNA polymerase-t7 promoter complex. SNAP output
1cf7 transcription-DNA X-ray (2.6 Å) Zheng N, Fraenkel E, Pabo CO, Pavletich NP (1999) "Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP." Genes Dev., 13, 666-674. Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor e2f-dp. SNAP output
1cgp transcription-DNA X-ray (3.0 Å) Schultz SC, Shields GC, Steitz TA (1991) "Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees." Science, 253, 1001-1007. Catabolite gene activator protein (cap)-DNA complex + adenosine-3',5'-cyclic-monophosphate. SNAP output
1cit transcription-DNA X-ray (2.7 Å) Meinke G, Sigler PB (1999) "DNA-binding mechanism of the monomeric orphan nuclear receptor NGFI-B." Nat.Struct.Biol., 6, 471-477. doi: 10.1038/8276. DNA-binding mechanism of the monomeric orphan nuclear receptor ngfi-b. SNAP output
1cjg transcription-DNA NMR Spronk CA, Bonvin AM, Radha PK, Melacini G, Boelens R, Kaptein R (1999) "The solution structure of Lac repressor headpiece 62 complexed to a symmetrical lac operator." Structure Fold.Des., 7, 1483-1492. doi: 10.1016/S0969-2126(00)88339-2. NMR structure of lac repressor hp62-DNA complex. SNAP output
1ckq protein-DNA X-ray (1.85 Å) Horvath M, Choi J, Kim Y, Wilkosz PA, Chandrasekhar K, Rosenberg JM "The Integration of Recognition and Cleavage: X-Ray Structures of Pre- Transition State and Post-Reactive DNA-Eco Ri Endonuclease Complexes." Pre-transition state eco ri endonuclease-cognate DNA (tcgcgaattcgcg) complex. SNAP output
1ckt gene regulation-DNA X-ray (2.5 Å) Ohndorf UM, Rould MA, He Q, Pabo CO, Lippard SJ (1999) "Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins." Nature, 399, 708-712. doi: 10.1038/21460. Crystal structure of hmg1 domain a bound to a cisplatin-modified DNA duplex. SNAP output
1cl8 protein-DNA X-ray (1.8 Å) Horvath M, Rosenberg JM "Iap (Inner-Adenine to Purine): A Cognate EcoRI-DNA Base Analog Complex." A pre-transition state eco ri endonuclease-cognate DNA (tcgcgapttcgcg) complex with DNA base analog purine (p). SNAP output
1clq transferase-DNA X-ray (2.7 Å) Shamoo Y, Steitz TA (1999) "Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex." Cell(Cambridge,Mass.), 99, 155-166. doi: 10.1016/S0092-8674(00)81647-5. Crystal structure of a replication fork DNA polymerase editing complex at 2.7 Å resolution. SNAP output
1cma transcription-DNA X-ray (2.8 Å) Somers WS, Phillips SE (1992) "Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by beta-strands." Nature, 359, 387-393. doi: 10.1038/359387a0. Met repressor-DNA complex + s-adenosyl-methionine. SNAP output
1co0 transcription NMR Brocchieri L, Zhou GP, Jardetzky O (2002) "Allostery and Induced Fit, NMR and Molecular Modeling Study of the trp-repressor - mtr DNA complex." Structures and Mechanisms, ACS Symposium Series, 827, 340-366. NMR study of trp repressor-mtr operator DNA complex. SNAP output
1cqt gene regulation-DNA X-ray (3.2 Å) Chasman D, Cepek K, Sharp PA, Pabo CO (1999) "Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: specific recognition of a protein-DNA interface." Genes Dev., 13, 2650-2657. doi: 10.1101/gad.13.20.2650. Crystal structure of a ternary complex containing an oca-b peptide, the oct-1 pou domain, and an octamer element. SNAP output
1crx replication-DNA X-ray (2.4 Å) Guo F, Gopaul DN, van Duyne GD (1997) "Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse." Nature, 389, 40-46. doi: 10.1038/37925. Cre recombinase-DNA complex reaction intermediate i. SNAP output
1cw0 hydrolase-DNA X-ray (2.3 Å) Tsutakawa SE, Jingami H, Morikawa K (1999) "Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex." Cell(Cambridge,Mass.), 99, 615-623. doi: 10.1016/S0092-8674(00)81550-0. Crystal structure analysis of very short patch repair (vsr) endonuclease in complex with a duplex DNA. SNAP output
1cyq hydrolase-DNA X-ray (1.93 Å) Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE, Monnat Jr RJ, Stoddard BL (1999) "A novel endonuclease mechanism directly visualized for I-PpoI." Nat.Struct.Biol., 6, 1096-1099. doi: 10.1038/70027. Intron encoded homing endonuclease i-ppoi (h98a)-DNA homing site complex. SNAP output
1cz0 hydrolase-DNA X-ray (2.1 Å) Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE, Monnat Jr RJ, Stoddard BL (1999) "A novel endonuclease mechanism directly visualized for I-PpoI." Nat.Struct.Biol., 6, 1096-1099. doi: 10.1038/70027. Intron encoded homing endonuclease i-ppoi-DNA complex lacking catalytic metal ion. SNAP output
1d02 hydrolase-DNA X-ray (1.7 Å) Deibert M, Grazulis S, Janulaitis A, Siksnys V, Huber R (1999) "Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution." EMBO J., 18, 5805-5816. doi: 10.1093/emboj/18.21.5805. Crystal structure of muni restriction endonuclease in complex with cognate DNA. SNAP output
1d0e transferase-DNA X-ray (3.0 Å) Najmudin S, Cote ML, Sun D, Yohannan S, Montano SP, Gu J, Georgiadis MM (2000) "Crystal structures of an N-terminal fragment from Moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain." J.Mol.Biol., 296, 613-632. doi: 10.1006/jmbi.1999.3477. Crystal structures of the n-terminal fragment from moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain. SNAP output
1d1u hydrolase-DNA X-ray (2.3 Å) Cote ML, Yohannan SJ, Georgiadis MM (2000) "Use of an N-terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing G-A mispairs." Acta Crystallogr.,Sect.D, 56, 1120-1131. doi: 10.1107/S0907444900008246. Use of an n-terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing g-a mispairs. SNAP output
1d2i hydrolase-DNA X-ray (1.7 Å) Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK (2000) "Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution." Nat.Struct.Biol., 7, 134-140. doi: 10.1038/72405. Crystal structure of restriction endonuclease bglii complexed with DNA 16-mer. SNAP output
1d3u gene regulation-DNA X-ray (2.4 Å) Littlefield O, Korkhin Y, Sigler PB (1999) "The structural basis for the oriented assembly of a TBP/TFB/promoter complex." Proc.Natl.Acad.Sci.USA, 96, 13668-13673. doi: 10.1073/pnas.96.24.13668. Tata-binding protein-transcription factor (ii)b-bre+tata-box complex from pyrococcus woesei. SNAP output
1d5y transcription-DNA X-ray (2.7 Å) Kwon HJ, Bennik MH, Demple B, Ellenberger T (2000) "Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA." Nat.Struct.Biol., 7, 424-430. doi: 10.1038/75213. Crystal structure of the e. coli rob transcription factor in complex with DNA. SNAP output
1d66 transcription-DNA X-ray (2.7 Å) Marmorstein R, Carey M, Ptashne M, Harrison SC (1992) "DNA recognition by GAL4: structure of a protein-DNA complex." Nature, 356, 408-414. doi: 10.1038/356408a0. DNA recognition by gal4: structure of a protein-DNA complex. SNAP output
1d8y transferase-DNA X-ray (2.08 Å) Teplova M, Wallace ST, Tereshko V, Minasov G, Symons AM, Cook PD, Manoharan M, Egli M (1999) "Structural origins of the exonuclease resistance of a zwitterionic RNA." Proc.Natl.Acad.Sci.USA, 96, 14240-14245. doi: 10.1073/pnas.96.25.14240. Crystal structure of the complex of DNA polymerase i klenow fragment with DNA. SNAP output
1dc1 hydrolase-DNA X-ray (1.7 Å) van der Woerd MJ, Pelletier JJ, Xu S, Friedman AM (2001) "Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis." Structure, 9, 133-144. doi: 10.1016/S0969-2126(01)00564-0. Restriction enzyme bsobi-DNA complex structure: encirclement of the DNA and histidine-catalyzed hydrolysis within a canonical restriction enzyme fold. SNAP output
1dct transferase-DNA X-ray (2.8 Å) Reinisch KM, Chen L, Verdine GL, Lipscomb WN (1995) "The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing." Cell(Cambridge,Mass.), 82, 143-153. doi: 10.1016/0092-8674(95)90060-8. DNA (cytosine-5) methylase from haeiii covalently bound to DNA. SNAP output
1ddn gene regulation-DNA X-ray (3.0 Å) White A, Ding X, vanderSpek JC, Murphy JR, Ringe D (1998) "Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex." Nature, 394, 502-506. doi: 10.1038/28893. Diphtheria tox repressor (c102d mutant)-tox DNA operator complex. SNAP output
1de8 lyase-DNA X-ray (2.95 Å) Mol CD, Izumi T, Mitra S, Tainer JA (2000) "DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected." Nature, 403, 451-456. doi: 10.1038/35000249. Human apurinic-apyrimidinic endonuclease-1 (ape1) bound to abasic DNA. SNAP output
1de9 lyase-DNA X-ray (3.0 Å) Mol CD, Izumi T, Mitra S, Tainer JA (2000) "DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination." Nature, 403, 451-456. doi: 10.1038/35000249. Human ape1 endonuclease with bound abasic DNA and mn2+ ion. SNAP output
1dew lyase-DNA X-ray (2.65 Å) Mol CD, Izumi T, Mitra S, Tainer JA (2000) "DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination." Nature, 403, 451-456. doi: 10.1038/35000249. Crystal structure of human ape1 bound to abasic DNA. SNAP output
1dfm hydrolase-DNA X-ray (1.5 Å) Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK (2000) "Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution." Nat.Struct.Biol., 7, 134-140. doi: 10.1038/72405. Crystal structure of restriction endonuclease bglii complexed with DNA 16-mer. SNAP output
1dgc transcription-DNA X-ray (3.0 Å) Konig P, Richmond TJ (1993) "The X-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility." J.Mol.Biol., 233, 139-154. doi: 10.1006/jmbi.1993.1490. The x-ray structure of the gcn4-bzip bound to atf-creb site DNA shows the complex depends on DNA flexibility. SNAP output
1dh3 transcription-DNA X-ray (3.0 Å) Schumacher MA, Goodman RH, Brennan RG (2000) "The structure of a CREB bZIP.somatostatin CRE complex reveals the basis for selective dimerization and divalent cation-enhanced DNA binding." J.Biol.Chem., 275, 35242-35247. doi: 10.1074/jbc.M007293200. Crystal structure of a creb bzip-cre complex reveals the basis for creb faimly selective dimerization and DNA binding. SNAP output
1diz hydrolase-DNA X-ray (2.5 Å) Hollis T, Ichikawa Y, Ellenberger T (2000) "DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA." EMBO J., 19, 758-766. doi: 10.1093/emboj/19.4.758. Crystal structure of e. coli 3-methyladenine DNA glycosylase (alka) complexed with DNA. SNAP output
1dmu hydrolase-DNA X-ray (2.2 Å) Newman M, Lunnen K, Wilson G, Greci J, Schildkraut I, Phillips SE (1998) "Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence." EMBO J., 17, 5466-5476. doi: 10.1093/emboj/17.18.5466. Crystal structure of the restriction endonuclease bgli (e.c.3.1.21.4) bound to its DNA recognition sequence. SNAP output
1dnk hydrolase-DNA X-ray (2.3 Å) Weston SA, Lahm A, Suck D (1992) "X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution." J.Mol.Biol., 226, 1237-1256. doi: 10.1016/0022-2836(92)91064-V. The x-ray structure of the dnase i-d(ggtatacc)2 complex at 2.3 angstroms resolution. SNAP output
1dp7 transcription-DNA X-ray (1.5 Å) Gajiwala KS, Chen H, Cornille F, Roques BP, Reith W, Mach B, Burley SK (2000) "Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding." Nature, 403, 916-921. doi: 10.1038/35002634. Cocrystal structure of rfx-dbd in complex with its cognate x-box binding site. SNAP output
1drg hydrolase, ligase-DNA X-ray (2.55 Å) Woods KC, Martin SS, Chu VC, Baldwin EP (2001) "Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction." J.Mol.Biol., 313, 49-69. doi: 10.1006/jmbi.2001.5012. Crystal structure of trimeric cre recombinase-lox complex. SNAP output
1dsc DNA-antibiotic NMR Lian C, Robinson H, Wang AH-J (1996) "Structure of Actinomycin D Bound with (Gaagcttc)2 and (Gatgcttc)2 and its Binding to the (Cag)N:(Ctg)N Triplet Sequence by NMR Analysis." J.Am.Chem.Soc., 118, 8791. doi: 10.1021/JA961631P. NMR study of DNA (5'-d(*gp*ap*ap*gp*cp*tp*tp*c)-3') self-complementary duplex complexed with actinomycin d, minimized average structure. SNAP output
1dsd DNA-antibiotic NMR Lian C, Robinson H, Wang AH-J (1996) "Structure of Actinomycin D Bound with (Gaagcttc)2 and (Gatgcttc)2 and its Binding to the (Cag)N:(Ctg)N Triplet Sequence by NMR Analysis." J.Am.Chem.Soc., 118, 8791. doi: 10.1021/JA961631P. NMR study of DNA (5'-d(*gp*ap*tp*gp*cp*tp*tp*c)-3') t:t mismatched duplex complexed with actinomycin d, minimized average structure. SNAP output
1dsz transcription-DNA X-ray (1.7 Å) Rastinejad F, Wagner T, Zhao Q, Khorasanizadeh S (2000) "Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1." EMBO J., 19, 1045-1054. doi: 10.1093/emboj/19.5.1045. Structure of the rxr-rar DNA-binding domain heterodimer in complex with the retinoic acid response element dr1. SNAP output
1du0 transcription-DNA X-ray (2.0 Å) Grant RA, Rould MA, Klemm JD, Pabo CO (2000) "Exploring the role of glutamine 50 in the homeodomain-DNA interface: crystal structure of engrailed (Gln50 --> ala) complex at 2.0 A." Biochemistry, 39, 8187-8192. doi: 10.1021/bi000071a. Engrailed homeodomain q50a variant DNA complex. SNAP output
1dux transcription-DNA X-ray (2.1 Å) Mo Y, Vaessen B, Johnston K, Marmorstein R (2000) "Structure of the elk-1-DNA complex reveals how DNA-distal residues affect ETS domain recognition of DNA." Nat.Struct.Biol., 7, 292-297. doi: 10.1038/74055. Elk-1-DNA structure reveals how residues distal from DNA-binding surface affect DNA-recognition. SNAP output
1e3m DNA binding X-ray (2.2 Å) Lamers MH, Perrakis A, Enzlin JH, Winterwerp HHK, De Wind N, Sixma TK (2000) "The Crystal Structure of DNA Mismatch Repair Protein Muts Binding to a G X T Mismatch." Nature, 407, 711. doi: 10.1038/35037523. The crystal structure of e. coli muts binding to DNA with a g:t mismatch. SNAP output
1e3o transcription X-ray (1.9 Å) Remenyi A, Tomilin A, Pohl E, Lins K, Philippsen A, Reinbold R, Scholer HR, Wilmanns M (2001) "Differential Dimer Activities of the Transcription Factor Oct-1 by DNA-Induced Interface Swapping." Mol.Cell, 8, 569. doi: 10.1016/S1097-2765(01)00336-7. Crystal structure of oct-1 pou dimer bound to more. SNAP output
1e7j protein-DNA NMR Cerdan R, Payet D, Yang J-C, Travers AA, Neuhaus D (2001) "Hmg-D Complexed to a Bulge DNA: An NMR Model." Protein Sci., 10, 504. doi: 10.1110/PS.35501. Hmg-d complexed to a bulge DNA. SNAP output
1ea4 gene regulation-DNA X-ray (2.95 Å) Costa M, Sola M, Del G, Eritja R, Hernaindez-Arriaga AM, Espinosa M, Gomis-Rueth FX, Coll M (2001) "Plasmid Transcriptional Repressor Copg Oligomerises to Render Helical Superstructures Unbound and in Complexes with Oligonucleotides." J.Mol.Biol., 310, 403. doi: 10.1006/JMBI.2001.4760. Transcriptional repressor copg-22bp dsDNA complex. SNAP output
1ebm lyase-DNA X-ray (2.1 Å) Bruner SD, Norman DP, Verdine GL (2000) "Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA." Nature, 403, 859-866. doi: 10.1038/35002510. Crystal structure of the human 8-oxoguanine glycosylase (hogg1) bound to a substrate oligonucleotide. SNAP output
1ecr replication-DNA X-ray (2.7 Å) Kamada K, Horiuchi T, Ohsumi K, Shimamoto N, Morikawa K (1996) "Structure of a replication-terminator protein complexed with DNA." Nature, 383, 598-603. doi: 10.1038/383598a0. Escherichia coli replication terminator protein (tus) complexed with DNA. SNAP output
1efa transcription-DNA X-ray (2.6 Å) Bell CE, Lewis M (2000) "A closer view of the conformation of the Lac repressor bound to operator." Nat.Struct.Biol., 7, 209-214. doi: 10.1038/78907. Crystal structure of the lac repressor dimer bound to operator and the anti-inducer onpf. SNAP output
1egw transcription-DNA X-ray (1.5 Å) Santelli E, Richmond TJ (2000) "Crystal structure of MEF2A core bound to DNA at 1.5 A resolution." J.Mol.Biol., 297, 437-449. doi: 10.1006/jmbi.2000.3568. Crystal structure of mef2a core bound to DNA. SNAP output
1ehl immune system X-ray (2.4 Å) Yokoyama H, Mizutani R, Satow Y, Komatsu Y, Ohtsuka E, Nikaido O (2000) "Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation." J.Mol.Biol., 299, 711-723. doi: 10.1006/jmbi.2000.3772. 64m-2 antibody fab complexed with d(5ht)(6-4)t. SNAP output
1ej9 isomerase-DNA X-ray (2.6 Å) Redinbo MR, Champoux JJ, Hol WG (2000) "Novel insights into catalytic mechanism from a crystal structure of human topoisomerase I in complex with DNA." Biochemistry, 39, 6832-6840. doi: 10.1021/bi992690t. Crystal structure of human topoisomerase i DNA complex. SNAP output
1emh hydrolase-DNA X-ray (1.8 Å) Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA (2000) "Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects." Proc.Natl.Acad.Sci.USA, 97, 5083-5088. doi: 10.1073/pnas.97.10.5083. Crystal structure of human uracil-DNA glycosylase bound to uncleaved substrate-containing DNA. SNAP output
1emj hydrolase-DNA X-ray (2.0 Å) Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA (2000) "Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects." Proc.Natl.Acad.Sci.USA, 97, 5083-5088. doi: 10.1073/pnas.97.10.5083. Uracil-DNA glycosylase bound to DNA containing a 4'-thio-2'deoxyuridine analog product. SNAP output
1eo3 hydrolase-DNA X-ray (2.0 Å) Horton NC, Connolly BA, Perona JJ (2000) "Inhibition of EcoRV Endonuclease by Deoxyribo-3'-S-phosphorothiolates: A High-Resolution X-ray Crystallographic Study." J.Am.Chem.Soc., 122, 3314-3324. doi: 10.1021/ja993719j. Inhibition of ecorv endonuclease by deoxyribo-3'-s-phosphorothiolates: a high resolution x-ray crystallographic study. SNAP output
1eo4 hydrolase-DNA X-ray (1.9 Å) Horton NC, Connolly BA, Perona JJ (2000) "Inhibition of EcoRV Endonuclease by Deoxyribo-3'-S-phosphorothiolates: A High-Resolution X-ray Crystallographic Study." J.Am.Chem.Soc., 122, 3314-3324. doi: 10.1021/ja993719j. Ecorv bound to mn2+ and cognate DNA containing a 3's substition at the cleavage site. SNAP output
1eon hydrolase-DNA X-ray (1.6 Å) Horton NC, Connolly BA, Perona JJ (2000) "Inhibition of EcoRV Endonuclease by Deoxyribo-3'-S-phosphorothiolates: A High-Resolution X-ray Crystallographic Study." J.Am.Chem.Soc., 122, 3314-3324. doi: 10.1021/ja993719j. Ecorv bound to 3'-s-phosphorothiolate DNA and ca2+. SNAP output
1eoo hydrolase-DNA X-ray (2.16 Å) Horton NC, Perona JJ (2000) "Crystallographic snapshots along a protein-induced DNA-bending pathway." Proc.Natl.Acad.Sci.USA, 97, 5729-5734. doi: 10.1073/pnas.090370797. Ecorv bound to cognate DNA. SNAP output
1eop hydrolase-DNA X-ray (2.6 Å) Horton NC, Perona JJ (2000) "Crystallographic snapshots along a protein-induced DNA-bending pathway." Proc.Natl.Acad.Sci.USA, 97, 5729-5734. doi: 10.1073/pnas.090370797. Ecorv bound to cognate DNA. SNAP output
1eqz structural protein-DNA X-ray (2.5 Å) Harp JM, Hanson BL, Timm DE, Bunick GJ (2000) "Asymmetries in the nucleosome core particle at 2.5 A resolution." Acta Crystallogr.,Sect.D, 56, 1513-1534. doi: 10.1107/S0907444900011847. X-ray structure of the nucleosome core particle at 2.5 Å resolution. SNAP output
1eri hydrolase-DNA X-ray (2.5 Å) Kim YC, Grable JC, Love R, Greene PJ, Rosenberg JM (1990) "Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing." Science, 249, 1307-1309. X-ray structure of the DNA-eco ri endonuclease-DNA recognition complex: the recognition network and the integration of recognition and cleavage. SNAP output
1esg hydrolase-DNA X-ray (1.9 Å) Viadiu H, Aggarwal AK (2000) "Structure of BamHI bound to nonspecific DNA: a model for DNA sliding." Mol.Cell, 5, 889-895. doi: 10.1016/S1097-2765(00)80329-9. Restriction endonuclease bamhi bound to a non-specific DNA.. SNAP output
1evw hydrolase-DNA X-ray (3.1 Å) Galburt EA, Chadsey MS, Jurica MS, Chevalier BS, Erho D, Tang W, Monnat Jr RJ, Stoddard BL (2000) "Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site." J.Mol.Biol., 300, 877-887. doi: 10.1006/jmbi.2000.3874. L116a mutant of the homing endonuclease i-ppoi complexed to homing site DNA.. SNAP output
1ewn hydrolase-DNA X-ray (2.1 Å) Lau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger T (2000) "Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG." Proc.Natl.Acad.Sci.USA, 97, 13573-13578. doi: 10.1073/pnas.97.25.13573. Crystal structure of the human aag DNA repair glycosylase complexed with 1,n6-ethenoadenine-DNA. SNAP output
1ewq replication-DNA X-ray (2.2 Å) Obmolova G, Ban C, Hsieh P, Yang W (2000) "Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA." Nature, 407, 703-710. doi: 10.1038/35037509. Crystal structure taq muts complexed with a heteroduplex DNA at 2.2 Å resolution. SNAP output
1exi transcription-DNA X-ray (3.12 Å) Heldwein EE, Brennan RG (2001) "Crystal structure of the transcription activator BmrR bound to DNA and a drug." Nature, 409, 378-382. doi: 10.1038/35053138. Crystal structure of transcription activator bmrr, from b. subtilis, bound to 21 base pair bmr operator and tpsb. SNAP output
1exj transcription-DNA X-ray (3.0 Å) Heldwein EE, Brennan RG (2001) "Crystal structure of the transcription activator BmrR bound to DNA and a drug." Nature, 409, 378-382. doi: 10.1038/35053138. Crystal structure of transcription activator bmrr, from b. subtilis, bound to 21 base pair bmr operator and tpp. SNAP output
1eyg replication-DNA X-ray (2.8 Å) Raghunathan S, Kozlov AG, Lohman TM, Waksman G (2000) "Structure of the DNA binding domain of E. coli SSB bound to ssDNA." Nat.Struct.Biol., 7, 648-652. doi: 10.1038/77943. Crystal structure of chymotryptic fragment of e. coli ssb bound to two 35-mer single strand dnas. SNAP output
1eyu hydrolase-DNA X-ray (1.78 Å) Horton JR, Cheng X (2000) "PvuII endonuclease contains two calcium ions in active sites." J.Mol.Biol., 300, 1049-1056. doi: 10.1006/jmbi.2000.3938. High resolution structure of the pvuii endonculease-cognate DNA complex at ph 4.6. SNAP output
1f0o hydrolase-DNA X-ray (2.5 Å) Horton JR, Cheng X (2000) "PvuII endonuclease contains two calcium ions in active sites." J.Mol.Biol., 300, 1049-1056. doi: 10.1006/jmbi.2000.3938. Pvuii endonuclease-cognate DNA complex (glutaraldehyde-crosslinked crystal) at ph 7.5 with two calcium ions at each active site. SNAP output
1f0v hydrolase-DNA X-ray (1.7 Å) Liu YS, Gotte G, Libonati M, Eisenberg DS (2001) "A domain-swapped RNase A dimer with implications for amyloid formation." Nat.Struct.Biol., 8, 211-214. doi: 10.1038/84941. Crystal structure of an rnase a dimer displaying a new type of 3d domain swapping. SNAP output
1f2i transcription-DNA X-ray (2.35 Å) Wang BS, Grant RA, Pabo CO (2001) "Selected peptide extension contacts hydrophobic patch on neighboring zinc finger and mediates dimerization on DNA." Nat.Struct.Biol., 8, 589-593. doi: 10.1038/89617. Cocrystal structure of selected zinc finger dimer bound to DNA. SNAP output
1f44 hydrolase, ligase-DNA X-ray (2.05 Å) Woods KC, Martin SS, Chu VC, Baldwin EP (2001) "Quasi-equivalence in site-specific recombinase structure and function: crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction." J.Mol.Biol., 313, 49-69. doi: 10.1006/jmbi.2001.5012. Crystal structure of trimeric cre recombinase-lox complex. SNAP output
1f4k replication-DNA X-ray (2.5 Å) Wilce JA, Vivian JP, Hastings AF, Otting G, Folmer RH, Duggin IG, Wake RG, Wilce MC (2001) "Structure of the RTP-DNA complex and the mechanism of polar replication fork arrest." Nat.Struct.Biol., 8, 206-210. doi: 10.1038/84934. Crystal structure of the replication terminator protein-b-site DNA complex. SNAP output
1f4r hydrolase-DNA X-ray (2.4 Å) Lau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger T (2000) "Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG." Proc.Natl.Acad.Sci.USA, 97, 13573-13578. doi: 10.1073/pnas.97.25.13573. Crystal structure of the human aag DNA repair glycosylase complexed with 1,n6-ethenoadenine-DNA. SNAP output
1f4s transcription-DNA NMR Cahuzac B, Cerdan R, Felenbok B, Guittet E (2001) "The solution structure of an AlcR-DNA complex sheds light onto the unique tight and monomeric DNA binding of a Zn(2)Cys(6) protein." Structure, 9, 827-836. doi: 10.1016/S0969-2126(01)00640-2. Structure of transcriptional factor alcr in complex with a target DNA. SNAP output
1f5e transcription-DNA NMR Cahuzac B, Cerdan R, Felenbok B, Guittet E (2001) "The solution structure of an AlcR-DNA complex sheds light onto the unique tight and monomeric DNA binding of a Zn(2)Cys(6) protein." Structure, 9, 827-836. doi: 10.1016/S0969-2126(01)00640-2. Structure of transcriptional factor alcr in complex with a target DNA. SNAP output
1f5t transcription-DNA X-ray (3.0 Å) Chen CS, White A, Love J, Murphy JR, Ringe D (2000) "Methyl groups of thymine bases are important for nucleic acid recognition by DtxR." Biochemistry, 39, 10397-10407. doi: 10.1021/bi0009284. Diphtheria tox repressor (c102d mutant) complexed with nickel and dtxr consensus binding sequence. SNAP output
1f66 structural protein-DNA X-ray (2.6 Å) Suto RK, Clarkson MJ, Tremethick DJ, Luger K (2000) "Crystal structure of a nucleosome core particle containing the variant histone H2A.Z." Nat.Struct.Biol., 7, 1121-1124. doi: 10.1038/81971. 2.6 a crystal structure of a nucleosome core particle containing the variant histone h2a.z. SNAP output
1f6o hydrolase-DNA X-ray (2.4 Å) Lau AY, Wyatt MD, Glassner BJ, Samson LD, Ellenberger T (2000) "Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG." Proc.Natl.Acad.Sci.USA, 97, 13573-13578. doi: 10.1073/pnas.97.25.13573. Crystal structure of the human aag DNA repair glycosylase complexed with DNA. SNAP output
1fiu hydrolase-DNA X-ray (1.6 Å) Deibert M, Grazulis S, Sasnauskas G, Siksnys V, Huber R (2000) "Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA." Nat.Struct.Biol., 7, 792-799. doi: 10.1038/79032. Tetrameric restriction endonuclease ngomiv in complex with cleaved DNA. SNAP output
1fja DNA-antibiotic NMR Chen H, Liu X, Patel DJ (1996) "DNA Bending and Unwinding Associated with Actinomycin D Antibiotics Bound to Partially Overlapping Sites on DNA." J.Mol.Biol., 258, 457. doi: 10.1006/JMBI.1996.0262. NMR study of deoxyribonucleic acid complexed with actinomycin d. SNAP output
1fjl transcription-DNA X-ray (2.0 Å) Wilson DS, Guenther B, Desplan C, Kuriyan J (1995) "High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA." Cell(Cambridge,Mass.), 82, 709-719. doi: 10.1016/0092-8674(95)90468-9. Homeodomain from the drosophila paired protein bound to a DNA oligonucleotide. SNAP output
1fjx transferase-DNA X-ray (2.26 Å) Vilkaitis G, Dong A, Weinhold E, Cheng X, Klimasauskas S (2000) "Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase." J.Biol.Chem., 275, 38722-38730. Structure of ternary complex of hhai methyltransferase mutant (t250g) in complex with DNA and adohcy. SNAP output
1flo ligase, lyase-DNA X-ray (2.65 Å) Chen Y, Narendra U, Iype LE, Cox MM, Rice PA (2000) "Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping." Mol.Cell, 6, 885-897. doi: 10.1016/S1097-2765(00)00086-1. Flp recombinase-holliday junction complex i. SNAP output
1fn7 hydrolase-DNA X-ray (2.6 Å) Norman DP, Bruner SD, Verdine GL (2001) "Coupling of substrate recognition and catalysis by a human base-excision DNA repair protein." J.Am.Chem.Soc., 123, 359-360. doi: 10.1021/ja003144m. Coupling of damage recognition and catalysis by a human base-excision DNA repair protein. SNAP output
1fok hydrolase-DNA X-ray (2.8 Å) Wah DA, Hirsch JA, Dorner LF, Schildkraut I, Aggarwal AK (1997) "Structure of the multimodular endonuclease FokI bound to DNA." Nature, 388, 97-100. doi: 10.1038/40446. Structure of restriction endonuclease foki bound to DNA. SNAP output
1fos transcription-DNA X-ray (3.05 Å) Glover JN, Harrison SC (1995) "Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA." Nature, 373, 257-261. doi: 10.1038/373257a0. Two human c-fos:c-jun:DNA complexes. SNAP output
1fw6 replication-DNA X-ray (2.7 Å) Junop MS, Obmolova G, Rausch K, Hsieh P, Yang W (2001) "Composite active site of an ABC ATPase: MutS uses ATP to verify mismatch recognition and authorize DNA repair." Mol.Cell, 7, 1-12. doi: 10.1016/S1097-2765(01)00149-6. Crystal structure of a taq muts-DNA-adp ternary complex. SNAP output
1fyl transcription-DNA X-ray (2.1 Å) Littlefield O, Nelson HC (2001) "Crystal packing interaction that blocks crystallization of a site-specific DNA binding protein-DNA complex." Proteins, 45, 219-228. doi: 10.1002/prot.1142. Serendipitous crystal structure containing the heat shock transcription factor's DNA binding domain and cognate DNA in a head-to-head orientation. SNAP output
1fym transcription-DNA X-ray (2.2 Å) Littlefield O, Nelson HC (2001) "Crystal packing interaction that blocks crystallization of a site-specific DNA binding protein-DNA complex." Proteins, 45, 219-228. doi: 10.1002/prot.1142. Serendipitous crystal structure containing the heat shock transcription factor's DNA binding domain and cognate DNA in a tail-to-tail orientation. SNAP output
1g2d transcription-DNA X-ray (2.2 Å) Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO (2001) "Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes." Structure, 9, 717-723. doi: 10.1016/S0969-2126(01)00632-3. Structure of a cys2his2 zinc finger-tata box complex (clone #2). SNAP output
1g2f transcription-DNA X-ray (2.0 Å) Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO (2001) "Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes." Structure, 9, 717-723. doi: 10.1016/S0969-2126(01)00632-3. Structure of a cys2his2 zinc finger-tata box complex (tatazf;clone #6). SNAP output
1g38 transferase-DNA X-ray (2.0 Å) Goedecke K, Pignot M, Goody RS, Scheidig AJ, Weinhold E (2001) "Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog." Nat.Struct.Biol., 8, 121-125. doi: 10.1038/84104. Adenine-specific methyltransferase m. taq i-DNA complex. SNAP output
1g3x DNA X-ray (2.7 Å) Malinina L, Soler-Lopez M, Aymami J, Subirana JA (2002) "Intercalation of an acridine-peptide drug in an AA/TT base step in the crystal structure of [d(CGCGAATTCGCG)](2) with six duplexes and seven Mg(2+) ions in the asymmetric unit." Biochemistry, 41, 9341-9348. doi: 10.1021/bi020135c. Intercalation of an 9acridine-peptide drug in a DNA dodecamer. SNAP output
1g4d viral protein-DNA NMR Wojciak JM, Iwahara J, Clubb RT (2001) "The Mu repressor-DNA complex contains an immobilized 'wing' within the minor groove." Nat.Struct.Biol., 8, 84-90. doi: 10.1038/89582. NMR structure of the mu bacteriophage repressor DNA-binding domain-DNA complex. SNAP output
1g9y hydrolase-DNA X-ray (2.05 Å) Chevalier BS, Monnat Jr RJ, Stoddard BL (2001) "The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites." Nat.Struct.Biol., 8, 312-316. doi: 10.1038/86181. Homing endonuclease i-crei - DNA substrate complex with calcium. SNAP output
1g9z hydrolase-DNA X-ray (1.8 Å) Chevalier BS, Monnat Jr RJ, Stoddard BL (2001) "The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites." Nat.Struct.Biol., 8, 312-316. doi: 10.1038/86181. Laglidadg homing endonuclease i-crei - DNA product complex with magnesium. SNAP output
1ga5 transcription-DNA X-ray (2.4 Å) Sierk ML, Zhao Q, Rastinejad F (2001) "DNA Deformability as a Recognition Feature in the RevErb Response Element." Biochemistry, 40, 12833-12843. doi: 10.1021/bi011086r. Crystal structure of the orphan nuclear receptor rev-erb(alpha) DNA-binding domain bound to its cognate response element. SNAP output
1gat transcription-DNA NMR Omichinski JG, Clore GM, Schaad O, Felsenfeld G, Trainor C, Appella E, Stahl SJ, Gronenborn AM (1993) "NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1." Science, 261, 438-446. doi: 10.1021/bi00131a004. Solution structure of the specific DNA complex of the zinc containing DNA binding domain of the erythroid transcription factor gata-1 by multidimensional NMR. SNAP output
1gau transcription-DNA NMR Omichinski JG, Clore GM, Schaad O, Felsenfeld G, Trainor C, Appella E, Stahl SJ, Gronenborn AM (1993) "NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1." Science, 261, 438-446. doi: 10.1021/bi00131a004. Solution structure of the specific DNA complex of the zinc containing DNA binding domain of the erythroid transcription factor gata-1 by multidimensional NMR. SNAP output
1gcc transcription-DNA NMR Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki M (1998) "A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA." EMBO J., 17, 5484-5496. doi: 10.1093/emboj/17.18.5484. Solution NMR structure of the complex of gcc-box binding domain of aterf1 and gcc-box DNA, minimized average structure. SNAP output
1gd2 transcription-DNA X-ray (2.0 Å) Fujii Y, Shimizu T, Toda T, Yanagida M, Hakoshima T (2000) "Structural basis for the diversity of DNA recognition by bZIP transcription factors." Nat.Struct.Biol., 7, 889-893. doi: 10.1038/82822. Crystal structure of bzip transcription factor pap1 bound to DNA. SNAP output
1gdt DNA binding protein-DNA X-ray (3.0 Å) Yang W, Steitz TA (1995) "Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site." Cell(Cambridge,Mass.), 82, 193-207. doi: 10.1016/0092-8674(95)90307-0. Crystal structure of a site-specific recombinase, gamma-delta resolvase complexed with a 34 bp cleavage site. SNAP output
1gji transcription-DNA X-ray (2.85 Å) Huang DB, Chen YQ, Ruetsche M, Phelps CB, Ghosh G (2001) "X-ray crystal structure of proto-oncogene product c-Rel bound to the CD28 response element of IL-2." Structure, 9, 669-678. doi: 10.1016/S0969-2126(01)00635-9. Crystal structure of c-rel bound to DNA. SNAP output
1glu transcription-DNA X-ray (2.9 Å) Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto KR, Sigler PB (1991) "Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA." Nature, 352, 497-505. doi: 10.1038/352497a0. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. SNAP output
1gm5 helicase X-ray (3.24 Å) Singleton MR, Scaife S, Wigley DB (2001) "Structural Analysis of DNA Replication Fork Reversal by Recg." Cell(Cambridge,Mass.), 107, 79. doi: 10.1016/S0092-8674(01)00501-3. Structure of recg bound to three-way DNA junction. SNAP output
1gt0 transcription X-ray (2.6 Å) Remenyi A, Lins K, Nissen LJ, Reinbold R, Scholer HR, Wilmanns M (2003) "Crystal Structure of a POU/Hmg/DNA Ternary Complex Suggests Differential Assembly of Oct4 and Sox2 on Two Enhancers." Genes Dev., 17, 2048. doi: 10.1101/GAD.269303. Crystal structure of a pou-hmg-DNA ternary complex. SNAP output
1gtw transcription-DNA X-ray (1.85 Å) Tahirov TH, Inoue-Bungo T, Sato K, Sasaki M, Ogata K "Structural Basis for Flexible Base Recognition by C/Ebpbeta." Crystal structure of c-ebpbeta bzip homodimer bound to a DNA fragment from the tom-1a promoter. SNAP output
1gu4 transcription-DNA X-ray (1.8 Å) Tahirov TH, Inoue-Bungo T, Sato K, Sasaki M, Ogata K "Structural Basis for Flexible Base Recognition by C/Ebpbeta." Crystal structure of c-ebpbeta bzip homodimer bound to a high affinity DNA fragment. SNAP output
1gu5 transcription-DNA X-ray (2.1 Å) Tahirov TH, Inoue-Bungo T, Sato K, Sasaki M, Ogata K "Structural Basis for Flexible Base Recognition by C/Ebpbeta." Crystal structure of c-ebpbeta bzip homodimer bound to a DNA fragment from the mim-1 promoter. SNAP output
1gxp transcriptional activator X-ray (2.5 Å) Blanco AG, Sola M, Gomis-Ruth FX, Coll M (2002) "Tandem DNA Recognition by Two-Component Signal Transduction Transcriptional Activator Phob." Structure, 10, 701. doi: 10.1016/S0969-2126(02)00761-X. Phob effector domain in complex with pho box DNA.. SNAP output
1h0m transcription-DNA X-ray (3.0 Å) Vannini A, Volpari C, Gargioli C, Muraglia E, Cortese R, De Francesco R, Neddermann P, Di Marco S (2002) "The Crystal Structure of the Quorum Sensing Protein Trar Bound to its Autoinducer and Target DNA." Embo J., 21, 4393. doi: 10.1093/EMBOJ/CDF459. Three-dimensional structure of the quorum sensing protein trar bound to its autoinducer and to its target DNA. SNAP output
1h38 transferase X-ray (2.9 Å) Tahirov TH, Temiakov D, Anikin M, Patlan V, Mcallister WT, Vassylyev DG, Yokoyama S (2002) "Structure of a T7 RNA Polymerase Elongation Complex at 2.9 A Resolution." Nature, 420, 43. doi: 10.1038/NATURE01129. Structure of a t7 RNA polymerase elongation complex at 2.9a resolution. SNAP output
1h6f transcription factor X-ray (1.7 Å) Coll M, Seidman JG, Muller CW (2002) "Structure of the DNA-Bound T-Box Domain of Human Tbx3, a Transcription Factor Responsible for Ulnar- Mammary Syndrome." Structure, 10, 343. doi: 10.1016/S0969-2126(02)00722-0. Human tbx3, a transcription factor responsible for ulnar-mammary syndrome, bound to a palindromic DNA site. SNAP output
1h88 transcription-DNA X-ray (2.8 Å) Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M, Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A, Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K (2002) "Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter." Cell(Cambridge,Mass.), 108, 57. doi: 10.1016/S0092-8674(01)00636-5. Crystal structure of ternary protein-DNA complex1. SNAP output
1h89 transcription-DNA X-ray (2.45 Å) Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M, Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A, Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K (2002) "Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter." Cell(Cambridge,Mass.), 108, 57. doi: 10.1016/S0092-8674(01)00636-5. Crystal structure of ternary protein-DNA complex2. SNAP output
1h8a transcription-DNA X-ray (2.23 Å) Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M, Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A, Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K (2002) "Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter." Cell(Cambridge,Mass.), 108, 57. doi: 10.1016/S0092-8674(01)00636-5. Crystal structure of ternary protein-DNA complex3. SNAP output
1h9d transcription factor X-ray (2.6 Å) Bravo J, Li Z, Speck NA, Warren AJ (2001) "The Leukemia-Associated Aml1 (Runx1)-Cbfbeta Complex Functions as a DNA-Induced Molecular Clamp." Nat.Struct.Biol., 8, 371. doi: 10.1038/86264. Aml1-cbf-beta-DNA complex. SNAP output
1h9t transcriptional regulation X-ray (3.25 Å) Van Aalten DMF, Dirusso CC, Knudsen J (2001) "The Structural Basis of Acyl Coenzyme A-Dependent Regulation of the Transcription Factor Fadr." Embo J., 20, 2041. doi: 10.1093/EMBOJ/20.8.2041. Fadr, fatty acid responsive transcription factor from e. coli in complex with fadb operator. SNAP output
1hao hydrolase-hydrolase inhibitor-DNA X-ray (2.8 Å) Padmanabhan K, Tulinsky A (1996) "An ambiguous structure of a DNA 15-mer thrombin complex." Acta Crystallogr.,Sect.D, 52, 272-282. doi: 10.1107/S0907444995013977. Complex of human alpha-thrombin with a 15mer oligonucleotide ggttggtgtggttgg (based on NMR model of DNA). SNAP output
1hap hydrolase-hydrolase inhibitor-DNA X-ray (2.8 Å) Padmanabhan K, Tulinsky A (1996) "An ambiguous structure of a DNA 15-mer thrombin complex." Acta Crystallogr.,Sect.D, 52, 272-282. doi: 10.1107/S0907444995013977. Complex of human alpha-thrombin with a 15mer oligonucleotide ggttggtgtggttgg (based on x-ray model of DNA). SNAP output
1hbx gene regulation X-ray (3.15 Å) Hassler M, Richmond TJ (2001) "The B-Box Dominates Sap-1/Srf Interactions in the Structure of the Ternary Complex." Embo J., 20, 3018. doi: 10.1093/EMBOJ/20.12.3018. Ternary complex of sap-1 and srf with specific sre DNA. SNAP output
1hcq transcription-DNA X-ray (2.4 Å) Schwabe JW, Chapman L, Finch JT, Rhodes D (1993) "The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements." Cell(Cambridge,Mass.), 75, 567-578. doi: 10.1016/0092-8674(93)90390-C. The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements. SNAP output
1hcr DNA binding protein-DNA X-ray (2.3 Å) Feng JA, Johnson RC, Dickerson RE (1994) "Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions." Science, 263, 348-355. Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions. SNAP output
1hdd transcription-DNA X-ray (2.8 Å) Kissinger CR, Liu BS, Martin-Blanco E, Kornberg TB, Pabo CO (1990) "Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions." Cell(Cambridge,Mass.), 63, 579-590. doi: 10.1016/0092-8674(90)90453-L. Crystal structure of an engrailed homeodomain-DNA complex at 2.8 angstroms resolution: a framework for understanding homeodomain-DNA interactions. SNAP output
1hf0 transcription X-ray (2.7 Å) Remenyi A, Tomilin A, Pohl E, Lins K, Philippsen A, Reinbold R, Scholer HR, Wilmanns M (2001) "Differential Dimer Activities of the Transcription Factor Oct-1 by DNA-Induced Interface Swapping." Mol.Cell, 8, 569. doi: 10.1016/S1097-2765(01)00336-7. Crystal structure of the DNA-binding domain of oct-1 bound to DNA as a dimer. SNAP output
1hht RNA polymerase X-ray (2.9 Å) Butcher SJ, Grimes JM, Makeyev EV, Bamford DH, Stuart DI (2001) "A Mechanism for Initiating RNA-Dependent RNA Polymerization." Nature, 410, 235. doi: 10.1038/35065653. RNA dependent RNA polymerase from dsrna bacteriophage phi6 plus template. SNAP output
1hi0 RNA polymerase X-ray (3.0 Å) Butcher SJ, Grimes JM, Makeyev EV, Bamford DH, Stuart DI (2001) "A Mechanism for Initiating RNA-Dependent RNA Polymerization." Nature, 410, 235. doi: 10.1038/35065653. RNA dependent RNA polymerase from dsrna bacteriophage phi6 plus initiation complex. SNAP output
1hjb transcription-DNA X-ray (3.0 Å) Tahirov TH, Inoue-Bungo T, Morii H, Fujikawa A, Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T, Yamamoto M, Ishii S, Ogata K (2001) "Structural Analyses of DNA Recognition by the Aml1/Runx-1 Runt Domain and its Allosteric Control by Cbfbeta." Cell(Cambridge,Mass.), 104, 755. doi: 10.1016/S0092-8674(01)00271-9. Crystal structure of runx-1-aml1-cbfalpha runt domain and c-ebpbeta bzip homodimer bound to a DNA fragment from the csf-1r promoter. SNAP output
1hjc transcription-DNA X-ray (2.65 Å) Tahirov TH, Inoue-Bungo T, Morii H, Fujikawa A, Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T, Yamamoto M, Ishii S, Ogata K (2001) "Structural Analyses of DNA Recognition by the Aml1/Runx-1 Runt Domain and its Allosteric Control by Cbfbeta." Cell(Cambridge,Mass.), 104, 755. doi: 10.1016/S0092-8674(01)00271-9. Crystal structure of runx-1-aml1-cbfalpha runt domain bound to a DNA fragment from the csf-1r promoter. SNAP output
1hlo transcription-DNA X-ray (2.8 Å) Brownlie P, Ceska T, Lamers M, Romier C, Stier G, Teo H, Suck D (1997) "The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control." Structure, 5, 509-520. doi: 10.1016/S0969-2126(97)00207-4. The crystal structure of an intact human max-DNA complex: new insights into mechanisms of transcriptional control. SNAP output
1hlv DNA binding protein-DNA X-ray (2.5 Å) Tanaka Y, Nureki O, Kurumizaka H, Fukai S, Kawaguchi S, Ikuta M, Iwahara J, Okazaki T, Yokoyama S (2001) "Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA." EMBO J., 20, 6612-6618. doi: 10.1093/emboj/20.23.6612. Crystal structure of cenp-b(1-129) complexed with the cenp-b box DNA. SNAP output
1hlz transcription-DNA X-ray (2.8 Å) Sierk ML, Zhao Q, Rastinejad F (2001) "DNA Deformability as a Recognition Feature in the RevErb Response Element." Biochemistry, 40, 12833-12843. doi: 10.1021/bi011086r. Crystal structure of the orphan nuclear receptor rev-erb(alpha) DNA-binding domain bound to its cognate response element. SNAP output
1hry DNA binding protein-DNA NMR Werner MH, Huth JR, Gronenborn AM, Clore GM (1995) "Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex." Cell(Cambridge,Mass.), 81, 704-705. doi: 10.1016/0092-8674(95)90532-4. The 3d structure of the human sry-DNA complex solved by multid-dimensional heteronuclear-edited and-filtered NMR. SNAP output
1hrz DNA binding protein-DNA NMR Werner MH, Huth JR, Gronenborn AM, Clore GM (1995) "Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex." Cell(Cambridge,Mass.), 81, 704-705. doi: 10.1016/0092-8674(95)90532-4. The 3d structure of the human sry-DNA complex solved by multi-dimensional heteronuclear-edited and-filtered NMR. SNAP output
1hu0 hydrolase-DNA X-ray (2.35 Å) Fromme JC, Bruner SD, Yang W, Karplus M, Verdine GL (2003) "Product-Assisted Catalysis in base-excision DNA Repair." Nat.Struct.Biol., 10, 204-211. doi: 10.1038/nsb902. Crystal structure of an hogg1-DNA borohydride trapped intermediate complex. SNAP output
1huo transferase-DNA X-ray (2.6 Å) Arndt JW, Gong W, Zhong X, Showalter AK, Liu J, Dunlap CA, Lin Z, Paxson C, Tsai MD, Chan MK (2001) "Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes." Biochemistry, 40, 5368-5375. doi: 10.1021/bi002176j. Crystal structure of DNA polymerase beta complexed with DNA and cr-tmppcp. SNAP output
1hut hydrolase-hydrolase inhibitor-DNA X-ray (2.9 Å) Padmanabhan K, Padmanabhan KP, Ferrara JD, Sadler JE, Tulinsky A (1993) "The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer." J.Biol.Chem., 268, 17651-17654. The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer. SNAP output
1huz transferase-DNA X-ray (2.6 Å) Arndt JW, Gong W, Zhong X, Showalter AK, Liu J, Dunlap CA, Lin Z, Paxson C, Tsai MD, Chan MK (2001) "Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes." Biochemistry, 40, 5368-5375. doi: 10.1021/bi002176j. Crystal structure of DNA polymerase complexed with DNA and cr-pcp. SNAP output
1hvn viral protein-DNA NMR South TL, Summers MF (1993) "Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein: NMR structure of the complex with the Psi-site analog, dACGCC." Protein Sci., 2, 3. Zinc-and sequence-dependent binding to nucleic acids by the n-terminal zinc finger domain of the hiv-1 nucleocapsid protein: NMR structure of the complex with the psi-site analog, d-acgcc. SNAP output
1hvo viral protein-DNA NMR South TL, Summers MF (1993) "Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein: NMR structure of the complex with the Psi-site analog, dACGCC." Protein Sci., 2, 3. Zinc-and sequence-dependent binding to nucleic acids by the n-terminal zinc finger domain of the hiv-1 nucleocapsid protein: NMR structure of the complex with the psi-site analog, d-acgcc. SNAP output
1hw2 transcription-DNA X-ray (3.25 Å) Xu Y, Heath RJ, Li Z, Rock CO, White SW (2001) "The FadR.DNA complex. Transcriptional control of fatty acid metabolism in Escherichia coli." J.Biol.Chem., 276, 17373-17379. doi: 10.1074/jbc.M100195200. Fadr-DNA complex: transcriptional control of fatty acid metabolism in echerichia coli. SNAP output
1hwt gene regulation-DNA X-ray (2.5 Å) King DA, Zhang L, Guarente L, Marmorstein R (1999) "Structure of a HAP1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein." Nat.Struct.Biol., 6, 64-71. doi: 10.1038/4940. Structure of a hap1-DNA complex reveals dramatically asymmetric DNA binding by a homodimeric protein. SNAP output
1hys transferase-DNA-RNA hybrid X-ray (3.0 Å) Sarafianos SG, Das K, Tantillo C, Clark Jr AD, Ding J, Whitcomb JM, Boyer PL, Hughes SH, Arnold E (2001) "Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA." EMBO J., 20, 1449-1461. doi: 10.1093/emboj/20.6.1449. Crystal structure of hiv-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. SNAP output
1i3j hydrolase-DNA X-ray (2.2 Å) Van Roey P, Waddling CA, Fox KM, Belfort M, Derbyshire V (2001) "Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate." EMBO J., 20, 3631-3637. doi: 10.1093/emboj/20.14.3631. Crystal structure of the DNA-binding domain of intron endonuclease i-tevi with its substrate. SNAP output
1i3w DNA-antibiotic X-ray (1.7 Å) Robinson H, Gao YG, Yang X, Sanishvili R, Joachimiak A, Wang AH (2001) "Crystallographic Analysis of a Novel Complex of Actinomycin D Bound to the DNA Decamer Cgatcgatcg." Biochemistry, 40, 5587. doi: 10.1021/BI002859Z. Actinomycin d binding to cgatcgatcg. SNAP output
1i6h transcription-DNA-RNA hybrid X-ray (3.3 Å) Gnatt AL, Cramer P, Fu J, Bushnell DA, Kornberg RD (2001) "Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution." Science, 292, 1876-1882. doi: 10.1126/science.1059495. RNA polymerase ii elongation complex. SNAP output
1i6j transferase-DNA X-ray (2.0 Å) Cote ML, Georgiadis MM (2001) "Structure of a pseudo-16-mer DNA with stacked guanines and two G-A mispairs complexed with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase." Acta Crystallogr.,Sect.D, 57, 1238-1250. doi: 10.1107/S090744490100943X. Crystal structure of a pseudo-16-mer DNA with stacked guanines and two g-a mispairs complexed with the n-terminal fragment of moloney murine leukemia virus reverse transcriptase. SNAP output
1i7d isomerase-DNA X-ray (2.05 Å) Changela A, DiGate RJ, Mondragon A (2001) "Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule." Nature, 411, 1077-1081. doi: 10.1038/35082615. Noncovalent complex of e.coli DNA topoisomerase iii with an 8-base single-stranded DNA oligonucleotide. SNAP output
1i8m immune system-DNA X-ray (2.1 Å) Tanner JJ, Komissarov AA, Deutscher SL (2001) "Crystal Structure of an Antigen-Binding Fragment Bound to Single-Stranded DNA." J.Mol.Biol., 314, 807-822. doi: 10.1006/jmbi.2001.5178. Crystal structure of a recombinant anti-single-stranded DNA antibody fragment complexed with dt5. SNAP output
1iaw hydrolase-DNA X-ray (2.4 Å) Huai Q, Colandene JD, Topal MD, Ke H (2001) "Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement." Nat.Struct.Biol., 8, 665-669. doi: 10.1038/90366. Crystal structure of naei complexed with 17mer DNA. SNAP output
1ic8 transcription-DNA X-ray (2.6 Å) Chi Y-I, Frantz JD, Oh B-C, Hansen L, Dhe-Paganon S, Shoelson SE (2002) "Diabetes mutations delineate an atypical POU domains in HNF1-Alpha." Mol.Cell, 10, 1129-1137. doi: 10.1016/S1097-2765(02)00704-9. Hepatocyte nuclear factor 1a bound to DNA : mody3 gene product. SNAP output
1id3 structural protein-DNA X-ray (3.1 Å) White CL, Suto RK, Luger K (2001) "Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions." EMBO J., 20, 5207-5218. doi: 10.1093/emboj/20.18.5207. Crystal structure of the yeast nucleosome core particle reveals fundamental differences in inter-nucleosome interactions. SNAP output
1if1 transcription-DNA X-ray (3.0 Å) Escalante CR, Yie J, Thanos D, Aggarwal AK (1998) "Structure of IRF-1 with bound DNA reveals determinants of interferon regulation." Nature, 391, 103-106. doi: 10.1038/34224. Interferon regulatory factor 1 (irf-1) complex with DNA. SNAP output
1ig4 transcription-DNA NMR Ohki I, Shimotake N, Fujita N, Jee J, Ikegami T, Nakao M, Shirakawa M (2001) "Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA." Cell(Cambridge,Mass.), 105, 487-497. doi: 10.1016/S0092-8674(01)00324-5. Solution structure of the methyl-cpg-binding domain of human mbd1 in complex with methylated DNA. SNAP output
1ig7 transcription-DNA X-ray (2.2 Å) Hovde S, Abate-Shen C, Geiger JH (2001) "Crystal structure of the Msx-1 homeodomain/DNA complex." Biochemistry, 40, 12013-12021. doi: 10.1021/bi0108148. Msx-1 homeodomain-DNA complex structure. SNAP output
1ig9 transferase-DNA X-ray (2.6 Å) Franklin MC, Wang J, Steitz TA (2001) "Structure of the Replicating Complex of a Pol Alpha Family DNA Polymerase." Cell(Cambridge,Mass.), 105, 657-667. doi: 10.1016/S0092-8674(01)00367-1. Structure of the replicating complex of a pol alpha family DNA polymerase. SNAP output
1ign DNA binding protein-DNA X-ray (2.25 Å) Konig P, Giraldo R, Chapman L, Rhodes D (1996) "The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA." Cell(Cambridge,Mass.), 85, 125-136. doi: 10.1016/S0092-8674(00)81088-0. DNA-binding domain of rap1 in complex with telomeric DNA site. SNAP output
1ihf transcription-DNA X-ray (2.5 Å) Rice PA, Yang S, Mizuuchi K, Nash HA (1996) "Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn." Cell(Cambridge,Mass.), 87, 1295-1306. doi: 10.1016/S0092-8674(00)81824-3. Integration host factor-DNA complex. SNAP output
1ijs virus-DNA X-ray (3.25 Å) Llamas-Saiz AL, Agbandje-McKenna M, Parker JS, Wahid AT, Parrish CR, Rossmann MG (1996) "Structural analysis of a mutation in canine parvovirus which controls antigenicity and host range." Virology, 225, 65-71. doi: 10.1006/viro.1996.0575. Cpv (strain d) mutant a300d, complex (viral coat-DNA), vp2, ph=7.5, t=4 degrees c. SNAP output
1ijw DNA binding protein-DNA X-ray (2.4 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations.. SNAP output
1imh transcription-DNA X-ray (2.86 Å) Stroud JC, Lopez-Rodriguez C, Rao A, Chen L (2002) "Structure of a TonEBP-DNA complex reveals DNA encircled by a transcription factor." Nat.Struct.Biol., 9, 90-94. doi: 10.1038/nsb749. Tonebp-DNA complex. SNAP output
1io4 transcription-DNA X-ray (3.0 Å) Tahirov TH, Inoue-Bungo T, Morii H, Fujikawa A, Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T, Yamamoto M, Ishii S, Ogata K (2001) "Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta." Cell(Cambridge,Mass.), 104, 755-767. doi: 10.1016/S0092-8674(01)00271-9. Crystal structure of runx-1-aml1-cbfalpha runt domain-cbfbeta core domain heterodimer and c-ebpbeta bzip homodimer bound to a DNA fragment from the csf-1r promoter. SNAP output
1ipp transcription-DNA X-ray (2.2 Å) Flick KE, Jurica MS, Monnat Jr RJ, Stoddard BL (1998) "DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI." Nature, 394, 96-101. doi: 10.1038/27952. Homing endonuclease-DNA complex. SNAP output
1iu3 replication inhibitor-DNA X-ray (3.0 Å) Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe M, Hiraga S, Yokoyama S (2004) "Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein." Nucleic Acids Res., 32, 82-92. doi: 10.1093/nar/gkh173. Crystal structure of the e.coli seqa protein complexed with hemimethylated DNA. SNAP output
1iv6 DNA binding protein-DNA NMR Nishikawa T, Okamura H, Nagadoi A, Konig P, Rhodes D, Nishimura Y (2001) "Solution structure of a telomeric DNA complex of human TRF1." Structure, 9, 1237-1251. doi: 10.1016/S0969-2126(01)00688-8. Solution structure of the DNA complex of human trf1. SNAP output
1ixy transferase-DNA X-ray (2.5 Å) Lariviere L, Morera S (2002) "A Base-flipping Mechanism for the T4 Phage beta-Glucosyltransferase and Identification of a Transition-state Analog." J.Mol.Biol., 324, 483-490. doi: 10.1016/S0022-2836(02)01091-4. Ternary complex of t4 phage bgt with udp and a 13 mer DNA duplex. SNAP output
1j1v replication-DNA X-ray (2.1 Å) Fujikawa N, Kurumizaka H, Nureki O, Terada T, Shirouzu M, Katayama T, Yokoyama S (2003) "Structural basis of replication origin recognition by the DnaA protein." NUCLEIC ACIDS RES., 31, 2077-2086. doi: 10.1093/nar/gkg309. Crystal structure of dnaa domainiv complexed with dnaabox DNA. SNAP output
1j3e replication-DNA X-ray (2.5 Å) Fujikawa N, Kurumizaka H, Nureki O, Tanaka Y, Yamazoe M, Hiraga S, Yokoyama S (2004) "Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein." Nucleic Acids Res., 32, 82-92. doi: 10.1093/nar/gkh173. Crystal structure of the e.coli seqa protein complexed with n6-methyladenine- guanine mismatch DNA. SNAP output
1j46 transcription-DNA NMR Murphy EC, Zhurkin VB, Louis JM, Cornilescu G, Clore GM (2001) "Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation." J.Mol.Biol., 312, 481-499. doi: 10.1006/jmbi.2001.4977. 3d solution NMR structure of the wild type hmg-box domain of the human male sex determining factor sry complexed to DNA. SNAP output
1j47 transcription-DNA NMR Murphy EC, Zhurkin VB, Louis JM, Cornilescu G, Clore GM (2001) "Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation." J.Mol.Biol., 312, 481-499. doi: 10.1006/jmbi.2001.4977. 3d solution NMR structure of the m9i mutant of the hmg-box domain of the human male sex determining factor sry complexed to DNA. SNAP output
1j4w transcription-DNA NMR Braddock DT, Louis JM, Baber JL, Levens D, Clore GM (2002) "Structure and dynamics of KH domains from FBP bound to single-stranded DNA." Nature, 415, 1051-1056. doi: 10.1038/4151051a. Complex of the kh3 and kh4 domains of fbp with a single_stranded 29mer DNA oligonucleotide from the fuse element of the c-myc oncogene. SNAP output
1j59 gene regulation-DNA X-ray (2.5 Å) Parkinson G, Wilson C, Gunasekera A, Ebright YW, Ebright RE, Berman HM (1996) "Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface." J.Mol.Biol., 260, 395-408. doi: 10.1006/jmbi.1996.0409. Catabolite gene activator protein (cap)-DNA complex + adenosine-3',5'-cyclic-monophosphate. SNAP output
1j5k transcription-DNA NMR Braddock DT, Baber JL, Levens D, Clore GM (2002) "Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA." EMBO J., 21, 3476-3485. doi: 10.1093/emboj/cdf352. Complex of the kh3 domain of hnrnp k with a single_stranded 10mer DNA oligonucleotide. SNAP output
1j5n DNA binding protein-DNA NMR Masse JE, Wong B, Yen Y-M, Allain FH-T, Johnson RC, Feigon J (2002) "The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding." J.Mol.Biol., 323, 263-284. doi: 10.1016/S0022-2836(02)00938-5. Solution structure of the non-sequence-specific hmgb protein nhp6a in complex with sry DNA. SNAP output
1j5o transferase-immune system-DNA X-ray (3.5 Å) Sarafianos SG, Das K, Clark Jr AD, Ding J, Boyer PL, Hughes SH, Arnold E (1999) "Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with beta-branched amino acids." Proc.Natl.Acad.Sci.USA, 96, 10027-10032. doi: 10.1073/pnas.96.18.10027. Crystal structure of met184ile mutant of hiv-1 reverse transcriptase in complex with double stranded DNA template-primer. SNAP output
1j75 immune system-DNA X-ray (1.85 Å) Schwartz T, Behlke J, Lowenhaupt K, Heinemann U, Rich A (2001) "Structure of the DLM-1-Z-DNA complex reveals a conserved family of Z-DNA-binding proteins." Nat.Struct.Biol., 8, 761-765. doi: 10.1038/nsb0901-761. Crystal structure of the DNA-binding domain zalpha of dlm-1 bound to z-DNA. SNAP output
1j9n DNA binding protein-DNA NMR Gomez-Pinto I, Marchan V, Gago F, Grandas A, Gonzalez C (2003) "Solution structure and stability of tryptophan-containing nucleopeptide duplexes." Chembiochem, 4, 40-49. doi: 10.1002/cbic.200390012. Solution structure of the nucleopeptide [ac-lys-trp-lys-hse(p3*dgcatcg)-ala]-[p5*dcgtagc]. SNAP output
1jb7 DNA-binding protein-DNA X-ray (1.86 Å) Horvath MP, Schultz SC (2001) "DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex." J.Mol.Biol., 310, 367-377. doi: 10.1006/jmbi.2001.4766. DNA g-quartets in a 1.86 Å resolution structure of an oxytricha nova telomeric protein-DNA complex. SNAP output
1je8 transcription-DNA X-ray (2.12 Å) Maris AE, Sawaya MR, Kaczor-Grzeskowiak M, Jarvis MR, Bearson SM, Kopka ML, Schroder I, Gunsalus RP, Dickerson RE (2002) "Dimerization allows DNA target site recognition by the NarL response regulator." Nat.Struct.Biol., 9, 771-778. doi: 10.1038/nsb845. Two-component response regulator narl-DNA complex: DNA bending found in a high affinity site. SNAP output
1jey DNA binding protein-DNA X-ray (2.5 Å) Walker JR, Corpina RA, Goldberg J (2001) "Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair." Nature, 412, 607-614. doi: 10.1038/35088000. Crystal structure of the ku heterodimer bound to DNA. SNAP output
1jfi transcription-DNA X-ray (2.62 Å) Kamada K, Shu F, Chen H, Malik S, Stelzer G, Roeder RG, Meisterernst M, Burley SK (2001) "Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex." Cell(Cambridge,Mass.), 106, 71-81. doi: 10.1016/S0092-8674(01)00417-2. Crystal structure of the nc2-tbp-DNA ternary complex. SNAP output
1jfs transcription-DNA X-ray (2.9 Å) Huffman JL, Lu F, Zalkin H, Brennan RG (2002) "Role of residue 147 in the gene regulatory function of the Escherichia coli purine repressor." Biochemistry, 41, 511-520. doi: 10.1021/bi0156660. Purine repressor mutant-hypoxanthine-purf operator complex. SNAP output
1jft transcription-DNA X-ray (2.5 Å) Huffman JL, Lu F, Zalkin H, Brennan RG (2002) "Role of residue 147 in the gene regulatory function of the Escherichia coli purine repressor." Biochemistry, 41, 511-520. doi: 10.1021/bi0156660. Purine repressor mutant-hypoxanthine-purf operator complex. SNAP output
1jgg transcription-DNA X-ray (2.0 Å) Hirsch JA, Aggarwal AK (1995) "Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity." EMBO J., 14, 6280-6291. Even-skipped homeodomain complexed to at-rich DNA. SNAP output
1jh9 transcription-DNA X-ray (2.55 Å) Huffman JL, Lu F, Zalkin H, Brennan RG (2002) "Role of residue 147 in the gene regulatory function of the Escherichia coli purine repressor." Biochemistry, 41, 511-520. doi: 10.1021/bi0156660. Purine repressor mutant-hypoxanthine-purf operator complex. SNAP output
1jj4 transcription-DNA X-ray (2.4 Å) Kim SS, Tam JK, Wang AF, Hegde RS (2000) "The structural basis of DNA target discrimination by papillomavirus E2 proteins." J.Biol.Chem., 275, 31245-31254. doi: 10.1074/jbc.M004541200. Human papillomavirus type 18 e2 DNA-binding domain bound to its DNA target. SNAP output
1jj6 DNA binding protein-DNA X-ray (2.3 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations.. SNAP output
1jj8 DNA binding protein-DNA X-ray (2.75 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations. SNAP output
1jk1 transcription-DNA X-ray (1.9 Å) Miller JC, Pabo CO (2001) "Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition." J.Mol.Biol., 313, 309-315. doi: 10.1006/jmbi.2001.4975. Zif268 d20a mutant bound to wt DNA site. SNAP output
1jk2 transcription-DNA X-ray (1.65 Å) Miller JC, Pabo CO (2001) "Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition." J.Mol.Biol., 313, 309-315. doi: 10.1006/jmbi.2001.4975. Zif268 d20a mutant bound to the gct DNA site. SNAP output
1jko DNA binding protein-DNA X-ray (2.24 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations. SNAP output
1jkp DNA binding protein-DNA X-ray (2.8 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations. SNAP output
1jkq DNA binding protein-DNA X-ray (2.86 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations. SNAP output
1jkr DNA binding protein-DNA X-ray (2.28 Å) Chiu TK, Sohn C, Dickerson RE, Johnson RC (2002) "Testing water-mediated DNA recognition by the Hin recombinase." EMBO J., 21, 801-814. doi: 10.1093/emboj/21.4.801. Testing the water-mediated hin recombinase DNA recognition by systematic mutations. SNAP output
1jmc replication-DNA X-ray (2.4 Å) Bochkarev A, Pfuetzner RA, Edwards AM, Frappier L (1997) "Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA." Nature, 385, 176-181. doi: 10.1038/385176a0. Single stranded DNA-binding domain of human replication protein a bound to single stranded DNA, rpa70 subunit, residues 183-420. SNAP output
1jnm transcription-DNA X-ray (2.2 Å) Kim Y, Podust LM "Crystal Structure of the Jun bZIP homodimer complexed with CRE." Crystal structure of the jun-cre complex. SNAP output
1jt0 transcription-DNA X-ray (2.9 Å) Schumacher MA, Miller MC, Grkovic S, Brown MH, Skurray RA, Brennan RG (2002) "Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR." EMBO J., 21, 1210-1218. doi: 10.1093/emboj/21.5.1210. Crystal structure of a cooperative qacr-DNA complex. SNAP output
1jwl transcription-DNA X-ray (4.0 Å) Bell CE, Lewis M (2001) "Crystallographic analysis of Lac repressor bound to natural operator O1." J.Mol.Biol., 312, 921-926. doi: 10.1006/jmbi.2001.5024. Structure of the dimeric lac repressor-operator o1-onpf complex. SNAP output
1jx4 transferase-DNA X-ray (1.7 Å) Ling H, Boudsocq F, Woodgate R, Yang W (2001) "Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication." Cell(Cambridge,Mass.), 107, 91-102. doi: 10.1016/S0092-8674(01)00515-3. Crystal structure of a y-family DNA polymerase in a ternary complex with DNA substrates and an incoming nucleotide. SNAP output
1jxl transferase-DNA X-ray (2.1 Å) Ling H, Boudsocq F, Woodgate R, Yang W (2001) "Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication." Cell(Cambridge,Mass.), 107, 91-102. doi: 10.1016/S0092-8674(01)00515-3. Crystal structure of a y-family DNA polymerase in a ternary complex with DNA substrates and an incoming nucleotide. SNAP output
1k3w hydrolase-DNA X-ray (1.42 Å) Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman SE, Kycia JH, Rieger RA, Grollman AP, Shoham G (2002) "Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate." EMBO J., 21, 789-800. doi: 10.1093/emboj/21.4.789. Crystal structure of a trapped reaction intermediate of the DNA repair enzyme endonuclease viii with DNA. SNAP output
1k3x hydrolase-DNA X-ray (1.25 Å) Zharkov DO, Golan G, Gilboa R, Fernandes AS, Gerchman SE, Kycia JH, Rieger RA, Grollman AP, Shoham G (2002) "Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate." EMBO J., 21, 789-800. doi: 10.1093/emboj/21.4.789. Crystal structure of a trapped reaction intermediate of the DNA repair enzyme endonuclease viii with brominated-DNA. SNAP output
1k4s isomerase-DNA X-ray (3.2 Å) Staker BL, Hjerrild K, Feese MD, Behnke CA, Burgin Jr AB, Stewart LJ (2002) "The mechanism of topoisomerase I poisoning by a camptothecin analog." Proc.Natl.Acad.Sci.USA, 99, 15387-15392. doi: 10.1073/pnas.242259599. Human DNA topoisomerase i in covalent complex with a 22 base pair DNA duplex. SNAP output
1k4t isomerase-DNA X-ray (2.1 Å) Staker BL, Hjerrild K, Feese MD, Behnke CA, Burgin Jr AB, Stewart LJ (2002) "The mechanism of topoisomerase I poisoning by a camptothecin analog." Proc.Natl.Acad.Sci.USA, 99, 15387-15392. doi: 10.1073/pnas.242259599. Human DNA topoisomerase i (70 kda) in complex with the poison topotecan and covalent complex with a 22 base pair DNA duplex. SNAP output
1k61 transcription-DNA X-ray (2.1 Å) Aishima J, Gitti RK, Noah JE, Gan HH, Schlick T, Wolberger C (2002) "A Hoogsteen base pair embedded in undistorted B-DNA." NUCLEIC ACIDS RES., 30, 5244-5252. doi: 10.1093/nar/gkf661. Matalpha2 homeodomain bound to DNA. SNAP output
1k6o transcription-DNA X-ray (3.19 Å) Mo Y, Ho W, Johnston K, Marmorstein R (2001) "Crystal structure of a ternary SAP-1/SRF/c-fos SRE DNA complex." J.Mol.Biol., 314, 495-506. doi: 10.1006/jmbi.2001.5138. Crystal structure of a ternary sap-1-srf-c-fos sre DNA complex. SNAP output
1k78 transcription-DNA X-ray (2.25 Å) Garvie CW, Hagman J, Wolberger C (2001) "Structural studies of Ets-1/Pax5 complex formation on DNA." Mol.Cell, 8, 1267-1276. doi: 10.1016/S1097-2765(01)00410-5. Pax5(1-149)+ets-1(331-440)+DNA. SNAP output
1k79 transcription-DNA X-ray (2.4 Å) Garvie CW, Hagman J, Wolberger C (2001) "Structural studies of Ets-1/Pax5 complex formation on DNA." Mol.Cell, 8, 1267-1276. doi: 10.1016/S1097-2765(01)00410-5. Ets-1(331-440)+ggaa duplex. SNAP output
1k7a transcription-DNA X-ray (2.8 Å) Garvie CW, Hagman J, Wolberger C (2001) "Structural studies of Ets-1/Pax5 complex formation on DNA." Mol.Cell, 8, 1267-1276. doi: 10.1016/S1097-2765(01)00410-5. Ets-1(331-440)+ggag duplex. SNAP output
1k82 hydrolase-DNA X-ray (2.1 Å) Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G (2002) "Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA." J.Biol.Chem., 277, 19811-19816. doi: 10.1074/jbc.M202058200. Crystal structure of e.coli formamidopyrimidine-DNA glycosylase (fpg) covalently trapped with DNA. SNAP output
1k8g DNA binding protein-DNA X-ray (2.6 Å) Classen S, Ruggles JA, Schultz SC (2001) "Crystal structure of the N-terminal domain of Oxytricha nova telomere end-binding protein alpha subunit both uncomplexed and complexed with telomeric ssDNA." J.Mol.Biol., 314, 1113-1125. doi: 10.1006/jmbi.2000.5191. Crystal structure of the n-terminal domain of oxytricha nova telomere end binding protein alpha subunit both uncomplexed and complexed with telomeric ssDNA. SNAP output
1kb2 transcription-DNA X-ray (2.7 Å) Shaffer PL, Gewirth DT (2002) "Structural basis of VDR-DNA interactions on direct repeat response elements." EMBO J., 21, 2242-2252. doi: 10.1093/emboj/21.9.2242. Crystal structure of vdr DNA-binding domain bound to mouse osteopontin (spp) response element. SNAP output
1kb4 transcription-DNA X-ray (2.8 Å) Shaffer PL, Gewirth DT (2002) "Structural basis of VDR-DNA interactions on direct repeat response elements." EMBO J., 21, 2242-2252. doi: 10.1093/emboj/21.9.2242. Crystal structure of vdr DNA-binding domain bound to a canonical direct repeat with three base pair spacer (dr3) response element. SNAP output
1kb6 transcription-DNA X-ray (2.7 Å) Shaffer PL, Gewirth DT (2002) "Structural basis of VDR-DNA interactions on direct repeat response elements." EMBO J., 21, 2242-2252. doi: 10.1093/emboj/21.9.2242. Crystal structure of vdr DNA-binding domain bound to rat osteocalcin (oc) response element. SNAP output
1kbu hydrolase, ligase-DNA X-ray (2.2 Å) Martin SS, Pulido E, Chu VC, Lechner TS, Baldwin EP (2002) "The Order of Strand Exchanges in Cre-LoxP Recombination and its Basis Suggested by the Crystal Structure of a Cre-LoxP Holliday Junction Complex." J.Mol.Biol., 319, 107-127. doi: 10.1016/S0022-2836(02)00246-2. Cre recombinase bound to a loxp holliday junction. SNAP output
1kc6 hydrolase-DNA X-ray (2.6 Å) Horton NC, Dorner LF, Perona JJ (2002) "Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation." Nat.Struct.Biol., 9, 42-47. doi: 10.1038/nsb741. Hincii bound to cognate DNA. SNAP output
1kc8 ribosome X-ray (3.01 Å) Hansen J, Moore PB, Steitz TA (2003) "Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit." J.Mol.Biol., 330, 1061-1075. doi: 10.1016/S0022-2836(03)00668-5. Co-crystal structure of blasticidin s bound to the 50s ribosomal subunit. SNAP output
1kdh transferase-DNA X-ray (3.0 Å) Delarue M, Boule JB, Lescar J, Expert-Bezancon N, Jourdan N, Sukumar N, Rougeon F, Papanicolaou C (2002) "Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase." EMBO J., 21, 427-439. doi: 10.1093/emboj/21.3.427. Binary complex of murine terminal deoxynucleotidyl transferase with a primer single stranded DNA. SNAP output
1keg immune system-DNA X-ray (2.4 Å) Yokoyama H, Mizutani R, Satow Y, Sato K, Komatsu Y, Ohtsuka E, Nikaido O (2012) "Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides." Acta Crystallogr.,Sect.D, 68, 232-238. doi: 10.1107/S0907444912000327. Antibody 64m-2 fab complexed with dtt(6-4)tt. SNAP output
1kfs transferase-DNA X-ray (2.1 Å) Brautigam CA, Steitz TA (1998) "Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates." J.Mol.Biol., 277, 363-377. doi: 10.1006/jmbi.1997.1586. DNA polymerase i klenow fragment (e.c.2.7.7.7) mutant-DNA complex. SNAP output
1kfv hydrolase-DNA X-ray (2.55 Å) Serre L, Pereira de Jesus K, Boiteux S, Zelwer C, Castaing B (2002) "Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA." EMBO J., 21, 2854-2865. doi: 10.1093/emboj/cdf304. Crystal structure of lactococcus lactis formamido-pyrimidine DNA glycosylase (alias fpg or mutm) non covalently bound to an ap site containing DNA.. SNAP output
1kix DNA binding protein-DNA X-ray (2.7 Å) Peersen OB, Ruggles JA, Schultz SC (2002) "Dimeric structure of the Oxytricha nova telomere end-binding protein alpha-subunit bound to ssDNA." Nat.Struct.Biol., 9, 182-187. Dimeric structure of the o. nova telomere end binding protein alpha subunit with bound ssDNA. SNAP output
1kln transferase-DNA X-ray (3.2 Å) Beese LS, Derbyshire V, Steitz TA (1993) "Structure of DNA polymerase I Klenow fragment bound to duplex DNA." Science, 260, 352-355. DNA polymerase i klenow fragment (e.c.2.7.7.7) mutant-DNA complex. SNAP output
1kqq transcription-DNA NMR Iwahara J, Iwahara M, Daughdrill GW, Ford J, Clubb RT (2002) "The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA." EMBO J., 21, 1197-1209. doi: 10.1093/emboj/21.5.1197. Solution structure of the dead ringer arid-DNA complex. SNAP output
1krp transferase-DNA X-ray (2.2 Å) Brautigam CA, Steitz TA (1998) "Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates." J.Mol.Biol., 277, 363-377. doi: 10.1006/jmbi.1997.1586. DNA polymerase i klenow fragment (e.c.2.7.7.7) mutant-DNA complex. SNAP output
1ksp transferase-DNA X-ray (2.3 Å) Brautigam CA, Steitz TA (1998) "Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates." J.Mol.Biol., 277, 363-377. doi: 10.1006/jmbi.1997.1586. DNA polymerase i klenow fragment (e.c.2.7.7.7) mutant-DNA complex. SNAP output
1ksx replication-DNA X-ray (3.2 Å) Enemark EJ, Stenlund A, Joshua-Tor L (2002) "Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex." EMBO J., 21, 1487-1496. doi: 10.1093/emboj/21.6.1487. Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex. SNAP output
1ksy replication-DNA X-ray (3.05 Å) Enemark EJ, Stenlund A, Joshua-Tor L (2002) "Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex." EMBO J., 21, 1487-1496. doi: 10.1093/emboj/21.6.1487. Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complex. SNAP output
1ku7 transcription-DNA X-ray (2.4 Å) Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA (2002) "Structure of the bacterial RNA polymerase promoter specificity sigma subunit." Mol.Cell, 9, 527-539. doi: 10.1016/S1097-2765(02)00470-7. Crystal structure of thermus aquatics RNA polymerase sigmaa subunit region 4 bound to-35 element DNA. SNAP output
1kx3 structural protein-DNA X-ray (2.0 Å) Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ (2002) "Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution." J.Mol.Biol., 319, 1097-1113. doi: 10.1016/S0022-2836(02)00386-8. X-ray structure of the nucleosome core particle, ncp146, at 2.0 Å resolution. SNAP output
1kx4 structural protein-DNA X-ray (2.6 Å) Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ (2002) "Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution." J.Mol.Biol., 319, 1097-1113. doi: 10.1016/S0022-2836(02)00386-8. X-ray structure of the nucleosome core particle, ncp146b, at 2.6 Å resolution. SNAP output
1kx5 structural protein-DNA X-ray (1.94 Å) Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ (2002) "Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution." J.Mol.Biol., 319, 1097-1113. doi: 10.1016/S0022-2836(02)00386-8. X-ray structure of the nucleosome core particle, ncp147, at 1.9 Å resolution. SNAP output
1l1m transcription regulator-DNA NMR Kalodimos CG, Bonvin AM, Salinas RK, Wechselberger R, Boelens R, Kaptein R (2002) "Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain." EMBO J., 21, 2866-2876. doi: 10.1093/emboj/cdf318. Solution structure of a dimer of lac repressor DNA-binding domain complexed to its natural operator o1. SNAP output
1l1t hydrolase-DNA X-ray (1.8 Å) Fromme JC, Verdine GL (2002) "Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM." Nat.Struct.Biol., 9, 544-552. Mutm (fpg) bound to abasic-site containing DNA. SNAP output
1l1v DNA-antibiotic NMR Chou SH, Chin KH, Chen FM (2002) "Looped Out and Perpendicular: Deformation of Watson-Crick Base Pair Associated with Actinomycin D Binding." Proc.Natl.Acad.Sci.USA, 99, 6625. doi: 10.1073/PNAS.102580399. Unusual actd-dna_ta complex structure. SNAP output
1l1z hydrolase-DNA X-ray (1.7 Å) Fromme JC, Verdine GL (2002) "Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM." Nat.Struct.Biol., 9, 544-552. Mutm (fpg) covalent-DNA intermediate. SNAP output
1l2b hydrolase-DNA X-ray (2.4 Å) Fromme JC, Verdine GL (2002) "Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM." Nat.Struct.Biol., 9, 544-552. Mutm (fpg) DNA end-product structure. SNAP output
1l2c hydrolase-DNA X-ray (2.2 Å) Fromme JC, Verdine GL (2002) "Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM." Nat.Struct.Biol., 9, 544-552. Mutm (fpg)-DNA estranged thymine mismatch recognition complex. SNAP output
1l2d hydrolase-DNA X-ray (2.0 Å) Fromme JC, Verdine GL (2002) "Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM." Nat.Struct.Biol., 9, 544-552. Mutm (fpg)-DNA estranged guanine mismatch recognition complex. SNAP output
1l3l transcription-DNA X-ray (1.66 Å) Zhang RG, Pappas T, Brace JL, Miller PC, Oulmassov T, Molyneaux JM, Anderson JC, Bashkin JK, Winans SC, Joachimiak A (2002) "Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA." Nature, 417, 971-974. doi: 10.1038/nature00833. Crystal structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA. SNAP output
1l3s transferase-DNA X-ray (1.7 Å) Johnson SJ, Taylor JS, Beese LS (2003) "Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations." Proc.Natl.Acad.Sci.USA, 100, 3895-3900. doi: 10.1073/pnas.0630532100. Crystal structure of bacillus DNA polymerase i fragment complexed to 9 base pairs of duplex DNA.. SNAP output
1l3t transferase-DNA X-ray (1.7 Å) Johnson SJ, Taylor JS, Beese LS (2003) "Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations." Proc.Natl.Acad.Sci.USA, 100, 3895-3900. doi: 10.1073/pnas.0630532100. Crystal structure of bacillus DNA polymerase i fragment product complex with 10 base pairs of duplex DNA following addition of a single dttp residue. SNAP output
1l3u transferase-DNA X-ray (1.8 Å) Johnson SJ, Taylor JS, Beese LS (2003) "Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations." Proc.Natl.Acad.Sci.USA, 100, 3895-3900. doi: 10.1073/pnas.0630532100. Crystal structure of bacillus DNA polymerase i fragment product complex with 11 base pairs of duplex DNA following addition of a dttp and a datp residue.. SNAP output
1l3v transferase-DNA X-ray (1.71 Å) Johnson SJ, Taylor JS, Beese LS (2003) "Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations." Proc.Natl.Acad.Sci.USA, 100, 3895-3900. doi: 10.1073/pnas.0630532100. Crystal structure of bacillus DNA polymerase i fragment product complex with 15 base pairs of duplex DNA following addition of dttp, datp, dctp, and dgtp residues.. SNAP output
1l5u transferase-DNA X-ray (1.95 Å) Johnson SJ, Taylor JS, Beese LS (2003) "Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations." Proc.Natl.Acad.Sci.USA, 100, 3895-3900. doi: 10.1073/pnas.0630532100. Crystal structure of bacillus DNA polymerase i fragment product complex with 12 base pairs of duplex DNA following addition of a dttp, a datp, and a dctp residue.. SNAP output
1lat transcription-DNA X-ray (1.9 Å) Gewirth DT, Sigler PB (1995) "The basis for half-site specificity explored through a non-cognate steroid receptor-DNA complex." Nat.Struct.Biol., 2, 386-394. doi: 10.1038/nsb0595-386. Glucocorticoid receptor mutant-DNA complex. SNAP output
1lau hydrolase-DNA X-ray (1.8 Å) Savva R, McAuley-Hecht K, Brown T, Pearl L (1995) "The structural basis of specific base-excision repair by uracil-DNA glycosylase." Nature, 373, 487-493. doi: 10.1038/373487a0. Uracil-DNA glycosylase. SNAP output
1lb2 gene regulation-DNA X-ray (3.1 Å) Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH (2002) "Structural basis of transcription activation: the CAP-alpha CTD-DNA complex." Science, 297, 1562-1566. doi: 10.1126/science.1076376. Structure of the e. coli alpha c-terminal domain of RNA polymerase in complex with cap and DNA. SNAP output
1lcc gene regulation-DNA NMR Chuprina VP, Rullmann JA, Lamerichs RM, van Boom JH, Boelens R, Kaptein R (1993) "Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics." J.Mol.Biol., 234, 446-462. doi: 10.1006/jmbi.1993.1598. Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. SNAP output
1lcd gene regulation-DNA NMR Chuprina VP, Rullmann JA, Lamerichs RM, van Boom JH, Boelens R, Kaptein R (1993) "Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics." J.Mol.Biol., 234, 446-462. doi: 10.1006/jmbi.1993.1598. Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. SNAP output
1le5 transcription-DNA X-ray (2.75 Å) Berkowitz B, Huang DB, Chen-Park FE, Sigler PB, Ghosh G (2002) "The X-ray crystal structure of the NF-kB p50/p65 heterodimer bound to the Interferon beta-kB site." J.Biol.Chem., 277, 24694-24700. doi: 10.1074/jbc.M200006200. Crystal structure of a nf-kb heterodimer bound to an ifnb-kb. SNAP output
1le8 transcription-DNA X-ray (2.3 Å) Ke A, Mathias JR, Vershon AK, Wolberger C (2002) "Structural and Thermodynamic Characterization of the DNA Binding Properties of a Triple Alanine Mutant of MATalpha2." Structure, 10, 961-971. doi: 10.1016/S0969-2126(02)00790-6. Crystal structure of the mata1-matalpha2-3a heterodimer bound to DNA complex. SNAP output
1le9 transcription-DNA X-ray (3.0 Å) Berkowitz B, Huang DB, Chen-Park FE, Sigler PB, Ghosh G (2002) "The x-ray crystal structure of the NF-kappa B p50.p65 heterodimer bound to the interferon beta -kappa B site." J.Biol.Chem., 277, 24694-24700. doi: 10.1074/jbc.M200006200. Crystal structure of a nf-kb heterodimer bound to the ig-hiv-kb siti. SNAP output
1lei transcription-DNA X-ray (2.7 Å) Chen-Park FE, Huang DB, Noro B, Thanos D, Ghosh G (2002) "The kB DNA sequence from the HIV Long Terminal Repeat functions as an allosteric regulator of HIV transcription." J.Biol.Chem., 277, 24701-24708. doi: 10.1074/jbc.M200007200. The kb DNA sequence from the hlv-ltr functions as an allosteric regulator of hiv transcription. SNAP output
1lfu transcription NMR Sprules T, Green N, Featherstone M, Gehring K (2003) "Lock and Key Binding of the HOX YPWM Peptide to the PBX Homeodomain." J.Biol.Chem., 278, 1053-1058. doi: 10.1074/jbc.M207504200. NMR solution structure of the extended pbx homeodomain bound to DNA. SNAP output
1lli transcription-DNA X-ray (2.1 Å) Lim WA, Hodel A, Sauer RT, Richards FM (1994) "The crystal structure of a mutant protein with altered but improved hydrophobic core packing." Proc.Natl.Acad.Sci.USA, 91, 423-427. doi: 10.1073/pnas.91.1.423. The crystal structure of a mutant protein with altered but improved hydrophobic core packing. SNAP output
1llm transcription-DNA X-ray (1.5 Å) Wolfe SA, Grant RA, Pabo CO (2003) "Structure of a designed dimeric zinc finger protein bound to DNA." Biochemistry, 42, 13401-13409. doi: 10.1021/bi034830b. Crystal structure of a zif23-gcn4 chimera bound to DNA. SNAP output
1lmb transcription-DNA X-ray (1.8 Å) Beamer LJ, Pabo CO (1992) "Refined 1.8 A crystal structure of the lambda repressor-operator complex." J.Mol.Biol., 227, 177-196. doi: 10.1016/0022-2836(92)90690-L. Refined 1.8 angstrom crystal structure of the lambda repressor-operator complex. SNAP output
1lo1 hormone-growth factor receptor-DNA NMR Gearhart MD, Holmbeck SMA, Evans RM, Dyson HJ, Wright PE (2003) "Monomeric Complex of Human Orphan Estrogen Related Receptor-2 with DNA: A Pseudo-dimer Interface Mediates Extended Half-site Recognition." J.Mol.Biol., 327, 819-832. doi: 10.1016/S0022-2836(03)00183-9. Estrogen related receptor 2 DNA binding domain in complex with DNA. SNAP output
1lpq isomerase-DNA X-ray (3.14 Å) Lesher DT, Pommier Y, Stewart L, Redinbo MR (2002) "8-Oxoguanine rearranges the active site of human topoisomerase I." Proc.Natl.Acad.Sci.USA, 99, 12102-12107. doi: 10.1073/pnas.192282699. Human DNA topoisomerase i (70 kda) in non-covalent complex with a 22 base pair DNA duplex containing an 8-oxog lesion. SNAP output
1lq1 transcription-DNA X-ray (2.3 Å) Zhao H, Msadek T, Zapf J, Madhusudan, Hoch JA, Varughese KI (2002) "DNA complexed structure of the key transcription factor initiating development in sporulating bacteria." Structure, 10, 1041-1050. doi: 10.1016/S0969-2126(02)00803-1. DNA complexed structure of the key transcription factor initiating development in sporulation bacteria. SNAP output
1lrr replication inhibitor-DNA X-ray (2.65 Å) Guarne A, Zhao Q, Guirlando R, Yang W (2002) "Insights into negative modulation of E. coli replication initiation from the structure of SeqA-hemimethylated DNA complex." NAT.STRUCT.BIOL., 9, 839-843. Crystal structure of e. coli seqa complexed with hemimethylated DNA. SNAP output
1lv5 transferase-DNA X-ray (1.95 Å) Johnson SJ, Taylor JS, Beese LS (2003) "Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations." Proc.Natl.Acad.Sci.USA, 100, 3895-3900. doi: 10.1073/pnas.0630532100. Crystal structure of the closed conformation of bacillus DNA polymerase i fragment bound to DNA and dctp. SNAP output
1lws hydrolase-DNA X-ray (3.5 Å) Moure CM, Gimble FS, Quiocho FA (2002) "Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence." Nat.Struct.Biol., 9, 764-770. doi: 10.1038/nsb840. Crystal structure of the intein homing endonuclease pi-scei bound to its recognition sequence. SNAP output
1lwt hydrolase-DNA X-ray (3.2 Å) Moure CM, Gimble FS, Quiocho FA (2002) "Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence." Nat.Struct.Biol., 9, 764-770. doi: 10.1038/nsb840. Crystal structure of the intein homing endonuclease pi-scei bound to its substrate DNA (ca2+ free). SNAP output
1lwv hydrolase-DNA X-ray (2.3 Å) Fromme JC, Bruner SD, Yang W, Karplus M, Verdine GL (2003) "Product-Assisted Catalysis in Base Excision DNA Repair." Nat.Struct.Biol., 10, 204-211. doi: 10.1038/nsb902. Borohydride-trapped hogg1 intermediate structure co-crystallized with 8-aminoguanine. SNAP output
1lww hydrolase-DNA X-ray (2.1 Å) Fromme JC, Bruner SD, Yang W, Karplus M, Verdine GL (2003) "Product-Assisted Catalysis in Base Excision DNA Repair." Nat.Struct.Biol., 10, 204-211. doi: 10.1038/nsb902. Borohydride-trapped hogg1 intermediate structure co-crystallized with 8-bromoguanine. SNAP output
1lwy hydrolase-DNA X-ray (2.01 Å) Fromme JC, Bruner SD, Yang W, Karplus M, Verdine GL (2003) "Product-Assisted Catalysis in Base Excision DNA Repair." Nat.Struct.Biol., 10, 204-211. doi: 10.1038/nsb902. Hogg1 borohydride-trapped intermediate without 8-oxoguanine. SNAP output
1m07 hydrolase-DNA X-ray (1.8 Å) Leu Y-J, Chern S-S, Wang S-C, Hsiao Y-Y, Amiraslanov I, Liaw Y-C, Liao Y-D (2003) "Residues involved in the catalysis, base specificity, and cytotoxicity of ribonuclease from Rana catesbeiana based upon mutagenesis and X-ray crystallography." J.Biol.Chem., 278, 7300-7309. doi: 10.1074/jbc.M206701200. Residues involved in the catalysis and base specificity of cytotoxic ribonuclease from bullfrog (rana catesbeiana). SNAP output
1m0e transferase-DNA X-ray (2.5 Å) Zhou L, Cheng X, Connolly BA, Dickman MJ, Hurd PJ, Hornby DP (2002) "ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASES." J.MOL.BIOL., 321, 591-599. doi: 10.1016/S0022-2836(02)00676-9. Zebularine: a novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferase. SNAP output
1m18 structural protein-DNA X-ray (2.45 Å) Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K (2003) "Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands." J.Mol.Biol., 326, 371-380. doi: 10.1016/S0022-2836(02)01407-9. Ligand binding alters the structure and dynamics of nucleosomal DNA. SNAP output
1m19 structural protein-DNA X-ray (2.3 Å) Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K (2003) "Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands." J.Mol.Biol., 326, 371-380. doi: 10.1016/S0022-2836(02)01407-9. Ligand binding alters the structure and dynamics of nucleosomal DNA. SNAP output
1m1a structural protein-DNA X-ray (2.65 Å) Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K (2003) "Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands." J.MOL.BIOL., 326, 371-380. doi: 10.1016/S0022-2836(02)01407-9. Ligand binding alters the structure and dynamics of nucleosomal DNA. SNAP output
1m3h hydrolase-DNA X-ray (2.05 Å) Chung SJ, Verdine GL (2004) "Structures of End Products Resulting from Lesion Processing by a DNA Glycosylase/Lyase." Chem.Biol., 11, 1643-1649. doi: 10.1016/j.chembiol.2004.09.014. Crystal structure of hogg1 d268e mutant with product oligonucleotide. SNAP output
1m3q hydrolase-DNA X-ray (1.9 Å) Chung SJ, Verdine GL (2004) "Structures of End Products Resulting from Lesion Processing by a DNA Glycosylase/Lyase." Chem.Biol., 11, 1643-1649. doi: 10.1016/j.chembiol.2004.09.014. Crystal structure of hogg1 d268e mutant with base-excised DNA and 8-aminoguanine. SNAP output
1m5r transferase-DNA X-ray (1.8 Å) Lariviere L, Morera S (2002) "A Base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition state analog." J.Mol.Biol., 324, 483-489. doi: 10.1016/S0022-2836(02)01091-4. Ternary complex of t4 phage bgt with udp and a 13 mer DNA duplex. SNAP output
1m5x hydrolase-DNA X-ray (2.25 Å) Chevalier B, Turmel M, Lemieux C, Monnat RJ, Stoddard BL (2003) "Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI." J.Mol.Biol., 329, 253-269. doi: 10.1016/S0022-2836(03)00447-9. Crystal structure of the homing endonuclease i-msoi bound to its DNA substrate. SNAP output
1m6x ligase, lyase-DNA X-ray (2.8 Å) Conway AB, Chen Y, Rice PA (2003) "Structural Plasticity of the Flp-Holliday Junction Complex." J.Mol.Biol., 326, 425-434. doi: 10.1016/S0022-2836(02)01370-0. Flpe-holliday junction complex. SNAP output
1ma7 hydrolase, ligase-DNA X-ray (2.3 Å) Martin SS, Chu VC, Baldwin EP (2003) "Modulation of the active complex assembly and turnover rate by protein-DNA interactions in Cre-LoxP recombination." Biochemistry, 42, 6814-6826. doi: 10.1021/bi0272306. Crystal structure of cre site-specific recombinase complexed with a mutant DNA substrate, loxp-a8-t27. SNAP output
1mdm transcription-DNA X-ray (2.8 Å) Garvie CW, Pufall MA, Graves BJ, Wolberger C (2002) "STRUCTURAL ANALYSIS OF THE AUTOINHIBITION OF ETS-1 AND ITS ROLE IN PROTEIN PARTNERSHIPS." J.Biol.Chem., 277, 45529-45536. doi: 10.1074/jbc.M206327200. Inhibited fragment of ets-1 and paired domain of pax5 bound to DNA. SNAP output
1mdy transcription-DNA X-ray (2.8 Å) Ma PC, Rould MA, Weintraub H, Pabo CO (1994) "Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation." Cell(Cambridge,Mass.), 77, 451-459. doi: 10.1016/0092-8674(94)90159-7. Crystal structure of myod bhlh domain bound to DNA: perspectives on DNA recognition and implications for transcriptional activation. SNAP output
1mey transferase-DNA X-ray (2.2 Å) Kim CA, Berg JM (1996) "A 2.2 A Resolution Crystal Structure of a Designed Zinc Finger Protein Bound to DNA." Nat.Struct.Biol., 3, 940-945. doi: 10.1038/nsb1196-940. Crystal structure of a designed zinc finger protein bound to DNA. SNAP output
1mhd complex (transcription activator-DNA) X-ray (2.8 Å) Shi Y, Wang YF, Jayaraman L, Yang H, Massague J, Pavletich NP (1998) "Crystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in TGF-beta signaling." Cell(Cambridge,Mass.), 94, 585-594. doi: 10.1016/S0092-8674(00)81600-1. Crystal structure of a smad mh1 domain bound to DNA. SNAP output
1mht transferase-DNA X-ray (2.6 Å) Klimasauskas S, Kumar S, Roberts RJ, Cheng X (1994) "HhaI methyltransferase flips its target base out of the DNA helix." Cell(Cambridge,Mass.), 76, 357-369. doi: 10.1016/0092-8674(94)90342-5. Covalent ternary structure of hhai methyltransferase, DNA and s-adenosyl-l-homocysteine. SNAP output
1mj1 ribosome cryo-EM (13.0 Å) Stark H, Rodnina MV, Wieden H-J, Zemlin F, Wintermeyer W, van Heel M (2002) "Ribosome Interactions of Aminoacyl-tRNA and Elongation Factor TU in the Codon Recognition Complex." Nat.Struct.Biol., 9, 849-854. Fitting the ternary complex of ef-tu-trna-gtp and ribosomal proteins into a 13 a cryo-EM map of the coli 70s ribosome. SNAP output
1mj2 transcription-DNA X-ray (2.4 Å) Garvie CW, Phillips SE (2000) "Direct and indirect readout in mutant Met repressor-operator complexes." Structure Fold.Des., 8, 905-914. doi: 10.1016/S0969-2126(00)00182-9. Methionine repressor mutant (q44k) plus corepressor (s-adenosyl methionine) complexed to a consensus operator sequence. SNAP output
1mje gene regulation-antitumor protein-DNA X-ray (3.5 Å) Yang H, Jeffrey PD, Miller J, Kinnucan E, Sun Y, Thoma NH, Zheng N, Chen PL, Lee WH, Pavletich NP (2002) "BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure." Science, 297, 1837-1848. doi: 10.1126/science.297.5588.1837. Structure of a brca2-dss1-ssDNA complex. SNAP output
1mjm transcription-DNA X-ray (2.2 Å) Garvie CW, Phillips SE (2000) "Direct and indirect readout in mutant Met repressor-operator complexes." Structure Fold.Des., 8, 905-914. doi: 10.1016/S0969-2126(00)00182-9. Methionine aporepressor mutant (q44k) complexed to half of the consensus operator sequence. SNAP output
1mjo transcription-DNA X-ray (2.1 Å) Garvie CW, Phillips SE (2000) "Direct and indirect readout in mutant Met repressor-operator complexes." Structure Fold.Des., 8, 905-914. doi: 10.1016/S0969-2126(00)00182-9. Methionine holorepressor mutant (q44k) plus corepressor (s-adenosyl methionine) complexed to the minimal met consensus operator with the central ta step mutated to at. SNAP output
1mjp transcription-DNA X-ray (3.4 Å) Garvie CW, Phillips SE (2000) "Direct and indirect readout in mutant Met repressor-operator complexes." Structure Fold.Des., 8, 905-914. doi: 10.1016/S0969-2126(00)00182-9. Methionine aporepressor mutant (q44k) complexed to the minimal met consensus operator. SNAP output
1mjq transcription-DNA X-ray (2.4 Å) Garvie CW, Phillips SE (2000) "Direct and indirect readout in mutant Met repressor-operator complexes." Structure Fold.Des., 8, 905-914. doi: 10.1016/S0969-2126(00)00182-9. Methionine repressor mutant (q44k) plus corepressor (s-adenosyl methionine) complexed to an altered met consensus operator sequence. SNAP output
1mm8 transcription-DNA X-ray (2.8 Å) Steiniger-White M, Bhasin A, Lovell S, Rayment I, Reznikoff WS (2002) "Evidence for "unseen" Transposase--DNA contacts." J.Mol.Biol., 322, 971-982. doi: 10.1016/S0022-2836(02)00877-X. Crystal structure of tn5 transposase complexed with me DNA. SNAP output
1mnm transcription-DNA X-ray (2.25 Å) Tan S, Richmond TJ (1998) "Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex." Nature, 391, 660-666. doi: 10.1038/35563. Yeast matalpha2-mcm1-DNA ternary transcription complex crystal structure. SNAP output
1mnn transcription-DNA X-ray (1.4 Å) Lamoureux JS, Stuart D, Tsang R, Wu C, Glover JN (2002) "Structure of the sporulation-specific transcription factor Ndt80 bound to DNA." Embo J., 21, 5721-5732. doi: 10.1093/emboj/cdf572. Structure of the sporulation specific transcription factor ndt80 bound to DNA. SNAP output
1mnv DNA-antibiotic X-ray (2.6 Å) Hou M-H, Robinson H, Gao Y-G, Wang AH-J (2002) "Crystal Structure of Actinomycin D Bound to the Ctg Triplet Repeat Sequences Linked to Neurological Diseases." Nucleic Acids Res., 30, 4910. doi: 10.1093/NAR/GKF619. Actinomycin d binding to atgctgcat. SNAP output
1mow hydrolase-DNA X-ray (2.4 Å) Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat Jr RJ, Stoddard BL (2002) "Design, Activity and Structure of a Highly Specific Artificial Endonuclease." Mol.Cell, 10, 895-905. doi: 10.1016/S1097-2765(02)00690-1. E-drei. SNAP output
1mq2 transferase-DNA X-ray (3.1 Å) Krahn JM, Beard WA, Miller H, Grollman AP, Wilson SH (2003) "Structure of DNA Polymerase beta with the Mutagenic DNA Lesion 8-oxodeoxyguanine Reveals Structural Insights into its Coding Potential." Structure, 11, 121-127. doi: 10.1016/S0969-2126(02)00930-9. Human DNA polymerase beta complexed with gapped DNA containing an 8-oxo-7,8-dihydro-guanine and damp. SNAP output
1mq3 transferase-DNA X-ray (2.8 Å) Krahn JM, Beard WA, Miller H, Grollman AP, Wilson SH (2003) "Structure of DNA Polymerase beta with the Mutagenic DNA Lesion 8-oxodeoxyguanine Reveals Structural Insights into its Coding Potential." Structure, 11, 121-127. doi: 10.1016/S0969-2126(02)00930-9. Human DNA polymerase beta complexed with gapped DNA containing an 8-oxo-7,8-dihydro-guanine template paired with dctp. SNAP output
1mse DNA binding protein-DNA NMR Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T, Kanai H, Sarai A, Ishii S, Nishimura Y (1994) "Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices." Cell(Cambridge,Mass.), 79, 639-648. doi: 10.1016/0092-8674(94)90549-5. Solution structure of a specific DNA complex of the myb DNA-binding domain with cooperative recognition helices. SNAP output
1msf DNA binding protein-DNA NMR Ogata K, Morikawa S, Nakamura H, Sekikawa A, Inoue T, Kanai H, Sarai A, Ishii S, Nishimura Y (1994) "Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices." Cell(Cambridge,Mass.), 79, 639-648. doi: 10.1016/0092-8674(94)90549-5. Solution structure of a specific DNA complex of the myb DNA-binding domain with cooperative recognition helices. SNAP output
1msw transcription-DNA-RNA X-ray (2.1 Å) Yin YW, Steitz TA (2002) "Structural Basis for the Transition from Initiation to Elongation Transcription in T7 RNA Polymerase." Science, 298, 1387-1395. doi: 10.1126/science.1077464. Structural basis for the transition from initiation to elongation transcription in t7 RNA polymerase. SNAP output
1mtl hydrolase-DNA X-ray (2.8 Å) Barrett TE, Savva R, Barlow T, Brown T, Jiricny J, Pearl LH (1998) "Structure of a DNA base-excision product resembling a cisplatin inter-strand adduct." Nat.Struct.Biol., 5, 697-701. doi: 10.1038/1394. Non-productive mug-DNA complex. SNAP output
1muh transcription-DNA X-ray (2.3 Å) Davies DR, Goryshin IY, Reznikoff WS, Rayment I (2000) "Three-dimensional structure of the Tn5 synaptic complex transposition intermediate." Science, 289, 77-85. doi: 10.1126/science.289.5476.77. Crystal structure of tn5 transposase complexed with transposon end DNA. SNAP output
1mus transcription-DNA X-ray (1.9 Å) Steiniger-White M, Rayment I, Reznikoff WS (2004) "Structure/function insights into Tn5 transposition." Curr.Opin.Struct.Biol., 14, 50-57. doi: 10.1016/j.sbi.2004.01.008. Crystal structure of tn5 transposase complexed with resolved outside end DNA. SNAP output
1mvm virus-DNA X-ray (3.5 Å) Llamas-Saiz AL, Agbandje-McKenna M, Wikoff WR, Bratton J, Tattersall P, Rossmann MG (1997) "Structure determination of minute virus of mice." Acta Crystallogr.,Sect.D, 53, 93-102. doi: 10.1107/S0907444996010566. Mvm(strain i), complex(viral coat-DNA), vp2, ph=7.5, t=4 degrees c. SNAP output
1mw8 isomerase X-ray (1.9 Å) Perry K, Mondragon A (2003) "Structure of a Complex between E. coli DNA Topoisomerase I and Single-Stranded DNA." Structure, 11, 1349-1358. doi: 10.1016/j.str.2003.09.013. Crystal structure of a complex between h365r mutant of 67 kda n-terminal fragment of e. coli DNA topoisomerase i and 5'-acttcgggatg-3'. SNAP output
1mwi hydrolase-DNA X-ray (2.35 Å) Barrett TE, Savva R, Panayotou G, Barlow T, Brown T, Jiricny J, Pearl LH (1998) "Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions." Cell(Cambridge,Mass.), 92, 117-129. doi: 10.1016/S0092-8674(00)80904-6. Crystal structure of a mug-DNA product complex. SNAP output
1mwj hydrolase-DNA X-ray (2.85 Å) Barrett TE, Scharer O, Savva R, Brown T, Jiricny J, Verdine GL, Pearl LH (1999) "Crystal Structure of a thwarted mismatch glycosylase DNA repair complex." Embo J., 18, 6599-6609. doi: 10.1093/emboj/18.23.6599. Crystal structure of a mug-DNA pseudo substrate complex. SNAP output
1n39 hydrolase, lyase-DNA X-ray (2.2 Å) Norman DP, Chung SJ, Verdine GL (2003) "Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase." Biochemistry, 42, 1564-1572. doi: 10.1021/bi026823d. Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase. SNAP output
1n3a hydrolase, lyase-DNA X-ray (2.2 Å) Norman DP, Chung SJ, Verdine GL (2003) "Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase." Biochemistry, 42, 1564-1572. doi: 10.1021/bi026823d. Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase. SNAP output
1n3c hydrolase, lyase-DNA X-ray (2.7 Å) Norman DP, Chung SJ, Verdine GL (2003) "Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase." Biochemistry, 42, 1564-1572. doi: 10.1021/bi026823d. Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase. SNAP output
1n3e hydrolase-DNA X-ray (2.5 Å) Chevalier B, Turmel M, Lemieux C, Monnat RJ, Stoddard BL (2003) "Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI." J.Mol.Biol., 329, 253-269. doi: 10.1016/S0022-2836(03)00447-9. Crystal structure of i-crei bound to a palindromic DNA sequence i (palindrome of left side of wildtype DNA target sequence). SNAP output
1n3f hydrolase-DNA X-ray (2.0 Å) Chevalier B, Turmel M, Lemieux C, Monnat RJ, Stoddard BL (2003) "Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI." J.Mol.Biol., 329, 253-269. doi: 10.1016/S0022-2836(03)00447-9. Crystal structure of i-crei bound to a palindromic DNA sequence ii (palindrome of right side of wildtype DNA target sequence). SNAP output
1n48 transferase-DNA X-ray (2.2 Å) Ling H, Boudsocq F, Woodgate R, Yang W "A Y-family polymerase complexed with abasic lesions: catching DNA with a loaded nucleoside triphosphate." Y-family DNA polymerase dpo4 in complex with DNA containing abasic lesion. SNAP output
1n56 transferase-DNA X-ray (2.4 Å) Ling H, Boudsocq F, Woodgate R, Yang W (2004) "Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts." Mol.Cell, 13, 751-762. doi: 10.1016/s1097-2765(04)00101-7. Y-family DNA polymerase dpo4 in complex with DNA containing abasic lesion. SNAP output
1n5y transferase-immune system-DNA X-ray (3.1 Å) Sarafianos SG, Clark Jr AD, Das K, Tuske S, Birktoft JJ, Ilankumaran P, Ramesha AR, Sayer JM, Jerina DM, Boyer PL, Hughes SH, Arnold E (2002) "Structure of HIV-1 Reverse Transcriptase with Pre-Translocation and Post-Translocation AZTMP-Terminated DNA." Embo J., 21, 6614-6624. doi: 10.1093/emboj/cdf637. Hiv-1 reverse transcriptase crosslinked to post-translocation aztmp-terminated DNA (complex p). SNAP output
1n6j transcription-DNA X-ray (2.2 Å) Han A, Pan F, Stroud JC, Youn HD, Liu JO, Chen L (2003) "Sequence-specific recruitment of transcriptional co-repressor Cabin1 by myocyte enhancer factor-2." Nature, 422, 730-734. doi: 10.1038/nature01555. Structural basis of sequence-specific recruitment of histone deacetylases by myocyte enhancer factor-2. SNAP output
1n6q transferase-immune system-DNA X-ray (3.0 Å) Sarafianos SG, Clark Jr AD, Das K, Tuske S, Birktoft JJ, Ilankumaran I, Ramesha AR, Sayer JM, Jerina DM, Boyer PL, Hughes SH, Arnold E (2002) "Structures of HIV-1 Reverse Transcriptase with Pre- and Post-translocation AZTMP-terminated DNA." Embo J., 21, 6614-6624. doi: 10.1093/emboj/cdf637. Hiv-1 reverse transcriptase crosslinked to pre-translocation aztmp-terminated DNA (complex n). SNAP output
1nfk transcription-DNA X-ray (2.3 Å) Ghosh G, van Duyne G, Ghosh S, Sigler PB (1995) "Structure of NF-kappa B p50 homodimer bound to a kappa B site." Nature, 373, 303-310. doi: 10.1038/373303a0. Structure of the nuclear factor kappa-b (nf-kb) p50 homodimer. SNAP output
1ng9 DNA binding protein X-ray (2.6 Å) Lamers MH, Winterwerp HHK, Sixma TK (2003) "The alternating ATPase domains of MutS control DNA mismatch repair." Embo J., 22, 746-756. doi: 10.1093/emboj/cdg064. E.coli muts r697a: an atpase-asymmetry mutant. SNAP output
1ngm transcription-DNA X-ray (2.95 Å) Juo ZS, Kassavetis GA, Wang J, Geiduschek EP, Sigler PB (2003) "Crystal structure of a transcription factor IIIB core interface ternary complex." Nature, 422, 534-539. doi: 10.1038/nature01534. Crystal structure of a yeast brf1-tbp-DNA ternary complex. SNAP output
1nh2 transcription-DNA X-ray (1.9 Å) Bleichenbacher M, Tan S, Richmond TJ (2003) "Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes." J.Mol.Biol., 332, 783-793. doi: 10.1016/S0022-2836(03)00887-8. Crystal structure of a yeast tfiia-tbp-DNA complex. SNAP output
1nh3 isomerase-DNA X-ray (3.1 Å) Chrencik JE, Burgin AB, Pommier Y, Stewart L, Redinbo MR (2003) "Structural Impact of the Leukemia Drug 1-beta-D-Arabinofuranosylcytosine (Ara-C) on the Covalent Human Topoisomerase I-DNA Complex." J.Biol.Chem., 278, 12461-12466. doi: 10.1074/jbc.M212930200. Human topoisomerase i ara-c complex. SNAP output
1njw transferase-DNA X-ray (1.9 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Guanine-thymine mismatch at the polymerase active site. SNAP output
1njx transferase-DNA X-ray (1.65 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Thymine-guanine mismatch at the polymerase active site. SNAP output
1njy transferase-DNA X-ray (2.0 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Thymine-thymine mismatch at the polymerase active site. SNAP output
1njz transferase-DNA X-ray (2.0 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Cytosine-thymine mismatch at the polymerase active site. SNAP output
1nk0 transferase-DNA X-ray (1.7 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Adenine-guanine mismatch at the polymerase active site. SNAP output
1nk2 DNA binding protein-DNA NMR Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti JA (1997) "Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity." Biochemistry, 36, 5372-5380. doi: 10.1021/bi9620060. Vnd-nk-2 homeodomain-DNA complex, NMR, 20 structures. SNAP output
1nk3 DNA binding protein-DNA NMR Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti JA (1997) "Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity." Biochemistry, 36, 5372-5380. doi: 10.1021/bi9620060. Vnd-nk-2 homeodomain-DNA complex, NMR, minimized average structure. SNAP output
1nk4 transferase-DNA X-ray (1.6 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Guanine-guanine mismatch at the polymerase active site. SNAP output
1nk5 transferase-DNA X-ray (2.1 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Adenine-adenine mismatch at the polymerase active site. SNAP output
1nk6 transferase-DNA X-ray (2.1 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Cytosine-cytosine mismatch at the polymerase active site. SNAP output
1nk7 transferase-DNA X-ray (1.9 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. Guanine-adenine mismatch at the polymerase active site. SNAP output
1nk8 transferase-DNA X-ray (1.9 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. A bacillus DNA polymerase i product complex bound to a guanine-thymine mismatch after a single round of primer extension, following incorporation of dctp.. SNAP output
1nk9 transferase-DNA X-ray (1.9 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. A bacillus DNA polymerase i product complex bound to a guanine-thymine mismatch after two rounds of primer extension, following incorporation of dctp and dgtp.. SNAP output
1nkb transferase-DNA X-ray (2.0 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. A bacillus DNA polymerase i product complex bound to a guanine-thymine mismatch after three rounds of primer extension, following incorporation of dctp, dgtp, and dttp.. SNAP output
1nkc transferase-DNA X-ray (1.8 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. A bacillus DNA polymerase i product complex bound to a guanine-thymine mismatch after five rounds of primer extension, following incorporation of dctp, dgtp, dttp, and datp.. SNAP output
1nke transferase-DNA X-ray (1.8 Å) Johnson SJ, Beese LS (2004) "Structures of mismatch replication errors observed in a DNA polymerase." Cell(Cambridge,Mass.), 116, 803-816. doi: 10.1016/S0092-8674(04)00252-1. A bacillus DNA polymerase i product complex bound to a cytosine-thymine mismatch after a single round of primer extension, following incorporation of dctp.. SNAP output
1nkp transcription-DNA X-ray (1.8 Å) Nair SK, Burley SK (2003) "X-ray structures of Myc-Max and Mad-Max recognizing DNA: Molecular bases of regulation by proto-oncogenic transcription factors." Cell(Cambridge,Mass.), 112, 193-205. doi: 10.1016/S0092-8674(02)01284-9. Crystal structure of myc-max recognizing DNA. SNAP output
1nlw transcription-DNA X-ray (2.0 Å) Nair SK, Burley SK (2003) "X-ray structures of Myc-Max and Mad-Max recognizing DNA: Molecular bases of regulation by proto-oncogenic transcription factors." Cell(Cambridge,Mass.), 112, 193-205. doi: 10.1016/S0092-8674(02)01284-9. Crystal structure of mad-max recognizing DNA. SNAP output
1nne DNA binding protein-DNA X-ray (3.11 Å) Alani E, Lee JY, Schofield MJ, Kijas AW, Hsieh P, Yang W (2003) "Crystal structure and biochemical analysis of the MutS-ADP-Beryllium Fluoride complex suggests a conserved mechanism for ATP interactions in mismatch repair." J.Biol.Chem., 278, 16088-16094. doi: 10.1074/jbc.M213193200. Crystal structure of the muts-adpbef3-DNA complex. SNAP output
1nnj hydrolase X-ray (1.9 Å) Pereira de Jesus K, Serre L, Zelwer C, Castaing B (2005) "Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA." Nucleic Acids Res., 33, 5936-5944. doi: 10.1093/nar/gki879. Crystal structure complex between the lactococcus lactis fpg and an abasic site containing DNA. SNAP output
1nop hydrolase-DNA X-ray (2.3 Å) Davies DR, Interthal H, Champoux JJ, Hol WGJ (2003) "Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide." Chem.Biol., 10, 139-147. doi: 10.1016/S1074-5521(03)00021-8. Crystal structure of human tyrosyl-DNA phosphodiesterase (tdp1) in complex with vanadate, DNA and a human topoisomerase i-derived peptide. SNAP output
1noy transferase-DNA X-ray (2.2 Å) Wang J, Yu P, Lin TC, Konigsberg WH, Steitz TA (1996) "Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions." Biochemistry, 35, 8110-8119. doi: 10.1021/bi960178r. DNA polymerase (e.c.2.7.7.7)-DNA complex. SNAP output
1nvp transcription-DNA X-ray (2.1 Å) Bleichenbacher M, Tan S, Richmond TJ (2003) "Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes." J.Mol.Biol., 332, 783-793. doi: 10.1016/S0022-2836(03)00887-8. Human tfiia-tbp-DNA complex. SNAP output
1nwq transcription-DNA X-ray (2.8 Å) Miller M, Shuman JD, Sebastian T, Dauter Z, Johnson PF (2003) "Structural Basis for DNA Recognition by the Basic Region Leucine Zipper Transcription Factor CCAAT/enhancer Binding Protein Alpha." J.Biol.Chem., 278, 15178-15184. doi: 10.1074/jbc.M300417200. Crystal structure of c-ebpalpha-DNA complex. SNAP output
1nzb replication-DNA X-ray (3.1 Å) Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck D (2003) "Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation." Nucleic Acids Res., 31, 5449-5460. doi: 10.1093/nar/gkg732. Crystal structure of wild type cre recombinase-loxp synapse. SNAP output
1o3q gene regulation-DNA X-ray (3.0 Å) Chen S, Vojtechovsky J, Parkinson GN, Ebright RH, Berman HM (2001) "Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking." J.Mol.Biol., 314, 63-74. doi: 10.1006/jmbi.2001.5089. Protein-DNA recognition and DNA deformation revealed in crystal structures of cap-DNA complexes. SNAP output
1o3r gene regulation-DNA X-ray (3.0 Å) Chen S, Vojtechovsky J, Parkinson GN, Ebright RH, Berman HM (2001) "Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking." J.Mol.Biol., 314, 63-74. doi: 10.1006/jmbi.2001.5089. Protein-DNA recognition and DNA deformation revealed in crystal structures of cap-DNA complexes. SNAP output
1o3s gene regulation-DNA X-ray (3.0 Å) Chen S, Gunasekera A, Zhang X, Kunkel TA, Ebright RH, Berman HM (2001) "Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: Alteration of DNA Binding Specificity Through Alteration of DNA Kinking." J.Mol.Biol., 314, 75-82. doi: 10.1006/jmbi.2001.5090. Protein-DNA recognition and DNA deformation revealed in crystal structures of cap-DNA complexes. SNAP output
1o3t gene regulation-DNA X-ray (2.8 Å) Chen S, Vojtechovsky J, Parkinson GN, Ebright RH, Berman HM (2001) "Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking." J.Mol.Biol., 314, 63-74. doi: 10.1006/jmbi.2001.5089. Protein-DNA recognition and DNA deformation revealed in crystal structures of cap-DNA complexes. SNAP output
1o4x transcription-DNA NMR Williams DC, Cai M, Clore GM (2004) "Molecular basis for synergistic transcriptional activation by Oct1 and Sox2 revealed from the solution structure of the 42-kDa Oct1.Sox2.Hoxb1-DNA ternary transcription factor complex." J.Biol.Chem., 279, 1449-1457. doi: 10.1074/jbc.M309790200. Ternary complex of the DNA binding domains of the oct1 and sox2 transcription factors with a 19mer oligonucleotide from the hoxb1 regulatory element. SNAP output
1oct transcription-DNA X-ray (3.0 Å) Klemm JD, Rould MA, Aurora R, Herr W, Pabo CO (1994) "Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules." Cell(Cambridge,Mass.), 77, 21-32. doi: 10.1016/0092-8674(94)90231-3. Crystal structure of the oct-1 pou domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. SNAP output
1odg hydrolase X-ray (2.8 Å) Bunting KA, Roe SM, Headley A, Brown T, Savva R, Pearl LH (2003) "Crystal Structure of the Escherichia Coli Dcm Very-Short-Patch DNA Repair Endonuclease Bound to its Reaction Product-Site in a DNA Superhelix." Nucleic Acids Res., 31, 1633. doi: 10.1093/NAR/GKG273. Very-short-patch DNA repair endonuclease bound to its reaction product site. SNAP output
1odh transcription factor-DNA X-ray (2.85 Å) Cohen SX, Moulin M, Hashemolhosseini S, Kilian K, Wegner M, Muller CW (2003) "Crystal Structure of the Gcm Domain-DNA Complex: A DNA-Binding Domain with a Novel Fold and Mode of Target Site Recognition." Embo J., 22, 1835. doi: 10.1093/EMBOJ/CDG182. Structure of the gcm domain bound to DNA. SNAP output
1oe4 hydrolase-DNA X-ray (2.0 Å) Wibley JEA, Waters TR, Haushalter K, Verdine GL, Pearl LH (2003) "Structure and Specificity of the Vertebrate Anti-Mutator Uracil-DNA Glycosylase Smug1." Mol.Cell, 11, 1647. doi: 10.1016/S1097-2765(03)00235-1. Xenopus smug1, an anti-mutator uracil-DNA glycosylase. SNAP output
1oe5 hydrolase-DNA X-ray (2.3 Å) Wibley JEA, Waters TR, Haushalter K, Verdine GL, Pearl LH (2003) "Structure and Specificity of the Vertebrate Anti-Mutator Uracil-DNA Glycosylase Smug1." Mol.Cell, 11, 1647. doi: 10.1016/S1097-2765(03)00235-1. Xenopus smug1, an anti-mutator uracil-DNA glycosylase. SNAP output
1oe6 hydrolase-DNA X-ray (2.65 Å) Wibley JEA, Waters TR, Haushalter K, Verdine GL, Pearl LH (2003) "Structure and Specificity of the Vertebrate Anti-Mutator Uracil-DNA Glycosylase Smug1." Mol.Cell, 11, 1647. doi: 10.1016/S1097-2765(03)00235-1. Xenopus smug1, an anti-mutator uracil-DNA glycosylase. SNAP output
1oh5 DNA binding X-ray (2.9 Å) Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK, Perrakis A, Sixma TK (2003) "Structures of E. Coli DNA Mismatch Repair Enzyme Muts in Complex with Different Mismatches: A Common Recognition Mode for Diverse Substrates." Nucleic Acids Res., 31, 4814. doi: 10.1093/NAR/GKG677. The crystal structure of e. coli muts binding to DNA with a c:a mismatch. SNAP output
1oh6 DNA binding X-ray (2.4 Å) Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK, Perrakis A, Sixma TK (2003) "Structures of E. Coli DNA Mismatch Repair Enzyme Muts in Complex with Different Mismatches: A Common Recognition Mode for Diverse Substrates." Nucleic Acids Res., 31, 4814. doi: 10.1093/NAR/GKG677. The crystal structure of e. coli muts binding to DNA with an a:a mismatch. SNAP output
1oh7 DNA binding X-ray (2.5 Å) Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK, Perrakis A, Sixma TK (2003) "Structures of E. Coli DNA Mismatch Repair Enzyme Muts in Complex with Different Mismatches: A Common Recognition Mode for Diverse Substrates." Nucleic Acids Res., 31, 4814. doi: 10.1093/NAR/GKG677. The crystal structure of e. coli muts binding to DNA with a g:g mismatch. SNAP output
1oh8 DNA binding X-ray (2.9 Å) Natrajan G, Lamers MH, Enzlin JH, Winterwerp HHK, Perrakis A, Sixma TK (2003) "Structures of E. Coli DNA Mismatch Repair Enzyme Muts in Complex with Different Mismatches: A Common Recognition Mode for Diverse Substrates." Nucleic Acids Res., 31, 4814. doi: 10.1093/NAR/GKG677. The crystal structure of e. coli muts binding to DNA with an unpaired thymidine. SNAP output
1oj8 hydrolase X-ray (1.7 Å) Tsai C-J, Liu J-H, Liao Y-D, Chen L-Y, Cheng P-T, Sun Y-J "Retro and Novel Binding Modes in Cytotoxic Ribonucleases from Rana Catesbeiana of Two Crystal Structures Complexed with (2',5'Cpg) and D(Apcpgpa)." Novel and retro binding modes in cytotoxic ribonucleases from rana catesbeiana of two crystal structures complexed with d(apcpgpa) and (2',5'cpg). SNAP output
1omh transferase-DNA X-ray (1.95 Å) Guasch A, Lucas M, Moncalian G, Cabezas M, Perez-Luque R, Gomis-Ruth FX, de la Cruz F, Coll M (2003) "Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC." Nat.Struct.Biol., 10, 1002-1010. doi: 10.1038/nsb1017. Conjugative relaxase trwc in complex with orit DNA. metal-free structure.. SNAP output
1orn hydrolase-DNA X-ray (1.7 Å) Fromme JC, Verdine GL (2003) "Structure of a Trapped Endonuclease III-DNA Covalent Intermediate." Embo J., 22, 3461-3471. doi: 10.1093/emboj/cdg311. Structure of a trapped endonuclease iii-DNA covalent intermediate: estranged-guanine complex. SNAP output
1orp hydrolase-DNA X-ray (2.2 Å) Fromme JC, Verdine GL (2003) "Structure of a Trapped Endonuclease III-DNA Covalent Intermediate." Embo J., 22, 3461-3471. doi: 10.1093/emboj/cdg311. Structure of a trapped endonuclease iii-DNA covalent intermediate: estranged-adenine complex. SNAP output
1osb transferase-DNA X-ray (2.65 Å) Guasch A, Lucas M, Moncalian G, Cabezas M, Perez-Luque R, Gomis-Ruth FX, de la Cruz F, Coll M (2003) "Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC." Nat.Struct.Biol., 10, 1002-1010. doi: 10.1038/nsb1017. Conjugative relaxase trwc in complex with orit DNA. metal-free structure.. SNAP output
1osl transcription-DNA NMR Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R (2004) "Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes." Science, 305, 386-389. doi: 10.1126/science.1097064. Solution structure of a dimeric lactose DNA-binding domain complexed to a nonspecific DNA sequence. SNAP output
1otc protein-DNA X-ray (2.8 Å) Horvath MP, Schweiker VL, Bevilacqua JM, Ruggles JA, Schultz SC (1998) "Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA." Cell(Cambridge,Mass.), 95, 963-974. doi: 10.1016/S0092-8674(00)81720-1. The o. nova telomere end binding protein complexed with single strand DNA. SNAP output
1oup hydrolase-DNA X-ray (2.3 Å) Li C-L, Hor L-I, Chang Z-F, Tsai L-C, Yang W-Z, Yuan HS (2003) "DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site." Embo J., 22, 4014-4025. doi: 10.1093/emboj/cdg377. Crystal structure of the periplasmic endonuclease vvn complexed with octamer double stranded DNA. SNAP output
1ouq replication-DNA X-ray (3.2 Å) Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck D (2003) "Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation." Nucleic Acids Res., 31, 5449-5460. doi: 10.1093/nar/gkg732. Crystal structure of wild-type cre recombinase-loxp synapse. SNAP output
1ouz transcription-DNA X-ray (2.41 Å) Lynch TW, Read EK, Mattis AN, Gardner JF, Rice PA (2003) "Integration Host Factor: putting a twist on protein-DNA recognition." J.Mol.Biol., 330, 493-502. doi: 10.1016/S0022-2836(03)00529-1. Crystal structure of a mutant ihf (betae44a) complexed with a variant h' site (t44a). SNAP output
1ovf DNA-antibiotic NMR Chin K-H, Chen F-M, Chou S-H (2003) "Solution Structure of the Actd-5'-Ccgtt(3)Gtgg-3' Complex: Drug Interaction with Tandem G.T Mismatches and Hairpin Loop Backbone." Nucleic Acids Res., 31, 2622. doi: 10.1093/NAR/GKG353. NMR structure of actd-5'-ccgttttgtgg-3' complex. SNAP output
1owf transcription-DNA X-ray (1.95 Å) Lynch TW, Read EK, Mattis AN, Gardner JF, Rice PA (2003) "Integration Host Factor: putting a twist on protein-DNA recognition." J.Mol.Biol., 330, 493-502. doi: 10.1016/S0022-2836(03)00529-1. Crystal structure of a mutant ihf (betae44a) complexed with the native h' site. SNAP output
1owg transcription-DNA X-ray (2.1 Å) Lynch TW, Read EK, Mattis AN, Gardner JF, Rice PA (2003) "Integration Host Factor: putting a twist on protein-DNA recognition." J.Mol.Biol., 330, 493-502. doi: 10.1016/S0022-2836(03)00529-1. Crystal structure of wt ihf complexed with an altered h' site (t44a). SNAP output
1owr transcription-DNA X-ray (3.0 Å) Stroud JC, Chen L (2003) "Structure of NFAT Bound to DNA as a Monomer." J.Mol.Biol., 334, 1009-1022. doi: 10.1016/j.jmb.2003.09.065. Crystal structure of human nfat1 bound monomerically to DNA. SNAP output
1ozj transcription-DNA X-ray (2.4 Å) Chai J, Wu J-W, Yan N, Massague J, Pavletich NP, Shi Y (2003) "Features of a Smad3 MH1-DNA complex. Roles of water and zinc in DNA binding." J.Biol.Chem., 278, 20327-20331. doi: 10.1074/jbc.C300134200. Crystal structure of smad3-mh1 bound to DNA at 2.4 Å resolution. SNAP output
1p34 structural protein-DNA X-ray (2.7 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3a structural protein-DNA X-ray (3.0 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3b structural protein-DNA X-ray (3.0 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3f structural protein-DNA X-ray (2.9 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3g structural protein-DNA X-ray (2.7 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3i structural protein-DNA X-ray (2.3 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3k structural protein-DNA X-ray (2.9 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3l structural protein-DNA X-ray (2.4 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3m structural protein-DNA X-ray (2.9 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3o structural protein-DNA X-ray (2.75 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p3p structural protein-DNA X-ray (2.7 Å) Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K (2004) "Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions." EMBO J., 23, 260-271. doi: 10.1038/sj.emboj.7600046. Crystallographic studies of nucleosome core particles containing histone 'sin' mutants. SNAP output
1p47 transcription-DNA X-ray (2.2 Å) Peisach E, Pabo CO (2003) "Constraints for Zinc Finger Linker Design as Inferred from X-ray Crystal Structure of Tandem Zif268-DNA Complexes." J.Mol.Biol., 330, 1-7. doi: 10.1016/S0022-2836(03)00572-2. Crystal structure of tandem zif268 molecules complexed to DNA. SNAP output
1p4e DNA binding protein-recombination-DNA X-ray (2.7 Å) Rice PA, Chen Y (2003) "The role of the conserved Trp330 in Flp-mediated recombination. Functional and structural analysis." J.Biol.Chem., 278, 24800-24807. doi: 10.1074/jbc.M300853200. Flpe w330f mutant-DNA holliday junction complex. SNAP output
1p51 DNA binding protein-DNA X-ray (2.5 Å) Swinger KK, Lemberg KM, Zhang Y, Rice PA (2003) "Flexible DNA bending in HU-DNA cocrystal structures." Embo J., 22, 3749-3760. doi: 10.1093/emboj/cdg351. Anabaena hu-DNA cocrystal structure (ahu6). SNAP output
1p59 hydrolase-DNA X-ray (2.5 Å) Fromme JC, Verdine GL (2003) "Structure of a Trapped Endonuclease III-DNA Covalent Intermediate." Embo J., 22, 3461-3471. doi: 10.1093/emboj/cdg311. Structure of a non-covalent endonuclease iii-DNA complex. SNAP output
1p5w virus-DNA X-ray (3.3 Å) Govindasamy L, Hueffer K, Parrish CR, Agbandje-McKenna M (2003) "Structures of host range-controlling regions of the capsids of canine and feline parvoviruses and mutants." J.Virol., 77, 12211-12221. doi: 10.1128/JVI.77.22.12211-12221.2003. The structures of host range controlling regions of the capsids of canine and feline parvoviruses and mutants. SNAP output
1p71 DNA binding protein-DNA X-ray (1.9 Å) Swinger KS, Lemberg KM, Zhang Y, Rice PA (2003) "Flexible DNA bending in HU-DNA cocrystal structures." Embo J., 22, 3749-3760. doi: 10.1093/emboj/cdg351. Anabaena hu-DNA corcrystal structure (tr3). SNAP output
1p78 DNA binding protein-DNA X-ray (2.25 Å) Swinger KS, Lemberg KM, Zhang Y, Rice PA (2003) "Flexible DNA bending in HU-DNA cocrystal structures." Embo J., 22, 3749-3760. doi: 10.1093/emboj/cdg351. Anabaena hu-DNA cocrystal structure (ahu2). SNAP output
1p7d DNA binding protein-DNA X-ray (2.95 Å) Aihara H, Kwon HJ, Nunes-Duby SE, Landy A, Ellenberger T (2003) "A Conformational Switch Controls the DNA Cleavage Activity of Lambda Integrase." Mol.Cell, 12, 187-198. doi: 10.1016/S1097-2765(03)00268-5. Crystal structure of the lambda integrase (residues 75-356) bound to DNA. SNAP output
1p7h transcription-DNA X-ray (2.6 Å) Giffin MJ, Stroud JC, Bates DL, von Koenig KD, Hardin J, Chen L (2003) "Structure of NFAT1 bound as a dimer to the HIV-1 LTR kappa B element." Nat.Struct.Biol., 10, 800-806. doi: 10.1038/nsb981. Structure of nfat1 bound as a dimer to the hiv-1 ltr kb element. SNAP output
1p8k hydrolase-DNA X-ray (2.6 Å) Bolduc JM, Spiegel PC, Chatterjee P, Brady KL, Downing ME, Caprara MG, Waring RB, Stoddard BL (2003) "Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor." Genes Dev., 17, 2875-2888. doi: 10.1101/gad.1109003. The structure and DNA recognition of a bifunctional homing endonuclease and group i intron splicing factor. SNAP output
1pa6 DNA binding protein-DNA X-ray (2.45 Å) Theobald DL, Schultz SC (2003) "Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttgagg. SNAP output
1par transcription-DNA X-ray (2.6 Å) Raumann BE, Rould MA, Pabo CO, Sauer RT (1994) "DNA recognition by beta-sheets in the Arc repressor-operator crystal structure." Nature, 367, 754-757. doi: 10.1038/367754a0. DNA recognition by beta-sheets in the arc repressor-operator crystal structure. SNAP output
1pdn gene regulation-DNA X-ray (2.5 Å) Xu W, Rould MA, Jun S, Desplan C, Pabo CO (1995) "Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations." Cell(Cambridge,Mass.), 80, 639-650. doi: 10.1016/0092-8674(95)90518-9. Crystal structure of a paired domain-DNA complex at 2.5 angstroms resolution reveals structural basis for pax developmental mutations. SNAP output
1per transcription-DNA X-ray (2.5 Å) Rodgers DW, Harrison SC (1993) "The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites." Structure, 1, 227-240. doi: 10.1016/0969-2126(93)90012-6. The complex between phage 434 repression DNA-binding domain and operator site or3: structural differences between consensus and non-consensus half-sites. SNAP output
1pfe DNA-antibiotic X-ray (1.1 Å) Cuesta-Seijo JA, Sheldrick GM (2005) "Structures of Complexes between Echinomycin and Duplex DNA." Acta Crystallogr.,Sect.D, 61, 442. doi: 10.1107/S090744490500137X. Echinomycin-(gcgtacgc)2 complex. SNAP output
1pfi virus fiber diffraction Liu DJ, Day LA (1994) "Pf1 virus structure: helical coat protein and DNA with paraxial phosphates." Science, 265, 671-674. Pf1 virus structure: helical coat protein and DNA with paraxial phosphates. SNAP output
1pgz DNA binding protein-DNA X-ray (2.6 Å) Myers JC, Moore SA, Shamoo Y (2003) "Structure-based incorporation of 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine into the human telomeric repeat DNA as a probe for UP1 binding and destabilization of G-tetrad structures." J.Biol.Chem., 278, 42300-42306. doi: 10.1074/jbc.M306147200. Crystal structure of up1 complexed with d(ttagggttag(6-mi)g); a human telomeric repeat containing 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine (6-mi). SNAP output
1ph1 DNA binding protein-DNA X-ray (2.51 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and Ssdna Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttggggt. SNAP output
1ph2 DNA binding protein-DNA X-ray (3.1 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttg. SNAP output
1ph3 DNA binding protein-DNA X-ray (2.3 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttggtg. SNAP output
1ph4 DNA binding protein-DNA X-ray (2.3 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttggcg. SNAP output
1ph5 DNA binding protein-DNA X-ray (2.3 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttg(3dr)gg. SNAP output
1ph6 DNA binding protein-DNA X-ray (2.1 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttgtgg. SNAP output
1ph7 DNA binding protein-DNA X-ray (2.9 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttgigg. SNAP output
1ph8 DNA binding protein-DNA X-ray (2.36 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and Ssdna Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttgcgg. SNAP output
1ph9 DNA binding protein-DNA X-ray (2.5 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA ggggttttgagg. SNAP output
1phj DNA binding protein-DNA X-ray (2.5 Å) Theobald DL, Schultz SC (2003) "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415. Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA gg(3dr)gttttgggg. SNAP output
1pji hydrolase-DNA X-ray (1.9 Å) Pereira de Jesus K, Serre L, Zelwer C, Castaing B (2005) "Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA." Nucleic Acids Res., 33, 5936-5944. doi: 10.1093/nar/gki879. Crystal structure of wild type lactococcus lactis fpg complexed to a 1,3 propanediol containing DNA. SNAP output
1pjj hydrolase-DNA X-ray (1.9 Å) Pereira de Jesus K, Serre L, Zelwer C, Castaing B (2005) "Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA." Nucleic Acids Res., 33, 5936-5944. doi: 10.1093/nar/gki879. Complex between the lactococcus lactis fpg and an abasic site containing DNA.. SNAP output
1pm5 hydrolase-DNA X-ray (1.95 Å) Pereira de Jesus K, Serre L, Zelwer C, Castaing B (2005) "Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA." Nucleic Acids Res., 33, 5936-5944. doi: 10.1093/nar/gki879. Crystal structure of wild type lactococcus lactis fpg complexed to a tetrahydrofuran containing DNA. SNAP output
1pnr transcription-DNA X-ray (2.7 Å) Schumacher MA, Choi KY, Zalkin H, Brennan RG (1994) "Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices." Science, 266, 763-770. Purine repressor-hypoxanthine-purf-operator complex. SNAP output
1po6 RNA binding protein-DNA X-ray (2.1 Å) Myers JC, Moore SA, Shamoo Y (2003) "Structure-based incorporation of 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine into the human telomeric repeat DNA as a probe for UP1 binding and destabilization of G-tetrad structures." J.BIOL.CHEM., 278, 42300-42306. doi: 10.1074/jbc.M306147200. Crystal structure of up1 complexed with d(tagg(6mi)ttaggg): a human telomeric repeat containing 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine (6mi). SNAP output
1pp7 transcription-DNA X-ray (2.45 Å) Schumacher MA, Lau AOT, Johnson PJ (2003) "Structural Basis of Core Promoter Recognition in a Primitive Eukaryote." Cell(Cambridge,Mass.), 115, 413-424. doi: 10.1016/S0092-8674(03)00887-0. Crystal structure of the t. vaginalis initiator binding protein bound to the ferredoxin inr. SNAP output
1pp8 transcription-DNA X-ray (3.05 Å) Schumacher MA, Lau AOT, Johnson PJ (2003) "Structural Basis of Core Promoter Recognition in a Primitive Eukaryote." Cell(Cambridge,Mass.), 115, 413-424. doi: 10.1016/S0092-8674(03)00887-0. Crystal structure of the t. vaginalis ibp39 initiator binding domain (ibd) bound to the alpha-scs inr element. SNAP output
1pt3 hydrolase-DNA X-ray (2.5 Å) Hsia KC, Chak KF, Liang PH, Cheng YS, Ku WY, Yuan HS (2004) "DNA binding and degradation by the HNH protein ColE7." STRUCTURE, 12, 205-214. doi: 10.1016/S0969-2126(04)00006-1. Crystal structures of nuclease-cole7 complexed with octamer DNA. SNAP output
1pue transcription-DNA X-ray (2.1 Å) Kodandapani R, Pio F, Ni CZ, Piccialli G, Klemsz M, McKercher S, Maki RA, Ely KR (1996) "A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex." Nature, 380, 456-460. doi: 10.1038/380456a0. Pu.1 ets domain-DNA complex. SNAP output
1puf transcription-DNA X-ray (1.9 Å) LARONDE-LEBLANC NA, Wolberger C (2003) "STRUCTURE OF HOXA9 AND PBX1 BOUND TO DNA: HOX HEXAPEPTIDE AND DNA RECOGNITION ANTERIOR TO POSTERIOR." Genes Dev., 17, 2060-2072. doi: 10.1101/gad.1103303. Crystal structure of hoxa9 and pbx1 homeodomains bound to DNA. SNAP output
1pv4 transcription-DNA X-ray (3.0 Å) Skordalakes E, Berger JM (2003) "Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading." Cell(Cambridge,Mass.), 114, 135-146. doi: 10.1016/S0092-8674(03)00512-9. X-ray crystal structure of the rho transcription termination factor in complex with single stranded DNA. SNAP output
1pvi hydrolase-DNA X-ray (2.6 Å) Cheng X, Balendiran K, Schildkraut I, Anderson JE (1994) "Structure of PvuII endonuclease with cognate DNA." EMBO J., 13, 3927-3935. Structure of pvuii endonuclease with cognate DNA. SNAP output
1pvp recombination-DNA X-ray (2.35 Å) Baldwin EP, Martin SS, Abel J, Gelato KA, Kim H, Schultz PG, Santoro SW (2003) "A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water." Chem.Biol., 10, 1085-1094. doi: 10.1016/j.chembiol.2003.10.015. Basis for a switch in substrate specificity: crystal structure of selected variant of cre site-specific recombinase, alshg bound to the engineered recognition site loxm7. SNAP output
1pvq recombination-DNA X-ray (2.75 Å) Baldwin EP, Martin SS, Abel J, Gelato KA, Kim H, Schultz PG, Santoro SW (2003) "A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water." Chem.Biol., 10, 1085-1094. doi: 10.1016/j.chembiol.2003.10.015. Basis for a switch in substrate specificity: crystal structure of selected variant of cre site-specific recombinase, lnsgg bound to the engineered recognition site loxm7. SNAP output
1pvr recombination-DNA X-ray (2.65 Å) Baldwin EP, Martin SS, Abel J, Gelato KA, Kim H, Schultz PG, Santoro SW (2003) "A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water." Chem.Biol., 10, 1085-1094. doi: 10.1016/j.chembiol.2003.10.015. Basis for a switch in substrate specificity: crystal structure of selected variant of cre site-specific recombinase, lnsgg bound to the loxp (wildtype) recognition site. SNAP output
1pyi transcription-DNA X-ray (3.2 Å) Marmorstein R, Harrison SC (1994) "Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a Zn2Cys6 binuclear cluster." Genes Dev., 8, 2504-2512. Crystal structure of a ppr1-DNA complex: DNA recognition by proteins containing a zn2cys6 binuclear cluster. SNAP output
1pzu transcription-DNA X-ray (3.1 Å) Jin L, Sliz P, Chen L, Macian F, Rao A, Hogan PG, Harrison SC (2003) "An asymmetric NFAT1 dimer on a pseudo-palindromic KB-like DNA site." Nat.Struct.Biol., 10, 807-811. doi: 10.1038/nsb975. An asymmetric nfat1-rhr homodimer on a pseudo-palindromic, kappa-b site. SNAP output
1q0t transferase-DNA X-ray (3.1 Å) Yang Z, Horton JR, Zhou L, Zhang XJ, Dong A, Zhang X, Schlagman SL, Kossykh V, Hattman S, Cheng X (2003) "Structure of the bacteriophage T4 DNA adenine methyltransferase." Nat.Struct.Biol., 10, 849-855. doi: 10.1038/nsb973. Ternary structure of t4dam with adohcy and DNA. SNAP output
1q3f hydrolase-DNA X-ray (1.9 Å) Bianchet MA, Seiple LA, Jiang YL, Ichikawa Y, Amzel LM, Stivers JT (2003) "Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase." Biochemistry, 42, 12455-12460. doi: 10.1021/bi035372+. Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA. SNAP output
1q3u replication-DNA X-ray (2.9 Å) Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck D (2003) "Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation." Nucleic Acids Res., 31, 5449-5460. doi: 10.1093/nar/gkg732. Crystal structure of a wild-type cre recombinase-loxp synapse: pre-cleavage complex. SNAP output
1q3v replication-DNA X-ray (2.91 Å) Ennifar E, Meyer JEW, Buchholz F, Stewart AF, Suck D (2003) "Crystal structure of a wild-type Cre recombinase-loxP synapse reveals a novel spacer conformation suggesting an alternative mechanism for DNA cleavage activation." Nucleic Acids Res., 31, 5449-5460. doi: 10.1093/nar/gkg732. Crystal structure of a wild-type cre recombinase-loxp synapse: phosphotyrosine covalent intermediate. SNAP output
1q9x transferase,replication-DNA X-ray (2.69 Å) Freisinger E, Grollman AP, Miller H, Kisker C (2004) "Lesion (in)tolerance reveals insights into DNA replication fidelity." Embo J., 23, 1494-1505. doi: 10.1038/sj.emboj.7600158. Crystal structure of enterobacteria phage rb69 gp43 DNA polymerase complexed with tetrahydrofuran containing DNA. SNAP output
1q9y transferase, replication-DNA X-ray (2.8 Å) Freisinger E, Grollman AP, Miller H, Kisker C (2004) "Lesion (in)tolerance reveals insights into DNA replication fidelity." Embo J., 23, 1494-1505. doi: 10.1038/sj.emboj.7600158. Crystal structure of enterobacteria phage rb69 gp43 DNA polymerase complexed with 8-oxoguanosine containing DNA. SNAP output
1qai transferase-DNA X-ray (2.3 Å) Najmudin S, Cote ML, Sun D, Yohannan S, Montano SP, Gu J, Georgiadis MM (2000) "Crystal structures of an N-terminal fragment from Moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain." J.Mol.Biol., 296, 613-622. doi: 10.1006/jmbi.1999.3477. Crystal structures of the n-terminal fragment from moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain. SNAP output
1qaj transferase-DNA X-ray (2.3 Å) Najmudin S, Cote ML, Sun D, Yohannan S, Montano SP, Gu J, Georgiadis MM (2000) "Crystal structures of an N-terminal fragment from Moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain." J.Mol.Biol., 296, 613-632. doi: 10.1006/jmbi.1999.3477. Crystal structures of the n-terminal fragment from moloney murine leukemia virus reverse transcriptase complexed with nucleic acid: functional implications for template-primer binding to the fingers domain. SNAP output
1qbj hydrolase-DNA X-ray (2.1 Å) Schwartz T, Rould MA, Lowenhaupt K, Herbert A, Rich A (1999) "Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA." Science, 284, 1841-1845. doi: 10.1126/science.284.5421.1841. Crystal structure of the zalpha z-DNA complex. SNAP output
1qln nucleotidyltransferase X-ray (2.4 Å) Cheetham GMT, Steitz TA (1999) "Structure of a Transcribing T7 RNA Polymerase Initiation Complex." Science, 286, 2305. doi: 10.1126/SCIENCE.286.5448.2305. Structure of a transcribing t7 RNA polymerase initiation complex. SNAP output
1qn3 tata box-binding protein (tbp) X-ray (1.95 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the c(-25) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qn4 tata box-binding protein (tbp) X-ray (1.86 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the t(-24) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qn5 tata box-binding protein (tbp) X-ray (1.93 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the g(-26) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qn6 tata box-binding protein (tbp) X-ray (2.1 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the t(-26) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qn7 tata box-binding protein (tbp) X-ray (2.3 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the t(-27) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qn8 tata box-binding protein (tbp) X-ray (2.1 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the t(-28) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qn9 tata box-binding protein (tbp) X-ray (1.9 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the c(-29) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qna tata box-binding protein (tbp) X-ray (1.8 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the t(-30) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qnb tata box-binding protein (tbp) X-ray (2.23 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the t(-25) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qnc tata box-binding protein (tbp) X-ray (2.3 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the a(-31) adenovirus major late promoter tata box variant bound to wild-type tbp (arabidopsis thaliana tbp isoform 2). tata element recognition by the tata box-binding protein has been conserved throughout evolution.. SNAP output
1qne tata box-binding protein (tbp) X-ray (1.9 Å) Patikoglou GA, Kim JL, Sun L, Yang S-H, Kodadek T, Burley SK (1999) "TATA Element Recognition by the TATA Box-Binding Protein Has Been Conserved Throughout Evolution." Genes Dev., 13, 3217. doi: 10.1101/GAD.13.24.3217. Crystal structure of the adenovirus major late promoter tata box bound to wild-type tbp (arabidopsis thaliana tbp isoform 2).. SNAP output
1qp0 transcription-DNA X-ray (2.9 Å) Glasfeld A, Koehler AN, Schumacher MA, Brennan RG (1999) "The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions." J.Mol.Biol., 291, 347-361. doi: 10.1006/jmbi.1999.2946. Purine repressor-hypoxanthine-palindromic operator complex. SNAP output
1qp4 transcription-DNA X-ray (3.0 Å) Glasfeld A, Koehler AN, Schumacher MA, Brennan RG (1999) "The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions." J.Mol.Biol., 291, 347-361. doi: 10.1006/jmbi.1999.2946. Purine repressor-hypoxanthine-palindromic operator complex. SNAP output
1qp7 transcription-DNA X-ray (2.9 Å) Glasfeld A, Koehler AN, Schumacher MA, Brennan RG (1999) "The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions." J.Mol.Biol., 291, 347-361. doi: 10.1006/jmbi.1999.2946. Purine repressor mutant-hypoxanthine-palindromic operator complex. SNAP output
1qp9 transcription-DNA X-ray (2.8 Å) Lukens AK, King DA, Marmorstein R (2000) "Structure of HAP1-PC7 bound to DNA: implications for DNA recognition and allosteric effects of DNA-binding on transcriptional activation." Nucleic Acids Res., 28, 3853-3863. doi: 10.1093/nar/28.20.3853. Structure of hap1-pc7 complexed to the uas of cyc7. SNAP output
1qpi transcription-DNA X-ray (2.5 Å) Orth P, Schnappinger D, Hillen W, Saenger W, Hinrichs W (2000) "Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system." Nat.Struct.Biol., 7, 215-219. doi: 10.1038/73324. Crystal structure of tetracycline repressor-operator complex. SNAP output
1qps hydrolase-DNA X-ray (2.5 Å) Horvath MM, Choi J, Kim Y, Wilkosz P, Rosenberg JM "The Integration of Recognition and Cleavage: X-Ray Structures of Pre- Transition State and Post-Reactive DNA-Eco RI Endonuclease Complexes." The crystal structure of a post-reactive cognate DNA-eco ri complex at 2.50 a in the presence of mn2+ ion. SNAP output
1qpz transcription-DNA X-ray (2.5 Å) Glasfeld A, Koehler AN, Schumacher MA, Brennan RG (1999) "The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions." J.Mol.Biol., 291, 347-361. doi: 10.1006/jmbi.1999.2946. Purine repressor-hypoxanthine-palindromic operator complex. SNAP output
1qqa gene regulation-DNA X-ray (3.0 Å) Glasfeld A, Koehler AN, Schumacher MA, Brennan RG (1999) "The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions." J.Mol.Biol., 291, 347-361. doi: 10.1006/jmbi.1999.2946. Purine repressor mutant-hypoxanthine-palindromic operator complex. SNAP output
1qqb gene regulation-DNA X-ray (2.7 Å) Glasfeld A, Koehler AN, Schumacher MA, Brennan RG (1999) "The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions." J.Mol.Biol., 291, 347-361. doi: 10.1006/jmbi.1999.2946. Purine repressor mutant-hypoxanthine-palindromic operator complex. SNAP output
1qrh hydrolase-DNA X-ray (2.5 Å) Choi J, Kim Y, Greene P, Hager P, Rosenberg JM "X-Ray Structure of the DNA-Eco RI Endonuclease Complexes with the ED144 and RK145 Mutations." X-ray structure of the DNA-eco ri endonuclease complexes with an r145k mutation at 2.7 a. SNAP output
1qri hydrolase-DNA X-ray (2.6 Å) Choi J, Kim Y, Greene P, Hager P, Rosenberg JM "X-Ray Structure of the DNA-Eco RI Endonuclease Complexes with the ED144 and RK145 Mutations." X-ray structure of the DNA-eco ri endonuclease complexes with an e144d mutation at 2.7 a. SNAP output
1qrv gene regulation-DNA X-ray (2.2 Å) Murphy IV FV, Sweet RM, Churchill ME (1999) "The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition." EMBO J., 18, 6610-6618. doi: 10.1093/emboj/18.23.6610. Crystal structure of the complex of hmg-d and DNA. SNAP output
1qsl transferase-DNA X-ray (2.2 Å) Brautigam CA, Aschheim K, Steitz TA (1999) "Structural elucidation of the binding and inhibitory properties of lanthanide (III) ions at the 3'-5' exonucleolytic active site of the Klenow fragment." Chem.Biol., 6, 901-908. doi: 10.1016/S1074-5521(00)80009-5. Klenow fragment complexed with single-stranded substrate and europium (iii) ion. SNAP output
1qss transferase-DNA X-ray (2.3 Å) Li Y, Mitaxov V, Waksman G (1999) "Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation." Proc.Natl.Acad.Sci.USA, 96, 9491-9496. doi: 10.1073/pnas.96.17.9491. Ddgtp-trapped closed ternary complex of the large fragment of DNA polymerase i from thermus aquaticus. SNAP output
1qsy transferase-DNA X-ray (2.3 Å) Li Y, Mitaxov V, Waksman G (1999) "Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation." Proc.Natl.Acad.Sci.USA, 96, 9491-9496. doi: 10.1073/pnas.96.17.9491. Ddatp-trapped closed ternary complex of the large fragment of DNA polymerase i from thermus aquaticus. SNAP output
1qtm transferase-DNA X-ray (2.3 Å) Li Y, Mitaxov V, Waksman G (1999) "Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation." Proc.Natl.Acad.Sci.USA, 96, 9491-9496. doi: 10.1073/pnas.96.17.9491. Ddttp-trapped closed ternary complex of the large fragment of DNA polymerase i from thermus aquaticus. SNAP output
1qum hydrolase-DNA X-ray (1.55 Å) Hosfield DJ, Guan Y, Haas BJ, Cunningham RP, Tainer JA (1999) "Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis." Cell(Cambridge,Mass.), 98, 397-408. doi: 10.1016/S0092-8674(00)81968-6. Crystal structure of escherichia coli endonuclease iv in complex with damaged DNA. SNAP output
1qx0 transferase-DNA X-ray (2.26 Å) Guasch A, Lucas M, Moncalian G, Cabezas M, Prez-Luque R, Gomis-Rth FX, de la Cruz F, Coll M (2003) "RECOGNITION AND PROCESSING OF THE ORIGIN OF TRANSFER DNA BY CONJUGATIVE RELAXASE TRWC." Nat.Struct.Biol., 10, 1002-1010. doi: 10.1038/nsb1017. Conjugative relaxase trwc in complex with orit DNA. metal-bound structure. SNAP output
1qzg DNA binding protein-DNA X-ray (1.9 Å) Lei M, Podell ER, Baumann P, Cech TR (2003) "DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA." Nature, 426, 198-203. doi: 10.1038/nature02092. Crystal structure of pot1 (protection of telomere)- ssDNA complex. SNAP output
1qzh DNA binding protein-DNA X-ray (2.4 Å) Lei M, Podell ER, Baumann P, Cech TR (2003) "DNA self-recognition in the structure of Pot1 bound to telomeric single-stranded DNA." Nature, 426, 198-203. doi: 10.1038/nature02092. Crystal structure of pot1 (protection of telomere)- ssDNA complex. SNAP output
1r0a transferase-immune system-DNA X-ray (2.8 Å) Peletskaya EN, Kogon AA, Tuske S, Arnold E, Hughes SH (2004) "Nonnucleoside inhibitor binding affects the interactions of the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase with DNA." J.Virol., 78, 3387-3397. doi: 10.1128/JVI.78.7.3387-3397.2004. Crystal structure of hiv-1 reverse transcriptase covalently tethered to DNA template-primer solved to 2.8 angstroms. SNAP output
1r0n transcription-DNA X-ray (2.6 Å) Devarakonda S, Harp JM, Kim Y, Ozyhar A, Rastinejad F (2003) "Structure of the heterodimeric Ecdysone Receptor DNA-binding complex." Embo J., 22, 5827-5840. doi: 10.1093/emboj/cdg569. Crystal structure of heterodimeric ecdsyone receptor DNA binding complex. SNAP output
1r0o transcription-DNA X-ray (2.24 Å) Devarakonda S, Harp JM, Kim Y, Ozyhar A, Rastinejad F (2003) "Structure of the Heterodimeric Ecdysone Receptor DNA-binding Complex." Embo J., 22, 5827-5840. doi: 10.1093/emboj/cdg569. Crystal structure of the heterodimeric ecdysone receptor DNA-binding complex. SNAP output
1r2y hydrolase-DNA X-ray (2.34 Å) Fromme JC, Verdine GL (2003) "DNA Lesion Recognition by the Bacterial Repair Enzyme MutM." J.Biol.Chem., 278, 51543-51548. doi: 10.1074/jbc.M307768200. Mutm (fpg) bound to 8-oxoguanine (oxog) containing DNA. SNAP output
1r2z hydrolase-DNA X-ray (1.63 Å) Fromme JC, Verdine GL (2003) "DNA Lesion Recognition by the Bacterial Repair Enzyme MutM." J.Biol.Chem., 278, 51543-51548. doi: 10.1074/jbc.M307768200. Mutm (fpg) bound to 5,6-dihydrouracil (dhu) containing DNA. SNAP output
1r49 isomerase-DNA X-ray (3.13 Å) Interthal H, Quigley PM, Hol WG, Champoux JJ (2004) "The role of lysine 532 in the catalytic mechanism of human topoisomerase I." J.Biol.Chem., 279, 2984-2992. doi: 10.1074/jbc.M309959200. Human topoisomerase i (topo70) double mutant k532r-y723f. SNAP output
1r4i transcription-DNA X-ray (3.1 Å) Shaffer PL, Jivan A, Dollins DE, Claessens F, Gewirth DT (2004) "Structural basis of androgen receptor binding to selective androgen response elements." Proc.Natl.Acad.Sci.USA, 101, 4758-4763. doi: 10.1073/pnas.0401123101. Crystal structure of androgen receptor DNA-binding domain bound to a direct repeat response element. SNAP output
1r4o transcription-DNA X-ray (2.5 Å) Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto KR, Sigler PB (1991) "Crystallographic Analysis of the Interaction of The Glucocorticoid Receptor with DNA." Nature, 352, 497-505. doi: 10.1038/352497a0. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. SNAP output
1r4r transcription-DNA X-ray (3.0 Å) Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto KR, Sigler PB (1991) "Crystallographic Analysis of the Interaction of the Glucocorticoid Receptor with DNA." Nature, 352, 497-505. doi: 10.1038/352497a0. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. SNAP output
1r71 transcription-DNA X-ray (2.2 Å) Khare D, Ziegelin G, Lanka E, Heinemann U (2004) "Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB." Nat.Struct.Mol.Biol., 11, 656-663. doi: 10.1038/nsmb773. Crystal structure of the DNA binding domain of korb in complex with the operator DNA. SNAP output
1r7m hydrolase-DNA X-ray (2.25 Å) Moure CM, Gimble FS, Quiocho FA (2003) "The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity." J.Mol.Biol., 334, 685-695. doi: 10.1016/j.jmb.2003.09.068. The homing endonuclease i-scei bound to its DNA recognition region. SNAP output
1r8d transcription-DNA X-ray (2.7 Å) Newberry KJ, Brennan RG (2004) "The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus." J.Biol.Chem., 279, 20356-20362. doi: 10.1074/jbc.M400960200. Crystal structure of mtan bound to DNA. SNAP output
1r8e transcription-DNA X-ray (2.4 Å) Newberry KJ, Brennan RG (2004) "The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus." J.Biol.Chem., 279, 20356-20362. doi: 10.1074/jbc.M400960200. Crystal structure of bmrr bound to DNA at 2.4a resolution. SNAP output
1r9s transcription-DNA-RNA hybrid X-ray (4.25 Å) Westover KD, Bushnell DA, Kornberg RD (2004) "Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center." Cell(Cambridge,Mass.), 119, 481-489. doi: 10.1016/j.cell.2004.10.016. RNA polymerase ii strand separated elongation complex, matched nucleotide. SNAP output
1r9t transcription-DNA-RNA hybrid X-ray (3.5 Å) Westover KD, Bushnell DA, Kornberg RD (2004) "Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center." Cell(Cambridge,Mass.), 119, 481-489. doi: 10.1016/j.cell.2004.10.016. RNA polymerase ii strand separated elongation complex, mismatched nucleotide. SNAP output
1ram transcription-DNA X-ray (2.7 Å) Chen YQ, Ghosh S, Ghosh G (1998) "A novel DNA recognition mode by the NF-kappa B p65 homodimer." Nat.Struct.Biol., 5, 67-73. doi: 10.1038/nsb0198-67. A novel DNA recognition mode by nf-kb p65 homodimer. SNAP output
1rb8 virus-DNA X-ray (3.5 Å) Bernal RA, Hafenstein S, Esmeralda R, Fane BA, Rossmann MG (2004) "The phiX174 Protein J Mediates DNA Packaging and Viral Attachment to Host Cells." J.Mol.Biol., 337, 1109-1122. doi: 10.1016/j.jmb.2004.02.033. The phix174 DNA binding protein j in two different capsid environments.. SNAP output
1rbj hydrolase-DNA X-ray (2.7 Å) Ko TP, Williams R, McPherson A (1996) "Structure of a ribonuclease B+d(pA)4 complex." Acta Crystallogr.,Sect.D, 52, 160-164. doi: 10.1107/S0907444995009127. Ribonuclease b complex with d(tetra-(deoxy-adenylate)). SNAP output
1rc8 transferase-DNA X-ray (2.75 Å) Eastberg JH, Pelletier J, Stoddard BL (2004) "Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase." Nucleic Acids Res., 32, 653-660. doi: 10.1093/nar/gkh212. T4 polynucleotide kinase bound to 5'-gtcac-3' ssDNA. SNAP output
1rcn hydrolase-DNA X-ray (2.32 Å) Fontecilla-Camps JC, de Llorens R, le Du MH, Cuchillo CM (1994) "Crystal structure of ribonuclease A.d(ApTpApApG) complex. Direct evidence for extended substrate recognition." J.Biol.Chem., 269, 21526-21531. Crystal structure of the ribonuclease a d(aptpapapg) complex : direct evidence for extended substrate recognition. SNAP output
1rcs transcription-DNA NMR Zhang H, Zhao D, Revington M, Lee W, Jia X, Arrowsmith C, Jardetzky O (1994) "The solution structures of the trp repressor-operator DNA complex." J.Mol.Biol., 238, 592-614. doi: 10.1006/jmbi.1994.1317. NMR study of trp repressor-operator DNA complex. SNAP output
1rep replication-DNA X-ray (2.6 Å) Komori H, Matsunaga F, Higuchi Y, Ishiai M, Wada C, Miki K (1999) "Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 A resolution." EMBO J., 18, 4597-4607. doi: 10.1093/emboj/18.17.4597. Crystal structure of replication initiator protein repe54 of mini-f plasmid complexed with an iteron DNA. SNAP output
1rff hydrolase-DNA X-ray (1.7 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octapeptide klnyydpr, and tetranucleotide agtt.. SNAP output
1rfi hydrolase-DNA X-ray (2.2 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, pentapeptide klnyk, and tetranucleotide agtc. SNAP output
1rg1 hydrolase-DNA X-ray (2.1 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide agtt. SNAP output
1rg2 hydrolase-DNA X-ray (2.1 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide agta. SNAP output
1rgt hydrolase-DNA X-ray (2.0 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide agtc. SNAP output
1rgu hydrolase-DNA X-ray (2.22 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. The crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide agtg. SNAP output
1rh0 hydrolase-DNA X-ray (2.3 Å) Davies DR, Interthal H, Champoux JJ, Hol WG (2004) "Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes." J.Med.Chem., 47, 829-837. doi: 10.1021/jm030487x. Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octopamine and trinucleotide gtt. SNAP output
1rh6 DNA binding protein-DNA X-ray (1.7 Å) Sam MD, Cascio D, Johnson RC, Clubb RT (2004) "Crystal structure of the excisionase-DNA complex from bacteriophage lambda." J.Mol.Biol., 338, 229-240. doi: 10.1016/j.jmb.2004.02.053. Bacteriophage lambda excisionase (xis)-DNA complex. SNAP output
1rio transcription-DNA X-ray (2.3 Å) Jain D, Nickels BE, Sun L, Hochschild A, Darst SA (2004) "Structure of a ternary transcription activation complex." Mol.Cell, 13, 45-53. doi: 10.1016/S1097-2765(03)00483-0. Structure of bacteriophage lambda ci-ntd in complex with sigma-region4 of thermus aquaticus bound to DNA. SNAP output
1rm1 transcription-DNA X-ray (2.5 Å) Jin X, Gewirth DT, Geiger JH "High Resolution Structure of a Yeast TFIIA/TBP/TATA-box DNA Complex." Structure of a yeast tfiia-tbp-tata-box DNA complex. SNAP output
1rnb endonuclease X-ray (1.9 Å) Baudet S, Janin J (1991) "Crystal structure of a barnase-d(GpC) complex at 1.9 A resolution." J.Mol.Biol., 219, 123-132. doi: 10.1016/0022-2836(91)90862-Z. Crystal structure of a barnase-d(*gp*c) complex at 1.9 angstroms resolution. SNAP output
1rpe gene regulation-DNA X-ray (2.5 Å) Shimon LJ, Harrison SC (1993) "The phage 434 OR2/R1-69 complex at 2.5 A resolution." J.Mol.Biol., 232, 826-838. doi: 10.1006/jmbi.1993.1434. The phage 434 or2-r1-69 complex at 2.5 angstroms resolution. SNAP output
1rpz transferase-DNA X-ray (2.9 Å) Eastberg JH, Pelletier J, Stoddard BL (2004) "Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase." Nucleic Acids Res., 32, 653-660. doi: 10.1093/nar/gkh212. T4 polynucleotide kinase bound to 5'-tgcac-3' ssDNA. SNAP output
1rr8 isomerase-DNA X-ray (2.6 Å) Chrencik JE, Staker BL, Burgin AB, Pourquier P, Pommier Y, Stewart L, Redinbo MR (2004) "Mechanisms of camptothecin resistance by human topoisomerase I mutations." J.Mol.Biol., 339, 773-784. doi: 10.1016/j.jmb.2004.03.077. Structural mechanisms of camptothecin resistance by mutations in human topoisomerase i. SNAP output
1rrc transferase-DNA X-ray (2.46 Å) Eastberg JH, Pelletier J, Stoddard BL (2004) "Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase." Nucleic Acids Res., 32, 653-660. doi: 10.1093/nar/gkh212. T4 polynucleotide kinase bound to 5'-gtc-3' ssDNA. SNAP output
1rrj isomerase-DNA X-ray (2.3 Å) Chrencik JE, Staker BL, Burgin AB, Pourquier P, Pommier Y, Stewart L, Redinbo MR (2004) "Mechanisms of camptothecin resistance by human topoisomerase I mutations." J.Mol.Biol., 339, 773-784. doi: 10.1016/j.jmb.2004.03.077. Structural mechanisms of camptothecin resistance by mutations in human topoisomerase i. SNAP output
1rrq hydrolase-DNA X-ray (2.22 Å) Fromme JC, Banerjee A, Huang SJ, Verdine GL (2004) "Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase." Nature, 427, 652-656. doi: 10.1038/nature02306. Muty adenine glycosylase in complex with DNA containing an a:oxog pair. SNAP output
1rrs hydrolase-DNA X-ray (2.4 Å) Fromme JC, Banerjee A, Huang SJ, Verdine GL (2004) "Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase." Nature, 427, 652-656. doi: 10.1038/nature02306. Muty adenine glycosylase in complex with DNA containing an abasic site. SNAP output
1rta hydrolase-DNA X-ray (2.5 Å) Birdsall DL, McPherson A (1992) "Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease A." J.Biol.Chem., 267, 22230-22236. Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease a. SNAP output
1rtd transferase-DNA X-ray (3.2 Å) Huang H, Chopra R, Verdine GL, Harrison SC (1998) "Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance." Science, 282, 1669-1675. doi: 10.1126/science.282.5394.1669. Structure of a catalytic complex of hiv-1 reverse transcriptase: implications for nucleoside analog drug resistance. SNAP output
1run transcription-DNA X-ray (2.7 Å) Parkinson G, Gunasekera A, Vojtechovsky J, Zhang X, Kunkel TA, Berman H, Ebright RH (1996) "Aromatic hydrogen bond in sequence-specific protein DNA recognition." Nat.Struct.Biol., 3, 837-841. doi: 10.1038/nsb1096-837. Catabolite gene activator protein (cap)-DNA complex + adenosine-3',5'-cyclic-monophosphate. SNAP output
1ruo transcription-DNA X-ray (2.7 Å) Parkinson G, Gunasekera A, Vojtechovsky J, Zhang X, Kunkel TA, Berman H, Ebright RH (1996) "Aromatic hydrogen bond in sequence-specific protein DNA recognition." Nat.Struct.Biol., 3, 837-841. doi: 10.1038/nsb1096-837. Catabolite gene activator protein (cap) mutant-DNA complex + adenosine-3',5'-cyclic-monophosphate. SNAP output
1rv5 hydrolase-DNA X-ray (2.1 Å) Horton NC, Perona JJ (1998) "Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT)." J.Mol.Biol., 277, 779-783. doi: 10.1006/jmbi.1998.1655. Complex of ecorv endonuclease with d(aaagat)-d(atctt). SNAP output
1rva hydrolase-DNA X-ray (2.0 Å) Kostrewa D, Winkler FK (1995) "Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution." Biochemistry, 34, 683-696. doi: 10.1021/bi00002a036. Mg2+ binding to the active site of eco rv endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 angstroms resolution. SNAP output
1rvb hydrolase-DNA X-ray (2.1 Å) Kostrewa D, Winkler FK (1995) "Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution." Biochemistry, 34, 683-696. doi: 10.1021/bi00002a036. Mg2+ binding to the active site of eco rv endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 angstroms resolution. SNAP output
1rvc hydrolase-DNA X-ray (2.1 Å) Kostrewa D, Winkler FK (1995) "Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution." Biochemistry, 34, 683-696. doi: 10.1021/bi00002a036. Mg2+ binding to the active site of eco rv endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 angstroms resolution. SNAP output
1rxv hydrolase-DNA X-ray (2.5 Å) Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B, Shen B, Tainer JA (2004) "Structural Basis for FEN-1 Substrate Specificity and PCNA-Mediated Activation in DNA Replication and Repair." Cell(Cambridge,Mass.), 116, 39-50. doi: 10.1016/S0092-8674(03)01036-5. Crystal structure of a. fulgidus fen-1 bound to DNA. SNAP output
1rxw hydrolase-DNA X-ray (2.0 Å) Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B, Shen B, Tainer JA (2004) "Structural Basis for FEN-1 Substrate Specificity and PCNA-Mediated Activation in DNA Replication and Repair." Cell(Cambridge,Mass.), 116, 39-50. doi: 10.1016/S0092-8674(03)01036-5. Crystal structure of a. fulgidus fen-1 bound to DNA. SNAP output
1ryr transferase-DNA X-ray (2.28 Å) Ling H, Boudsocq F, Plosky B, Woodgate R, Yang W (2003) "Replication of a Cis-Syn Thymine Dimer at Atomic Resolution." Nature, 424, 1083-1087. doi: 10.1038/nature01919. Replication of a cis-syn thymine dimer at atomic resolution. SNAP output
1rys transferase-DNA X-ray (2.03 Å) Ling H, Boudsocq F, Plosky B, Woodgate R, Yang W (2003) "Replication of a Cis-Syn Thymine Dimer at Atomic Resolution." Nature, 424, 1083-1087. doi: 10.1038/nature01919. Replication of a cis-syn thymine dimer at atomic resolution. SNAP output
1rz9 viral protein-DNA X-ray (3.1 Å) Hickman AB, Ronning DR, Perez ZN, Kotin RM, Dyda F (2004) "The nuclease domain of adeno-associated virus rep coordinates replication initiation using two distinct DNA recognition interfaces." Mol.Cell, 13, 403-414. doi: 10.1016/S1097-2765(04)00023-1. Crystal structure of aav rep complexed with the rep-binding sequence. SNAP output
1rzr transcription-transport protein-DNA X-ray (2.8 Å) Schumacher MA, Allen GS, Diel M, Seidel G, Hillen W, Brennan RG (2004) "Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P." Cell(Cambridge,Mass.), 118, 731-741. doi: 10.1016/j.cell.2004.08.027. Crystal structure of transcriptional regulator-phosphoprotein-DNA complex. SNAP output
1rzt transferase-DNA X-ray (2.1 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Blanco L, Kunkel TA, Pedersen LC (2004) "A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology." Mol.Cell, 13, 561-572. doi: 10.1016/S1097-2765(04)00061-9. Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule. SNAP output
1s0m transferase-DNA X-ray (2.7 Å) Ling H, Sayer JM, Plosky BS, Yagi H, Boudsocq F, Woodgate R, Jerina DM, Yang W (2004) "Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase." Proc.Natl.Acad.Sci.USA, 101, 2265-2269. doi: 10.1073/pnas.0308332100. Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase. SNAP output
1s0n transferase-DNA X-ray (2.8 Å) Ling H, Boudsocq F, Woodgate R, Yang W (2004) "Snapshots of Replication through an Abasic Lesion; Structural Basis for Base Substitutions and Frameshifts." Mol.Cell, 13, 751-762. doi: 10.1016/S1097-2765(04)00101-7. Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift. SNAP output
1s0o transferase-DNA X-ray (2.1 Å) Ling H, Boudsocq F, Woodgate R, Yang W (2004) "Snapshots of Replication through an Abasic Lesion; Structural Basis for Base Substitutions and Frameshifts." Mol.Cell, 13, 751-762. doi: 10.1016/S1097-2765(04)00101-7. Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift. SNAP output
1s0v transferase-DNA-RNA hybrid X-ray (3.2 Å) Temiakov D, Patlan V, Anikin M, McAllister WT, Yokoyama S, Vassylyev DG (2004) "Structural basis for substrate selection by t7 RNA polymerase." Cell(Cambridge,Mass.), 116, 381-391. doi: 10.1016/S0092-8674(04)00059-5. Structural basis for substrate selection by t7 RNA polymerase. SNAP output
1s10 transferase-DNA X-ray (2.1 Å) Ling H, Boudsocq F, Woodgate R, Yang W (2004) "Snapshots of Replication through an Abasic Lesion; Structural Basis for Base Substitutions and Frameshifts." Mol.Cell, 13, 751-762. doi: 10.1016/S1097-2765(04)00101-7. Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift. SNAP output
1s32 structural protein-DNA X-ray (2.05 Å) Edayathumangalam RS, Weyermann P, Gottesfeld JM, Dervan PB, Luger K (2004) "Molecular Recognition of the Nucleosomal 'Supergroove'." Proc.Natl.Acad.Sci.USA, 101, 6864-6869. doi: 10.1073/pnas.0401743101. Molecular recognition of the nucleosomal 'supergroove'. SNAP output
1s40 cell cycle-DNA NMR Mitton-Fry RM, Anderson EM, Theobald DL, Glustrom LW, Wuttke DS (2004) "Structural basis for telomeric single-stranded DNA recognition by yeast Cdc13." J.Mol.Biol., 338, 241-255. doi: 10.1016/j.jmb.2004.01.063. Solution structure of the cdc13 DNA-binding domain complexed with a single-stranded telomeric DNA 11-mer. SNAP output
1s6m DNA binding protein-DNA X-ray (2.28 Å) Boer R, Russi S, Guasch A, Lucas M, Blanco AG, Perez-Luque R, Coll M, de la Cruz F (2006) "Unveiling the molecular mechanism of a conjugative relaxase: The structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site." J.Mol.Biol., 358, 857-869. doi: 10.1016/j.jmb.2006.02.018. Conjugative relaxase trwc in complex with orit DNA. metal-bound structure. SNAP output
1s76 transferase X-ray (2.88 Å) Yin YW, Steitz TA (2004) "The structural mechanism of translocation and helicase activity in T7 RNA polymerase." Cell(Cambridge,Mass.), 116, 393-404. doi: 10.1016/S0092-8674(04)00120-5. T7 RNA polymerase alpha beta methylene atp elongation complex. SNAP output
1s77 transferase X-ray (2.69 Å) Yin YW, Steitz TA (2004) "The structural mechanism of translocation and helicase activity in T7 RNA polymerase." Cell(Cambridge,Mass.), 116, 393-404. doi: 10.1016/S0092-8674(04)00120-5. T7 rnap product pyrophosphate elongation complex. SNAP output
1s97 transferase-DNA X-ray (2.4 Å) Trincao J, Johnson RE, Wolfle WT, Escalante CR, Prakash S, Prakash L, Aggarwal AK (2004) "Dpo4 is hindered in extending a G.T mismatch by a reverse wobble." Nat.Struct.Mol.Biol., 11, 457-462. doi: 10.1038/nsmb755. Dpo4 with gt mismatch. SNAP output
1s9f transferase-DNA X-ray (2.0 Å) Trincao J, Johnson RE, Wolfle WT, Escalante CR, Prakash S, Prakash L, Aggarwal AK (2004) "Dpo4 is hindered in extending a G.T mismatch by a reverse wobble." Nat.Struct.Mol.Biol., 11, 457-462. doi: 10.1038/nsmb755. Dpo with at matched. SNAP output
1s9k transcription-DNA X-ray (3.1 Å) Wang D, Stroud JC, Chen L "Crystal Structure of Human NFAT1 and Fos-Jun on the IL-2 ARRE1 Site." Crystal structure of human nfat1 and fos-jun on the il-2 arre1 site. SNAP output
1sa3 hydrolase-DNA X-ray (1.95 Å) Xu QS, Kucera RB, Roberts RJ, Guo HC (2004) "An Asymmetric Complex of Restriction Endonuclease MspI on Its Palindromic DNA Recognition Site." STRUCTURE, 12, 1741-1747. doi: 10.1016/j.str.2004.07.014. An asymmetric complex of restriction endonuclease mspi on its palindromic DNA recognition site. SNAP output
1sax transcription-DNA X-ray (2.8 Å) Garcia-Castellanos R, Mallorqui-Fernandez G, Marrero A, Potempa J, Coll M, Gomis-Ruth FX (2004) "On the transcriptional regulation of methicillin resistance: MecI repressor in complex with its operator." J.Biol.Chem., 279, 17888-17896. doi: 10.1074/jbc.M313123200. Three-dimensional structure of s.aureus methicillin-resistance regulating transcriptional repressor meci in complex with 25-bp ds-DNA. SNAP output
1sc7 isomerase-DNA X-ray (3.0 Å) Staker BL, Feese MD, Cushman M, Pommier Y, Zembower D, Stewart L, Burgin AB (2005) "Structures of three classes of anticancer agents bound to the human topoisomerase I-DNA covalent complex." J.Med.Chem., 48, 2336-2345. doi: 10.1021/jm049146p. Human DNA topoisomerase i (70 kda) in complex with the indenoisoquinoline mj-ii-38 and covalent complex with a 22 base pair DNA duplex. SNAP output
1seu isomerase-DNA X-ray (3.0 Å) Staker BL, Feese MD, Cushman M, Pommier Y, Zembower D, Stewart L, Burgin AB (2005) "Structures of three classes of anticancer agents bound to the human topoisomerase I-DNA covalent complex." J.Med.Chem., 48, 2336-2345. doi: 10.1021/jm049146p. Human DNA topoisomerase i (70 kda) in complex with the indolocarbazole sa315f and covalent complex with a 22 base pair DNA duplex. SNAP output
1sfo transcription-DNA-RNA hybrid X-ray (3.61 Å) Westover KD, Bushnell DA, Kornberg RD (2004) "Structural Basis of Transcription: Separation of RNA from DNA by RNA Polymerase II." Science, 303, 1014-1016. doi: 10.1126/science.1090839. RNA polymerase ii strand separated elongation complex. SNAP output
1sfu DNA binding protein-DNA X-ray (2.0 Å) Ha SC, Lokanath NK, Van Quyen D, Wu CA, Lowenhaupt K, Rich A, Kim YG, Kim KK (2004) "A poxvirus protein forms a complex with left-handed Z-DNA: crystal structure of a Yatapoxvirus Zalpha bound to DNA." Proc.Natl.Acad.Sci.USA, 101, 14367-14372. doi: 10.1073/pnas.0405586101. Crystal structure of the viral zalpha domain bound to left-handed z-DNA. SNAP output
1si2 gene regulation-RNA-DNA X-ray (2.6 Å) Ma JB, Ye K, Patel DJ (2004) "Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain." Nature, 429, 318-322. doi: 10.1038/nature02519. Crystal structure of the paz domain of human eif2c1 in complex with a 9-mer sirna-like duplex of deoxynucleotide overhang. SNAP output
1skm transferase-DNA X-ray (2.2 Å) Horton JR, Ratner G, Banavali NK, Huang N, Choi Y, Maier MA, Marquez VE, MacKerell AD, Cheng X (2004) "Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase." Nucleic Acids Res., 32, 3877-3886. doi: 10.1093/nar/gkh701. Hhai methyltransferase in complex with DNA containing an abasic south carbocyclic sugar at its target site. SNAP output
1skn transcription-DNA X-ray (2.5 Å) Rupert PB, Daughdrill GW, Bowerman B, Matthews BW (1998) "A new DNA-binding motif in the Skn-1 binding domain-DNA complex." Nat.Struct.Biol., 5, 484-491. doi: 10.1038/nsb0698-484. The binding domain of skn-1 in complex with DNA: a new DNA-binding motif. SNAP output
1skr transferase-electron transport-DNA X-ray (2.4 Å) Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T (2004) "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat.Struct.Mol.Biol., 11, 784-790. doi: 10.1038/nsmb792. T7 DNA polymerase complexed to DNA primer-template and ddatp. SNAP output
1sks transferase-electron transport-DNA X-ray (2.3 Å) Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T (2004) "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat.Struct.Mol.Biol., 11, 784-790. doi: 10.1038/nsmb792. Binary 3' complex of t7 DNA polymerase with a DNA primer-template containing a cis-syn thymine dimer on the template. SNAP output
1skw transferase-electron transport-DNA X-ray (2.3 Å) Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T (2004) "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat.Struct.Mol.Biol., 11, 784-790. doi: 10.1038/nsmb792. Binary 3' complex of t7 DNA polymerase with a DNA primer-template containing a disordered cis-syn thymine dimer on the template. SNAP output
1sl0 transferase-electron transport-DNA X-ray (3.2 Å) Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T (2004) "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat.Struct.Mol.Biol., 11, 784-790. doi: 10.1038/nsmb792. Ternary 3' complex of t7 DNA polymerase with a DNA primer-template containing a disordered cis-syn thymine dimer on the template and an incoming nucleotide. SNAP output
1sl1 transferase-electron transport-DNA X-ray (2.2 Å) Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T (2004) "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat.Struct.Mol.Biol., 11, 784-790. doi: 10.1038/nsmb792. Binary 5' complex of t7 DNA polymerase with a DNA primer-template containing a cis-syn thymine dimer on the template. SNAP output
1sl2 transferase-electron transport-DNA X-ray (2.3 Å) Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T (2004) "Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7." Nat.Struct.Mol.Biol., 11, 784-790. doi: 10.1038/nsmb792. Ternary 5' complex of t7 DNA polymerase with a DNA primer-template containing a cis-syn thymine dimer on the template and an incoming nucleotide. SNAP output
1srs transcription-DNA X-ray (3.2 Å) Pellegrini L, Tan S, Richmond TJ (1995) "Structure of serum response factor core bound to DNA." Nature, 376, 490-498. doi: 10.1038/376490a0. Serum response factor (srf) core complexed with specific sre DNA. SNAP output
1ssp hydrolase-DNA X-ray (1.9 Å) Parikh SS, Mol CD, Slupphaug G, Bharati S, Krokan HE, Tainer JA (1998) "Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA." EMBO J., 17, 5214-5226. doi: 10.1093/emboj/17.17.5214. Wild-type uracil-DNA glycosylase bound to uracil-containing DNA. SNAP output
1stx hydrolase-DNA X-ray (2.1 Å) Horton NC, Perona JJ (2004) "DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites." Biochemistry, 43, 6841-6857. doi: 10.1021/bi0499056. Structure of the k38a mutant of ecorv bound to cognate DNA and mn2+. SNAP output
1suz hydrolase-DNA X-ray (1.8 Å) Horton NC, Perona JJ (2004) "DNA Cleavage by EcoRV Endonuclease: Two Metal Ions in Three Metal Ion Binding Sites." Biochemistry, 43, 6841-6857. doi: 10.1021/bi0499056. The structure of k92a ecorv bound to cognate DNA and mg2+. SNAP output
1svc transcription-DNA X-ray (2.6 Å) Muller CW, Rey FA, Sodeoka M, Verdine GL, Harrison SC (1995) "Structure of the NF-kappa B p50 homodimer bound to DNA." Nature, 373, 311-317. doi: 10.1038/373311a0. Nfkb p50 homodimer bound to DNA. SNAP output
1sx5 hydrolase-DNA X-ray (1.5 Å) Horton NC, Perona JJ (2004) "DNA cleavage by EcoRV endonuclease: Two metal ions in three metal ion binding sites." Biochemistry, 43, 6841-6857. doi: 10.1021/bi0499056. K38a ecorv bound to cleaved DNA and mn2+: p1 crystal form. SNAP output
1sx8 hydrolase-DNA X-ray (2.15 Å) Horton NC, Perona JJ (2004) "DNA Cleavage by EcoRV Endonuclease: Two Metal Ions in Three Metal Ion Binding Sites." Biochemistry, 43, 6841-6857. doi: 10.1021/bi0499056. Ecorv bound to cognate DNA and mn2+. SNAP output
1sxp transferase-DNA X-ray (2.5 Å) Lariviere L, Morera S (2004) "Structural evidence of a passive base flipping mechanism for {beta}-Glucosyltransferase." J.Biol.Chem., 279, 34715-34720. doi: 10.1074/jbc.M404394200. Bgt in complex with a 13mer DNA containing a central a:g mismatch. SNAP output
1sxq transferase-DNA X-ray (1.8 Å) Lariviere L, Morera S (2004) "Structural evidence of a passive base flipping mechanism for {beta}-Glucosyltransferase." J.Biol.Chem., 279, 34715-34720. doi: 10.1074/jbc.M404394200. Bgt in complex with a 13mer DNA containing a central c:g base pair and udp. SNAP output
1t03 transferase-antibody-DNA X-ray (3.1 Å) Tuske S, Sarafianos SG, Clark Jr AD, Ding J, Naeger LK, White KL, Miller MD, Gibbs CS, Boyer PL, Clark P, Wang G, Gaffney BL, Jones RA, Jerina DM, Hughes SH, Arnold E (2004) "Structure of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir." Nat.Struct.Mol.Biol., 11, 469-474. doi: 10.1038/nsmb760. Hiv-1 reverse transcriptase crosslinked to tenofovir terminated template-primer (complex p). SNAP output
1t05 transferase-DNA X-ray (3.0 Å) Tuske S, Sarafianos SG, Clark Jr AD, Ding J, Naeger LK, White KL, Miller MD, Gibbs CS, Boyer PL, Clark P, Wang G, Gaffney BL, Jones RA, Jerina DM, Hughes SH, Arnold E (2004) "Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir." Nat.Struct.Mol.Biol., 11, 469-474. doi: 10.1038/nsmb760. Hiv-1 reverse transcriptase crosslinked to template-primer with tenofovir-diphosphate bound as the incoming nucleotide substrate. SNAP output
1t2k transcription-DNA X-ray (3.0 Å) Panne D, Maniatis T, Harrison SC (2004) "Crystal structure of ATF-2/c-Jun and IRF-3 bound to the interferon-beta enhancer." Embo J., 23, 4384-4393. doi: 10.1038/sj.emboj.7600453. Structure of the DNA binding domains of irf3, atf-2 and jun bound to DNA. SNAP output
1t2s nucleic acid binding protein-DNA NMR Lingel A, Simon B, Izaurralde E, Sattler M (2004) "Nucleic acid 3'-end recognition by the Argonaute2 PAZ domain." Nat.Struct.Mol.Biol., 11, 576-577. doi: 10.1038/nsmb777. Structural basis for 3' end recognition of nucleic acids by the drosophila argonaute 2 paz domain. SNAP output
1t2t hydrolase-DNA X-ray (2.5 Å) Edgell DR, Derbyshire V, Van Roey P, LaBonne S, Stanger MJ, Li Z, Boyd TM, Shub DA, Belfort M (2004) "Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor." Nat.Struct.Mol.Biol., 11, 936-944. doi: 10.1038/nsmb823. Crystal structure of the DNA-binding domain of intron endonuclease i-tevi with operator site. SNAP output
1t38 transferase-DNA X-ray (3.2 Å) Daniels DS, Woo TT, Luu KX, Noll DM, Clarke ND, Pegg AE, Tainer JA (2004) "DNA binding and nucleotide flipping by the human DNA repair protein AGT." Nat.Struct.Mol.Biol., 11, 714-720. doi: 10.1038/nsmb791. Human o6-alkylguanine-DNA alkyltransferase bound to DNA containing o6-methylguanine. SNAP output
1t39 transferase-DNA X-ray (3.3 Å) Daniels DS, Woo TT, Luu KX, Noll DM, Clarke ND, Pegg AE, Tainer JA (2004) "DNA binding and nucleotide flipping by the human DNA repair protein AGT." Nat.Struct.Mol.Biol., 11, 714-720. doi: 10.1038/nsmb791. Human o6-alkylguanine-DNA alkyltransferase covalently crosslinked to DNA. SNAP output
1t3n replication-DNA X-ray (2.3 Å) Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK (2004) "Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing." Nature, 430, 377-380. doi: 10.1038/nature02692. Structure of the catalytic core of DNA polymerase iota in complex with DNA and dttp. SNAP output
1t7p transferase-DNA X-ray (2.2 Å) Doublie S, Tabor S, Long AM, Richardson CC, Ellenberger T (1998) "Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution." Nature, 391, 251-258. doi: 10.1038/34593. T7 DNA polymerase complexed to DNA primer-template,a nucleoside triphosphate, and its processivity factor thioredoxin. SNAP output
1t8e transferase-electron transport-DNA X-ray (2.54 Å) Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T (2004) "Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase." Embo J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354. T7 DNA polymerase ternary complex with dctp at the insertion site.. SNAP output
1t8i isomerase-DNA X-ray (3.0 Å) Staker BL, Feese MD, Cushman M, Pommier Y, Zembower D, Stewart L, Burgin AB (2005) "Structures of three classes of anticancer agents bound to the human topoisomerase I-DNA covalent complex." J.Med.Chem., 48, 2336-2345. doi: 10.1021/jm049146p. Human DNA topoisomerase i (70 kda) in complex with the poison camptothecin and covalent complex with a 22 base pair DNA duplex. SNAP output
1t9i hydrolase-DNA X-ray (1.6 Å) Chevalier B, Sussman D, Otis C, Noel AJ, Turmel M, Lemieux C, Stephens K, Monnat Jr RJ, Stoddard BL (2004) "Metal-Dependent DNA Cleavage Mechanism of the I-CreI LAGLIDADG Homing Endonuclease." Biochemistry, 43, 14015-14026. doi: 10.1021/bi048970c. I-crei(d20n)-DNA complex. SNAP output
1t9j hydrolase-DNA X-ray (2.0 Å) Chevalier B, Sussman D, Otis C, Noel AJ, Turmel M, Lemieux C, Stephens K, Monnat Jr RJ, Stoddard BL (2004) "Metal-Dependent DNA Cleavage Mechanism of the I-CreI LAGLIDADG Homing Endonuclease." Biochemistry, 43, 14015-14026. doi: 10.1021/bi048970c. I-crei(q47e)-DNA complex. SNAP output
1tau transferase-DNA X-ray (3.0 Å) Eom SH, Wang J, Steitz TA (1996) "Structure of Taq ploymerase with DNA at the polymerase active site." Nature, 382, 278-281. doi: 10.1038/382278a0. Taq polymerase (e.c.2.7.7.7)-DNA-b-octylglucoside complex. SNAP output
1tc3 DNA binding protein-DNA X-ray (2.45 Å) van Pouderoyen G, Ketting RF, Perrakis A, Plasterk RH, Sixma TK (1997) "Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA." EMBO J., 16, 6044-6054. doi: 10.1093/emboj/16.19.6044. Transposase tc3a1-65 from caenorhabditis elegans. SNAP output
1tdz hydrolase-DNA X-ray (1.8 Å) Coste F, Ober M, Carell T, Boiteux S, Zelwer C, Castaing B (2004) "Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase." J.Biol.Chem., 279, 44074-44083. doi: 10.1074/jbc.M405928200. Crystal structure complex between the lactococcus lactis fpg (mutm) and a fapy-dg containing DNA. SNAP output
1tez lyase-DNA X-ray (1.8 Å) Mees A, Klar T, Gnau P, Hennecke U, Eker APM, Carell T, Essen L-O (2004) "Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair." Science, 306, 1789-1793. doi: 10.1126/science.1101598. Complex between DNA and the DNA photolyase from anacystis nidulans. SNAP output
1tf3 transcription-DNA NMR Foster MP, Wuttke DS, Radhakrishnan I, Case DA, Gottesfeld JM, Wright PE (1997) "Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA." Nat.Struct.Biol., 4, 605-608. doi: 10.1038/nsb0897-605. Tfiiia finger 1-3 bound to DNA, NMR, 22 structures. SNAP output
1tf6 transcription-DNA X-ray (3.1 Å) Nolte RT, Conlin RM, Harrison SC, Brown RS (1998) "Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex." Proc.Natl.Acad.Sci.USA, 95, 2938-2943. doi: 10.1073/pnas.95.6.2938. Co-crystal structure of xenopus tfiiia zinc finger domain bound to the 5s ribosomal RNA gene internal control region. SNAP output
1tgh transcription-DNA X-ray (2.9 Å) Juo ZS, Chiu TK, Leiberman PM, Baikalov I, Berk AJ, Dickerson RE (1996) "How proteins recognize the TATA box." J.Mol.Biol., 261, 239-254. doi: 10.1006/jmbi.1996.0456. Tata binding protein (tbp)-DNA complex. SNAP output
1tk0 transferase-electron transport-DNA X-ray (2.3 Å) Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T (2004) "Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase." Embo J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354. T7 DNA polymerase ternary complex with 8 oxo guanosine and ddctp at the insertion site. SNAP output
1tk5 transferase-electron transport-DNA X-ray (2.2 Å) Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T (2004) "Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase." Embo J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354. T7 DNA polymerase binary complex with 8 oxo guanosine in the templating strand. SNAP output
1tk8 transferase-electron transport-DNA X-ray (2.5 Å) Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T (2004) "Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase." Embo J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354. T7 DNA polymerase ternary complex with 8 oxo guanosine and damp at the elongation site. SNAP output
1tkd transferase-electron transport-DNA X-ray (2.49 Å) Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T (2004) "Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase." Embo J., 23, 3452-3461. doi: 10.1038/sj.emboj.7600354. T7 DNA polymerase ternary complex with 8 oxo guanosine and dcmp at the elongation site. SNAP output
1tl8 isomerase-DNA X-ray (3.1 Å) Ioanoviciu A, Antony S, Pommier Y, Staker BL, Stewart L, Cushman M (2005) "Synthesis and Mechanism of Action Studies of a Series of Norindenoisoquinoline Topoisomerase I Poisons Reveal an Inhibitor with a Flipped Orientation in the Ternary DNA-Enzyme-Inhibitor Complex As Determined by X-ray Crystallographic Analysis." J.Med.Chem., 48, 4803-4814. doi: 10.1021/jm050076b. Human DNA topoisomerase i (70 kda) in complex with the indenoisoquinoline ai-iii-52 and covalent complex with a 22 base pair DNA duplex. SNAP output
1tn9 integrase-DNA NMR Wojciak JM, Connolly KM, Clubb RT (1999) "NMR structure of the Tn916 integrase-DNA complex." Nat.Struct.Biol., 6, 366-373. doi: 10.1038/7603. The solution structure of tn916 integrase n-terminal domain-DNA complex. SNAP output
1tqe transcription-protein binding-DNA X-ray (2.7 Å) Han A, He J, Wu Y, Liu JO, Chen L (2005) "Mechanism of Recruitment of Class II Histone Deacetylases by Myocyte Enhancer Factor-2." J.Mol.Biol., 345, 91-102. doi: 10.1016/j.jmb.2004.10.033. Mechanism of recruitment of class ii histone deacetylases by myocyte enhancer factor-2. SNAP output
1tro transcription-DNA X-ray (1.9 Å) Otwinowski Z, Schevitz RW, Zhang RG, Lawson CL, Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB (1988) "Crystal structure of trp repressor/operator complex at atomic resolution." Nature, 335, 321-329. doi: 10.1038/335321a0. Crystal structure of trp repressor operator complex at atomic resolution. SNAP output
1trr transcription-DNA X-ray (2.4 Å) Lawson CL, Carey J (1993) "Tandem binding in crystals of a trp repressor/operator half-site complex." Nature, 366, 178-182. doi: 10.1038/366178a0. Tandem binding in crystals of a trp repressor-operator half-site complex. SNAP output
1tsr antitumor protein-DNA X-ray (2.2 Å) Cho Y, Gorina S, Jeffrey PD, Pavletich NP (1994) "Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations." Science, 265, 346-355. P53 core domain in complex with DNA. SNAP output
1ttu transcription X-ray (2.85 Å) Kovall RA, Hendrickson WA (2004) "Crystal structure of the nuclear effector of Notch signaling, CSL, bound to DNA." Embo J., 23, 3441-3451. doi: 10.1038/sj.emboj.7600349. Crystal structure of csl bound to DNA. SNAP output
1tup antitumor protein-DNA X-ray (2.2 Å) Cho Y, Gorina S, Jeffrey PD, Pavletich NP (1994) "Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations." Science, 265, 346-355. Tumor suppressor p53 complexed with DNA. SNAP output
1tv9 transferase-DNA X-ray (2.0 Å) Krahn JM, Beard WM, Wilson SH (2004) "STRUCTURAL INSIGHTS INTO DNA POLYMERASE BETA DETERRENTS FOR MISINCORPORATION SUPPORT OF AN INDUCED-FIT MECHANISM FOR FIDELITY." Structure, 12, 1823-1832. doi: 10.1016/j.str.2004.08.001. Human DNA polymerase beta complexed with nicked DNA containing a mismatched template adenine and incoming cytidine. SNAP output
1tva transferase-DNA X-ray (2.6 Å) Krahn JM, Beard WA, Wilson SH (2004) "Structural insights into DNA polymerase Beta deterrents for misincorporation support an induced-fit mechanism for fidelity." Structure, 12, 1823-1832. doi: 10.1016/j.str.2004.08.001. Human DNA polymerase beta complexed with nicked DNA containing a mismatched template thymidine and incoming cytidine. SNAP output
1tw8 hydrolase-DNA X-ray (2.8 Å) Etzkorn C, Horton NC (2004) "Ca2+ binding in the active site of HincII: implications for the catalytic mechanism." Biochemistry, 43, 13256-13270. Hincii bound to ca2+ and cognate DNA gtcgac. SNAP output
1tx3 hydrolase-DNA X-ray (2.5 Å) Etzkorn C, Horton NC (2004) "Ca2+ binding in the active site of HincII: implications for the catalytic mechanism." Biochemistry, 43, 13256-13270. doi: 10.1021/bi0490082. Hincii bound to cognate DNA. SNAP output
1u0c hydrolase-DNA X-ray (2.5 Å) Sussman D, Chadsey M, Fauce S, Engel A, Bruett A, Monnat R, Stoddard BL, Seligman LM (2004) "Isolation and characterization of new homing endonuclease specificities at individual target site positions." J.Mol.Biol., 342, 31-41. doi: 10.1016/j.jmb.2004.07.031. Y33c mutant of homing endonuclease i-crei. SNAP output
1u0d hydrolase-DNA X-ray (2.9 Å) Sussman D, Chadsey M, Fauce S, Engel A, Bruett A, Monnat R, Stoddard BL, Seligman LM (2004) "Isolation and characterization of new homing endonuclease specificities at individual target site positions." J.Mol.Biol., 342, 31-41. doi: 10.1016/j.jmb.2004.07.031. Y33h mutant of homing endonuclease i-crei. SNAP output
1u1k transport protein-DNA X-ray (2.0 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggtt 7da ggg); a human telomeric repeat containing 7-deaza-adenine. SNAP output
1u1l transport protein-DNA X-ray (2.0 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggtt prn ggg); a human telomeric repeat containing nebularine. SNAP output
1u1m transport protein-DNA X-ray (2.0 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggtta 7gu gg); a human telomeric repeat containing 7-deaza-guanine. SNAP output
1u1n transport protein-DNA X-ray (2.1 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggtta (prn)gg); a human telomeric repeat containing nebularine. SNAP output
1u1o transport protein-DNA X-ray (2.0 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggttag(di)g); a human telomeric repeat containing inosine. SNAP output
1u1p transport protein-DNA X-ray (1.9 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggtta 2pr gg); a human telomeric repeat containing 2-aminopurine. SNAP output
1u1q transport protein-DNA X-ray (1.8 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggtta(di)gg); a human telomeric repeat containing inosine. SNAP output
1u1r transport protein-DNA X-ray (1.8 Å) Myers JC, Shamoo Y (2004) "Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM)." J.Mol.Biol., 342, 743-756. doi: 10.1016/j.jmb.2004.07.029. Crystal structure of up1 complexed with d(ttagggttag(2pr)g); a human telomeric repeat containing 2-aminopurine. SNAP output
1u1y virus-RNA X-ray (2.85 Å) Horn WT, Convery MA, Stonehouse NJ, Adams CJ, Liljas L, Phillips SE, Stockley PG (2004) "The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions." Rna, 10, 1776-1782. doi: 10.1261/rna.7710304. Crystal structure of a complex between wt bacteriophage ms2 coat protein and an f5 aptamer RNA stemloop with 2aminopurine substituted at the-10 position. SNAP output
1u35 structural protein-DNA X-ray (3.0 Å) Chakravarthy S, Gundimella SK, Caron C, Perche PY, Pehrson JR, Khochbin S, Luger K (2005) "Structural characterization of the histone variant macroH2A." Mol.Cell.Biol., 25, 7616-7624. doi: 10.1128/MCB.25.17.7616-7624.2005. Crystal structure of the nucleosome core particle containing the histone domain of macroh2a. SNAP output
1u3e DNA binding protein-DNA X-ray (2.92 Å) Shen BW, Landthaler M, Shub DA, Stoddard BL (2004) "DNA Binding and Cleavage by the HNH Homing Endonuclease I-HmuI." J.Mol.Biol., 342, 43-56. doi: 10.1016/j.jmb.2004.07.032. DNA binding and cleavage by the hnh homing endonuclease i-hmui. SNAP output
1u45 transferase-DNA X-ray (2.01 Å) Hsu GW, Ober M, Carell T, Beese LS (2004) "Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase." Nature, 431, 217-221. doi: 10.1038/nature02908. 8oxoguanine at the pre-insertion site of the polymerase active site. SNAP output
1u47 transferase-DNA X-ray (2.0 Å) Hsu GW, Ober M, Carell T, Beese LS (2004) "Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase." Nature, 431, 217-221. doi: 10.1038/nature02908. Cytosine-8-oxoguanine base pair at the polymerase active site. SNAP output
1u48 transferase-DNA X-ray (2.1 Å) Hsu GW, Ober M, Carell T, Beese LS (2004) "Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase." Nature, 431, 217-221. doi: 10.1038/nature02908. Extension of a cytosine-8-oxoguanine base pair. SNAP output
1u49 transferase-DNA X-ray (2.15 Å) Hsu GW, Ober M, Carell T, Beese LS (2004) "Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase." Nature, 431, 217-221. doi: 10.1038/nature02908. Adenine-8oxoguanine mismatch at the polymerase active site. SNAP output
1u4b transferase-DNA X-ray (1.6 Å) Hsu GW, Ober M, Carell T, Beese LS (2004) "Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase." Nature, 431, 217-221. doi: 10.1038/nature02908. Extension of an adenine-8oxoguanine mismatch. SNAP output
1u78 DNA binding protein-DNA X-ray (2.69 Å) Watkins S, van Pouderoyen G, Sixma TK (2004) "Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA." Nucleic Acids Res., 32, 4306-4312. doi: 10.1093/nar/gkh770. Structure of the bipartite DNA-binding domain of tc3 transposase bound to transposon DNA. SNAP output
1u8b metal binding protein-DNA X-ray (2.1 Å) He C, Hus JC, Sun LJ, Zhou P, Norman DP, Dotsch V, Wei H, Gross JD, Lane WS, Wagner G, Verdine GL (2005) "A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli ada." Mol.Cell, 20, 117-129. doi: 10.1016/j.molcel.2005.08.013. Crystal structure of the methylated n-ada-DNA complex. SNAP output
1u8r metal-binding protein,transcription-DNA X-ray (2.75 Å) Wisedchaisri G, Holmes RK, Hol WGJ (2004) "Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions." J.Mol.Biol., 342, 1155-1169. doi: 10.1016/j.jmb.2004.07.083. Crystal structure of an ider-DNA complex reveals a conformational change in activated ider for base-specific interactions. SNAP output
1ua0 transferase-DNA X-ray (2.1 Å) Hsu GW, Kiefer JR, Burnouf D, Becherel OJ, Fuchs RPP, Beese LS (2004) "Observing translesion synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase." J.Biol.Chem., 279, 50280-50285. doi: 10.1074/jbc.M409224200. Aminofluorene DNA adduct at the pre-insertion site of a DNA polymerase. SNAP output
1ua1 transferase-DNA X-ray (2.0 Å) Hsu GW, Kiefer JR, Becherel OJ, Fuchs RPP, Beese LS (2004) "Observing translesion synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase." J.Biol.Chem., 279, 50280-50285. doi: 10.1074/jbc.M409224200. Structure of aminofluorene adduct paired opposite cytosine at the polymerase active site.. SNAP output
1uaa hydrolase-DNA X-ray (3.0 Å) Korolev S, Hsieh J, Gauss GH, Lohman TM, Waksman G (1997) "Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP." Cell(Cambridge,Mass.), 90, 635-647. doi: 10.1016/S0092-8674(00)80525-5. E. coli rep helicase-DNA complex. SNAP output
1ubd transcription-DNA X-ray (2.5 Å) Houbaviy HB, Usheva A, Shenk T, Burley SK (1996) "Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator." Proc.Natl.Acad.Sci.USA, 93, 13577-13582. doi: 10.1073/pnas.93.24.13577. Co-crystal structure of human yy1 zinc finger domain bound to the adeno-associated virus p5 initiator element. SNAP output
1unj DNA-antibiotic X-ray (2.5 Å) Alexopoulos EC, Jares-Erijman EA, Jovin TM, Klement R, Machinek R, Sheldrick GM, Uson I (2005) "Crystal and Solution Structures of 7-Amino-Actinomycin D Complexes with D(Ttagbrut), D(Ttagtt) and D(Tttagttt)." Acta Crystallogr.,Sect.D, 61, 407. doi: 10.1107/S090744490500082X. Crystal structure of a 7-aminoactinomycin d complex with non-complementary DNA. SNAP output
1unm DNA-antibiotic X-ray (2.0 Å) Alexopoulos EC, Jares-Erijman EA, Jovin TM, Klement R, Machinek R, Sheldrick GM, Uson I (2005) "Crystal and Solution Structures of 7-Amino-Actinomycin D Complexes with D(Ttagbrut), D(Ttagtt) and D(Tttagttt)." Acta Crystallogr.,Sect.D, 61, 407. doi: 10.1107/S090744490500082X. Crystal structure of 7-aminoactinomycin d with non-complementary DNA. SNAP output
1uut hydrolase-DNA X-ray (2.0 Å) Hickman AB, Ronning DR, Perez ZN, Kotin RM, Dyda F (2004) "The Nuclease Domain of Adeno-Associated Virus Rep Coordinates Replication Initiation Using Two Distinct DNA Recognition Interfaces." Mol.Cell, 13, 403. doi: 10.1016/S1097-2765(04)00023-1. The nuclease domain of adeno-associated virus rep complexed with the rbe' stemloop of the viral inverted terminal repeat. SNAP output
1v14 hydrolase X-ray (2.9 Å) Mate MJ, Kleanthous C (2004) "Structure-Based Analysis of the Metal-Dependent Mechanism of H-N-H Endonucleases." J.Biol.Chem., 279, 34763. doi: 10.1074/JBC.M403719200. Crystal structure of the colicin e9, mutant his103ala, in complex with mg+2 and dsDNA (resolution 2.9a). SNAP output
1v15 hydrolase X-ray (2.4 Å) Mate MJ, Kleanthous C (2004) "Structure-Based Analysis of the Metal-Dependent Mechanism of H-N-H Endonucleases." J.Biol.Chem., 279, 34763. doi: 10.1074/JBC.M403719200. Crystal structure of the colicin e9, mutant his103ala, in complex with zn+2 and dsDNA (resolution 2.4a). SNAP output
1vas hydrolase-DNA X-ray (2.75 Å) Vassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai S, Ohtsuka E, Morikawa K (1995) "Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition." Cell(Cambridge,Mass.), 83, 773-782. doi: 10.1016/0092-8674(95)90190-6. Atomic model of a pyrimidine dimer specific excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition. SNAP output
1vfc structural protein-DNA NMR Hanaoka S, Nagadoi A, Nishimura Y (2005) "Comparison between TRF2 and TRF1 of their telomeric DNA-bound structures and DNA-binding activities." Protein Sci., 14, 119-130. doi: 10.1110/ps.04983705. Solution structure of the DNA complex of human trf2. SNAP output
1vkx transcription-DNA X-ray (2.9 Å) Chen FE, Huang DB, Chen YQ, Ghosh G (1998) "Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA." Nature, 391, 410-413. doi: 10.1038/34956. Crystal structure of the nfkb p50-p65 heterodimer complexed to the immunoglobulin kb DNA. SNAP output
1vol transcription-DNA X-ray (2.7 Å) Nikolov DB, Chen H, Halay ED, Usheva AA, Hisatake K, Lee DK, Roeder RG, Burley SK (1995) "Crystal structure of a TFIIB-TBP-TATA-element ternary complex." Nature, 377, 119-128. doi: 10.1038/377119a0. Tfiib (human core domain)-tbp (a.thaliana)-tata element ternary complex. SNAP output
1vpw transcription-DNA X-ray (2.7 Å) Arvidson DN, Lu F, Faber C, Zalkin H, Brennan RG (1998) "The structure of PurR mutant L54M shows an alternative route to DNA kinking." Nat.Struct.Biol., 5, 436-441. doi: 10.1038/nsb0698-436. Structure of the purr mutant, l54m, bound to hypoxanthine and purf operator DNA. SNAP output
1vq5 ribosome X-ray (2.6 Å) Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA (2005) "Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction." Mol.Cell, 20, 437-448. doi: 10.1016/j.molcel.2005.09.006. The structure of the transition state analogue "raa" bound to the large ribosomal subunit of haloarcula marismortui. SNAP output
1vqp ribosome X-ray (2.25 Å) Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA (2005) "Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction." Mol.Cell, 20, 437-448. doi: 10.1016/j.molcel.2005.09.006. The structure of the transition state analogue "rap" bound to the large ribosomal subunit of haloarcula marismortui. SNAP output
1vrl hydrolase-DNA X-ray (2.5 Å) Fromme JC, Banerjee A, Huang SJ, Verdine GL (2004) "Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase." Nature, 427, 652-656. doi: 10.1038/nature02306. Muty adenine glycosylase in complex with DNA and soaked adenine free base. SNAP output
1vrr hydrolase-DNA X-ray (2.7 Å) Townson SA, Samuelson JC, Xu SY, Aggarwal AK (2005) "Implications for Switching Restriction Enzyme Specificities from the Structure of BstYI Bound to a BglII DNA Sequence." Structure, 13, 791-801. doi: 10.1016/j.str.2005.02.018. Crystal structure of the restriction endonuclease bstyi complex with DNA. SNAP output
1vs2 DNA-antibiotic X-ray (2.0 Å) Wang AH, Ughetto G, Quigley GJ, Rich A (1986) "Interactions of Quinoxaline Antibiotic and DNA: The Molecular Structure of a Triostin A-D(Gcgtacgc) Complex." J.Biomol.Struct.Dyn., 4, 319. Interactions of quinoxaline antibiotic and DNA: the molecular structure of a triostin a-d(gcgtacgc) complex. SNAP output
1vtg DNA-antibiotic X-ray (1.67 Å) Wang AH, Ughetto G, Quigley GJ, Hakoshima T, van der Marel GA, van Boom JH, Rich A (1984) "The molecular structure of a DNA-triostin A complex." Science, 225, 1115-1121. The molecular structure of a DNA-triostin a complex. SNAP output
1vtl transcription-DNA X-ray (2.25 Å) Kim JL, Nikolov DB, Burley SK (1993) "Co-Crystal Structure of TBP Recognizing the Minor Groove of a TATA Element." Nature, 365, 520-527. doi: 10.1038/365520a0. Co-crystal structure of tbp recognizing the minor groove of a tata element. SNAP output
1vtn transcription-DNA X-ray (2.5 Å) Clark KL, Halay ED, Lai E, Burley SK (1993) "Co-Crystal Structure of the HNF-3/Fork Head DNA-Recognition Motif Resembles Histone H5." Nature, 364, 412-420. doi: 10.1038/364412a0. Co-crystal structure of the hnf-3-fork head DNA-recognition motif resembles histone h5. SNAP output
1vto transcription-DNA X-ray (1.9 Å) Kim JL, Burley SK (1994) "1.9 A Resolution Refined Structure of TBP Recognizing the Minor Groove of TATAAAAG." Nat.Struct.Biol., 1, 638-653. 1.9 Å resolution refined structure of tbp recognizing the minor groove of tataaaag. SNAP output
1w0t DNA binding protein X-ray (2.0 Å) Court RI, Chapman LM, Fairall L, Rhodes D (2005) "How the Human Telomeric Proteins Trf1 and Trf2 Recognize Telomeric DNA: A View from High-Resolution Crystal Structures." Embo Rep., 6, 39. doi: 10.1038/SJ.EMBOR.7400314. Htrf1 DNA-binding domain in complex with telomeric DNA.. SNAP output
1w0u DNA binding protein X-ray (1.8 Å) Court RI, Chapman LM, Fairall L, Rhodes D (2005) "How the Human Telomeric Proteins Trf1 and Trf2 Recognize Telomeric DNA: A View from High-Resolution Crystal Structures." Embo Rep., 6, 39. doi: 10.1038/SJ.EMBOR.7400314. Htrf2 DNA-binding domain in complex with telomeric DNA.. SNAP output
1w36 recombination X-ray (3.1 Å) Singleton MR, Dillingham MS, Gaudier M, Kowalczykowski SC, Wigley DB (2004) "Crystal Structure of Recbcd Enzyme Reveals a Machine for Processing DNA Breaks." Nature, 432, 187. doi: 10.1038/NATURE02988. Recbcd:DNA complex. SNAP output
1w7a DNA binding X-ray (2.27 Å) Lamers MH, Georgijevic D, Lebbink J, Winterwerp HHK, Agianian B, De Wind N, Sixma TK (2004) "ATP Increases the Affinity between Muts ATPase Domains: Implications for ATP Hydrolysis and Conformational Changes." J.Biol.Chem., 279, 43879. doi: 10.1074/JBC.M406380200. Atp bound muts. SNAP output
1wb9 DNA-binding X-ray (2.1 Å) Lebbink JHG, Georgijevic D, Natrajan G, Fish A, Winterwerp HHK, Sixma TK, De Wind N (2006) "Dual Role of Muts Glutamate 38 in DNA Mismatch Discrimination and in the Authorization of Repair." Embo J., 25, 409. doi: 10.1038/SJ.EMBOJ.7600936. Crystal structure of e. coli DNA mismatch repair enzyme muts, e38t mutant, in complex with a g.t mismatch. SNAP output
1wbb DNA-binding X-ray (2.5 Å) Lebbink JHG, Georgijevic D, Natrajan G, Fish A, Winterwerp HHK, Sixma TK, De Wind N (2006) "Dual Role of Muts Glutamate 38 in DNA Mismatch Discrimination and in the Authorization of Repair." Embo J., 25, 409. doi: 10.1038/SJ.EMBOJ.7600936. Crystal structure of e. coli DNA mismatch repair enzyme muts, e38a mutant, in complex with a g.t mismatch. SNAP output
1wbd DNA-binding X-ray (2.4 Å) Lebbink JHG, Georgijevic D, Natrajan G, Fish A, Winterwerp HHK, Sixma TK, De Wind N (2006) "Dual Role of Muts Glutamate 38 in DNA Mismatch Discrimination and in the Authorization of Repair." Embo J., 25, 409. doi: 10.1038/SJ.EMBOJ.7600936. Crystal structure of e. coli DNA mismatch repair enzyme muts, e38q mutant, in complex with a g.t mismatch. SNAP output
1wd0 structural protein-DNA X-ray (1.9 Å) Ko TP, Chu HM, Chen CY, Chou CC, Wang AH (2004) "Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers." Acta Crystallogr.,Sect.D, 60, 1381-1387. doi: 10.1107/S0907444904012065. Crystal structures of the hyperthermophilic chromosomal protein sac7d in complex with DNA decamers. SNAP output
1wd1 structural protein-DNA X-ray (2.2 Å) Ko TP, Chu HM, Chen CY, Chou CC, Wang AH (2004) "Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers." Acta Crystallogr.,Sect.D, 60, 1381-1387. doi: 10.1107/S0907444904012065. Crystal structures of the hyperthermophilic chromosomal protein sac7d in complex with DNA decamers. SNAP output
1wet transcription-DNA X-ray (2.6 Å) Schumacher MA, Glasfeld A, Zalkin H, Brennan RG (1997) "The X-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity." J.Biol.Chem., 272, 22648-22653. doi: 10.1074/jbc.272.36.22648. Structure of the purr-guanine-purf operator complex. SNAP output
1wtb transcription-DNA NMR Enokizono Y, Konishi Y, Nagata K, Ouhashi K, Uesugi S, Ishikawa F, Katahira M (2005) "Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D." J.Biol.Chem., 280, 18862-18870. doi: 10.1074/jbc.M411822200. Complex structure of the c-terminal RNA-binding domain of hnrnp d (auf1) with telomere DNA. SNAP output
1wte hydrolase-DNA X-ray (1.9 Å) Hashimoto H, Shimizu T, Imasaki T, Kato M, Shichijo N, Kita K, Sato M (2005) "Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA." J.Biol.Chem., 280, 5605-5610. doi: 10.1074/jbc.M411684200. Crystal structure of type ii restrcition endonuclease, ecoo109i complexed with cognate DNA. SNAP output
1wto DNA binding protein-DNA X-ray (1.5 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d double mutant v26f-m29f in complex with DNA gcgatcgc. SNAP output
1wtp DNA binding protein-DNA X-ray (1.9 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d single mutant m29f in complex with DNA gcga(ubr)cgc. SNAP output
1wtq DNA binding protein-DNA X-ray (1.7 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d single mutant m29f in complex with DNA gtaattac. SNAP output
1wtr DNA binding protein-DNA X-ray (1.8 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d single mutant m29a in complex with DNA gcgatcgc. SNAP output
1wtv DNA binding protein-DNA X-ray (1.6 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d single mutant m29a in complex with DNA gtaattac. SNAP output
1wtw DNA binding protein-DNA X-ray (2.2 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d single mutant v26a in complex with DNA gcgatcgc. SNAP output
1wtx DNA binding protein-DNA X-ray (2.2 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." NUCLEIC ACIDS RES., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d single mutant v26a in complex with DNA gtaattac. SNAP output
1wvl structural protein-DNA X-ray (2.6 Å) Wu SW, Ko TP, Chou CC, Wang AH (2005) "Design and characterization of a multimeric DNA binding protein using Sac7d and GCN4 as templates." Proteins, 60, 617-628. doi: 10.1002/prot.20524. Crystal structure of multimeric DNA-binding protein sac7d-gcn4 with DNA decamer. SNAP output
1x0f transcription-DNA NMR Enokizono Y, Konishi Y, Nagata K, Ouhashi K, Uesugi S, Ishikawa F, Katahira M (2005) "Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D." J.Biol.Chem., 280, 18862-18870. doi: 10.1074/jbc.M411822200. Complex structure of the c-terminal RNA-binding domain of hnrnp d(auf1) with telomeric DNA. SNAP output
1x9m transferase-electron transport-DNA X-ray (2.1 Å) Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC, Romano LJ, Ellenberger T (2004) "Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis." Proc.Natl.Acad.Sci.USA, 101, 16186-16191. doi: 10.1073/pnas.0406516101. T7 DNA polymerase in complex with an n-2-acetylaminofluorene-adducted DNA. SNAP output
1x9n ligase-DNA X-ray (3.0 Å) Pascal JM, O'Brien PJ, Tomkinson AE, Ellenberger T (2004) "Human DNA ligase I completely encircles and partially unwinds nicked DNA." Nature, 432, 473-478. doi: 10.1038/nature03082. Crystal structure of human DNA ligase i bound to 5'-adenylated, nicked DNA. SNAP output
1x9s transferase-electron transport-DNA X-ray (2.7 Å) Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC, Romano LJ, Ellenberger T (2004) "Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis." Proc.Natl.Acad.Sci.Usa, 101, 16186-16191. doi: 10.1073/pnas.0406516101. T7 DNA polymerase in complex with a primer-template DNA containing a disordered n-2 aminofluorene on the template, crystallized with dideoxy-ctp as the incoming nucleotide.. SNAP output
1x9w transferase-electron transport-DNA X-ray (2.3 Å) Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC, Romano LJ, Ellenberger T (2004) "Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis." Proc.Natl.Acad.Sci.Usa, 101, 16186-16191. doi: 10.1073/pnas.0406516101. T7 DNA polymerase in complex with a primer-template DNA containing a disordered n-2 aminofluorene on the template, crystallized with dideoxy-atp as the incoming nucleotide.. SNAP output
1xbr transcription-DNA X-ray (2.5 Å) Muller CW, Herrmann BG (1997) "Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor." Nature, 389, 884-888. doi: 10.1038/39929. T domain from xenopus laevis bound to DNA. SNAP output
1xc8 hydrolase-DNA X-ray (1.95 Å) Coste F, Ober M, Carell T, Boiteux S, Zelwer C, Castaing B (2004) "Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase." J.Biol.Chem., 279, 44074-44083. doi: 10.1074/jbc.M405928200. Crystal structure complex between the wild-type lactococcus lactis fpg (mutm) and a fapy-dg containing DNA. SNAP output
1xc9 transferase-DNA X-ray (1.9 Å) Hsu GW, Huang X, Luneva NP, Geacintov NE, Beese LS (2005) "Structure of a High Fidelity DNA Polymerase Bound to a Benzo[a]pyrene Adduct That Blocks Replication." J.Biol.Chem., 280, 3764-3770. doi: 10.1074/jbc.M411276200. Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication. SNAP output
1xf2 immune system-DNA X-ray (2.3 Å) Schuermann JP, Prewitt SP, Davies C, Deutscher SL, Tanner JJ (2005) "Evidence for Structural Plasticity of Heavy Chain Complementarity-determining Region 3 in Antibody-ssDNA Recognition." J.Mol.Biol., 347, 965-978. doi: 10.1016/j.jmb.2005.02.008. Structure of fab DNA-1 complexed with dt3. SNAP output
1xhu hydrolase-DNA X-ray (2.95 Å) Etzkorn C, Horton NC (2004) "Mechanistic Insights from the Structures of HincII Bound to Cognate DNA Cleaved from Addition of Mg(2+) and Mn(2+)." J.Mol.Biol., 343, 833-849. doi: 10.1016/j.jmb.2004.08.082. Hincii bound to cleaved, cognate DNA containing gtcgac. SNAP output
1xhv hydrolase-DNA X-ray (2.5 Å) Etzkorn C, Horton NC (2004) "Mechanistic Insights from the Structures of HincII Bound to Cognate DNA Cleaved from Addition of Mg(2+) and Mn(2+)." J.Mol.Biol., 343, 833-849. doi: 10.1016/j.jmb.2004.08.082. Hincii bound to cleaved cognate DNA gtcgac and mn2+. SNAP output
1xhz transferase-DNA X-ray (2.7 Å) Kamtekar S, Berman AJ, Wang J, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2004) "Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage phi29." Mol.Cell, 16, 609-618. doi: 10.1016/j.molcel.2004.10.019. Phi29 DNA polymerase, orthorhombic crystal form, ssDNA complex. SNAP output
1xi1 transferase-DNA X-ray (2.2 Å) Wang J, Kamtekar S, Berman AJ, Steitz TA (2005) "Correction of X-ray intensities from single crystals containing lattice-translocation defects." Acta Crystallogr.,Sect.D, 61, 67-74. doi: 10.1107/S0907444904026721. Phi29 DNA polymerase ssDNA complex, monoclinic crystal form. SNAP output
1xjv transcription-DNA X-ray (1.73 Å) Lei M, Podell ER, Cech TR (2004) "Structure of human POT1 bound to telomeric single-stranded DNA provides a model for chromosome end-protection." Nat.Struct.Mol.Biol., 11, 1223-1229. doi: 10.1038/nsmb867. Crystal structure of human pot1 bound to telomeric single-stranded DNA (ttagggttag). SNAP output
1xns hydrolase, ligase-DNA X-ray (2.8 Å) Ghosh K, Lau CK, Guo F, Segall AM, Van Duyne GD (2005) "Peptide trapping of the Holliday junction intermediate in Cre-loxP site-specific recombination." J.Biol.Chem., 280, 8290-8299. doi: 10.1074/jbc.M411668200. Peptide trapped holliday junction intermediate in cre-loxp recombination. SNAP output
1xo0 hydrolase, ligase-DNA X-ray (2.0 Å) Ghosh K, Lau CK, Guo F, Segall AM, Van Duyne GD (2005) "Peptide trapping of the Holliday junction intermediate in Cre-loxP site-specific recombination." J.Biol.Chem., 280, 8290-8299. doi: 10.1074/jbc.M411668200. High resolution structure of the holliday junction intermediate in cre-loxp site-specific recombination. SNAP output
1xpx transcription regulation-DNA X-ray (2.8 Å) Yousef MS, Matthews BW (2005) "Structural Basis of Prospero-DNA Interaction: Implications for Transcription Regulationin Developing Cells." STRUCTURE, 13, 601-607. doi: 10.1016/j.str.2005.01.023. Structural basis of prospero-DNA interaction; implications for transcription regulation in developing cells. SNAP output
1xs9 transcription-DNA NMR Dangi B, Gronenborn AM, Rosner JL, Martin RG (2004) "Versatility of the carboxy-terminal domain of the alpha subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA." Mol.Microbiol., 54, 45-59. doi: 10.1111/j.1365-2958.2004.04250.x. A model of the ternary complex formed between mara, the alpha-ctd of RNA polymerase and DNA. SNAP output
1xsd transcription-DNA X-ray (2.7 Å) Safo MK, Zhao Q, Ko T-P, Musayev FN, Robinson H, Scarsdale N, Wang AH-J, Archer GL (2005) "Crystal structures of the BlaI repressor from Staphylococcus aureus and its complex with DNA: insights into transcriptional regulation of the bla and mec operons." J.Bacteriol., 187, 1833-1844. doi: 10.1128/JB.187.5.1833-1844.2005. Crystal structure of the blai repressor in complex with DNA. SNAP output
1xsl transferase-DNA X-ray (2.3 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA, Pedersen LC (2005) "A closed conformation for the Pol lambda catalytic cycle." Nat.Struct.Mol.Biol., 12, 97-98. doi: 10.1038/nsmb876. Crystal structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap. SNAP output
1xsn transferase-DNA X-ray (1.95 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA, Pedersen LC (2005) "A closed conformation for the Pol lambda catalytic cycle." Nat.Struct.Mol.Biol., 12, 97-98. doi: 10.1038/nsmb876. Crystal structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddttp. SNAP output
1xsp transferase-DNA X-ray (2.2 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Kunkel TA, Pedersen LC (2005) "A closed conformation for the Pol lambda catalytic cycle." Nat.Struct.Mol.Biol., 12, 97-98. doi: 10.1038/nsmb876. Crystal structure of human DNA polymerase lambda in complex with nicked DNA and pyrophosphate. SNAP output
1xvk DNA-antibiotic X-ray (1.26 Å) Cuesta-Seijo JA, Sheldrick GM (2005) "Structures of Complexes between Echinomycin and Duplex DNA." Acta Crystallogr.,Sect.D, 61, 442. doi: 10.1107/S090744490500137X. X-ray structure of an echinomycin-(gcgtacgc)2 complex. SNAP output
1xvn DNA-antibiotic X-ray (1.5 Å) Cuesta-Seijo JA, Sheldrick GM (2005) "Structures of Complexes between Echinomycin and Duplex DNA." Acta Crystallogr.,Sect.D, 61, 442. doi: 10.1107/S090744490500137X. Echinomycin (acgtacgt)2 complex. SNAP output
1xvr DNA-antibiotic X-ray (1.4 Å) Cuesta-Seijo JA, Sheldrick GM (2005) "Structures of Complexes between Echinomycin and Duplex DNA." Acta Crystallogr.,Sect.D, 61, 442. doi: 10.1107/S090744490500137X. Echinomycin (cgtacg)2 complex. SNAP output
1xyi structural protein-DNA X-ray (1.45 Å) Chen C-Y, Ko T-P, Lin T-W, Chou C-C, Chen C-J, Wang AH-J (2005) "Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d." Nucleic Acids Res., 33, 430-438. doi: 10.1093/nar/gki191. Hyperthermophile chromosomal protein sac7d double mutant val26ala-met29ala in complex with DNA gcgatcgc. SNAP output
1y1w transcription,transferase-DNA-RNA hybrid X-ray (4.0 Å) Kettenberger H, Armache K-J, Cramer P (2004) "Complete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS." Mol.Cell, 16, 955-965. doi: 10.1016/j.molcel.2004.11.040. Complete RNA polymerase ii elongation complex. SNAP output
1y6f transferase-DNA X-ray (2.4 Å) Lariviere L, Sommer N, Morera S (2005) "Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase." J.Mol.Biol., 352, 139-150. doi: 10.1016/j.jmb.2005.07.007. Alpha-glucosyltransferase in complex with udp-glucose and DNA containing an abasic site. SNAP output
1y6g transferase-DNA X-ray (2.8 Å) Lariviere L, Sommer N, Morera S (2005) "Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase." J.Mol.Biol., 352, 139-150. doi: 10.1016/j.jmb.2005.07.007. Alpha-glucosyltransferase in complex with udp and a 13_mer DNA containing a hmu base at 2.8 Å resolution. SNAP output
1y77 transcription,transferase-DNA-RNA hybrid X-ray (4.5 Å) Kettenberger H, Armache K-J, Cramer P (2004) "Complete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS." Mol.Cell, 16, 955-965. doi: 10.1016/j.molcel.2004.11.040. Complete RNA polymerase ii elongation complex with substrate analogue gmpcpp. SNAP output
1y8z transferase-DNA X-ray (1.9 Å) Lariviere L, Sommer N, Morera S (2005) "Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase." J.Mol.Biol., 352, 139-150. doi: 10.1016/j.jmb.2005.07.007. Alpha-glucosyltransferase in complex with udp and a 13-mer DNA containing a hmu base at 1.9 Å resolution. SNAP output
1ya6 transferase-DNA X-ray (2.4 Å) Lariviere L, Sommer N, Morera S (2005) "Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase." J.Mol.Biol., 352, 139-150. doi: 10.1016/j.jmb.2005.07.007. Alpha-glucosyltransferase in complex with udp and a 13-mer DNA containing a central a:g mismatch. SNAP output
1yf3 transferase-DNA X-ray (2.29 Å) Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X (2005) "Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase." Cell(Cambridge,Mass.), 121, 349-361. doi: 10.1016/j.cell.2005.02.021. T4dam in complex with adohcy and 13-mer oligonucleotide making non- and semi-specific (~1-4) contact. SNAP output
1yfh transferase-DNA X-ray (3.01 Å) Duguid EM, Rice PA, He C (2005) "The structure of the human AGT protein bound to DNA and its implications for damage detection." J.Mol.Biol., 350, 657-666. doi: 10.1016/j.jmb.2005.05.028. Wt human o6-alkylguanine-DNA alkyltransferase bound to DNA containing an alkylated cytosine. SNAP output
1yfi hydrolase-DNA X-ray (2.7 Å) Xu QS, Roberts RJ, Guo H-C (2005) "Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure." Protein Sci., 14, 2590-2600. doi: 10.1110/ps.051565105. Crystal structure of restriction endonuclease mspi in complex with its cognate DNA in p212121 space group. SNAP output
1yfj transferase-DNA X-ray (2.69 Å) Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X (2005) "Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase." Cell(Cambridge,Mass.), 121, 349-361. doi: 10.1016/j.cell.2005.02.021. T4dam in complex with adohcy and 15-mer oligonucleotide showing semi-specific and specific contact. SNAP output
1yfl transferase-DNA X-ray (3.09 Å) Horton JR, Liebert K, Hattman S, Jeltsch A, Cheng X (2005) "Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase." Cell(Cambridge,Mass.), 121, 349-361. doi: 10.1016/j.cell.2005.02.021. T4dam in complex with sinefungin and 16-mer oligonucleotide showing semi-specific and specific contact and flipped base. SNAP output
1ynw transcription-DNA X-ray (3.0 Å) Shaffer PL, Gewirth DT (2004) "Structural analysis of RXR-VDR interactions on DR3 DNA." J.Steroid Biochem.Mol.Biol., 89-90, 215-219. doi: 10.1016/j.jsbmb.2004.03.084. Crystal structure of vitamin d receptor and 9-cis retinoic acid receptor DNA-binding domains bound to a dr3 response element. SNAP output
1yo5 transcription-DNA X-ray (2.0 Å) Wang Y, Feng L, Said M, Balderman S, Fayazi Z, Liu Y, Ghosh D, Gulick AM (2005) "Analysis of the 2.0 A Crystal Structure of the Protein-DNA Complex of the Human PDEF Ets Domain Bound to the Prostate Specific Antigen Regulatory Site." Biochemistry, 44, 7095-7106. doi: 10.1021/bi047352t. Analysis of the 2.0a crystal structure of the protein-DNA complex of human pdef ets domain bound to the prostate specific antigen regulatory site. SNAP output
1yqk hydrolase-DNA X-ray (2.5 Å) Banerjee A, Yang W, Karplus M, Verdine GL (2005) "Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA." Nature, 434, 612-618. doi: 10.1038/nature03458. Human 8-oxoguanine glycosylase crosslinked with guanine containing DNA. SNAP output
1yql hydrolase-DNA X-ray (2.6 Å) Banerjee A, Yang W, Karplus M, Verdine GL (2005) "Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA." Nature, 434, 612-618. doi: 10.1038/nature03458. Catalytically inactive hogg1 crosslinked with 7-deaza-8-azaguanine containing DNA. SNAP output
1yqm hydrolase-DNA X-ray (2.5 Å) Banerjee A, Yang W, Karplus M, Verdine GL (2005) "Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA." Nature, 434, 612-618. doi: 10.1038/nature03458. Catalytically inactive human 8-oxoguanine glycosylase crosslinked to 7-deazaguanine containing DNA. SNAP output
1yqr hydrolase-DNA X-ray (2.43 Å) Banerjee A, Yang W, Karplus M, Verdine GL (2005) "Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA." Nature, 434, 612-618. doi: 10.1038/nature03458. Catalytically inactive human 8-oxoguanine glycosylase crosslinked to oxog containing DNA. SNAP output
1yrn DNA binding protein-DNA X-ray (2.5 Å) Li T, Stark MR, Johnson AD, Wolberger C (1995) "Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA." Science, 270, 262-269. Crystal structure of the mata1-matalpha2 homeodomain heterodimer bound to DNA. SNAP output
1ysa transcription-DNA X-ray (2.9 Å) Ellenberger TE, Brandl CJ, Struhl K, Harrison SC (1992) "The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex." Cell(Cambridge,Mass.), 71, 1223-1237. doi: 10.1016/S0092-8674(05)80070-4. The gcn4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex. SNAP output
1ytb transcription-DNA X-ray (1.8 Å) Kim Y, Geiger JH, Hahn S, Sigler PB (1993) "Crystal structure of a yeast TBP/TATA-box complex." Nature, 365, 512-520. doi: 10.1038/365512a0. Crystal structure of a yeast tbp-tata-box complex. SNAP output
1ytf transcription-DNA X-ray (2.5 Å) Tan S, Hunziker Y, Sargent DF, Richmond TJ (1996) "Crystal structure of a yeast TFIIA/TBP/DNA complex." Nature, 381, 127-134. doi: 10.1038/381127a0. Yeast tfiia-tbp-DNA complex. SNAP output
1yui DNA binding protein-DNA NMR Omichinski JG, Pedone PV, Felsenfeld G, Gronenborn AM, Clore GM (1997) "The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode." Nat.Struct.Biol., 4, 122-132. doi: 10.1038/nsb0297-122. Solution NMR structure of the gaga factor-DNA complex, regularized mean structure. SNAP output
1yuj DNA binding protein-DNA NMR Omichinski JG, Pedone PV, Felsenfeld G, Gronenborn AM, Clore GM (1997) "The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode." Nat.Struct.Biol., 4, 122-132. doi: 10.1038/nsb0297-122. Solution NMR structure of the gaga factor-DNA complex, 50 structures. SNAP output
1z19 DNA binding protein-DNA X-ray (2.8 Å) Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy A, Ellenberger T (2005) "A structural basis for allosteric control of DNA recombination by lambda integrase." Nature, 435, 1059-1066. doi: 10.1038/nature03657. Crystal structure of a lambda integrase(75-356) dimer bound to a coc' core site. SNAP output
1z1b DNA binding protein-DNA X-ray (3.8 Å) Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy A, Ellenberger T (2005) "A structural basis for allosteric control of DNA recombination by lambda integrase." Nature, 435, 1059-1066. doi: 10.1038/nature03657. Crystal structure of a lambda integrase dimer bound to a coc' core site. SNAP output
1z1c virus-DNA X-ray (3.5 Å) Kontou M, Govindasamy L, Nam HJ, Bryant N, Llamas-Saiz AL, Foces-Foces C, Hernando E, Rubio MP, McKenna R, Almendral JM, Agbandje-McKenna M (2005) "Structural determinants of tissue tropism and in vivo pathogenicity for the parvovirus minute virus of mice." J.Virol., 79, 10931-10943. doi: 10.1128/JVI.79.17.10931-10943.2005. Structural determinants of tissue tropism and in vivo pathogenicity for the parvovirus minute virus of mice. SNAP output
1z1g DNA binding protein-DNA X-ray (4.4 Å) Biswas T, Aihara H, Radman-Livaja M, Filman D, Landy A, Ellenberger T (2005) "A structural basis for allosteric control of DNA recombination by lambda integrase." Nature, 435, 1059-1066. doi: 10.1038/nature03657. Crystal structure of a lambda integrase tetramer bound to a holliday junction. SNAP output
1z63 hydrolase-DNA complex X-ray (3.0 Å) Durr H, Korner C, Muller M, Hickmann V, Hopfner KP (2005) "X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA." Cell(Cambridge,Mass.), 121, 363-373. doi: 10.1016/j.cell.2005.03.026. Sulfolobus solfataricus swi2-snf2 atpase core in complex with dsDNA. SNAP output
1z9c transcription-DNA X-ray (2.64 Å) Hong M, Fuangthong M, Helmann JD, Brennan RG (2005) "Structure of an OhrR-ohrA Operator Complex Reveals the DNA Binding Mechanism of the MarR Family." Mol.Cell, 20, 131-141. doi: 10.1016/j.molcel.2005.09.013. Crystal structure of ohrr bound to the ohra promoter: structure of marr family protein with operator DNA. SNAP output
1zaa transcription-DNA X-ray (2.1 Å) Pavletich NP, Pabo CO (1991) "Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A." Science, 252, 809-817. Zinc finger-DNA recognition: crystal structure of a zif268-DNA complex at 2.1 angstroms. SNAP output
1zay transcription-DNA X-ray (2.7 Å) Zheleznova EE, Brennan RG "The Roles of Exocyclic Groups in the Central Base-Pair Step in Modulating the Affinity of PurR for its Operator." Purine repressor-hypoxanthine-modified-purf-operator complex. SNAP output
1zbb structural protein-DNA X-ray (9.0 Å) Schalch T, Duda S, Sargent DF, Richmond TJ (2005) "X-ray structure of a tetranucleosome and its implications for the chromatin fibre." Nature, 436, 138-141. doi: 10.1038/nature03686. Structure of the 4_601_167 tetranucleosome. SNAP output
1zbi hydrolase-RNA-DNA X-ray (1.85 Å) Nowotny M, Gaidamakov SA, Crouch RJ, Yang W (2005) "Crystal Structures of RNase H Bound to an RNA/DNA Hybrid: Substrate Specificity and Metal-Dependent Catalysis." Cell(Cambridge,Mass.), 121, 1005-1016. doi: 10.1016/j.cell.2005.04.024. Bacillus halodurans rnase h catalytic domain mutant d132n in complex with 12-mer RNA-DNA hybrid. SNAP output
1zbl hydrolase-RNA-DNA X-ray (2.2 Å) Nowotny M, Gaidamakov SA, Crouch RJ, Yang W (2005) "Crystal Structures of RNase H Bound to an RNA/DNA Hybrid: Substrate Specificity and Metal-Dependent Catalysis." Cell(Cambridge,Mass.), 121, 1005-1016. doi: 10.1016/j.cell.2005.04.024. Bacillus halodurans rnase h catalytic domain mutant d192n in complex with 12-mer RNA-DNA hybrid. SNAP output
1zet replication-DNA X-ray (2.3 Å) Wang J (2005) "DNA polymerases: Hoogsteen base-pairing in DNA replication?." Nature, 437, E6-7; discussion E7. doi: 10.1038/nature04199. X-ray data do not support hoogsteen base-pairing during replication by human polymerase iota. SNAP output
1zg1 transcription-DNA X-ray (2.3 Å) Maris AE, Kaczor-Grzeskowiak M, Ma Z, Kopka ML, Gunsalus RP, Dickerson RE (2005) "Primary and Secondary Modes of DNA Recognition by the NarL Two-Component Response Regulator." Biochemistry, 44, 14538-14552. doi: 10.1021/bi050734u. Narl complexed to nirb promoter non-palindromic tail-to-tail DNA site. SNAP output
1zg5 transcription-DNA X-ray (2.3 Å) Maris AE, Kaczor-Grzeskowiak M, Ma Z, Kopka ML, Gunsalus RP, Dickerson RE (2005) "Primary and Secondary Modes of DNA Recognition by the NarL Two-Component Response Regulator." Biochemistry, 44, 14538-14552. doi: 10.1021/bi050734u. Narl complexed to narg-89 promoter palindromic tail-to-tail DNA site. SNAP output
1zgw transcription regulator-DNA NMR He C, Hus JC, Sun LJ, Zhou P, Norman DP, Doetsch V, Wei H, Gross JD, Lane WS, Wagner G, Verdine GL (2005) "A Methylation-Dependent Electrostatic Switch Controls DNA Repair and Transcriptional Activation by E. coli Ada." Mol.Cell, 20, 117-129. doi: 10.1016/j.molcel.2005.08.013. NMR structure of e. coli ada protein in complex with DNA. SNAP output
1zjm DNA-lyase-transferase X-ray (2.1 Å) Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH (2005) "Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate." STRUCTURE, 13, 1225-1233. doi: 10.1016/j.str.2005.05.010. Human DNA polymerase beta complexed with DNA containing an a-a mismatched primer terminus. SNAP output
1zjn DNA-lyase-transferase X-ray (2.61 Å) Batra VK, Beard WA, Shock DD, Pedersen LC, Wilson SH (2005) "Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate." STRUCTURE, 13, 1225-1233. doi: 10.1016/j.str.2005.05.010. Human DNA polymerase beta complexed with DNA containing an a-a mismatched primer terminus with dgtp. SNAP output
1zla structural protein-DNA X-ray (2.9 Å) Barbera AJ, Chodaparambil JV, Kelley-Clarke B, Joukov V, Walter JC, Luger K, Kaye KM (2006) "The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA." Science, 311, 856-861. doi: 10.1126/science.1120541. X-ray structure of a kaposi's sarcoma herpesvirus lana peptide bound to the nucleosomal core. SNAP output
1zlk transcription-DNA X-ray (3.1 Å) Wisedchaisri G, Wu M, Rice AE, Roberts DM, Sherman DR, Hol WGJ (2005) "Structures of Mycobacterium tuberculosis DosR and DosR-DNA complex involved in gene activation during adaptation to hypoxic latency." J.Mol.Biol., 354, 630-641. doi: 10.1016/j.jmb.2005.09.048. Crystal structure of the mycobacterium tuberculosis hypoxic response regulator dosr c-terminal domain-DNA complex. SNAP output
1zm5 DNA binding protein-DNA X-ray (2.5 Å) Boer R, Russi S, Guasch A, Lucas M, Blanco AG, Perez-Luque R, Coll M, de la Cruz F (2006) "Unveiling the Molecular Mechanism of a Conjugative Relaxase: The Structure of TrwC Complexed with a 27-mer DNA Comprising the Recognition Hairpin and the Cleavage Site." J.Mol.Biol., 358, 857-869. doi: 10.1016/j.jmb.2006.02.018. Conjugative relaxase trwc in complex with orit DNA, cooper-bound structure. SNAP output
1zme transcription-DNA X-ray (2.5 Å) Swaminathan K, Flynn P, Reece RJ, Marmorstein R (1997) "Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster." Nat.Struct.Biol., 4, 751-759. doi: 10.1038/nsb0997-751. Crystal structure of put3-DNA complex. SNAP output
1zns hydrolase-DNA X-ray (2.5 Å) Doudeva LG, Huang H, Hsia KC, Shi Z, Li CL, Shen Y, Cheng YS, Yuan HS (2006) "Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+." Protein Sci., 15, 269-280. doi: 10.1110/ps.051903406. Crystal structure of n-cole7-12-bp DNA-zn complex. SNAP output
1zq3 transcription-DNA NMR Baird-Titus JM, Clark-Baldwin K, Dave V, Caperelli CA, Ma J, Rance M (2006) "The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site." J.Mol.Biol., 356, 1137-1151. doi: 10.1016/j.jmb.2005.12.007. NMR solution structure of the bicoid homeodomain bound to the consensus DNA binding site taatcc. SNAP output
1zqa transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of kcl (150 millimolar) at ph 7.5. SNAP output
1zqb transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of bacl2 (150 millimolar). SNAP output
1zqc transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of cacl2 (15 millimolar). SNAP output
1zqd transferase-DNA X-ray (3.5 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of cacl2 (150 millimolar). SNAP output
1zqe transferase-DNA X-ray (3.7 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of crcl3 (saturated solution). SNAP output
1zqf transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of cscl (150 millimolar). SNAP output
1zqg transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of a sodium-free artificial mother liquor at ph 6.5. SNAP output
1zqh transferase-DNA X-ray (3.1 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of a sodium-free artificial mother liquor at ph 7.5. SNAP output
1zqi transferase-DNA X-ray (2.7 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of kcl (150 millimolar). SNAP output
1zqj transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of cacl2 (15 millimolar) and mgcl2 (15 millimolar). SNAP output
1zqk transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of kcl (75 millimolar) and mgcl2 (75 millimolar). SNAP output
1zql transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of mncl2 (15 millimolar) and mgcl2 (15 millimolar). SNAP output
1zqm transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of mncl2 (15 millimolar). SNAP output
1zqn transferase-DNA X-ray (3.0 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of bacl2 (15 millimolar) and nacl (15 millimolar). SNAP output
1zqo transferase-DNA X-ray (3.2 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of cacl2 (15 millimolar) and nacl (15 millimolar). SNAP output
1zqp transferase-DNA X-ray (2.8 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of kcl (75 millimolar) and nacl (75 millimolar). SNAP output
1zqq transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of mncl2 (15 millimolar) and nacl (15 millimolar). SNAP output
1zqr transferase-DNA X-ray (3.7 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (e.c.2.7.7.7)-DNA complex, soaked in the presence of nicl2. SNAP output
1zqs transferase-DNA X-ray (3.3 Å) Pelletier H, Sawaya MR (1996) "Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis." Biochemistry, 35, 12778-12787. doi: 10.1021/bi960790i. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of tlcl (0.5 millimolar). SNAP output
1zqt transferase-DNA X-ray (3.4 Å) Pelletier H, Sawaya MR, Wolfle W, Wilson SH, Kraut J (1996) "A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta." Biochemistry, 35, 12762-12777. doi: 10.1021/bi9529566. DNA polymerase beta (pol b) (e.c.2.7.7.7) complexed with seven base pairs of DNA; soaked in the presence of datp (0.01 millimolar) and zncl2 (0.02 millimolar). SNAP output
1zr2 recombination-DNA X-ray (3.9 Å) Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley ND, Steitz TA (2005) "Structure of a synaptic gamma delta resolvase tetramer covalently linked to two cleaved DNAs." Science, 309, 1210-1215. doi: 10.1126/science.1112064. Structure of a synaptic gamma-delta resolvase tetramer covalently linked to two cleaved dnas. SNAP output
1zr4 recombination-DNA X-ray (3.4 Å) Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley ND, Steitz TA (2005) "Structure of a synaptic gamma delta resolvase tetramer covalently linked to two cleaved DNAs." Science, 309, 1210-1215. doi: 10.1126/science.1112064. Structure of a synaptic gamma-delta resolvase tetramer covalently linked to two cleaved dnas. SNAP output
1zrc gene regulation-DNA X-ray (2.8 Å) Napoli AA, Lawson CL, Ebright RH, Berman HM (2006) "Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps." J.Mol.Biol., 357, 173-183. doi: 10.1016/j.jmb.2005.12.051. 4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-icap38 DNA. SNAP output
1zrd gene regulation-DNA X-ray (2.8 Å) Napoli AA, Lawson CL, Ebright RH, Berman HM (2006) "Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps." J.Mol.Biol., 357, 173-183. doi: 10.1016/j.jmb.2005.12.051. 4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-[6a;17t]icap38 DNA. SNAP output
1zre gene regulation-DNA X-ray (2.8 Å) Napoli AA, Lawson CL, Ebright RH, Berman HM (2006) "Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps." J.Mol.Biol., 357, 173-183. doi: 10.1016/j.jmb.2005.12.051. 4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-[6g;17c]icap38 DNA. SNAP output
1zrf gene regulation-DNA X-ray (2.1 Å) Napoli AA, Lawson CL, Ebright RH, Berman HM (2006) "Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps." J.Mol.Biol., 357, 173-183. doi: 10.1016/j.jmb.2005.12.051. 4 crystal structures of cap-DNA with all base-pair substitutions at position 6, cap-[6c;17g]icap38 DNA. SNAP output
1zs4 transcription-DNA X-ray (1.7 Å) Jain D, Kim Y, Maxwell KL, Beasley S, Zhang R, Gussin GN, Edwards AM, Darst SA (2005) "Crystal Structure of Bacteriophage lambdacII and Its DNA Complex." Mol.Cell, 19, 259-269. doi: 10.1016/j.molcel.2005.06.006. Structure of bacteriophage lambda cii protein in complex with DNA. SNAP output
1ztg DNA, RNA binding protein-DNA X-ray (3.0 Å) Yoga YMK, Traore DAK, Sidiqi M, Szeto C, Pendini NR, Barker A, Leedman PJ, Wilce JA, Wilce MCJ (2012) "Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides." Nucleic Acids Res., 40, 5101-5114. doi: 10.1093/nar/gks058. Human alpha polyc binding protein kh1. SNAP output
1ztt transferase-DNA X-ray (1.85 Å) Goodwin KD, Long EC, Georgiadis MM (2005) "A host-guest approach for determining drug-DNA interactions: an example using netropsin." Nucleic Acids Res., 33, 4106-4116. doi: 10.1093/nar/gki717. Netropsin bound to d(cttaattcgaattaag) in complex with mmlv rt catalytic fragment. SNAP output
1ztw transferase-DNA X-ray (1.8 Å) Goodwin KD, Long EC, Georgiadis MM (2005) "A host-guest approach for determining drug-DNA interactions: an example using netropsin." Nucleic Acids Res., 33, 4106-4116. doi: 10.1093/nar/gki717. D(cttaattcgaattaag) complexed with moloney murine leukemia virus reverse transcriptase catalytic fragment. SNAP output
1zvv transcription-DNA X-ray (2.98 Å) Schumacher MA, Seidel G, Hillen W, Brennan RG (2006) "Phosphoprotein Crh-Ser46-P displays altered binding to CcpA to effect carbon catabolite regulation." J.Biol.Chem., 281, 6793-6800. doi: 10.1074/jbc.M509977200. Crystal structure of a ccpa-crh-DNA complex. SNAP output
1zx4 cell cycle X-ray (2.98 Å) Schumacher MA, Funnell BE (2005) "Structures of ParB bound to DNA reveal mechanism of partition complex formation." Nature, 438, 516-519. doi: 10.1038/nature04149. Structure of parb bound to DNA. SNAP output
1zyq transferase-electron transport-DNA X-ray (2.7 Å) Brieba LG, Kokoska RJ, Bebenek K, Kunkel TA, Ellenberger T (2005) "A lysine residue in the fingers subdomain of t7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine." Structure, 13, 1653-1659. doi: 10.1016/j.str.2005.07.020. T7 DNA polymerase in complex with 8og and incoming ddatp. SNAP output
1zzi structural protein-DNA X-ray (1.8 Å) Backe PH, Messias AC, Ravelli RB, Sattler M, Cusack S (2005) "X-Ray Crystallographic and NMR Studies of the Third KH Domain of hnRNP K in Complex with Single-Stranded Nucleic Acids." STRUCTURE, 13, 1055-1067. doi: 10.1016/j.str.2005.04.008. Crystal structure analysis of the third kh domain of hnrnp k in complex with ssDNA. SNAP output
1zzj structural protein-DNA X-ray (2.3 Å) Backe PH, Messias AC, Ravelli RB, Sattler M, Cusack S (2005) "X-Ray Crystallographic and NMR Studies of the Third KH Domain of hnRNP K in Complex with Single-Stranded Nucleic Acids." STRUCTURE, 13, 1055-1067. doi: 10.1016/j.str.2005.04.008. Structure of the third kh domain of hnrnp k in complex with 15-mer ssDNA. SNAP output
209d DNA-antibiotic X-ray (3.0 Å) Shinomiya M, Chu W, Carlson RG, Weaver RF, Takusagawa F (1995) "Structural, Physical, and Biological Characteristics of RNA.DNA Binding Agent N8-Actinomycin D." Biochemistry, 34, 8481. doi: 10.1021/BI00026A032. Structural, physical and biological characteristics of RNA:DNA binding agent n8-actinomycin d. SNAP output
2a07 transcription-DNA X-ray (1.9 Å) Stroud JC, Wu Y, Bates DL, Han A, Nowick K, Paabo S, Tong H, Chen L (2006) "Structure of the Forkhead Domain of FOXP2 Bound to DNA." Structure, 14, 159-166. doi: 10.1016/j.str.2005.10.005. Crystal structure of foxp2 bound specifically to DNA.. SNAP output
2a0i hydrolase-DNA X-ray (2.72 Å) Larkin C, Datta S, Harley MJ, Anderson BJ, Ebie A, Hargreaves V, Schildbach JF (2005) "Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the f factor relaxase." Structure, 13, 1533-1544. doi: 10.1016/j.str.2005.06.013. F factor trai relaxase domain bound to f orit single-stranded DNA. SNAP output
2a3v recombination X-ray (2.8 Å) MacDonald D, Demarre G, Bouvier M, Mazel D, Gopaul DN (2006) "Structural basis for broad DNA-specificity in integron recombination." Nature, 440, 1157-1162. doi: 10.1038/nature04643. Structural basis for broad DNA-specificity in integron recombination. SNAP output
2a66 transcription-DNA X-ray (2.2 Å) Solomon IH, Hager JM, Safi R, McDonnell DP, Redinbo MR, Ortlund EA (2005) "Crystal Structure of the Human LRH-1 DBD-DNA Complex Reveals Ftz-F1 Domain Positioning is Required for Receptor Activity." J.Mol.Biol., 354, 1091-1102. doi: 10.1016/j.jmb.2005.10.009. Human liver receptor homologue DNA-binding domain (hlrh-1 dbd) in complex with dsDNA from the hcyp7a1 promoter. SNAP output
2a6o transcription-DNA X-ray (2.6 Å) Ronning DR, Guynet C, Ton-Hoang B, Perez ZN, Ghirlando R, Chandler M, Dyda F (2005) "Active site sharing and subterminal hairpin recognition in a new class of DNA transposases." Mol.Cell, 20, 143-154. doi: 10.1016/j.molcel.2005.07.026. Crystal structure of the ishp608 transposase in complex with stem-loop DNA. SNAP output
2ac0 apoptosis-DNA X-ray (1.8 Å) Kitayner M, Rozenberg H, Kessler N, Rabinovich D, Shaulov L, Haran TE, Shakked Z (2006) "Structural Basis of DNA Recognition by p53 Tetramers." Mol.Cell, 22, 741-753. doi: 10.1016/j.molcel.2006.05.015. Structural basis of DNA recognition by p53 tetramers (complex i). SNAP output
2acj hydrolase-DNA X-ray (2.6 Å) Ha SC, Lowenhaupt K, Rich A, Kim YG, Kim KK (2005) "Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases." Nature, 437, 1183-1186. doi: 10.1038/nature04088. Crystal structure of the b-z junction containing DNA bound to z-DNA binding proteins. SNAP output
2adw DNA-antibiotic X-ray (1.6 Å) Cuesta-Seijo JA, Weiss MS, Sheldrick GM (2006) "Serendipitous Sad Phasing of an Echinomycin-(Acgtacgt)2 Bisintercalation Complex." Acta Crystallogr.,Sect.D, 62, 417. doi: 10.1107/S0907444906003763. Crystal structure of echinomycin-(acgtacgt)2 solved by sad. SNAP output
2ady apoptosis-DNA X-ray (2.5 Å) Kitayner M, Rozenberg H, Kessler N, Rabinovich D, Shaulov L, Haran TE, Shakked Z (2006) "Structural Basis of DNA Recognition by p53 Tetramers." Mol.Cell, 22, 741-753. doi: 10.1016/j.molcel.2006.05.015. Structural basis of DNA recognition by p53 tetramers (complex iv). SNAP output
2ago transferase-DNA X-ray (2.85 Å) Vaisman A, Ling H, Woodgate R, Yang W (2005) "Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis." Embo J., 24, 2957-2967. doi: 10.1038/sj.emboj.7600786. Fidelity of dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. SNAP output
2agp transferase-DNA X-ray (2.9 Å) Vaisman A, Ling H, Woodgate R, Yang W (2005) "Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis." Embo J., 24, 2957-2967. doi: 10.1038/sj.emboj.7600786. Fidelity of dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. SNAP output
2agq transferase-DNA X-ray (2.1 Å) Vaisman A, Ling H, Woodgate R, Yang W (2005) "Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis." Embo J., 24, 2957-2967. doi: 10.1038/sj.emboj.7600786. Fidelity of dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. SNAP output
2ahi apoptosis-DNA X-ray (1.85 Å) Kitayner M, Rozenberg H, Kessler N, Rabinovich D, Shaulov L, Haran TE, Shakked Z (2006) "Structural Basis of DNA Recognition by p53 Tetramers." Mol.Cell, 22, 741-753. doi: 10.1016/j.molcel.2006.05.015. Structural basis of DNA recognition by p53 tetramers (complex iii). SNAP output
2ajq transferase,transcription-DNA X-ray (2.6 Å) Brieba L, Ellenberger T "Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing." Structure of replicative DNA polymerase provides insigts into the mechanisms for processivity, frameshifting and editing. SNAP output
2alz transferase-DNA X-ray (2.5 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2005) "Human DNA Polymerase iota Incorporates dCTP Opposite Template G via a G.C+ Hoogsteen Base Pair." Structure, 13, 1569-1577. doi: 10.1016/j.str.2005.08.010. Ternary complex of hpoli with DNA and dctp. SNAP output
2aoq hydrolase-DNA X-ray (2.2 Å) Lee JY, Chang J, Joseph N, Ghirlando R, Rao DN, Yang W (2005) "MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage." Mol.Cell, 20, 155-166. doi: 10.1016/j.molcel.2005.08.019. Crystal structure of muth-unmethylated DNA complex. SNAP output
2aor hydrolase-DNA X-ray (2.0 Å) Lee JY, Chang J, Joseph N, Ghirlando R, Rao DN, Yang W (2005) "MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage." Mol.Cell, 20, 155-166. doi: 10.1016/j.molcel.2005.08.019. Crystal structure of muth-hemimethylated DNA complex. SNAP output
2aq4 transferase X-ray (2.32 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2005) "Rev1 employs a novel mechanism of DNA synthesis using a protein template." Science, 309, 2219-2222. doi: 10.1126/science.1116336. Ternary complex of the catalytic core of rev1 with DNA and dctp.. SNAP output
2as5 transcription-DNA X-ray (2.7 Å) Wu Y, Borde M, Heissmeyer V, Feuerer M, Lapan AD, Stroud JC, Bates DL, Guo L, Han A, Ziegler SF, Mathis D, Benoist C, Chen L, Rao A (2006) "FOXP3 Controls Regulatory T Cell Function through Cooperation with NFAT." Cell(Cambridge,Mass.), 126, 375-387. doi: 10.1016/j.cell.2006.05.042. Structure of the DNA binding domains of nfat and foxp2 bound specifically to DNA.. SNAP output
2asd transferase-DNA X-ray (1.95 Å) Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ (2006) "Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion." Plos Biol., 4, 1-18. doi: 10.1371/journal.pbio.0040011. Oxog-modified insertion ternary complex. SNAP output
2asj transferase-DNA X-ray (2.35 Å) Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ (2006) "Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion." Plos Biol., 4, 1-18. doi: 10.1371/journal.pbio.0040011. Oxog-modified preinsertion binary complex. SNAP output
2asl transferase-DNA X-ray (2.65 Å) Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ (2006) "Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion." Plos Biol., 4, 1-18. doi: 10.1371/journal.pbio.0040011. Oxog-modified postinsertion binary complex. SNAP output
2ata apoptosis-DNA X-ray (2.2 Å) Kitayner M, Rozenberg H, Kessler N, Rabinovich D, Shaulov L, Haran TE, Shakked Z (2006) "Structural Basis of DNA Recognition by p53 Tetramers." Mol.Cell, 22, 741-753. doi: 10.1016/j.molcel.2006.05.015. Structural basis of DNA recognition by p53 tetramers (complex ii). SNAP output
2atl transferase-DNA X-ray (2.8 Å) Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ (2006) "Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion." Plos Biol., 4, 1-18. doi: 10.1371/journal.pbio.0040011. Unmodified insertion ternary complex. SNAP output
2au0 transferase-DNA X-ray (2.7 Å) Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ (2006) "Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion." Plos Biol., 4, 1-18. doi: 10.1371/journal.pbio.0040011. Unmodified preinsertion binary complex. SNAP output
2axy DNA binding protein-DNA X-ray (1.7 Å) Du Z, Lee JK, Tjhen R, Li S, Pan H, Stroud RM, James TL (2005) "Crystal Structure of the First KH Domain of Human Poly(C)-binding Protein-2 in Complex with a C-rich Strand of Human Telomeric DNA at 1.7 A." J.Biol.Chem., 280, 38823-38830. doi: 10.1074/jbc.M508183200. Crystal structure of kh1 domain of human poly(c)-binding protein-2 with c-rich strand of human telomeric DNA. SNAP output
2ayb transcription-DNA X-ray (3.2 Å) Hooley E, Fairweather V, Clarke AR, Gaston K, Brady RL (2006) "The recognition of local DNA conformation by the human papillomavirus type 6 E2 protein." Nucleic Acids Res., 34, 3897-3908. doi: 10.1093/nar/gkl466. Crystal structure of hpv6a e2 DNA binding domain bound to a 16 base pair DNA target. SNAP output
2ayg transcription-DNA X-ray (3.1 Å) Hooley E, Fairweather V, Clarke AR, Gaston K, Brady RL (2006) "The recognition of local DNA conformation by the human papillomavirus type 6 E2 protein." Nucleic Acids Res., 34, 3897-3908. doi: 10.1093/nar/gkl466. Crystal structure of hpv6a e2 DNA binding domain bound to an 18 base pair DNA target. SNAP output
2b0d hydrolase-DNA X-ray (2.0 Å) Hiller DA, Rodriguez AM, Perona JJ (2005) "Non-cognate Enzyme-DNA Complex: Structural and Kinetic Analysis of EcoRV Endonuclease Bound to the EcoRI Recognition Site GAATTC." J.Mol.Biol., 354, 121-136. doi: 10.1016/j.jmb.2005.09.046. Ecorv restriction endonuclease-gaattc-ca2+. SNAP output
2b0e hydrolase-DNA X-ray (1.9 Å) Hiller DA, Rodriguez AM, Perona JJ (2005) "Non-cognate Enzyme-DNA Complex: Structural and Kinetic Analysis of EcoRV Endonuclease Bound to the EcoRI Recognition Site GAATTC." J.Mol.Biol., 354, 121-136. doi: 10.1016/j.jmb.2005.09.046. Ecorv restriction endonuclease-gaautc-ca2+. SNAP output
2b9s isomerase-DNA X-ray (2.27 Å) Davies DR, Mushtaq A, Interthal H, Champoux JJ, Hol WG (2006) "The Structure of the Transition State of the Heterodimeric Topoisomerase I of Leishmania donovani as a Vanadate Complex with Nicked DNA." J.Mol.Biol., 357, 1202-1210. doi: 10.1016/j.jmb.2006.01.022. Crystal structure of heterodimeric l. donovani topoisomerase i-vanadate-DNA complex. SNAP output
2bam hydrolase-DNA X-ray (2.0 Å) Viadiu H, Aggarwal AK (1998) "The role of metals in catalysis by the restriction endonuclease BamHI." Nat.Struct.Biol., 5, 910-916. doi: 10.1038/2352. Restriction endonuclease bamhi complex with DNA and calcium ions (pre-reactive complex).. SNAP output
2bcq transferase, lyase-DNA X-ray (1.65 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2006) "Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase." Cell(Cambridge,Mass.), 124, 331-342. doi: 10.1016/j.cell.2005.10.039. DNA polymerase lambda in complex with a DNA duplex containing an unpaired dtmp. SNAP output
2bcr transferase, lyase-DNA X-ray (1.75 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2006) "Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase." Cell(Cambridge,Mass.), 124, 331-342. doi: 10.1016/j.cell.2005.10.039. DNA polymerase lambda in complex with a DNA duplex containing an unpaired damp. SNAP output
2bcs transferase, lyase-DNA X-ray (2.2 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2006) "Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase." Cell(Cambridge,Mass.), 124, 331-342. doi: 10.1016/j.cell.2005.10.039. DNA polymerase lambda in complex with a DNA duplex containing an unpaired dcmp. SNAP output
2bcu transferase, lyase-DNA X-ray (2.2 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2006) "Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase." Cell(Cambridge,Mass.), 124, 331-342. doi: 10.1016/j.cell.2005.10.039. DNA polymerase lambda in complex with a DNA duplex containing an unpaired damp and a t:t mismatch. SNAP output
2bcv transferase, lyase-DNA X-ray (2.0 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2006) "Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase." Cell(Cambridge,Mass.), 124, 331-342. doi: 10.1016/j.cell.2005.10.039. DNA polymerase lambda in complex with dttp and a DNA duplex containing an unpaired dtmp. SNAP output
2bdp transferase-DNA X-ray (1.8 Å) Kiefer JR, Mao C, Braman JC, Beese LS (1998) "Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal." Nature, 391, 304-307. doi: 10.1038/34693. Crystal structure of bacillus DNA polymerase i fragment complexed to 9 base pairs of duplex DNA. SNAP output
2bgw hydrolase X-ray (2.8 Å) Newman M, Murray-Rust J, Lally J, Rudolf J, Fadden A, Knowles PP, White MF, McDonald NQ (2005) "Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition." EMBO J., 24, 895-905. doi: 10.1038/sj.emboj.7600581. Xpf from aeropyrum pernix, complex with DNA. SNAP output
2bjc transcription regulator NMR Salinas RK, Folkers GE, Bonvin AMJJ, Das D, Boelens R, Kaptein R (2005) "Altered Specificity in DNA Binding by the Lac Repressor: A Mutant Lac Headpiece that Mimics the Gal Repressor." Chembiochem, 6, 1628. doi: 10.1002/CBIC.200500049. NMR structure of a protein-DNA complex of an altered specificity mutant of the lac repressor headpiece that mimics the gal repressor. SNAP output
2bnw DNA-binding-regulatory protein X-ray (2.45 Å) Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger W (2006) "Structures of Omega Repressors Bound to Direct and Inverted DNA Repeats Explain Modulation of Transcription." Nucleic Acids Res., 34, 1450. doi: 10.1093/NAR/GKL015. Structural basis for cooperative binding of ribbon-helix-helix omega repressor to direct DNA heptad repeats. SNAP output
2bnz DNA binding protein-DNA X-ray (2.6 Å) Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger W (2006) "Structures of Omega Repressors Bound to Direct and Inverted DNA Repeats Explain Modulation of Transcription." Nucleic Acids Res., 34, 1450. doi: 10.1093/NAR/GKL015. Structural basis for cooperative binding of ribbon-helix-helix omega repressor to inverted DNA heptad repeats. SNAP output
2bop transcription-DNA X-ray (1.7 Å) Hegde RS, Grossman SR, Laimins LA, Sigler PB (1992) "Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target." Nature, 359, 505-512. doi: 10.1038/359505a0. Crystal structure at 1.7 angstroms of the bovine papillomavirus-1 e2 DNA-binding domain bound to its DNA target. SNAP output
2bpa virus-DNA X-ray (3.0 Å) McKenna R, Xia D, Willingmann P, Ilag LL, Krishnaswamy S, Rossmann MG, Olson NH, Baker TS, Incardona NL (1992) "Atomic structure of single-stranded DNA bacteriophage phi X174 and its functional implications." Nature, 355, 137-143. doi: 10.1038/355137a0. Atomic structure of single-stranded DNA bacteriophage phix174 and its functional implications. SNAP output
2bpf transferase-DNA X-ray (2.9 Å) Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut J (1994) "Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP." Science, 264, 1891-1903. Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddctp. SNAP output
2bpg transferase-DNA X-ray (3.6 Å) Pelletier H, Sawaya MR, Kumar A, Wilson SH, Kraut J (1994) "Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP." Science, 264, 1891-1903. Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddctp. SNAP output
2bq3 transferase X-ray (2.0 Å) Zang H, Goodenough AK, Choi JY, Irimia A, Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M, Guengerich FP (2005) "DNA Adduct Bypass Polymerization by Sulfolobus Solfataricus DNA Polymerase Dpo4: Analysis and Crystal Structures of Multiple Base Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine." J.Biol.Chem., 280, 29750. doi: 10.1074/JBC.M504756200. DNA adduct bypass polymerization by sulfolobus solfataricus dpo4. analysis and crystal structures of multiple base-pair substitution and frameshift products with the adduct 1,n2-ethenoguanine. SNAP output
2bqr transferase X-ray (2.37 Å) Zang H, Goodenough AK, Choi JY, Irimia A, Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M, Guengerich FP (2005) "DNA Adduct Bypass Polymerization by Sulfolobus Solfataricus DNA Polymerase Dpo4: Analysis and Crystal Structures of Multiple Base Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine." J.Biol.Chem., 280, 29750. doi: 10.1074/JBC.M504756200. DNA adduct bypass polymerization by sulfolobus solfataricus dpo4. analysis and crystal structures of multiple base-pair substitution and frameshift products with the adduct 1,n2-ethenoguanine. SNAP output
2bqu transferase X-ray (2.5 Å) Zang H, Goodenough AK, Choi JY, Irimia A, Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M, Guengerich FP (2005) "DNA Adduct Bypass Polymerization by Sulfolobus Solfataricus DNA Polymerase Dpo4: Analysis and Crystal Structures of Multiple Base Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine." J.Biol.Chem., 280, 29750. doi: 10.1074/JBC.M504756200. DNA adduct bypass polymerization by sulfolobus solfataricus dpo4. analysis and crystal structures of multiple base-pair substitution and frameshift products with the adduct 1,n2-ethenoguanine. SNAP output
2br0 transferase X-ray (2.17 Å) Zang H, Goodenough AK, Choi JY, Irimia A, Loukachevitch LV, Kozekov ID, Angel KC, Rizzo CJ, Egli M, Guengerich FP (2005) "DNA Adduct Bypass Polymerization by Sulfolobus Solfataricus DNA Polymerase Dpo4: Analysis and Crystal Structures of Multiple Base Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine." J.Biol.Chem., 280, 29750. doi: 10.1074/JBC.M504756200. DNA adduct bypass polymerization by sulfolobus solfataricus dpo4. analysis and crystal structures of multiple base-pair substitution and frameshift products with the adduct 1,n2-ethenoguanine. SNAP output
2bsq transcription X-ray (3.0 Å) Mattison K, Wilbur JS, So M, Brennan RG (2006) "Structure of Fitab from Neisseria Gonorrhoeae Bound to DNA Reveals a Tetramer of Toxin-Antitoxin Heterodimers Containing Pin Domains and Ribbon-Helix-Helix Motifs." J.Biol.Chem., 281, 37942. doi: 10.1074/JBC.M605198200. Fitab bound to DNA. SNAP output
2bzf DNA binding protein X-ray (2.87 Å) Bradley CM, Ronning DR, Ghirlando R, Craigie R, Dyda F (2005) "Structural Basis for DNA Bridging by Barrier-to-Autointegration Factor." Nat.Struct.Mol.Biol., 12, 935. doi: 10.1038/NSMB989. Structural basis for DNA bridging by barrier-to-autointegration factor (baf). SNAP output
2c22 polymerase X-ray (2.56 Å) Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch LV, Egli M, Guengerich FP (2006) "Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 281, 2358. doi: 10.1074/JBC.M510889200. Efficient and high fidelity incorporation of dctp opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus solfataricus DNA polymerase dpo4. SNAP output
2c28 polymerase X-ray (2.27 Å) Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch LV, Egli M, P Guengerich F (2006) "Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 281, 2358. doi: 10.1074/JBC.M510889200. Efficient and high fidelity incorporation of dctp opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus solfataricus DNA polymerase dpo4. SNAP output
2c2d polymerase X-ray (2.57 Å) Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch LV, Egli M, P Guengerich F (2006) "Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 281, 2358. doi: 10.1074/JBC.M510889200. Efficient and high fidelity incorporation of dctp opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus solfataricus DNA polymerase dpo4. SNAP output
2c2e polymerase X-ray (2.61 Å) Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch LV, Egli M, P Guengerich F (2006) "Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 281, 2358. doi: 10.1074/JBC.M510889200. Efficient and high fidelity incorporation of dctp opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus solfataricus DNA polymerase dpo4. SNAP output
2c2r polymerase X-ray (2.55 Å) Zang H, Irimia A, Choi J-Y, Angel KC, Loukachevitch LV, Egli M, Guengerich FP (2006) "Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus Solfataricus DNA Polymerase Dpo4." J.Biol.Chem., 281, 2358. doi: 10.1074/JBC.M510889200. Efficient and high fidelity incorporation of dctp opposite 7,8- dihydro-8-oxodeoxyguanosine by sulfolobus solfataricus DNA polymerase dpo4. SNAP output
2c5r DNA-binding protein-DNA X-ray (2.9 Å) Albert A, Munoz-Espin D, Jimenez M, Asensio JL, Hermoso JA, Salas M, Meijer WJJ (2005) "Structural Basis for Membrane Anchorage of Viral Phi 29 DNA During Replication." J.Biol.Chem., 280, 42486. doi: 10.1074/JBC.C500429200. The structure of phage phi29 replication organizer protein p16.7 in complex with double stranded DNA. SNAP output
2c62 transcription X-ray (1.74 Å) Werten S, Moras D (2006) "A Global Transcription Cofactor Bound to Juxtaposed Strands of Unwound DNA." Nat.Struct.Mol.Biol., 13, 181. doi: 10.1038/NSMB1044. Crystal structure of the human transcription cofactor pc4 in complex with single-stranded DNA. SNAP output
2c6y transcription regulation X-ray (2.4 Å) Tsai K-L, Huang C-Y, Chang C-H, Sun Y-J, Chuang W-J, Hsiao C-D (2006) "Crystal Structure of the Human Foxk1A-DNA Complex and its Implications on the Diverse Binding Specificity of Winged Helix/Forkhead Proteins." J.Biol.Chem., 281, 17400. doi: 10.1074/JBC.M600478200. Crystal structure of interleukin enhancer-binding factor 1 bound to DNA. SNAP output
2c7a receptor-DNA X-ray (2.5 Å) Roemer SC, Donham DC, Sherman L, Pon VH, Edwards DP, Churchill MEA (2006) "Structure of the Progesterone Receptor-Deoxyribonucleic Acid Complex: Novel Interactions Required for Binding to Half-Site Response Elements." Mol.Endocrinol., 20, 3042. doi: 10.1210/ME.2005-0511. Structure of the progesterone receptor-DNA complex. SNAP output
2c7o transferase-DNA X-ray (1.9 Å) Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DTF, Klimasauskas S, Jones AC (2005) "Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes." Nucleic Acids Res., 33, 6953. doi: 10.1093/NAR/GKI995. Hhai DNA methyltransferase complex with 13mer oligonucleotide containing 2-aminopurine adjacent to the target base (pcgc:gmgc) and sah. SNAP output
2c7p transferase-DNA X-ray (1.7 Å) Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DTF, Klimasauskas S, Jones AC (2005) "Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes." Nucleic Acids Res., 33, 6953. doi: 10.1093/NAR/GKI995. Hhai DNA methyltransferase complex with oligonucleotide containing 2- aminopurine opposite to the target base (gcgc:gmpc) and sah. SNAP output
2c7q transferase-DNA X-ray (1.85 Å) Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DTF, Klimasauskas S, Jones AC (2005) "Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes." Nucleic Acids Res., 33, 6953. doi: 10.1093/NAR/GKI995. Hhai DNA methyltransferase complex with oligonucleotide containing 2- aminopurine outside the recognition sequence (paired with g) and sah. SNAP output
2c7r transferase-DNA X-ray (1.9 Å) Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DTF, Klimasauskas S, Jones AC (2005) "Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes." Nucleic Acids Res., 33, 6953. doi: 10.1093/NAR/GKI995. Hhai DNA methyltransferase (t250g mutant) complex with oligonucleotide containing 2-aminopurine as a target base (gpgc:gmgc) and sah. SNAP output
2c9l viral protein X-ray (2.25 Å) Petosa C, Morand P, Baudin F, Moulin M, Artero JB, Muller CW (2006) "Structural Basis of Lytic Cycle Activation by the Epstein-Barr Virus Zebra Protein." Mol.Cell, 21, 565. doi: 10.1016/J.MOLCEL.2006.01.006. Structure of the epstein-barr virus zebra protein. SNAP output
2c9n viral protein X-ray (3.3 Å) Petosa C, Morand P, Baudin F, Moulin M, Artero JB, Muller CW (2006) "Structural Basis of Lytic Cycle Activation by the Epstein-Barr Virus Zebra Protein." Mol.Cell, 21, 565. doi: 10.1016/J.MOLCEL.2006.01.006. Structure of the epstein-barr virus zebra protein at approximately 3. 5 angstrom resolution. SNAP output
2cax transcriptional repressor X-ray (2.9 Å) Weihofen WA, Cicek A, Pratto F, Alonso JC, Saenger W (2006) "Structures of Omega Repressors Bound to Direct and Inverted DNA Repeats Explain Modulation of Transcription." Nucleic Acids Res., 34, 1450. doi: 10.1093/NAR/GKL015. Structural basis for cooperative binding of ribbon-helix-helix repressor omega to mutated direct DNA heptad repeats. SNAP output
2ccz DNA-replication X-ray (2.7 Å) Huang C-Y, Hsu C-H, Sun Y-J, Wu H-N, Hsiao C-D (2006) "Complexed Crystal Structure of Replication Restart Primsome Protein Prib Reveals a Novel Single-Stranded DNA-Binding Mode." Nucleic Acids Res., 34, 3878. doi: 10.1093/NAR/GKL536. Crystal structure of e. coli primosomol protein prib bound to ssDNA. SNAP output
2cdm DNA-DNA-binding protein X-ray (2.7 Å) Boer R, Russi S, Guasch A, Lucas M, Blanco AG, Perez-Luque R, Coll M, De La Cruz F (2006) "Unveiling the Molecular Mechanism of a Conjugative Relaxase: The Structure of Trwc Complexed with a 27-mer DNA Comprising the Recognition Hairpin and the Cleavage Site." J.Mol.Biol., 358, 857. doi: 10.1016/J.JMB.2006.02.018. The structure of trwc complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site. SNAP output
2cgp transcription-DNA X-ray (2.2 Å) Passner JM, Steitz TA (1997) "The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer." Proc.Natl.Acad.Sci.USA, 94, 2843-2847. doi: 10.1073/pnas.94.7.2843. Catabolite gene activator protein-DNA complex, adenosine-3',5'-cyclic-monophosphate. SNAP output
2crx hydrolase, ligase-DNA X-ray (2.5 Å) Gopaul DN, Guo F, Van Duyne GD (1998) "Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination." EMBO J., 17, 4175-4187. doi: 10.1093/emboj/17.14.4175. Structure of the holliday junction intermediate in cre-loxp site-specific recombination. SNAP output
2cv5 structural protein-DNA X-ray (2.5 Å) Tsunaka Y, Kajimura N, Tate S, Morikawa K (2005) "Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle." Nucleic Acids Res., 33, 3424-3434. doi: 10.1093/nar/gki663. Crystal structure of human nucleosome core particle. SNAP output
2d45 transcription-DNA X-ray (3.8 Å) Safo MK, Ko TP, Musayev FN, Zhao Q, Wang AH, Archer GL (2006) "Structure of the MecI repressor from Staphylococcus aureus in complex with the cognate DNA operator of mec." Acta Crystallogr.,Sect.F, 62, 320-324. doi: 10.1107/S1744309106009742. Crystal structure of the meci-meca repressor-operator complex. SNAP output
2d55 DNA-antibiotic X-ray (3.0 Å) Kamitori S, Takusagawa F (1992) "Crystal Structure of the 2:1 Complex between D(Gaagcttc) and the Anticancer Drug Actinomycin D." J.Mol.Biol., 225, 445. doi: 10.1016/0022-2836(92)90931-9. Structural, physical and biological characteristics of RNA.DNA binding agent n8-actinomycin d. SNAP output
2d5v transcription-DNA X-ray (2.0 Å) Iyaguchi D, Yao M, Watanabe N, Nishihira J, Tanaka I (2007) "DNA recognition mechanism of the ONECUT homeodomain of transcription factor HNF-6." Structure, 15, 75-83. doi: 10.1016/j.str.2006.11.004. Crystal structure of hnf-6alpha DNA-binding domain in complex with the ttr promoter. SNAP output
2d7d hydrolase-DNA X-ray (2.1 Å) Eryilmaz J, Ceschini S, Ryan J, Geddes S, Waters TR, Barrett TE (2006) "Structural insights into the cryptic DNA-dependent ATPase activity of UvrB." J.Mol.Biol., 357, 62-72. doi: 10.1016/j.jmb.2005.12.059. Structural insights into the cryptic DNA dependent atp-ase activity of uvrb. SNAP output
2d7g hydrolase X-ray (3.3 Å) Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D (2007) "Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA." EMBO J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697. Crystal structure of the aa complex of the n-terminal domain of pria. SNAP output
2d7h hydrolase X-ray (3.0 Å) Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D (2007) "Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA." EMBO J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697. Crystal structure of the ccc complex of the n-terminal domain of pria. SNAP output
2da8 DNA-antibiotic NMR Addess KJ, Sinsheimer JS, Feigon J (1993) "Solution Structure of a Complex between [N-Mecys3,N-Mecys7]Tandem and [D(Gatatc)]2." Biochemistry, 32, 2498. doi: 10.1021/BI00061A006. Solution structure of a complex between (n-mecys3,n-mecys7)tandem and (d(gatatc))2. SNAP output
2ddg hydrolase-DNA X-ray (2.1 Å) Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui R (2007) "Crystal structure of family 5 uracil-DNA glycosylase bound to DNA." J.Mol.Biol., 373, 839-850. doi: 10.1016/j.jmb.2007.08.022. Crystal structure of uracil-DNA glycosylase in complex with ap:g containing DNA. SNAP output
2dem hydrolase-DNA X-ray (1.95 Å) Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui R (2007) "Crystal structure of family 5 uracil-DNA glycosylase bound to DNA." J.Mol.Biol., 373, 839-850. doi: 10.1016/j.jmb.2007.08.022. Crystal structure of uracil-DNA glycosylase in complex with ap:a containing DNA. SNAP output
2dgc transcription-DNA X-ray (2.2 Å) Keller W, Konig P, Richmond TJ (1995) "Crystal structure of a bZIP/DNA complex at 2.2 A: determinants of DNA specific recognition." J.Mol.Biol., 254, 657-667. doi: 10.1006/jmbi.1995.0645. Gcn4 basic domain, leucine zipper complexed with atf-creb site DNA. SNAP output
2dlc ligase-trna X-ray (2.4 Å) Tsunoda M, Kusakabe Y, Tanaka N, Ohno S, Nakamura M, Senda T, Moriguchi T, Asai N, Sekine M, Yokogawa T, Nishikawa K, Nakamura KT (2007) "Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms." Nucleic Acids Res., 35, 4289-4300. doi: 10.1093/nar/gkm417. Crystal structure of the ternary complex of yeast tyrosyl-trna synthetase. SNAP output
2dnj hydrolase-DNA X-ray (2.0 Å) Lahm A, Suck D (1991) "DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex." J.Mol.Biol., 222, 645-667. doi: 10.1016/0022-2836(91)90502-W. Dnase i-induced DNA conformation. 2 angstroms structure of a dnase i-octamer complex. SNAP output
2dp6 hydrolase-DNA X-ray (1.8 Å) Kosaka H, Nakagawa N, Masui R, Kuramitsu S "Structure of Family 5 Uracil-DNA Glycosylase Bound to DNA Reveals Insights into the Mechanism for Substrate Recognition and Catalysis." Crystal structure of uracil-DNA glycosylase in complex with ap:c containing DNA. SNAP output
2dpd DNA binding protein-DNA X-ray (3.17 Å) Vivian JP, Wilce J, Wilce MCJ "Crystal structure of the Replication Termination Protein in complex with a pseudosymmetric B-site." Crystal structure of the replication termination protein in complex with a pseudosymmetric b-site. SNAP output
2dpi transferase-DNA X-ray (2.3 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2006) "Hoogsteen base pair formation promotes synthesis opposite the 1,N(6)-ethenodeoxyadenosine lesion by human DNA polymerase iota." Nat.Struct.Mol.Biol., 13, 619-625. doi: 10.1038/nsmb1118. Ternary complex of hpoli with DNA and dctp. SNAP output
2dpj transferase-DNA X-ray (2.3 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2006) "Hoogsteen base pair formation promotes synthesis opposite the 1,N(6)-ethenodeoxyadenosine lesion by human DNA polymerase iota." Nat.Struct.Mol.Biol., 13, 619-625. doi: 10.1038/nsmb1118. Structure of hpoli with DNA and dttp. SNAP output
2dpu DNA binding protein-DNA X-ray (3.1 Å) Vivian JP, Wilce J, Wilce MCJ "Crystal structure of the replication termination protein in complex with a pseudosymmetric 21mer B-site DNA." Crystal structure of the replication termination protein in complex with a pseudosymmetric 21mer b-site DNA. SNAP output
2drp transcription-DNA X-ray (2.8 Å) Fairall L, Schwabe JW, Chapman L, Finch JT, Rhodes D (1993) "The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition." Nature, 366, 483-487. doi: 10.1038/366483a0. The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger-DNA recognition. SNAP output
2dtu transferase-DNA X-ray (2.37 Å) Hogg M, Aller P, Konigsberg W, Wallace SS, Doublie S (2007) "Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family." J.Biol.Chem., 282, 1432-1444. doi: 10.1074/jbc.M605675200. Crystal structure of the beta hairpin loop deletion variant of rb69 gp43 in complex with DNA containing an abasic site analog. SNAP output
2dwl hydrolase-DNA X-ray (3.2 Å) Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D (2007) "Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA." EMBO J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697. Crystal structure of the pria protein complexed with oligonucleotides. SNAP output
2dwm hydrolase-DNA X-ray (3.15 Å) Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D (2007) "Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA." EMBO J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697. Crystal structure of the pria protein complexed with oligonucleotides. SNAP output
2dwn hydrolase-DNA X-ray (3.35 Å) Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D (2007) "Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA." EMBO J., 26, 2584-2593. doi: 10.1038/sj.emboj.7601697. Crystal structure of the pria protein complexed with oligonucleotides. SNAP output
2dy4 transferase-DNA X-ray (2.65 Å) Aller P, Rould MA, Hogg M, Wallace SS, Doublie S (2007) "A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol." Proc.Natl.Acad.Sci.USA, 104, 814-818. doi: 10.1073/pnas.0606648104. Crystal structure of rb69 gp43 in complex with DNA containing thymine glycol. SNAP output
2e1c transcription-DNA X-ray (2.1 Å) Yokoyama K, Ishijima SA, Koike H, Kurihara C, Shimowasa A, Kabasawa M, Kawashima T, Suzuki M (2007) "Feast/Famine Regulation by Transcription Factor FL11 for the Survival of the Hyperthermophilic Archaeon Pyrococcus OT3." Structure, 15, 1542-1554. doi: 10.1016/j.str.2007.10.015. Structure of putative hth-type transcriptional regulator ph1519-DNA complex. SNAP output
2e2h transcription,transferase-DNA-RNA hybrid X-ray (3.95 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex at 5 mm mg2+ with gtp. SNAP output
2e2i transcription,transferase-DNA-RNA hybrid X-ray (3.41 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex in 5 mm mg+2 with 2'-dgtp. SNAP output
2e2j transcription,transferase-DNA-RNA hybrid X-ray (3.5 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex in 5 mm mg+2 with gmpcpp. SNAP output
2e42 transcription-DNA X-ray (1.8 Å) Tahirov TH, Inoue-Bungo T, Sato K, Shiina M, Hamada K, Ogata K "Structural Basis for Flexible Base Recognition by C/Ebpbeta." Crystal structure of c-ebpbeta bzip homodimer v285a mutant bound to a high affinity DNA fragment. SNAP output
2e43 transcription-DNA X-ray (2.1 Å) Tahirov TH, Inoue-Bungo T, Sato K, Shiina M, Hamada K, Ogata K "Structural Basis for Flexible Base Recognition by C/Ebpbeta." Crystal structure of c-ebpbeta bzip homodimer k269a mutant bound to a high affinity DNA fragment. SNAP output
2e52 hydrolase-DNA X-ray (2.0 Å) Watanabe N, Takasaki Y, Sato C, Ando S, Tanaka I (2009) "Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations." Acta Crystallogr.,Sect.D, 65, 1326-1333. doi: 10.1107/S0907444909041134. Crystal structural analysis of hindiii restriction endonuclease in complex with cognate DNA at 2.0 angstrom resolution. SNAP output
2ea0 hydrolase-DNA X-ray (1.4 Å) Golan G, Zharkov DO, Grollman AP, Shoham G "Active site plasticity of endonuclease VIII: Conformational changes compensating for different substrate and mutations of critical residues." Crystal structure of the DNA repair enzyme endonuclease-viii (nei) from e. coli in complex with ap-site containing DNA substrate. SNAP output
2efw replication-DNA X-ray (2.5 Å) Vivian JP, Porter CJ, Wilce JA, Wilce MCJ (2007) "An asymmetric structure of the Bacillus subtilis replication terminator protein in complex with DNA." J.Mol.Biol., 370, 481-491. doi: 10.1016/j.jmb.2007.02.067. Crystal structure of the rtp:nrb complex from bacillus subtilis. SNAP output
2er8 transcription activator-DNA X-ray (2.85 Å) Fitzgerald MX, Rojas JR, Kim JM, Kohlhaw GB, Marmorstein R (2006) "Structure of a Leu3-DNA complex: recognition of everted CGG half-sites by a Zn2Cys6 binuclear cluster protein." Structure, 14, 725-735. doi: 10.1016/j.str.2005.11.025. Crystal structure of leu3 DNA-binding domain complexed with a 12mer DNA duplex. SNAP output
2ere transcription activator-DNA X-ray (3.0 Å) Fitzgerald MX, Rojas JR, Kim JM, Kohlhaw GB, Marmorstein R (2006) "Structure of a Leu3-DNA complex: recognition of everted CGG half-sites by a Zn2Cys6 binuclear cluster protein." Structure, 14, 725-735. doi: 10.1016/j.str.2005.11.025. Crystal structure of a leu3 DNA-binding domain complexed with a 15mer DNA duplex. SNAP output
2erg transcription activator-DNA X-ray (3.15 Å) Fitzgerald MX, Rojas JR, Kim JM, Kohlhaw GB, Marmorstein R (2006) "Structure of a Leu3-DNA complex: recognition of everted CGG half-sites by a Zn2Cys6 binuclear cluster protein." Structure, 14, 725-735. doi: 10.1016/j.str.2005.11.025. Crystal structure of leu3 DNA-binding domain with a single h50c mutation complexed with a 15mer DNA duplex. SNAP output
2es2 gene regulation X-ray (1.78 Å) Max KE, Zeeb M, Bienert R, Balbach J, Heinemann U (2006) "T-rich DNA single strands bind to a preformed site on the bacterial cold shock protein Bs-CspB." J.Mol.Biol., 360, 702-714. doi: 10.1016/j.jmb.2006.05.044. Crystal structure analysis of the bacillus subtilis cold shock protein bs-cspb in complex with hexathymidine. SNAP output
2etw cell cycle-DNA X-ray (1.67 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Principles of protein-DNA recognition revealed in the structural analysis of ndt80-mse DNA complexes. SNAP output
2euv cell cycle-DNA X-ray (1.94 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Principles of protein-DNA recognition revealed in the structural analysis of ndt80-mse DNA complexes. SNAP output
2euw cell cycle-DNA X-ray (1.68 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse mutant ma4t). SNAP output
2eux cell cycle-DNA X-ray (1.57 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse variant va4g). SNAP output
2euz cell cycle-DNA X-ray (1.56 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse mutant mc5t). SNAP output
2evf cell cycle-DNA X-ray (1.56 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse mutant ma6t). SNAP output
2evg cell cycle-DNA X-ray (1.55 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse mutant ma7t). SNAP output
2evh cell cycle-DNA X-ray (1.989 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse mutant ma7g). SNAP output
2evi cell cycle-DNA X-ray (1.8 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of a ndt80-DNA complex (mse mutant ma8t). SNAP output
2evj cell cycle-DNA X-ray (1.89 Å) Lamoureux JS, Glover JN (2006) "Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes." Structure, 14, 555-565. doi: 10.1016/j.str.2005.11.017. Structure of an ndt80-DNA complex (mse mutant ma9c). SNAP output
2ewj replication-DNA X-ray (2.7 Å) Mulcair MD, Schaeffer PM, Oakley AJ, Cross HF, Neylon C, Hill TM, Dixon NE (2006) "A molecular mousetrap determines polarity of termination of DNA replication in E. coli." Cell(Cambridge,Mass.), 125, 1309-1319. doi: 10.1016/j.cell.2006.04.040. Escherichia coli replication terminator protein (tus) complexed with DNA- locked form. SNAP output
2ex5 hydrolase-DNA X-ray (2.2 Å) Spiegel PC, Chevalier B, Sussman D, Turmel M, Lemieux C, Stoddard BL (2006) "The structure of I-CeuI homing endonuclease: Evolving asymmetric DNA recognition from a symmetric protein scaffold." Structure, 14, 869-880. doi: 10.1016/j.str.2006.03.009. Group i intron-encoded homing endonuclease i-ceui complexed with DNA. SNAP output
2exf viral protein-DNA NMR Bourbigot S, Ramalanjaona N, Boudier C, Salgado GF, Roques BP, Mely Y, Bouaziz S, Morellet N (2008) "How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription." J.Mol.Biol., 383, 1112-1128. doi: 10.1016/j.jmb.2008.08.046. Solution structure of the hiv-1 nucleocapsid (ncp7(12-55)) complexed with the DNA (-) primer binding site. SNAP output
2ezd DNA binding protein-DNA NMR Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R, Gronenborn AM, Clore GM (1997) "The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif." Nat.Struct.Biol., 4, 657-665. doi: 10.1038/nsb0897-657. Solution structure of a complex of the second DNA binding domain of human hmg-i(y) bound to DNA dodecamer containing the prdii site of the interferon-beta promoter, NMR, minimized average structure. SNAP output
2eze DNA binding protein-DNA NMR Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R, Gronenborn AM, Clore GM (1997) "The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif." Nat.Struct.Biol., 4, 657-665. doi: 10.1038/nsb0897-657. Solution structure of a complex of the second DNA binding domain of human hmg-i(y) bound to DNA dodecamer containing the prdii site of the interferon-beta promoter, NMR, 35 structures. SNAP output
2ezf DNA binding protein-DNA NMR Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R, Gronenborn AM, Clore GM (1997) "The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif." Nat.Struct.Biol., 4, 657-665. doi: 10.1038/nsb0897-657. Solution structure of a complex of the third DNA binding domain of human hmg-i(y) bound to DNA dodecamer containing the prdii site of the interferon-beta promoter, NMR, minimized average structure. SNAP output
2ezg DNA binding protein-DNA NMR Huth JR, Bewley CA, Nissen MS, Evans JN, Reeves R, Gronenborn AM, Clore GM (1997) "The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif." Nat.Struct.Biol., 4, 657-665. doi: 10.1038/nsb0897-657. Solution structure of a complex of the third DNA binding domain of human hmg-i(y) bound to DNA dodecamer containing the prdii site of the interferon-beta promoter, NMR, 35 structures. SNAP output
2ezv hydrolase-DNA X-ray (2.4 Å) Vanamee ES, Viadiu H, Kucera R, Dorner L, Picone S, Schildkraut I, Aggarwal AK (2005) "A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA." Embo J., 24, 4198-4208. doi: 10.1038/sj.emboj.7600880. Crystal structure of tetrameric restriction endonuclease sfii bound to cognate DNA.. SNAP output
2f03 hydrolase-DNA X-ray (3.05 Å) Vanamee ES, Viadiu H, Kucera R, Dorner L, Picone S, Schildkraut I, Aggarwal AK (2005) "A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA." Embo J., 24, 4198-4208. doi: 10.1038/sj.emboj.7600880. Crystal structure of tetrameric restriction endonuclease sfii in complex with cognate DNA (partial bound form). SNAP output
2f55 hydrolase-DNA X-ray (3.3 Å) Mackintosh SG, Lu JZ, Jordan JB, Harrison MK, Sikora B, Sharma SD, Cameron CE, Raney KD, Sakon J (2006) "Structural and biological identification of residues on the surface of NS3 helicase required for optimal replication of the hepatitis C virus." J.Biol.Chem., 281, 3528-3535. doi: 10.1074/jbc.M512100200. Two hepatitis c virus ns3 helicase domains complexed with the same strand of DNA. SNAP output
2f5n hydrolase-DNA X-ray (2.0 Å) Banerjee A, Santos WL, Verdine GL (2006) "Structure of a DNA glycosylase searching for lesions." Science, 311, 1153-1157. doi: 10.1126/science.1120288. Mutm crosslinked to undamaged DNA sampling a:t base pair ic1. SNAP output
2f5o hydrolase-DNA X-ray (2.05 Å) Banerjee A, Santos WL, Verdine GL (2006) "Structure of a DNA glycosylase searching for lesions." Science, 311, 1153-1157. doi: 10.1126/science.1120288. Mutm crosslinked to undamaged DNA sampling g:c base pair ic3. SNAP output
2f5p hydrolase-DNA X-ray (2.0 Å) Banerjee A, Santos WL, Verdine GL (2006) "Structure of a DNA glycosylase searching for lesions." Science, 311, 1153-1157. doi: 10.1126/science.1120288. Mutm crosslinked to undamaged DNA sampling a:t base pair ic2. SNAP output
2f5q hydrolase-DNA X-ray (2.35 Å) Banerjee A, Santos WL, Verdine GL (2006) "Structure of a DNA glycosylase searching for lesions." Science, 311, 1153-1157. doi: 10.1126/science.1120288. Catalytically inactive (e3q) mutm crosslinked to oxog:c containing DNA cc2. SNAP output
2f5s hydrolase-DNA X-ray (2.35 Å) Banerjee A, Santos WL, Verdine GL (2006) "Structure of a DNA glycosylase searching for lesions." Science, 311, 1153-1157. doi: 10.1126/science.1120288. Catalytically inactive (e3q) mutm crosslinked to oxog:c containing DNA cc1. SNAP output
2f8n structural protein-DNA X-ray (2.9 Å) Chakravarthy S, Luger K "Nucleosomes containing the histone domain of macroH2A: In vitro possibilities." 2.9 angstrom x-ray structure of hybrid macroh2a nucleosomes. SNAP output
2f8x transcription-DNA X-ray (3.25 Å) Nam Y, Sliz P, Song L, Aster JC, Blacklow SC (2006) "Structural basis for cooperativity in recruitment of MAML coactivators to Notch transcription complexes." Cell(Cambridge,Mass.), 124, 973-983. doi: 10.1016/j.cell.2005.12.037. Crystal structure of activated notch, csl and maml on hes-1 promoter DNA sequence. SNAP output
2fcc hydrolase X-ray (2.3 Å) Golan G, Zharkov DO, Grollman AP, Dodson ML, McCullough AK, Lloyd RS, Shoham G (2006) "Structure of T4 Pyrimidine Dimer Glycosylase in a Reduced Imine Covalent Complex with Abasic Site-containing DNA." J.Mol.Biol., 362, 241-258. doi: 10.1016/j.jmb.2006.06.059. Crystal structure of t4 pyrimidine dimer glycosylase (t4-pdg) covalently complexed with a DNA substrate containing abasic site. SNAP output
2fd8 oxidoreductase-DNA X-ray (2.3 Å) Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) "Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB." Nature, 439, 879-884. doi: 10.1038/nature04561. Crystal structure of alkb in complex with fe(ii), 2-oxoglutarate, and methylated trinucleotide t-mea-t. SNAP output
2fdc DNA binding protein-DNA X-ray (3.3 Å) Truglio JJ, Karakas E, Rhau B, Wang H, DellaVecchia MJ, Van Houten B, Kisker C (2006) "Structural basis for DNA recognition and processing by UvrB." Nat.Struct.Mol.Biol., 13, 360-364. doi: 10.1038/nsmb1072. Structural basis of DNA damage recognition and processing by uvrb: crystal structure of a uvrb-DNA complex. SNAP output
2fdf oxidoreductase-DNA X-ray (2.1 Å) Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) "Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB." Nature, 439, 879-884. doi: 10.1038/nature04561. Crystal structure of alkb in complex with co(ii), 2-oxoglutarate, and methylated trinucleotide t-mea-t. SNAP output
2fdg oxidoreductase-DNA X-ray (2.2 Å) Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) "Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB." Nature, 439, 879-884. doi: 10.1038/nature04561. Crystal structure of alkb in complex with fe(ii), succinate, and methylated trinucleotide t-mea-t. SNAP output
2fdh oxidoreductase-DNA X-ray (2.1 Å) Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) "Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB." Nature, 439, 879-884. doi: 10.1038/nature04561. Crystal structure of alkb in complex with mn(ii), 2-oxoglutarate, and methylated trinucleotide t-mea-t. SNAP output
2fdi oxidoreductase-DNA X-ray (1.8 Å) Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) "Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB." Nature, 439, 879-884. doi: 10.1038/nature04561. Crystal structure of alkb in complex with fe(ii), 2-oxoglutarate, and methylated trinucleotide t-mea-t (air 3 hours). SNAP output
2fdk oxidoreductase-DNA X-ray (2.3 Å) Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) "Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB." Nature, 439, 879-884. doi: 10.1038/nature04561. Crystal structure of alkb in complex with fe(ii), 2-oxoglutarate, and methylated trinucleotide t-mea-t (air 9 days). SNAP output
2ff0 hormone-growth factor-DNA NMR Little TH, Zhang Y, Matulis CK, Weck J, Zhang Z, Ramachandran A, Mayo KE, Radhakrishnan I (2006) "Sequence-specific deoxyribonucleic Acid (DNA) recognition by steroidogenic factor 1: a helix at the carboxy terminus of the DNA binding domain is necessary for complex stability." Mol.Endocrinol., 20, 831-843. doi: 10.1210/me.2005-0384. Solution structure of steroidogenic factor 1 DNA binding domain bound to its target sequence in the inhibin alpha-subunit promoter. SNAP output
2fio transcription-DNA X-ray (2.7 Å) Badia D, Camacho A, Perez-Lago L, Escandon C, Salas M, Coll M (2006) "The structure of phage phi29 transcription regulator p4-DNA complex reveals an N-hook motif for DNA." Mol.Cell, 22, 73-81. doi: 10.1016/j.molcel.2006.02.019. Phage phi29 transcription regulator p4-DNA complex. SNAP output
2fj7 structural protein-DNA X-ray (3.2 Å) Bao Y, White CL, Luger K (2006) "Nucleosome Core Particles Containing a Poly(dA.dT) Sequence Element Exhibit a Locally Distorted DNA Structure." J.Mol.Biol., 361, 617-624. doi: 10.1016/j.jmb.2006.06.051. Crystal structure of nucleosome core particle containing a poly (da.dt) sequence element. SNAP output
2fjv transferase-DNA X-ray (2.05 Å) Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson WD, Georgiadis MM, Long EC (2006) "A High-Throughput, High-Resolution Strategy for the Study of Site-Selective DNA Binding Agents: Analysis of a "Highly Twisted" Benzimidazole-Diamidine." J.Am.Chem.Soc., 128, 7846-7854. doi: 10.1021/ja0600936. Rt29 bound to d(cttaattcgaattaag) in complex with mmlv rt catalytic fragment. SNAP output
2fjw transferase-DNA X-ray (1.95 Å) Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson WD, Georgiadis MM, Long EC (2006) "A High-Throughput, High-Resolution Strategy for the Study of Site-Selective DNA Binding Agents: Analysis of a "Highly Twisted" Benzimidazole-Diamidine." J.Am.Chem.Soc., 128, 7846-7854. doi: 10.1021/ja0600936. D(cttgaatgcattcaag) in complex with mmlv rt catalytic fragment. SNAP output
2fjx transferase-DNA X-ray (1.8 Å) Goodwin KD, Lewis MA, Tanious FA, Tidwell RR, Wilson WD, Georgiadis MM, Long EC (2006) "A High-Throughput, High-Resolution Strategy for the Study of Site-Selective DNA Binding Agents: Analysis of a "Highly Twisted" Benzimidazole-Diamidine." J.Am.Chem.Soc., 128, 7846-7854. doi: 10.1021/ja0600936. Rt29 bound to d(cttgaatgcattcaag) in complex with mmlv rt catalytic fragment. SNAP output
2fkc hydrolase-DNA X-ray (2.39 Å) Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X (2006) "DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion." Nucleic Acids Res., 34, 939-948. doi: 10.1093/nar/gkj484. Crystal form i of pre-reactive complex of restriction endonuclease hinp1i with cognate DNA and calcium ion. SNAP output
2fkh hydrolase-DNA X-ray (3.09 Å) Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X (2006) "DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion." Nucleic Acids Res., 34, 939-948. doi: 10.1093/nar/gkj484. Crystal form ii of pre-reactive complex of restriction endonuclease hinp1i with cognate DNA and calcium ions. SNAP output
2fl3 hydrolase-DNA X-ray (2.39 Å) Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X (2006) "DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion." Nucleic Acids Res., 34, 939-948. doi: 10.1093/nar/gkj484. Binary complex of restriction endonuclease hinp1i with cognate DNA. SNAP output
2flc hydrolase-DNA X-ray (2.59 Å) Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X (2006) "DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion." Nucleic Acids Res., 34, 939-948. doi: 10.1093/nar/gkj484. Post-reactive complex of restriction endonuclease hinp1i with nicked cognate DNA and magnesium ions. SNAP output
2fld hydrolase-DNA X-ray (2.0 Å) Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Stoddard BL, Baker D (2006) "Computational redesign of endonuclease DNA binding and cleavage specificity." Nature, 441, 656-659. doi: 10.1038/nature04818. I-msoi re-designed for altered DNA cleavage specificity. SNAP output
2fll replication-DNA X-ray (2.6 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2006) "An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site." Structure, 14, 749-755. doi: 10.1016/j.str.2006.01.010. Ternary complex of human DNA polymerase iota with DNA and dttp. SNAP output
2fln replication-DNA X-ray (2.5 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2006) "An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site." Structure, 14, 749-755. doi: 10.1016/j.str.2006.01.010. Binary complex of catalytic core of human DNA polymerase iota with DNA (template a). SNAP output
2flp replication-DNA X-ray (2.4 Å) Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2006) "An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site." Structure, 14, 749-755. doi: 10.1016/j.str.2006.01.010. Binary complex of the catalytic core of human DNA polymerase iota with DNA (template g). SNAP output
2fmp transferase-DNA X-ray (1.65 Å) Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC, Wilson SH (2006) "Magnesium-induced assembly of a complete DNA polymerase catalytic complex." Structure, 14, 757-766. doi: 10.1016/j.str.2006.01.011. DNA polymerase beta with a terminated gapped DNA substrate and ddctp with sodium in the catalytic site. SNAP output
2fmq transferase-DNA X-ray (2.2 Å) Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC, Wilson SH (2006) "Magnesium-induced assembly of a complete DNA polymerase catalytic complex." Structure, 14, 757-766. doi: 10.1016/j.str.2006.01.011. Sodium in active site of DNA polymerase beta. SNAP output
2fms transferase-DNA X-ray (2.0 Å) Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC, Wilson SH (2006) "Magnesium-induced assembly of a complete DNA polymerase catalytic complex." Structure, 14, 757-766. doi: 10.1016/j.str.2006.01.011. DNA polymerase beta with a gapped DNA substrate and dumpnpp with magnesium in the catalytic site. SNAP output
2fo1 gene regulation-signalling protein-DNA X-ray (3.12 Å) Wilson JJ, Kovall RA (2006) "Crystal structure of the CSL-Notch-Mastermind ternary complex bound to DNA." Cell(Cambridge,Mass.), 124, 985-996. doi: 10.1016/j.cell.2006.01.035. Crystal structure of the csl-notch-mastermind ternary complex bound to DNA. SNAP output
2fqz hydrolase-DNA X-ray (2.0 Å) Bochtler M, Szczepanowski RH, Tamulaitis G, Grazulis S, Czapinska H, Manakova E, Siksnys V (2006) "Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease." Embo J., 25, 2219-2229. doi: 10.1038/sj.emboj.7601096. Metal-depleted ecl18ki in complex with uncleaved DNA. SNAP output
2fr4 immune system-DNA X-ray (1.95 Å) Ou Z, Bottoms CA, Henzl MT, Tanner JJ (2007) "Impact of DNA hairpin folding energetics on antibody-ssDNA association." J.Mol.Biol., 374, 1029-1040. doi: 10.1016/j.jmb.2007.09.084. Structure of fab DNA-1 complexed with a stem-loop DNA ligand. SNAP output
2fvp transferase-DNA X-ray (2.25 Å) Montano SP, Cote ML, Roth MJ, Georgiadis MM (2006) "Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus." Nucleic Acids Res., 34, 5353-5360. doi: 10.1093/nar/gkl693. A structural study of the ca dinucleotide step in the integrase processing site of moloney murine leukemia virus. SNAP output
2fvq transferase-DNA X-ray (2.3 Å) Montano SP, Cote ML, Roth MJ, Georgiadis MM (2006) "Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus." Nucleic Acids Res., 34, 5353-5360. doi: 10.1093/nar/gkl693. A structural study of the ca dinucleotide step in the integrase processing site of moloney murine leukemia virus. SNAP output
2fvr transferase-DNA X-ray (2.2 Å) Montano SP, Cote ML, Roth MJ, Georgiadis MM (2006) "Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus." Nucleic Acids Res., 34, 5353-5360. doi: 10.1093/nar/gkl693. A structural study of the ca dinucleotide step in the integrase processing site of moloney murine leukemia virus. SNAP output
2fvs transferase-DNA X-ray (2.35 Å) Montano SP, Cote ML, Roth MJ, Georgiadis MM (2006) "Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus." Nucleic Acids Res., 34, 5353-5360. doi: 10.1093/nar/gkl693. A structural study of the ca dinucleotide step in the integrase processing site of moloney murine leukemia virus. SNAP output
2g1p transferase-DNA X-ray (1.89 Å) Horton JR, Liebert K, Bekes M, Jeltsch A, Cheng X (2006) "Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase." J.Mol.Biol., 358, 559-570. doi: 10.1016/j.jmb.2006.02.028. Structure of e. coli DNA adenine methyltransferase (dam). SNAP output
2g8f hydrolase-RNA-DNA X-ray (1.65 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain e188a mutant in complex with mg2+ and RNA-DNA hybrid (non-p nick at the active site). SNAP output
2g8h hydrolase-RNA-DNA X-ray (1.85 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain d192n mutant in complex with mg2+ and RNA-DNA hybrid (non-p nick at the active site). SNAP output
2g8i hydrolase-RNA-DNA X-ray (1.65 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain d192n mutant in complex with mn2+ and RNA-DNA hybrid (non-p nick at the active site). SNAP output
2g8k hydrolase-RNA-DNA X-ray (1.65 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain d192n mutant in complex with ca2+ and RNA-DNA hybrid (non-p nick at the active site). SNAP output
2g8u hydrolase-RNA-DNA X-ray (2.7 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain d132n mutant in complex with mg2+ and RNA-DNA hybrid (non-p nick at the active site). SNAP output
2g8v hydrolase-RNA-DNA X-ray (1.85 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain e188a mutant in complex with mg2+ and RNA-DNA hybrid (reaction product). SNAP output
2g8w hydrolase-RNA-DNA X-ray (2.05 Å) Nowotny M, Yang W (2006) "Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release." Embo J., 25, 1924-1933. doi: 10.1038/sj.emboj.7601076. B. halodurans rnase h catalytic domain e188a mutant in complex with ca2+ and RNA-DNA hybrid. SNAP output
2gat transcription-DNA NMR Tjandra N, Omichinski JG, Gronenborn AM, Clore GM, Bax A (1997) "Use of dipolar 1H-15N and 1H-13C couplings in the structure determination of magnetically oriented macromolecules in solution." Nat.Struct.Biol., 4, 732-738. doi: 10.1038/nsb0997-732. Solution structure of the c-terminal domain of chicken gata-1 bound to DNA, NMR, regularized mean structure. SNAP output
2gb7 hydrolase-DNA X-ray (1.7 Å) Bochtler M, Szczepanowski RH, Tamulaitis G, Grazulis S, Czapinska H, Manakova E, Siksnys V (2006) "Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease." Embo J., 25, 2219-2229. doi: 10.1038/sj.emboj.7601096. Metal-depleted ecl18ki in complex with uncleaved, modified DNA. SNAP output
2ge5 hydrolase-DNA X-ray (2.4 Å) Hiller DA, Perona JJ (2006) "Positively Charged C-Terminal Subdomains of EcoRV Endonuclease: Contributions to DNA Binding, Bending, and Cleavage." Biochemistry, 45, 11453-11463. doi: 10.1021/bi0606400. Ecorv restriction endonuclease c-terminal deletion mutant-gatatc-ca2+. SNAP output
2geq transcription-DNA X-ray (2.3 Å) Ho WC, Fitzgerald MX, Marmorstein R (2006) "Structure of the p53 Core Domain Dimer Bound to DNA." J.Biol.Chem., 281, 20494-20502. doi: 10.1074/jbc.M603634200. Crystal structure of a p53 core dimer bound to DNA. SNAP output
2gie hydrolase-DNA X-ray (2.6 Å) Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC (2006) "Alteration of Sequence Specificity of the Type II Restriction Endonuclease HincII through an Indirect Readout Mechanism." J.Biol.Chem., 281, 23852-23869. doi: 10.1074/jbc.M512339200. Hincii bound to cognate DNA gttaac. SNAP output
2gig hydrolase-DNA X-ray (1.83 Å) Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC (2006) "Alteration of Sequence Specificity of the Type II Restriction Endonuclease HincII through an Indirect Readout Mechanism." J.Biol.Chem., 281, 23852-23869. doi: 10.1074/jbc.M512339200. Alteration of sequence specificity of the type ii restriction endonuclease hincii through an indirect readout mechanism. SNAP output
2gih hydrolase-DNA X-ray (2.5 Å) Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC (2006) "Alteration of Sequence Specificity of the Type II Restriction Endonuclease HincII through an Indirect Readout Mechanism." J.Biol.Chem., 281, 23852-23869. doi: 10.1074/jbc.M512339200. Q138f hincii bound to cognate DNA gtcgac and ca2+. SNAP output
2gii hydrolase-DNA X-ray (2.3 Å) Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC (2006) "Alteration of Sequence Specificity of the Type II Restriction Endonuclease HincII through an Indirect Readout Mechanism." J.Biol.Chem., 281, 23852-23869. doi: 10.1074/jbc.M512339200. Q138f hincii bound to cognate DNA gttaac. SNAP output
2gij hydrolase-DNA X-ray (1.93 Å) Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC (2006) "Alteration of Sequence Specificity of the Type II Restriction Endonuclease HincII through an Indirect Readout Mechanism." J.Biol.Chem., 281, 23852-23869. doi: 10.1074/jbc.M512339200. Q138f hincii bound to cognate DNA gttaac and ca2+. SNAP output
2gkd toxin-DNA NMR Singh S, Hager MH, Zhang C, Griffith BR, Lee MS, Hallenga K, Markley JL, Thorson JS (2006) "Structural insight into the self-sacrifice mechanism of enediyne resistance." Acs Chem.Biol., 1, 451-460. doi: 10.1021/cb6002898. Structural insight into self-sacrifice mechanism of enediyne resistance. SNAP output
2gli transcription-DNA X-ray (2.6 Å) Pavletich NP, Pabo CO (1993) "Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers." Science, 261, 1701-1707. Five-finger gli-DNA complex. SNAP output
2glo transcription-DNA NMR Cordier F, Hartmann B, Rogowski M, Affolter M, Grzesiek S (2006) "DNA recognition by the brinker repressor - an extreme case of coupling between binding and folding." J.Mol.Biol., 361, 659-672. doi: 10.1016/j.jmb.2006.06.045. Solution structure of the brinker DNA binding domain in complex with the omb enhancer. SNAP output
2gm4 recombination, DNA X-ray (3.5 Å) Kamtekar S, Ho RS, Cocco MJ, Li W, Wenwieser SV, Boocock MR, Grindley ND, Steitz TA (2006) "Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination." Proc.Natl.Acad.Sci.Usa, 103, 10642-10647. doi: 10.1073/pnas.0604062103. An activated, tetrameric gamma-delta resolvase: hin chimaera bound to cleaved DNA. SNAP output
2gws transferase-DNA X-ray (2.4 Å) Picher AJ, Garcia-Diaz M, Bebenek K, Pedersen LC, Kunkel TA, Blanco L (2006) "Promiscuous mismatch extension by human DNA polymerase lambda." Nucleic Acids Res., 34, 3259-3266. doi: 10.1093/nar/gkl377. Crystal structure of human DNA polymerase lambda with a g-g mismatch in the primer terminus. SNAP output
2gxa replication-DNA X-ray (3.15 Å) Enemark EJ, Joshua-Tor L (2006) "Mechanism of DNA translocation in a replicative hexameric helicase." Nature, 442, 270-275. doi: 10.1038/nature04943. Crystal structure of papillomavirus e1 hexameric helicase with ssDNA and mgadp. SNAP output
2gzk DNA-structural protein NMR Stott K, Tang GS, Lee KB, Thomas JO (2006) "Structure of a Complex of Tandem HMG Boxes and DNA." J.Mol.Biol., 360, 90-104. doi: 10.1016/j.jmb.2006.04.059. Structure of a complex of tandem hmg boxes and DNA. SNAP output
2h1k transcription-DNA X-ray (2.42 Å) Longo A, Guanga GP, Rose RB (2007) "Structural basis for induced fit mechanisms in DNA recognition by the pdx1 homeodomain." Biochemistry, 46, 2948-2957. doi: 10.1021/bi060969l. Crystal structure of the pdx1 homeodomain in complex with DNA. SNAP output
2h1o gene regulation-DNA complex X-ray (3.0 Å) Mattison K, Wilbur JS, So M, Brennan RG (2006) "Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs." J.Biol.Chem., 281, 37942-37951. doi: 10.1074/jbc.M605198200. Structure of fitab bound to ir36 DNA fragment. SNAP output
2h27 transferase-DNA X-ray (2.3 Å) Lane WJ, Darst SA (2006) "The structural basis for promoter -35 element recognition by the group IV sigma factors." Plos Biol., 4, e269. doi: 10.1371/journal.pbio.0040269. Crystal structure of escherichia coli sigmae region 4 bound to its-35 element DNA. SNAP output
2h3a immune system-DNA NMR Madl T, Van Melderen L, Mine N, Respondek M, Oberer M, Keller W, Khatai L, Zangger K (2006) "Structural Basis for Nucleic Acid and Toxin Recognition of the Bacterial Antitoxin CcdA." J.Mol.Biol., 364, 170-185. doi: 10.1016/j.jmb.2006.08.082. Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin ccda. SNAP output
2h3c immune system-DNA NMR Madl T, Van Melderen L, Mine N, Respondek M, Oberer M, Keller W, Khatai L, Zangger K (2006) "Structural Basis for Nucleic Acid and Toxin Recognition of the Bacterial Antitoxin CcdA." J.Mol.Biol., 364, 170-185. doi: 10.1016/j.jmb.2006.08.082. Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin ccda. SNAP output
2h7f isomerase-DNA X-ray (2.7 Å) Perry K, Hwang Y, Bushman FD, Van Duyne GD (2006) "Structural basis for specificity in the poxvirus topoisomerase." Mol.Cell, 23, 343-354. doi: 10.1016/j.molcel.2006.06.015. Structure of variola topoisomerase covalently bound to DNA. SNAP output
2h7g isomerase-DNA X-ray (1.9 Å) Perry K, Hwang Y, Bushman FD, Van Duyne GD (2006) "Structural basis for specificity in the poxvirus topoisomerase." Mol.Cell, 23, 343-354. doi: 10.1016/j.molcel.2006.06.015. Structure of variola topoisomerase non-covalently bound to DNA. SNAP output
2h7h viral protein-DNA X-ray (2.3 Å) Kim Y, Borovilos M "Crystal structure of the JUN BZIP homodimer complexed with AP-1 DNA." Crystal structure of the jun bzip homodimer complexed with ap-1 DNA. SNAP output
2h8c hydrolase-DNA X-ray (3.1 Å) Macmaster R, Sedelnikova S, Baker PJ, Bolt EL, Lloyd RG, Rafferty JB (2006) "RusA Holliday junction resolvase: DNA complex structure--insights into selectivity and specificity." Nucleic Acids Res., 34, 5577-5584. doi: 10.1093/nar/gkl447. Structure of rusa d70n in complex with DNA. SNAP output
2h8r transcription activator-DNA X-ray (3.2 Å) Lu P, Rha GB, Chi YI (2007) "Structural basis of disease-causing mutations in hepatocyte nuclear factor 1beta." Biochemistry, 46, 12071-12080. doi: 10.1021/bi7010527. Hepatocyte nuclear factor 1b bound to DNA: mody5 gene product. SNAP output
2han transcription-DNA X-ray (1.95 Å) Jakob M, Kolodziejczyk R, Orlowski M, Krzywda S, Kowalska A, Dutko-Gwozdz J, Gwozdz T, Kochman M, Jaskolski M, Ozyhar A (2007) "Novel DNA-binding element within the C-terminal extension of the nuclear receptor DNA-binding domain." Nucleic Acids Res., 35, 2705-2718. doi: 10.1093/nar/gkm162. Structural basis of heterodimeric ecdysteroid receptor interaction with natural response element hsp27 gene promoter. SNAP output
2hap gene regulation-DNA X-ray (2.5 Å) King DA, Zhang L, Guarente L, Marmorstein R (1999) "Structure of HAP1-18-DNA implicates direct allosteric effect of protein-DNA interactions on transcriptional activation." Nat.Struct.Biol., 6, 22-27. doi: 10.1038/4893. Structure of a hap1-18-DNA complex reveals that protein-DNA interactions can have direct allosteric effects on transcriptional activation. SNAP output
2hax gene regulation-DNA X-ray (1.29 Å) Max KE, Zeeb M, Bienert R, Balbach J, Heinemann U (2007) "Common mode of DNA binding to cold shock domains. Crystal structure of hexathymidine bound to the domain-swapped form of a major cold shock protein from Bacillus caldolyticus." Febs J., 274, 1265-1279. doi: 10.1111/j.1742-4658.2007.05672.x. Crystal structure of bacillus caldolyticus cold shock protein in complex with hexathymidine. SNAP output
2hdc protein-DNA NMR Jin C, Marsden I, Chen X, Liao X (1999) "Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex." J.Mol.Biol., 289, 683-690. doi: 10.1006/jmbi.1999.2819. Structure of transcription factor genesis-DNA complex. SNAP output
2hdd transcription-DNA X-ray (1.9 Å) Tucker-Kellogg L, Rould MA, Chambers KA, Ades SE, Sauer RT, Pabo CO (1997) "Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity." Structure, 5, 1047-1054. doi: 10.1016/S0969-2126(97)00256-6. Engrailed homeodomain q50k variant DNA complex. SNAP output
2heo immune system-DNA X-ray (1.7 Å) Magis C, Gasparini D, Lecoq A, Le Du MH, Stura E, Charbonnier JB, Mourier G, Boulain JC, Pardo L, Caruana A, Joly A, Lefranc M, Masella M, Menez A, Cuniasse P (2006) "Structure-based secondary structure-independent approach to design protein ligands: Application to the design of Kv1.2 potassium channel blockers." J.Am.Chem.Soc., 128, 16190-16205. doi: 10.1021/ja0646491. General structure-based approach to the design of protein ligands: application to the design of kv1.2 potassium channel blockers.. SNAP output
2hhq transferase-DNA X-ray (1.8 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. O6-methyl-guanine:t pair in the polymerase-10 basepair position. SNAP output
2hhs transferase-DNA X-ray (1.8 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. O6-methyl:c pair in the polymerase-10 basepair position. SNAP output
2hht transferase-DNA X-ray (2.05 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. C:o6-methyl-guanine pair in the polymerase-2 basepair position. SNAP output
2hhu transferase-DNA X-ray (1.8 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. C:o6-methyl-guanine in the polymerase postinsertion site (-1 basepair position). SNAP output
2hhv transferase-DNA X-ray (1.55 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. T:o6-methyl-guanine in the polymerase-2 basepair position. SNAP output
2hhw transferase-DNA X-ray (1.88 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. Ddttp:o6-methyl-guanine pair in the polymerase active site, in the closed conformation. SNAP output
2hhx transferase-DNA X-ray (2.26 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. O6-methyl-guanine in the polymerase template preinsertion site. SNAP output
2hmi immune system-DNA X-ray (2.8 Å) Ding J, Das K, Hsiou Y, Sarafianos SG, Clark Jr AD, Jacobo-Molina A, Tantillo C, Hughes SH, Arnold E (1998) "Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution." J.Mol.Biol., 284, 1095-1111. doi: 10.1006/jmbi.1998.2208. Hiv-1 reverse transcriptase-fragment of fab 28-DNA complex. SNAP output
2hof recombination-DNA X-ray (2.4 Å) Ghosh K, Guo F, Van Duyne GD (2007) "Synapsis of loxP sites by Cre recombinase." J.Biol.Chem., 282, 24004-24016. doi: 10.1074/jbc.M703283200. Crystal structure of the pre-cleavage synaptic complex in the cre-loxp site-specific recombination. SNAP output
2hoi recombination-DNA X-ray (2.601 Å) Ghosh K, Guo F, Van Duyne GD (2007) "Synapsis of loxP sites by Cre recombinase." J.Biol.Chem., 282, 24004-24016. doi: 10.1074/jbc.M703283200. Crystal structure of the tetrameric pre-cleavage synaptic complex in the cre-loxp site-specific recombination. SNAP output
2hos transcription-DNA X-ray (1.9 Å) Simon MD, Feldman ME, Rauh D, Maris AE, Wemmer DE, Shokat KM (2006) "Structure and properties of a re-engineered homeodomain protein-DNA interface." Acs Chem.Biol., 1, 755-760. doi: 10.1021/cb6003756. Phage-selected homeodomain bound to unmodified DNA. SNAP output
2hot transcription-DNA X-ray (2.19 Å) Simon MD, Feldman ME, Rauh D, Maris AE, Wemmer DE, Shokat KM (2006) "Structure and properties of a re-engineered homeodomain protein-DNA interface." Acs Chem.Biol., 1, 755-760. doi: 10.1021/cb6003756. Phage selected homeodomain bound to modified DNA. SNAP output
2hr1 transferase-DNA X-ray (1.96 Å) Shieh FK, Youngblood B, Reich NO (2006) "The Role of Arg165 Towards Base Flipping, Base Stabilization and Catalysis in M.HhaI." J.Mol.Biol., 362, 516-527. doi: 10.1016/j.jmb.2006.07.030. Ternary structure of wt m.hhai c5-cytosine DNA methyltransferase with unmodified DNA and adohcy. SNAP output
2ht0 transcription-DNA X-ray (2.0 Å) Swinger KK, Rice PA (2007) "Structure-based Analysis of HU-DNA Binding." J.Mol.Biol., 365, 1005-1016. doi: 10.1016/j.jmb.2006.10.024. Ihf bound to doubly nicked DNA. SNAP output
2hvh transferase-DNA X-ray (2.492 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. Ddctp:o6meg pair in the polymerase active site (0 position). SNAP output
2hvi transferase-DNA X-ray (1.98 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. Ddctp:g pair in the polymerase active site (0 position). SNAP output
2hvr ligase-RNA-DNA X-ray (2.45 Å) Nandakumar J, Shuman S, Lima CD (2006) "RNA Ligase Structures Reveal the Basis for RNA Specificity and Conformational Changes that Drive Ligation Forward." Cell(Cambridge,Mass.), 127, 71-84. doi: 10.1016/j.cell.2006.08.038. Structure of t4 RNA ligase 2 with nicked 5'-adenylated nucleic acid duplex containing a 3'-deoxyribonucleotide at the nick. SNAP output
2hvs ligase-DNA-RNA X-ray (2.5 Å) Nandakumar J, Shuman S, Lima CD (2006) "RNA Ligase Structures Reveal the Basis for RNA Specificity and Conformational Changes that Drive Ligation Forward." Cell(Cambridge,Mass.), 127, 71-84. doi: 10.1016/j.cell.2006.08.038. Structure of t4 RNA ligase 2 with nicked 5'-adenylated nucleic acid duplex containing a 2'-deoxyribonucleotide at the nick. SNAP output
2hw3 transferase-DNA X-ray (1.98 Å) Warren JJ, Forsberg LJ, Beese LS (2006) "The structural basis for the mutagenicity of O6-methyl-guanine lesions." Proc.Natl.Acad.Sci.Usa, 103, 19701-19706. doi: 10.1073/pnas.0609580103. T:o6-methyl-guanine pair in the polymerase postinsertion site (-1 basepair position). SNAP output
2hzv metal binding protein-DNA X-ray (3.1 Å) Schreiter ER, Wang SC, Zamble DB, Drennan CL (2006) "NikR-operator complex structure and the mechanism of repressor activation by metal ions." Proc.Natl.Acad.Sci.Usa, 103, 13676-13681. doi: 10.1073/pnas.0606247103. Nikr-operator DNA complex. SNAP output
2i05 replication-DNA X-ray (2.6 Å) Oakley AJ, Mulcair MD, Schaeffer PM, Dixon NE "Polarity of Termination of DNA Replication in E. coli." Escherichia coli replication terminator protein (tus) complexed with tera DNA. SNAP output
2i06 replication-DNA X-ray (2.2 Å) Oakley AJ, Mulcair MD, Schaeffer PM, Dixon NE "Polarity of Termination of DNA Replication in E. coli." Escherichia coli replication terminator protein (tus) complexed with DNA- locked form. SNAP output
2i0q structural protein-DNA X-ray (1.91 Å) Buczek P, Horvath MP (2006) "Structural reorganization and the cooperative binding of single-stranded telomere DNA in Sterkiella nova." J.Biol.Chem., 281, 40124-40134. doi: 10.1074/jbc.M607749200. Crystal structure of a telomere single-strand DNA-protein complex from o. nova with full-length alpha and beta telomere proteins. SNAP output
2i13 DNA binding protein-DNA X-ray (1.96 Å) Segal DJ, Crotty JW, Bhakta MS, Barbas CF, Horton NC (2006) "Structure of Aart, a Designed Six-finger Zinc Finger Peptide, Bound to DNA." J.Mol.Biol., 363, 405-421. doi: 10.1016/j.jmb.2006.08.016. Aart, a six finger zinc finger designed to recognize ann triplets. SNAP output
2i3p hydrolase-DNA X-ray (2.3 Å) Rosen LE, Morrison HA, Masri S, Brown MJ, Springstubb B, Sussman D, Stoddard BL, Seligman LM (2006) "Homing endonuclease I-CreI derivatives with novel DNA target specificities." Nucleic Acids Res., 34, 4791-4800. doi: 10.1093/nar/gkl645. K28r mutant of homing endonuclease i-crei. SNAP output
2i3q hydrolase-DNA X-ray (2.3 Å) Rosen LE, Morrison HA, Masri S, Brown MJ, Springstubb B, Sussman D, Stoddard BL, Seligman LM (2006) "Homing endonuclease I-CreI derivatives with novel DNA target specificities." Nucleic Acids Res., 34, 4791-4800. doi: 10.1093/nar/gkl645. Q44v mutant of homing endonuclease i-crei. SNAP output
2i5s hydrolase-DNA X-ray (1.9 Å) Lee JE, Bae E, Bingman CA, Phillips Jr GN, Raines RT (2008) "Structural basis for catalysis by onconase." J.Mol.Biol., 375, 165-177. doi: 10.1016/j.jmb.2007.09.089. Crystal structure of onconase with bound nucleic acid. SNAP output
2i5w hydrolase, lyase-DNA X-ray (2.6 Å) Banerjee A, Verdine GL (2006) "A nucleobase lesion remodels the interaction of its normal neighbor in a DNA glycosylase complex." Proc.Natl.Acad.Sci.Usa, 103, 15020-15025. doi: 10.1073/pnas.0603644103. Structure of hogg1 crosslinked to DNA sampling a normal g adjacent to an oxog. SNAP output
2i9g transferase-DNA X-ray (2.1 Å) Batra VK, Shock DD, Prasad R, Beard WA, Hou EW, Pedersen LC, Sayer JM, Yagi H, Kumar S, Jerina DM, Wilson SH (2006) "Structure of DNA polymerase beta with a benzo[c]phenanthrene diol epoxide-adducted template exhibits mutagenic features." Proc.Natl.Acad.Sci.Usa, 103, 17231-17236. doi: 10.1073/pnas.0605069103. DNA polymerase beta with a benzo[c]phenanthrene diol epoxide adducted guanine base. SNAP output
2i9k transferase-DNA X-ray (2.65 Å) Youngblood B, Shieh FK, De Los Rios S, Perona JJ, Reich NO (2006) "Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI." J.Mol.Biol., 362, 334-346. doi: 10.1016/j.jmb.2006.07.031. Engineered extrahelical base destabilization enhances sequence discrimination of DNA methyltransferase m.hhai. SNAP output
2i9t transcription-DNA X-ray (2.8 Å) Escalante CR, Shen L, Thanos D, Aggarwal AK (2002) "Structure of NF-kappaB p50/p65 heterodimer bound to the PRDII DNA element from the interferon-beta promoter." Structure, 10, 383-391. doi: 10.1016/S0969-2126(02)00723-2. Structure of nf-kb p65-p50 heterodimer bound to prdii element of b-interferon promoter. SNAP output
2ia6 transferase-DNA X-ray (2.5 Å) Bauer J, Xing G, Yagi H, Sayer JM, Jerina DM, Ling H (2007) "A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment." Proc.Natl.Acad.Sci.Usa, 104, 14905-14910. doi: 10.1073/pnas.0700717104. Bypass of major benzopyrene-dg adduct by y-family DNA polymerase with unique structural gap. SNAP output
2ibk transferase-DNA X-ray (2.25 Å) Bauer J, Xing G, Yagi H, Sayer JM, Jerina DM, Ling H (2007) "A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment." Proc.Natl.Acad.Sci.Usa, 104, 14905-14910. doi: 10.1073/pnas.0700717104. Bypass of major benzopyrene-dg adduct by y-family DNA polymerase with unique structural gap. SNAP output
2ibs transferase-DNA X-ray (2.4 Å) Lenz T, Bonnist EYM, Pljevaljcic G, Neely RK, Dryden DTF, Scheidig AJ, Jones AC, Weinhold E (2007) "2-Aminopurine Flipped into the Active Site of the Adenine-Specific DNA Methyltransferase M.TaqI: Crystal Structures and Time-Resolved Fluorescence." J.Am.Chem.Soc., 129, 6240-6248. doi: 10.1021/ja069366n. Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing 2-aminopurine at the target position. SNAP output
2ibt transferase-DNA X-ray (1.7 Å) Lenz T, Bonnist EYM, Pljevaljcic G, Neely RK, Dryden DTF, Scheidig AJ, Jones AC, Weinhold E (2007) "2-Aminopurine Flipped into the Active Site of the Adenine-Specific DNA Methyltransferase M.TaqI: Crystal Structures and Time-Resolved Fluorescence." J.Am.Chem.Soc., 129, 6240-6248. doi: 10.1021/ja069366n. Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing 2-aminopurine at the target position and an abasic site analog at the target base partner position. SNAP output
2ief DNA binding protein-DNA X-ray (2.601 Å) Abbani MA, Papagiannis CV, Sam MD, Cascio D, Johnson RC, Clubb RT (2007) "Structure of the cooperative Xis-DNA complex reveals a micronucleoprotein filament that regulates phage lambda intasome assembly." Proc.Natl.Acad.Sci.Usa, 104, 2109-2114. doi: 10.1073/pnas.0607820104. Structure of the cooperative excisionase (xis)-DNA complex reveals a micronucleoprotein filament. SNAP output
2ih2 transferase-DNA X-ray (1.61 Å) Lenz T, Scheidig AJ, Weinhold E "Influence of the target base partner on the methylation rate of the adenine-specific DNA methyltransferase M.TaqI." Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing 5-methylpyrimidin-2(1h)-one at the target base partner position. SNAP output
2ih4 transferase-DNA X-ray (2.1 Å) Lenz T, Scheidig AJ, Weinhold E "Influence of the target base partner on the methylation rate of the adenine-specific DNA methyltransferase M.TaqI." Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing pyrrolo-dc at the target base partner position. SNAP output
2ih5 transferase-DNA X-ray (1.8 Å) Lenz T, Scheidig AJ, Weinhold E "Influence of the target base partner on the methylation rate of the adenine-specific DNA methyltransferase M.TaqI." Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing an abasic site analog at the target base partner position. SNAP output
2ihm transferase-DNA X-ray (2.4 Å) Moon AF, Garcia-Diaz M, Bebenek K, Davis BJ, Zhong X, Ramsden DA, Kunkel TA, Pedersen LC (2007) "Structural insight into the substrate specificity of DNA Polymerase mu." Nat.Struct.Mol.Biol., 14, 45-53. doi: 10.1038/nsmb1180. Polymerase mu in ternary complex with gapped 11mer DNA duplex and bound incoming nucleotide. SNAP output
2ihn hydrolase-DNA X-ray (3.0 Å) Devos JM, Tomanicek SJ, Jones CE, Nossal NG, Mueser TC (2007) "Crystal structure of bacteriophage T4 5' nuclease in complex with a branched DNA reveals how FEN-1 family nucleases bind their substrates." J.Biol.Chem., 282, 31713-31724. doi: 10.1074/jbc.M703209200. Co-crystal of bacteriophage t4 rnase h with a fork DNA substrate. SNAP output
2iie recombination-DNA X-ray (2.41 Å) Bao Q, Chen H, Liu Y, Yan J, Droge P, Davey CA (2007) "A Divalent Metal-mediated Switch Controlling Protein-induced DNA Bending." J.Mol.Biol., 367, 731-740. doi: 10.1016/j.jmb.2006.09.082. Single chain integration host factor protein (scihf2) in complex with DNA. SNAP output
2iif recombination-DNA X-ray (2.72 Å) Bao Q, Chen H, Liu Y, Yan J, Droge P, Davey CA (2007) "A Divalent Metal-mediated Switch Controlling Protein-induced DNA Bending." J.Mol.Biol., 367, 731-740. doi: 10.1016/j.jmb.2006.09.082. Single chain integration host factor mutant protein (scihf2-k45ae) in complex with DNA. SNAP output
2imw transferase-DNA X-ray (2.05 Å) Fiala KA, Brown JA, Ling H, Kshetry AK, Zhang J, Taylor JS, Yang W, Suo Z (2007) "Mechanism of Template-independent Nucleotide Incorporation Catalyzed by a Template-dependent DNA Polymerase." J.Mol.Biol., 365, 590-602. doi: 10.1016/j.jmb.2006.10.008. Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase. SNAP output
2irf gene regulation-DNA X-ray (2.2 Å) Fujii Y, Shimizu T, Kusumoto M, Kyogoku Y, Taniguchi T, Hakoshima T (1999) "Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences." EMBO J., 18, 5028-5041. doi: 10.1093/emboj/18.18.5028. Crystal structure of an irf-2-DNA complex.. SNAP output
2is1 hydrolase-DNA X-ray (2.9 Å) Lee JY, Yang W (2006) "UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke." Cell(Cambridge,Mass.), 127, 1349-1360. doi: 10.1016/j.cell.2006.10.049. Crystal structure of uvrd-DNA-so4 complex. SNAP output
2is2 hydrolase-DNA X-ray (3.0 Å) Lee JY, Yang W (2006) "UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke." Cell(Cambridge,Mass.), 127, 1349-1360. doi: 10.1016/j.cell.2006.10.049. Crystal structure of uvrd-DNA binary complex. SNAP output
2is4 hydrolase-DNA X-ray (2.6 Å) Lee JY, Yang W (2006) "UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke." Cell(Cambridge,Mass.), 127, 1349-1360. doi: 10.1016/j.cell.2006.10.049. Crystal structure of uvrd-DNA-adpnp ternary complex. SNAP output
2is6 hydrolase-DNA X-ray (2.2 Å) Lee JY, Yang W (2006) "UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke." Cell(Cambridge,Mass.), 127, 1349-1360. doi: 10.1016/j.cell.2006.10.049. Crystal structure of uvrd-DNA-adpmgf3 ternary complex. SNAP output
2iso transferase-DNA X-ray (2.1 Å) Sucato CA, Upton TG, Kashemirov BA, Batra VK, Martinek V, Xiang Y, Beard WA, Pedersen LC, Wilson SH, McKenna CE, Florian J, Warshel A, Goodman MF (2007) "Modifying the beta,gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of DNA Polymerase beta." Biochemistry, 46, 461-471. doi: 10.1021/bi061517b. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-difluoromethylene triphosphate. SNAP output
2isp transferase-DNA X-ray (2.2 Å) Sucato CA, Upton TG, Kashemirov BA, Batra VK, Martinek V, Xiang Y, Beard WA, Pedersen LC, Wilson SH, McKenna CE, Florian J, Warshel A, Goodman MF (2007) "Modifying the beta,gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of DNA Polymerase beta." Biochemistry, 46, 461-471. doi: 10.1021/bi061517b. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-methylene triphosphate. SNAP output
2isz transcription-DNA X-ray (2.403 Å) Wisedchaisri G, Chou CJ, Wu M, Roach C, Rice AE, Holmes RK, Beeson C, Hol WG (2007) "Crystal structures, metal activation, and DNA-binding properties of two-domain IdeR from Mycobacterium tuberculosis." Biochemistry, 46, 436-447. doi: 10.1021/bi0609826. Crystal structure of a two-domain ider-DNA complex crystal form i. SNAP output
2it0 transcription-DNA X-ray (2.6 Å) Wisedchaisri G, Chou CJ, Wu M, Roach C, Rice AE, Holmes RK, Beeson C, Hol WG (2007) "Crystal structures, metal activation, and DNA-binding properties of two-domain IdeR from Mycobacterium tuberculosis." Biochemistry, 46, 436-447. doi: 10.1021/bi0609826. Crystal structure of a two-domain ider-DNA complex crystal form ii. SNAP output
2itl DNA binding protein-DNA X-ray (1.65 Å) Bochkareva E, Martynowski D, Seitova A, Bochkarev A (2006) "Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA." Embo J., 25, 5961-5969. doi: 10.1038/sj.emboj.7601452. The origin binding domain of the sv40 large t antigen bound to the functional pen palindrome DNA (23 bp). SNAP output
2ivh hydrolase X-ray (2.8 Å) Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS (2007) "Structural Basis for Sequence-Dependent DNA Cleavage by Nonspecific Endonucleases." Nucleic Acids Res., 35, 584. doi: 10.1093/NAR/GKL621. Crystal structure of the nuclease domain of cole7 (h545q mutant) in complex with an 18-bp duplex DNA. SNAP output
2ivk hydrolase X-ray (2.9 Å) Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS (2007) "Structural Basis for Sequence-Dependent DNA Cleavage by Nonspecific Endonucleases." Nucleic Acids Res., 35, 584. doi: 10.1093/NAR/GKL621. Crystal structure of the periplasmic endonuclease vvn complexed with a 16-bp DNA. SNAP output
2j6s transferase-DNA X-ray (2.5 Å) Eoff RL, Irimia A, Egli M, Guengerich FP (2007) "Sulfolobus Solfataricus DNA Polymerase Dpo4 is Partially Inhibited by "Wobble" Pairing between O6- Methylguanine and Cytosine, But Accurate Bypass is Preferred." J.Biol.Chem., 282, 1456. doi: 10.1074/JBC.M609661200. Ternary complex of sulfolobus solfataricus dpo4 DNA polymerase, o6- methylguanine modified DNA, and datp.. SNAP output
2j6t transferase-DNA X-ray (2.6 Å) Eoff RL, Irimia A, Egli M, Guengerich FP (2007) "Sulfolobus Solfataricus DNA Polymerase Dpo4 is Partially Inhibited by "Wobble" Pairing between O6- Methylguanine and Cytosine, But Accurate Bypass is Preferred." J.Biol.Chem., 282, 1456. doi: 10.1074/JBC.M609661200. Ternary complex of sulfolobus solfataricus dpo4 DNA polymerase, o6- methylguanine modified DNA, and datp.. SNAP output
2j6u transferase-DNA X-ray (2.5 Å) Eoff RL, Irimia A, Egli M, Guengerich FP (2007) "Sulfolobus Solfataricus DNA Polymerase Dpo4 is Partially Inhibited by "Wobble" Pairing between O6- Methylguanine and Cytosine, But Accurate Bypass is Preferred." J.Biol.Chem., 282, 1456. doi: 10.1074/JBC.M609661200. Ternary complex of sulfolobus solfataricus dpo4 DNA polymerase, o6- methylguanine modified DNA, and dgtp.. SNAP output
2ja5 transferase X-ray (3.8 Å) Brueckner F, Hennecke U, Carell T, Cramer P (2007) "Cpd Damage Recognition by Transcribing RNA Polymerase II." Science, 315, 859. doi: 10.1126/SCIENCE.1135400. Cpd lesion containing RNA polymerase ii elongation complex a. SNAP output
2ja6 transferase X-ray (4.0 Å) Brueckner F, Hennecke U, Carell T, Cramer P (2007) "CPD damage recognition by transcribing RNA polymerase II." Science, 315, 859-862. doi: 10.1126/science.1135400. Cpd lesion containing RNA polymerase ii elongation complex b. SNAP output
2ja7 transferase X-ray (3.8 Å) Brueckner F, Hennecke U, Carell T, Cramer P (2007) "Cpd Damage Recognition by Transcribing RNA Polymerase II." Science, 315, 859. doi: 10.1126/SCIENCE.1135400. Cpd lesion containing RNA polymerase ii elongation complex c. SNAP output
2ja8 transferase X-ray (3.8 Å) Brueckner F, Hennecke U, Carell T, Cramer P (2007) "Cpd Damage Recognition by Transcribing RNA Polymerase II." Science, 315, 859. doi: 10.1126/SCIENCE.1135400. Cpd lesion containing RNA polymerase ii elongation complex d. SNAP output
2jef transferase-DNA X-ray (2.17 Å) Eoff RL, Angel KC, Egli M, Guengerich FP (2007) "Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus Solfataricus DNA Polymerase Dpo4: Steady-State and Pre-Steady-State Kinetics and X-Ray Crystallography of Correct and Incorrect Pairing." J.Biol.Chem., 282, 13573. doi: 10.1074/JBC.M700656200. The molecular basis of selectivity of nucleotide triphosphate incorporation opposite o6-benzylguanine by sulfolobus solfataricus DNA polymerase iv: steady-state and pre-steady-state and x-ray crystallography of correct and incorrect pairing. SNAP output
2jeg transferase X-ray (2.38 Å) Eoff RL, Angel KC, Egli M, Guengerich FP (2007) "Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus Solfataricus DNA Polymerase Dpo4: Steady-State and Pre-Steady-State Kinetics and X-Ray Crystallography of Correct and Incorrect Pairing." J.Biol.Chem., 282, 13573. doi: 10.1074/JBC.M700656200. The molecular basis of selectivity of nucleoside triphosphate incorporation opposite o6-benzylguanine by sulfolobus solfataricus DNA polymerase iv: steady-state and pre-steady-state kinetics and x- ray crystallography of correct and incorrect pairing. SNAP output
2jei transferase X-ray (2.39 Å) Eoff RL, Angel KC, Egli M, Guengerich FP (2007) "Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus Solfataricus DNA Polymerase Dpo4: Steady-State and Pre-Steady-State Kinetics and X-Ray Crystallography of Correct and Incorrect Pairing." J.Biol.Chem., 282, 13573. doi: 10.1074/JBC.M700656200. The molecular basis of selectivity of nucleoside triphosphate incorporation opposite o6-benzylguanine by sulfolobus solfataricus DNA polymerase iv: steady-state and pre-steady-state kinetics and x- ray crystallography of correct and incorrect pairing. SNAP output
2jej transferase X-ray (1.86 Å) Eoff RL, Angel KC, Egli M, Guengerich FP (2007) "Molecular Basis of Selectivity of Nucleoside Triphosphate Incorporation Opposite O6-Benzylguanine by Sulfolobus Solfataricus DNA Polymerase Dpo4: Steady-State and Pre-Steady-State Kinetics and X-Ray Crystallography of Correct and Incorrect Pairing." J.Biol.Chem., 282, 13573. doi: 10.1074/JBC.M700656200. The molecular basis of selectivity of nucleoside triphosphate incorporation opposite o6-benzylguanine by sulfolobus solfataricus DNA polymerase iv: steady-state and pre-steady-state kinetics and x- ray crystallography of correct and incorrect pairing. SNAP output
2jg3 transferase-DNA X-ray (1.9 Å) Pljevaljcic G, Schmidt F, Scheidig AJ, Lurz R, Weinhold E (2007) "Quantitative Labeling of Long Plasmid DNA with Nanometer Precision." Chembiochem, 8, 1516. doi: 10.1002/CBIC.200700294. Mtaqi with baz. SNAP output
2jlg transferase X-ray (2.8 Å) Poranen MM, Salgado PS, Koivunen MRL, Wright S, Bamford DH, Stuart DI, Grimes JM (2008) "Structural Explanation for the Role of Mn2+ in the Activity of {Phi}6 RNA-Dependent RNA Polymerase." Nucleic Acids Res., 36, 6633. doi: 10.1093/NAR/GKN632. Structural explanation for the role of mn in the activity of phi6 RNA-dependent RNA polymerase. SNAP output
2jp9 transcription-DNA NMR Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA, Dyson HJ, Wright PE (2007) "Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA." J.Mol.Biol., 372, 1227-1245. doi: 10.1016/j.jmb.2007.07.017. Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA. SNAP output
2jpa transcription-DNA NMR Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA, Dyson HJ, Wright PE (2007) "Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA." J.Mol.Biol., 372, 1227-1245. doi: 10.1016/j.jmb.2007.07.017. Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA. SNAP output
2jx1 transcription-DNA NMR Gamsjaeger R, Swanton MK, Kobus FJ, Lehtomaki E, Lowry JA, Kwan AH, Matthews JM, Mackay JP "Structure of the fifth zinc finger of Myelin Transcription Factor 1 in complex with RARE DNA." Structure of the fifth zinc finger of myelin transcription factor 1 in complex with rare DNA. SNAP output
2jxi DNA binding protein, DNA NMR Halouska S, Zhou Y, Becker DF, Powers R (2008) "Solution structure of the Pseudomonas putida protein PpPutA45 and its DNA complex." Proteins, 75, 12-27. doi: 10.1002/prot.22217. Solution structure of the DNA-binding domain of pseudomonas putida proline utilization a (puta) bound to gttgca DNA sequence. SNAP output
2jzw viral protein-DNA NMR Bourbigot S, Ramalanjaona N, Boudier C, Salgado GF, Roques BP, Mely Y, Bouaziz S, Morellet N (2008) "How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription." J.Mol.Biol., 383, 1112-1128. doi: 10.1016/j.jmb.2008.08.046. How the hiv-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription. SNAP output
2k1n transcription-DNA NMR Sullivan DM, Bobay BG, Kojetin DJ, Thompson RJ, Rance M, Strauch MA, Cavanagh J (2008) "Insights into the Nature of DNA Binding of AbrB-like Transcription Factors." Structure, 16, 1702-1713. doi: 10.1016/j.str.2008.08.014. DNA bound structure of the n-terminal domain of abrb. SNAP output
2k7f replication-DNA NMR Kobayashi M, Ab E, Bonvin AM, Siegal G (2010) "Structure of the DNA-bound BRCA1 C-terminal region from human replication factor C p140 and model of the protein-DNA complex." J.Biol.Chem., 285, 10087-10097. doi: 10.1074/jbc.M109.054106. Haddock calculated model of the complex between the brct region of rfc p140 and dsDNA. SNAP output
2kae transcription-DNA NMR Lowry JA, Gamsjaeger R, Thong SY, Hung W, Kwan AH, Broitman-Maduro G, Matthews JM, Maduro M, Mackay JP (2009) "Structural Analysis of MED-1 Reveals Unexpected Diversity in the Mechanism of DNA Recognition by GATA-type Zinc Finger Domains." J.Biol.Chem., 284, 5827-5835. doi: 10.1074/jbc.M808712200. Data-driven model of med1:DNA complex. SNAP output
2kdz transcription-DNA NMR Lou YC, Wei SY, Rajasekaran M, Chou CC, Hsu HM, Tai JH, Chen C (2009) "NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis." Nucleic Acids Res. doi: 10.1093/nar/gkp097. Structure of the r2r3 DNA binding domain of myb1 protein from protozoan parasite trichomonas vaginalis in complex with mre-1-mre-2r DNA. SNAP output
2kei transcription-DNA NMR Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk H, Bonvin AM, Kaptein R, Boelens R (2009) "Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes." J.Mol.Biol., 390, 478-489. doi: 10.1016/j.jmb.2009.05.022. Refined solution structure of a dimer of lac repressor DNA-binding domain complexed to its natural operator o1. SNAP output
2kej transcription-DNA NMR Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk H, Bonvin AM, Kaptein R, Boelens R (2009) "Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes." J.Mol.Biol., 390, 478-489. doi: 10.1016/j.jmb.2009.05.022. Solution structure of a dimer of lac repressor DNA-binding domain complexed to its natural operator o2. SNAP output
2kek transcription-DNA NMR Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk H, Bonvin AM, Kaptein R, Boelens R (2009) "Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes." J.Mol.Biol., 390, 478-489. doi: 10.1016/j.jmb.2009.05.022. Solution structure of a dimer of lac repressor DNA-binding domain complexed to its natural operator o3. SNAP output
2kfn transferase-DNA X-ray (2.03 Å) Brautigam CA, Sun S, Piccirilli JA, Steitz TA (1999) "Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli." Biochemistry, 38, 696-704. doi: 10.1021/bi981537g. Klenow fragment with bridging-sulfur substrate and manganese. SNAP output
2kfz transferase-DNA X-ray (2.03 Å) Brautigam CA, Sun S, Piccirilli JA, Steitz TA (1999) "Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli." Biochemistry, 38, 696-704. doi: 10.1021/bi981537g. Klenow fragment with bridging-sulfur substrate and zinc only. SNAP output
2kkf DNA binding protein-DNA NMR Cierpicki T, Risner LE, Grembecka J, Lukasik SM, Popovic R, Omonkowska M, Shultis DD, Zeleznik-Le NJ, Bushweller JH (2010) "Structure of the MLL CXXC domain-DNA complex and its functional role in MLL-AF9 leukemia." Nat.Struct.Mol.Biol., 17, 62-68. doi: 10.1038/nsmb.1714. Solution structure of mll cxxc domain in complex with palindromic cpg DNA. SNAP output
2kmk DNA binding protein-DNA NMR Lee S, Doddapaneni K, Hogue A, McGhee L, Meyers S, Wu Z (2010) "Solution structure of Gfi-1 zinc domain bound to consensus DNA." J.Mol.Biol., 397, 1055-1066. doi: 10.1016/j.jmb.2010.02.006. Gfi-1 zinc fingers 3-5 complexed with DNA. SNAP output
2kn7 hydrolase-DNA NMR Das D, Folkers GE, van Dijk M, Jaspers NGJ, Hoeijmakers JHJ, Kaptein R, Boelens R (2012) "The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition." Structure, 20, 667-675. doi: 10.1016/j.str.2012.02.009. Structure of the xpf-single strand DNA complex. SNAP output
2ko0 transcription-DNA NMR Campagne S, Saurel O, Gervais V, Milon A (2010) "Structural determinants of specific DNA-recognition by the THAP zinc finger." Nucleic Acids Res. doi: 10.1093/nar/gkq053. Solution structure of the thap zinc finger of thap1 in complex with its DNA target. SNAP output
2ktq transferase-DNA X-ray (2.3 Å) Li Y, Korolev S, Waksman G (1998) "Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation." EMBO J., 17, 7514-7525. doi: 10.1093/emboj/17.24.7514. Open ternary complex of the large fragment of DNA polymerase i from thermus aquaticus. SNAP output
2kv6 DNA binding protein-DNA NMR Huang H, Kozekov ID, Kozekova A, Rizzo CJ, McCullough AK, Lloyd RS, Stone MP (2010) "Minor Groove Orientation of the KWKK Peptide Tethered via the N-Terminal Amine to the Acrolein-Derived 1,N(2)-gamma-Hydroxypropanodeoxyguanosine Lesion with a Trimethylene Linkage ." Biochemistry, 49, 6155-6164. doi: 10.1021/bi100364f. Tetrapeptide kwkk conjugated to oligonucleotide duplex by a trimethylene tether. SNAP output
2ky8 transcription-DNA NMR Scarsdale JN, Webb HD, Ginder GD, Williams DC (2011) "Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence." Nucleic Acids Res., 39, 6741-6752. doi: 10.1093/nar/gkr262. Solution structure and dynamic analysis of chicken mbd2 methyl binding domain bound to a target methylated DNA sequence. SNAP output
2kzm transferase-DNA X-ray (2.6 Å) Brautigam CA, Sun S, Piccirilli JA, Steitz TA (1999) "Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli." Biochemistry, 38, 696-704. doi: 10.1021/bi981537g. Klenow fragment with normal substrate and zinc and manganese. SNAP output
2kzz transferase-DNA X-ray (2.25 Å) Brautigam CA, Sun S, Piccirilli JA, Steitz TA (1999) "Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli." Biochemistry, 38, 696-704. doi: 10.1021/bi981537g. Klenow fragment with normal substrate and zinc only. SNAP output
2l1g transcription-DNA NMR Campagne S, Gervais V, Saurel O, Milon A "RDC refined solution structure of the THAP zinc finger of THAP1 in complex with its 16bp RRM1 DNA target." Rdc refined solution structure of the thap zinc finger of thap1 in complex with its 16bp rrm1 DNA target. SNAP output
2l45 viral protein-DNA NMR Quintal S, Viegas A, Erhardt S, Cabrita EJ, Farrell NP (2012) "Platinated DNA affects zinc finger conformation. Interaction of a platinated single-stranded oligonucleotide and the C-terminal zinc finger of nucleocapsid protein HIVNCp7." Biochemistry, 51, 1752-1761. doi: 10.1021/bi201834g. C-terminal zinc knuckle of the hivncp7 with DNA. SNAP output
2l46 viral protein-DNA NMR Quintal S, Viegas A, Erhardt S, Cabrita EJ, Farrell NP (2012) "Platinated DNA affects zinc finger conformation. Interaction of a platinated single-stranded oligonucleotide and the C-terminal zinc finger of nucleocapsid protein HIVNCp7." Biochemistry, 51, 1752-1761. doi: 10.1021/bi201834g. C-terminal zinc finger of the hivncp7 with platinated DNA. SNAP output
2l4l viral protein-DNA NMR Bazzi A, Zargarian L, Chaminade F, Boudier C, De Rocquigny H, Rene B, Mely Y, Fosse P, Mauffret O (2011) "Structural insights into the cTAR DNA recognition by the HIV-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC." Nucleic Acids Res., 39, 3903-3916. doi: 10.1093/nar/gkq1290. Structural insights into the ctar DNA recognition by the hiv-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of nc. SNAP output
2ld5 transcription-DNA NMR Zhang Y, Larsen CA, Stadler HS, Ames JB (2011) "Structural basis for sequence specific DNA binding and protein dimerization of HOXA13." Plos One, 6, e23069. doi: 10.1371/journal.pone.0023069. Solution NMR-derived complex structure of hoxa13 DNA binding domain bound to DNA. SNAP output
2lef gene regulation-DNA NMR Love JJ, Li X, Case DA, Giese K, Grosschedl R, Wright PE (1995) "Structural basis for DNA bending by the architectural transcription factor LEF-1." Nature, 376, 791-795. doi: 10.1038/376791a0. Lef1 hmg domain (from mouse), complexed with DNA (15bp), NMR, 12 structures. SNAP output
2lev transcription regulator-DNA multiple methods: solution nmr, solution scattering Cordeiro TN, Schmidt H, Madrid C, Juarez A, Bernado P, Griesinger C, Garcia J, Pons M (2011) "Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler." Plos Pathog., 7, e1002380. doi: 10.1371/journal.ppat.1002380. Structure of the DNA complex of the c-terminal domain of ler. SNAP output
2lex transcription-DNA NMR Yamasaki K, Kigawa T, Watanabe S, Inoue M, Yamasaki T, Seki M, Shinozaki K, Yokoyama S (2012) "Structural basis for sequence-spscific DNA recognition by an Arabidopsis WRKY transcription factor." J.Biol.Chem. doi: 10.1074/jbc.M111.279844. Complex of the c-terminal wrky domain of atwrky4 and a w-box DNA. SNAP output
2lkx transcription-DNA NMR Chaney BA, Clark-Baldwin K, Dave V, Ma J, Rance M (2005) "Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome." Biochemistry, 44, 7497-7511. doi: 10.1021/bi0473253. NMR structure of the homeodomain of pitx2 in complex with a taatcc DNA binding site. SNAP output
2lt7 metal binding protein-DNA NMR Buck-Koehntop BA, Stanfield RL, Ekiert DC, Martinez-Yamout MA, Dyson HJ, Wilson IA, Wright PE (2012) "Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso." Proc.Natl.Acad.Sci.USA, 109, 15229-15234. doi: 10.1073/pnas.1213726109. Solution NMR structure of kaiso zinc finger DNA binding domain in complex with kaiso binding site DNA. SNAP output
2ltt transcription, DNA binding protein-DNA NMR Rossi P, Barbieri CM, Aramini JM, Bini E, Lee HW, Janjua H, Xiao R, Acton TB, Montelione GT (2013) "Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome." Nucleic Acids Res., 41, 2756-2768. doi: 10.1093/nar/gks1348. Solution NMR structure of ydbc:dt19g1 complex. northeast structural genomics consortium (nesg) target kr150. SNAP output
2m2w transferase-DNA NMR Wu WJ, Su MI, Wu JL, Kumar S, Lim LH, Wang CW, Nelissen FH, Chen MC, Doreleijers JF, Wijmenga SS, Tsai MD (2014) "How a low-fidelity DNA polymerase chooses non-Watson-Crick from Watson-Crick incorporation." J.Am.Chem.Soc., 136, 4927-4937. doi: 10.1021/ja4102375. Ternary complex of asfv pol x with DNA and mgdgtp. SNAP output
2map transcription-DNA NMR Campagne S, Marsh ME, Capitani G, Vorholt JA, Allain FH (2014) "Structural basis for -10 promoter element melting by environmentally induced sigma factors." Nat.Struct.Mol.Biol., 21, 269-276. doi: 10.1038/nsmb.2777. Solution structure of the complex formed by the region 2 of e. coli sigmae and its cognate -10 promoter element non template strand tgtcaaa.. SNAP output
2me6 transcription-DNA NMR Proudfoot A, Wuthrich K, Serrano P, Geralt M "NMR Structure of the homeodomain transcription factor Gbx1 from Homo sapiens in complex with the DNA sequence CGACTAATTAGTCG." NMR structure of the homeodomain transcription factor gbx1 from homo sapiens in complex with the DNA sequence cgactaattagtcg. SNAP output
2mf8 metal binding protein-DNA NMR Gamsjaeger R, O'Connell MR, Cubeddu L, Shepherd NE, Lowry JA, Kwan AH, Vandevenne M, Swanton MK, Matthews JM, Mackay JP (2013) "A structural analysis of DNA binding by myelin transcription factor 1 double zinc fingers." J.Biol.Chem., 288, 35180-35191. doi: 10.1074/jbc.M113.482075. Haddock model of myt1 f4f5 - DNA complex. SNAP output
2mna DNA binding protein-DNA NMR Gamsjaeger R, Kariawasam R, Gimenez AX, Touma C, McIlwain E, Bernardo RE, Shepherd NE, Ataide SF, Dong Q, Richard DJ, White MF, Cubeddu L (2015) "The structural basis of DNA binding by the single-stranded DNA-binding protein from Sulfolobus solfataricus." Biochem.J., 465, 337-346. doi: 10.1042/BJ20141140. The structural basis of DNA binding by the single-stranded DNA-binding protein from sulfolobus solfataricus. SNAP output
2moe hydrolase-DNA NMR Walavalkar NM, Cramer JM, Buchwald WA, Scarsdale JN, Williams DC (2015) "Solution structure and intramolecular exchange of methyl-cytosine binding domain protein 4 (MBD4) on DNA suggests a mechanism to scan for mCpG/TpG mismatches." Nucleic Acids Res., 42, 11218-11232. doi: 10.1093/nar/gku782. Solution structure of mbd4 methyl-cytosine binding domain bound to methylated DNA. SNAP output
2mru DNA binding protein-DNA NMR Zorzini V, Buts L, Schrank E, Sterckx YG, Respondek M, Engelberg-Kulka H, Loris R, Zangger K, van Nuland NA (2015) "Escherichia coli antitoxin MazE as transcription factor: insights into MazE-DNA binding." Nucleic Acids Res., 43, 1241-1256. doi: 10.1093/nar/gku1352. Structure of truncated ecmaze-DNA complex. SNAP output
2mxf transcription regulator-DNA NMR Ding P, McFarland KA, Jin S, Tong G, Duan B, Yang A, Hughes TR, Liu J, Dove SL, Navarre WW, Xia B (2015) "A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT." Plos Pathog., 11, e1004967. doi: 10.1371/journal.ppat.1004967. Structure of the DNA complex of the c-terminal domain of mvat. SNAP output
2n21 hydrolase-DNA NMR Heddi B, Cheong VV, Martadinata H, Phan AT (2015) "Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide-quadruplex complex." Proc.Natl.Acad.Sci.USA. doi: 10.1073/pnas.1422605112. Solution structure of complex between DNA g-quadruplex and g-quadruplex recognition domain of rhau. SNAP output
2n8a transferase NMR Eustermann S, Wu WF, Langelier MF, Yang JC, Easton LE, Riccio AA, Pascal JM, Neuhaus D (2015) "Structural Basis of Detection and Signaling of DNA Single-Strand Breaks by Human PARP-1." Mol.Cell, 60, 742-754. doi: 10.1016/j.molcel.2015.10.032. 1h, 13c and 15n chemical shift assignments and solution structure for parp-1 f1f2 domains in complex with a DNA single-strand break. SNAP output
2nbj DNA binding protein-DNA NMR Paquet F, Loth K, Landon C "First 3D structure of an atypical protein-DNA complex." DNA-archeal mc1 protein complex structure by NMR. SNAP output
2nl8 DNA binding protein-DNA X-ray (2.3 Å) Bochkareva E, Martynowski D, Seitova A, Bochkarev A (2006) "Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA." Embo J., 25, 5961-5969. doi: 10.1038/sj.emboj.7601452. The origin binding domain of the sv40 large t antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3). SNAP output
2nll transcription-DNA X-ray (1.9 Å) Rastinejad F, Perlmann T, Evans RM, Sigler PB (1995) "Structural determinants of nuclear receptor assembly on DNA direct repeats." Nature, 375, 203-211. doi: 10.1038/375203a0. Retinoid x receptor-thyroid hormone receptor DNA-binding domain heterodimer bound to thyroid response element DNA. SNAP output
2nmv hydrolase-DNA X-ray (2.95 Å) Waters TR, Eryilmaz J, Geddes S, Barrett TE (2006) "Damage detection by the UvrABC pathway: crystal structure of UvrB bound to fluorescein-adducted DNA." Febs Lett., 580, 6423-6427. doi: 10.1016/j.febslet.2006.10.051. Damage detection by the uvrabc pathway: crystal structure of uvrb bound to fluorescein-adducted DNA. SNAP output
2nny transcription-DNA X-ray (2.58 Å) Lamber EP, Vanhille L, Textor LC, Kachalova GS, Sieweke MH, Wilmanns M (2008) "Regulation of the transcription factor Ets-1 by DNA-mediated homo-dimerization." Embo J., 27, 2006-2017. doi: 10.1038/emboj.2008.117. Crystal structure of the ets1 dimer DNA complex.. SNAP output
2nob hydrolase, lyase-DNA X-ray (2.1 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of catalytically inactive h270a human 8-oxoguanine glycosylase crosslinked to 8-oxoguanine DNA. SNAP output
2noe hydrolase, lyase-DNA X-ray (2.2 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of catalytically inactive g42a human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA. SNAP output
2nof hydrolase, lyase-DNA X-ray (2.35 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of q315f human 8-oxoguanine glycosylase proximal crosslink to 8-oxoguanine DNA. SNAP output
2noh hydrolase, lyase-DNA X-ray (2.01 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of catalytically inactive q315a human 8-oxoguanine glycosylase complexed to 8-oxoguanine DNA. SNAP output
2noi hydrolase, lyase-DNA X-ray (2.35 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of g42a human 8-oxoguanine glycosylase crosslinked to undamaged g-containing DNA. SNAP output
2nol hydrolase, lyase-DNA X-ray (2.57 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of catalytically inactive human 8-oxoguanine glycosylase distal crosslink to oxog DNA. SNAP output
2noz hydrolase, lyase-DNA X-ray (2.43 Å) Radom CT, Banerjee A, Verdine GL (2007) "Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations." J.Biol.Chem., 282, 9182-9194. doi: 10.1074/jbc.M608989200. Structure of q315f human 8-oxoguanine glycosylase distal crosslink to 8-oxoguanine DNA. SNAP output
2np2 DNA binding protein-DNA X-ray (3.02 Å) Mouw KW, Rice PA (2007) "Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA-bending protein Hbb." Mol.Microbiol., 63, 1319-1330. doi: 10.1111/j.1365-2958.2007.05586.x. Hbb-DNA complex. SNAP output
2np6 transferase-DNA X-ray (2.1 Å) Lenz T, Scheidig AJ, Weinhold E "Caught in the act II: Visualization of an intermediate in the DNA base-flipping pathway induced by the adenine-specific DNA methyltransferase M.TaqI." Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing an abasic site analog at the target position. SNAP output
2np7 transferase-DNA X-ray (1.9 Å) Lenz T, Scheidig AJ, Weinhold E "Caught in the act II: Visualization of an intermediate in the DNA base-flipping pathway induced by the adenine-specific DNA methyltransferase M.TaqI." Crystal structure of the adenine-specific DNA methyltransferase m.taqi complexed with the cofactor analog aeta and a 10 bp DNA containing an abasic site analog at the target position and pyrrolo-dc at the target base partner position. SNAP output
2nq9 hydrolase-DNA X-ray (1.45 Å) Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Bjoras M, Cunningham RP, Tainer JA (2008) "DNA apurinic-apyrimidinic site binding and excision by endonuclease IV." Nat.Struct.Mol.Biol., 15, 515-522. doi: 10.1038/nsmb.1414. High resolution crystal structure of escherichia coli endonuclease iv (endo iv) y72a mutant bound to damaged DNA. SNAP output
2nqb structural protein-DNA X-ray (2.3 Å) Chakravarthy S, Luger K "Comparative analysis of nucleosome structures from different species." Drosophila nucleosome structure. SNAP output
2nqj hydrolase X-ray (2.45 Å) Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Bjoras M, Cunningham RP, Tainer JA (2008) "DNA apurinic-apyrimidinic site binding and excision by endonuclease IV." Nat.Struct.Mol.Biol., 15, 515-522. doi: 10.1038/nsmb.1414. Crystal structure of escherichia coli endonuclease iv (endo iv) e261q mutant bound to damaged DNA. SNAP output
2nra replication-DNA X-ray (3.1 Å) Swan MK, Bastia D, Davies C (2006) "Crystal structure of pi initiator protein-iteron complex of plasmid R6K: implications for initiation of plasmid DNA replication." Proc.Natl.Acad.Sci.Usa, 103, 18481-18486. doi: 10.1073/pnas.0609046103. Crystal structure of pi initiator protein in complex with iteron DNA. SNAP output
2ntc DNA binding protein-DNA X-ray (2.4 Å) Meinke G, Phelan P, Moine S, Bochkareva E, Bochkarev A, Bullock PA, Bohm A (2007) "The Crystal Structure of the SV40 T-Antigen Origin Binding Domain in Complex with DNA." Plos Biol., 5, e23. doi: 10.1371/journal.pbio.0050023. Crystal structure of sv40 large t antigen origin binding domain with DNA. SNAP output
2ntz cell cycle-DNA X-ray (3.35 Å) Schumacher MA, Mansoor A, Funnell BE (2007) "Structure of a four-way bridged ParB-DNA complex provides insight into P1 segrosome assembly." J.Biol.Chem., 282, 10456-10464. doi: 10.1074/jbc.M610603200. Structure of a parb-DNA complex reveals a double b-box interaction. SNAP output
2nvq transcription,transferase-DNA-RNA hybrid X-ray (2.9 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex in 150 mm mg+2 with 2'dutp. SNAP output
2nvt transcription,transferase-DNA-RNA hybrid X-ray (3.36 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex in 150 mm mg+2 with gmpcpp. SNAP output
2nvx transcription,transferase-DNA-RNA hybrid X-ray (3.6 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex in 5 mm mg+2 with 2'-dutp. SNAP output
2nvz transcription,transferase-DNA-RNA hybrid X-ray (4.3 Å) Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD (2006) "Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis." Cell(Cambridge,Mass.), 127, 941-954. doi: 10.1016/j.cell.2006.11.023. RNA polymerase ii elongation complex with utp, updated 11-2006. SNAP output
2nzd structural protein-DNA X-ray (2.65 Å) Ong MS, Richmond TJ, Davey CA (2007) "DNA stretching and extreme kinking in the nucleosome core." J.Mol.Biol., 368, 1067-1074. doi: 10.1016/j.jmb.2007.02.062. Nucleosome core particle containing 145 bp of DNA. SNAP output
2o19 isomerase-DNA X-ray (2.45 Å) Changela A, Digate RJ, Mondragon A (2007) "Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate." J.Mol.Biol., 368, 105-118. doi: 10.1016/j.jmb.2007.01.065. Structure of e. coli topoisomersae iii in complex with an 8-base single stranded oligonucleotide. frozen in glycerol at ph 5.5. SNAP output
2o49 transcription-DNA X-ray (2.0 Å) Yamasaki K, Akiba T, Yamasaki T, Harata K (2007) "Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1." Nucleic Acids Res., 35, 5073-5084. doi: 10.1093/nar/gkm504. Crystal structure of the n-terminal cut domain of satb1 bound to matrix attachment region DNA. SNAP output
2o4a transcription-DNA X-ray (1.75 Å) Yamasaki K, Akiba T, Yamasaki T, Harata K (2007) "Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1." Nucleic Acids Res., 35, 5073-5084. doi: 10.1093/nar/gkm504. Crystal structure of the n-terminal cut domain of satb1 bound to matrix attachment region DNA. SNAP output
2o4i hydrolase-DNA X-ray (3.5 Å) Brucet M, Querol-Audi J, Serra M, Ramirez-Espain X, Bertlik K, Ruiz L, Lloberas J, Macias MJ, Fita I, Celada A (2007) "Structure of the dimeric exonuclease TREX1 in complex with DNA displays a proline-rich binding site for WW Domains." J.Biol.Chem., 282, 14547-14557. doi: 10.1074/jbc.M700236200. Structure of trex1 in complex with DNA. SNAP output
2o54 isomerase-DNA X-ray (2.5 Å) Changela A, Digate RJ, Mondragon A (2007) "Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate." J.Mol.Biol., 368, 105-118. doi: 10.1016/j.jmb.2007.01.065. Structure of e. coli topoisomerase iii in complex with an 8-base single stranded oligonucleotide. frozen in glycerol at ph 7.0. SNAP output
2o59 isomerase-DNA X-ray (2.5 Å) Changela A, Digate RJ, Mondragon A (2007) "Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate." J.Mol.Biol., 368, 105-118. doi: 10.1016/j.jmb.2007.01.065. Structure of e. coli topoisomerase iii in complex with an 8-base single stranded oligonucleotide. frozen in glycerol ph 8.0. SNAP output
2o5c isomerase-DNA X-ray (2.35 Å) Changela A, Digate RJ, Mondragon A (2007) "Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate." J.Mol.Biol., 368, 105-118. doi: 10.1016/j.jmb.2007.01.065. Structure of e. coli topoisomerase iii in complex with an 8-base single stranded oligonucleotide. frozen in glucose ph 5.5. SNAP output
2o5e isomerase-DNA X-ray (2.5 Å) Changela A, Digate RJ, Mondragon A (2007) "Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate." J.Mol.Biol., 368, 105-118. doi: 10.1016/j.jmb.2007.01.065. Structure of e. coli topoisomerase iii in complex with an 8-base single stranded oligonucleotide. frozen in glucose ph 7.0. SNAP output
2o5i transferase-DNA-RNA hybrid X-ray (2.5 Å) Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I (2007) "Structural basis for transcription elongation by bacterial RNA polymerase." Nature, 448, 157-162. doi: 10.1038/nature05932. Crystal structure of the t. thermophilus RNA polymerase elongation complex. SNAP output
2o5j transferase-DNA-RNA hybrid X-ray (3.0 Å) Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R (2007) "Structural basis for substrate loading in bacterial RNA polymerase." Nature, 448, 163-168. doi: 10.1038/nature05931. Crystal structure of the t. thermophilus rnap polymerase elongation complex with the ntp substrate analog. SNAP output
2o61 transcription-DNA X-ray (2.8 Å) Panne D, Maniatis T, Harrison SC (2007) "An Atomic Model of the Interferon-beta Enhanceosome." Cell(Cambridge,Mass.), 129, 1111-1123. doi: 10.1016/j.cell.2007.05.019. Crystal structure of nfkb, irf7, irf3 bound to the interferon-b enhancer. SNAP output
2o6g transcription-DNA X-ray (3.1 Å) Panne D, Maniatis T, Harrison SC (2007) "An Atomic Model of the Interferon-beta Enhanceosome." Cell(Cambridge,Mass.), 129, 1111-1123. doi: 10.1016/j.cell.2007.05.019. Crystal structure of irf-3 bound to the interferon-b enhancer. SNAP output
2o6m hydrolase-DNA X-ray (2.3 Å) Eastberg JH, Eklund J, Monnat R, Stoddard BL (2007) "Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism." Biochemistry, 46, 7215-7225. doi: 10.1021/bi700418d. H98q mutant of the homing endonuclease i-ppoi complexed with DNA. SNAP output
2o8b DNA binding protein-DNA X-ray (2.75 Å) Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich PL, Beese LS (2007) "Structure of the Human MutSalpha DNA Lesion Recognition Complex." Mol.Cell, 26, 579-592. doi: 10.1016/j.molcel.2007.04.018. Human mutsalpha (msh2-msh6) bound to adp and a g t mispair. SNAP output
2o8c DNA binding protein-DNA X-ray (3.37 Å) Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich PL, Beese LS (2007) "Structure of the Human MutSalpha DNA Lesion Recognition Complex." Mol.Cell, 26, 579-592. doi: 10.1016/j.molcel.2007.04.018. Human mutsalpha (msh2-msh6) bound to adp and an o6-methyl-guanine t mispair. SNAP output
2o8d DNA binding protein-DNA X-ray (3.0 Å) Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich PL, Beese LS (2007) "Structure of the Human MutSalpha DNA Lesion Recognition Complex." Mol.Cell, 26, 579-592. doi: 10.1016/j.molcel.2007.04.018. Human mutsalpha (msh2-msh6) bound to adp and a g du mispair. SNAP output
2o8e DNA binding protein-DNA X-ray (3.3 Å) Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich PL, Beese LS (2007) "Structure of the Human MutSalpha DNA Lesion Recognition Complex." Mol.Cell, 26, 579-592. doi: 10.1016/j.molcel.2007.04.018. Human mutsalpha (msh2-msh6) bound to a g t mispair, with adp bound to msh2 only. SNAP output
2o8f DNA binding protein-DNA X-ray (3.25 Å) Warren JJ, Pohlhaus TJ, Changela A, Iyer RR, Modrich PL, Beese LS (2007) "Structure of the Human MutSalpha DNA Lesion Recognition Complex." Mol.Cell, 26, 579-592. doi: 10.1016/j.molcel.2007.04.018. Human mutsalpha (msh2-msh6) bound to DNA with a single base t insert. SNAP output
2o8k transcription-DNA NMR Doucleff M, Pelton JG, Lee PS, Nixon BT, Wemmer DE (2007) "Structural basis of DNA recognition by the alternative sigma-factor, sigma54." J.Mol.Biol., 369, 1070-1078. doi: 10.1016/j.jmb.2007.04.019. NMR structure of the sigma-54 rpon domain bound to the-24 promoter element. SNAP output
2o93 transcription-DNA X-ray (3.05 Å) Bates DL, Barthel KK, Wu Y, Kalhor R, Stroud JC, Giffin MJ, Chen L (2008) "Crystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element." Structure, 16, 684-694. doi: 10.1016/j.str.2008.01.020. Crystal structure of nfat bound to the hiv-1 ltr tandem kappab enhancer element. SNAP output
2o9l RNA polymerase sigma factor rpon-DNA NMR Doucleff M, Pelton JG, Lee PS, Nixon BT, Wemmer DE (2007) "Structural basis of DNA recognition by the alternative sigma-factor, sigma54." J.Mol.Biol., 369, 1070-1078. doi: 10.1016/j.jmb.2007.04.019. Amber refined NMR structure of the sigma-54 rpon domain bound to the-24 promoter element. SNAP output
2oa8 hydrolase-DNA X-ray (2.1 Å) de Silva U, Choudhury S, Bailey SL, Harvey S, Perrino FW, Hollis T (2007) "The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals a Polyproline II Helix for Protein Partnering." J.Biol.Chem., 282, 10537-10543. doi: 10.1074/jbc.M700039200. Crystal structure of mtrex1 with ssDNA. SNAP output
2oaa hydrolase-DNA X-ray (1.5 Å) Kaus-Drobek M, Czapinska H, Sokolowska M, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M (2007) "Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically." Nucleic Acids Res., 35, 2035-2046. doi: 10.1093/nar/gkm064. Restriction endonuclease mvai-cognate DNA substrate complex. SNAP output
2odi hydrolase-DNA X-ray (1.45 Å) Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M (2007) "Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA." J.Mol.Biol., 369, 722-734. doi: 10.1016/j.jmb.2007.03.018. Restriction endonuclease bcni-cognate DNA substrate complex. SNAP output
2oeh transcription-DNA NMR Cai S, Zhu L, Zhang Z, Chen Y (2007) "Determination of the three-dimensional structure of the Mrf2-DNA complex using paramagnetic spin labeling." Biochemistry, 46, 4943-4950. doi: 10.1021/bi061738h. Determination of the three-dimensional structure of the mrf2-DNA complex using paramagnetic spin labeling. SNAP output
2ofi 3-methyladenine DNA glycosylase i-DNA X-ray (1.85 Å) Metz AH, Hollis T, Eichman BF (2007) "DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG)." Embo J., 26, 2411-2420. doi: 10.1038/sj.emboj.7601649. Crystal structure of 3-methyladenine DNA glycosylase i (tag) bound to DNA-3ma. SNAP output
2og0 DNA binding protein-DNA X-ray (1.9 Å) Papagiannis CV, Sam MD, Abbani MA, Yoo D, Cascio D, Clubb RT, Johnson RC (2007) "Fis targets assembly of the xis nucleoprotein filament to promote excisive recombination by phage lambda." J.Mol.Biol., 367, 328-343. doi: 10.1016/j.jmb.2006.12.071. Crystal structure of the lambda xis-DNA complex. SNAP output
2oh2 transferase-DNA X-ray (3.05 Å) Lone S, Townson SA, Uljon SN, Johnson RE, Brahma A, Nair DT, Prakash S, Prakash L, Aggarwal AK "Ternary complex of the catalytic core of human DNA polymerase Kappa with DNA and dTT." Ternary complex of human DNA polymerase. SNAP output
2ok0 immune system-DNA X-ray (1.89 Å) Sanguineti S, Centeno Crowley JM, Lodeiro Merlo MF, Cerutti ML, Wilson IA, Goldbaum FA, Stanfield RL, de Prat-Gay G (2007) "Specific recognition of a DNA immunogen by its elicited antibody." J.Mol.Biol., 370, 183-195. doi: 10.1016/j.jmb.2007.04.046. Fab ed10-DNA complex. SNAP output
2opf hydrolase-DNA X-ray (1.85 Å) Golan G, Zharkov DO, Grollman AP, Shoham G "Active site plasticity of endonuclease VIII: Conformational changes compensating for different substrates and mutations of critical residues." Crystal structure of the DNA repair enzyme endonuclease-viii (nei) from e. coli (r252a) in complex with ap-site containing DNA substrate. SNAP output
2oq4 hydrolase-DNA X-ray (2.6 Å) Golan G, Zharkov DO, Grollman AP, Shoham G "Active site plasticity of endonuclease VIII: Conformational changes compensating for different substrates and mutations of critical residues." Crystal structure of the DNA repair enzyme endonuclease-viii (nei) from e. coli (e2q) in complex with ap-site containing DNA substrate. SNAP output
2or1 gene regulation-DNA X-ray (2.5 Å) Aggarwal AK, Rodgers DW, Drottar M, Ptashne M, Harrison SC (1988) "Recognition of a DNA operator by the repressor of phage 434: a view at high resolution." Science, 242, 899-907. Recognition of a DNA operator by the repressor of phage 434. a view at high resolution. SNAP output
2ost hydrolase-DNA X-ray (3.1 Å) Zhao L, Bonocora RP, Shub DA, Stoddard BL (2007) "The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif." Embo J., 26, 2432-2442. doi: 10.1038/sj.emboj.7601672. The structure of a bacterial homing endonuclease : i-ssp6803i. SNAP output
2owo ligase-DNA X-ray (2.3 Å) Nandakumar J, Nair PA, Shuman S (2007) "Last Stop on the Road to Repair: Structure of E. coli DNA Ligase Bound to Nicked DNA-Adenylate." Mol.Cell, 26, 257-271. doi: 10.1016/j.molcel.2007.02.026. Last stop on the road to repair: structure of e.coli DNA ligase bound to nicked DNA-adenylate. SNAP output
2oxm hydrolase-DNA X-ray (2.5 Å) Parker JB, Bianchet MA, Krosky DJ, Friedman JI, Amzel LM, Stivers JT (2007) "Enzymatic capture of an extrahelical thymine in the search for uracil in DNA." Nature, 449, 433-437. doi: 10.1038/nature06131. Crystal structure of a ung2-modified DNA complex that represent a stabilized short-lived extrahelical state in ezymatic DNA base flipping. SNAP output
2oxv hydrolase-DNA X-ray (1.95 Å) Sapienza PJ, Rosenberg JM, Jen-Jacobson L (2007) "Structural and thermodynamic basis for enhanced DNA binding by a promiscuous mutant EcoRI endonuclease." Structure, 15, 1368-1382. doi: 10.1016/j.str.2007.09.014. Structure of the a138t promiscuous mutant of the ecori restriction endonuclease bound to its cognate recognition site.. SNAP output
2oyq transferase-DNA X-ray (2.86 Å) Zahn KE, Belrhali H, Wallace SS, Doublie S (2007) "Caught bending the a-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide." Biochemistry, 46, 10551-10561. doi: 10.1021/bi7008807. Crystal structure of rb69 gp43 in complex with DNA with 5-nimp opposite an abasic site analog. SNAP output
2oyt hydrolase-DNA X-ray (2.0 Å) Parker JB, Bianchet MA, Krosky DJ, Friedman JI, Amzel LM, Stivers JT (2007) "Enzymatic capture of an extrahelical thymine in the search for uracil in DNA." Nature, 449, 433-437. doi: 10.1038/nature06131. Crystal structure of ung2-DNA(tm). SNAP output
2ozm transferase-DNA X-ray (2.86 Å) Zahn KE, Belrhail H, Wallace SS, Doublie S (2007) "Caught Bending the A-Rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide." Biochemistry, 46, 10551-10561. doi: 10.1021/bi7008807. Crystal structure of rb69 gp43 in complex with DNA with 5-nitp opposite an abasic site analog. SNAP output
2ozs transferase-DNA X-ray (2.75 Å) Zahn KE, Belrhali H, Wallace SS, Doublie S (2007) "Caught bending the a-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide." Biochemistry, 46, 10551-10561. doi: 10.1021/bi7008807. Crystal structure of rb69 gp43 in complex with DNA with datp opposite dtmp. SNAP output
2p0j hydrolase-DNA X-ray (2.1 Å) Townson SA, Samuelson JC, Bao Y, Xu SY, Aggarwal AK (2007) "BstYI Bound to Noncognate DNA Reveals a "Hemispecific" Complex: Implications for DNA Scanning." Structure, 15, 449-459. doi: 10.1016/j.str.2007.03.002. Structure of restriction endonuclease bstyi bound to non-cognate DNA. SNAP output
2p2r RNA and DNA binding protein-DNA X-ray (1.6 Å) Fenn S, Du Z, Lee JK, Tjhen R, Stroud RM, James TL (2007) "Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6 A resolution." Nucleic Acids Res., 35, 2651-2660. doi: 10.1093/nar/gkm139. Crystal structure of the third kh domain of human poly(c)-binding protein-2 in complex with c-rich strand of human telomeric DNA. SNAP output
2p5g transferase-DNA X-ray (2.8 Å) Zahn KE, Belrhali H, Wallace SS, Doublie S (2007) "Caught bending the a-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide." Biochemistry, 46, 10551-10561. doi: 10.1021/bi7008807. Crystal structure of rb69 gp43 in complex with DNA with damp opposite an abasic site analog in a 21mer template. SNAP output
2p5l transcription repressor X-ray (2.85 Å) Garnett JA, Marincs F, Baumberg S, Stockley PG, Phillips SE (2008) "Structure and function of the arginine repressor-operator complex from Bacillus subtilis." J.Mol.Biol., 379, 284-298. doi: 10.1016/j.jmb.2008.03.007. Crystal structure of a dimer of n-terminal domains of ahrc in complex with an 18bp DNA operator site. SNAP output
2p5o transferase-DNA X-ray (2.8 Å) Hogg M, Wallace SS, Doublie S (2004) "Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site." Embo J., 23, 1483-1493. doi: 10.1038/sj.emboj.760015. Crystal structure of rb69 gp43 in complex with DNA containing an abasic site analog. SNAP output
2p66 transferase, lyase-DNA X-ray (2.5 Å) Prasad R, Batra VK, Yang X-P, Krahn JM, Pedersen LC, Beard WA, Wilson SH (2005) "Structural insight into the DNA Polymerase beta deoxyribose phosphate lyase mechanism." DNA REPAIR, 4, 1347-1357. doi: 10.1016/j.dnarep.2005.08.009. Human DNA polymerase beta complexed with tetrahydrofuran (abasic site) containing DNA. SNAP output
2p6r DNA binding protein-DNA X-ray (3.0 Å) Buttner K, Nehring S, Hopfner KP (2007) "Structural basis for DNA duplex separation by a superfamily-2 helicase." Nat.Struct.Mol.Biol., 14, 647-652. doi: 10.1038/nsmb1246. Crystal structure of superfamily 2 helicase hel308 in complex with unwound DNA. SNAP output
2p7c transcription regulator NMR Boudet J, Duval V, Van Melckebeke H, Blackledge M, Amoroso A, Joris B, Simorre JP (2007) "Conformational and thermodynamic changes of the repressor/DNA operator complex upon monomerization shed new light on regulation mechanisms of bacterial resistance against beta-lactam antibiotics." Nucleic Acids Res., 35, 4384-4395. doi: 10.1093/nar/gkm448. Solution structure of the bacillus licheniformis blai monomeric form in complex with the blap half-operator.. SNAP output
2pe5 transcription-DNA X-ray (3.5 Å) Daber R, Stayrook S, Rosenberg A, Lewis M (2007) "Structural analysis of lac repressor bound to allosteric effectors." J.Mol.Biol., 370, 609-619. doi: 10.1016/j.jmb.2007.04.028. Crystal structure of the lac repressor bound to onpg in repressed state. SNAP output
2pfj hydrolase-DNA X-ray (3.1 Å) Hadden JM, Declais AC, Carr SB, Lilley DM, Phillips SE (2007) "The structural basis of Holliday junction resolution by T7 endonuclease I." Nature, 449, 621-624. doi: 10.1038/nature06158. Crystal structure of t7 endo i resolvase in complex with a holliday junction. SNAP output
2pfn transferase, lyase-DNA X-ray (1.9 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2007) "Role of the catalytic metal during polymerization by DNA polymerase lambda." DNA Repair, 6, 1333-1340. doi: 10.1016/j.dnarep.2007.03.005. Na in the active site of DNA polymerase lambda. SNAP output
2pfo transferase, lyase-DNA X-ray (2.0 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2007) "Role of the catalytic metal during polymerization by DNA polymerase lambda." DNA Repair, 6, 1333-1340. doi: 10.1016/j.dnarep.2007.03.005. DNA polymerase lambda in complex with DNA and dupnpp. SNAP output
2pfp transferase, lyase-DNA X-ray (2.1 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2007) "Role of the catalytic metal during polymerization by DNA polymerase lambda." DNA Repair, 6, 1333-1340. doi: 10.1016/j.dnarep.2007.03.005. DNA polymerase lambda in complex with DNA and dctp. SNAP output
2pfq transferase, lyase-DNA X-ray (2.1 Å) Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA (2007) "Role of the catalytic metal during polymerization by DNA polymerase lambda." DNA Repair, 6, 1333-1340. doi: 10.1016/j.dnarep.2007.03.005. Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal. SNAP output
2pi0 transcription activator-DNA X-ray (2.31 Å) Escalante CR, Nistal-Villan E, Shen L, Garcia-Sastre A, Aggarwal AK (2007) "Structure of IRF-3 bound to the PRDIII-I regulatory element of the human interferon-beta enhancer." Mol.Cell, 26, 703-716. doi: 10.1016/j.molcel.2007.04.022. Crystal structure of irf-3 bound to the prdiii-i regulatory element of the human interferon-b enhancer. SNAP output
2pi4 transferase-DNA X-ray (2.5 Å) Kennedy WP, Momand JR, Yin YW (2007) "Mechanism for de novo RNA synthesis and initiating nucleotide specificity by t7 RNA polymerase." J.Mol.Biol., 370, 256-268. doi: 10.1016/j.jmb.2007.03.041. T7rnap complexed with a phi10 protein and initiating gtps.. SNAP output
2pi5 transferase-DNA X-ray (2.9 Å) Kennedy WP, Momand JR, Yin YW (2007) "Mechanism for de novo RNA synthesis and initiating nucleotide specificity by t7 RNA polymerase." J.Mol.Biol., 370, 256-268. doi: 10.1016/j.jmb.2007.03.041. T7 RNA polymerase complexed with a phi10 promoter. SNAP output
2pjr hydrolase-DNA X-ray (2.9 Å) Velankar SS, Soultanas P, Dillingham MS, Subramanya HS, Wigley DB (1999) "Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism." Cell(Cambridge,Mass.), 97, 75-98. doi: 10.1016/S0092-8674(00)80716-3. Helicase product complex. SNAP output
2ppb transferase-DNA-RNA X-ray (3.0 Å) Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R (2007) "Structural basis for substrate loading in bacterial RNA polymerase." Nature, 448, 163-168. doi: 10.1038/nature05931. Crystal structure of the t. thermophilus rnap polymerase elongation complex with the ntp substrate analog and antibiotic streptolydigin. SNAP output
2pqu RNA and DNA binding protein-DNA X-ray (2.12 Å) Du Z, Lee JK, Fenn S, Tjhen R, Stroud RM, James TL (2007) "X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2." Rna, 13, 1043-1051. doi: 10.1261/rna.410107. Crystal structure of kh1 domain of human pcbp2 complexed to single-stranded 12-mer telomeric DNA. SNAP output
2prt transcription-DNA X-ray (3.15 Å) Stoll R, Lee BM, Debler EW, Laity JH, Wilson IA, Dyson HJ, Wright PE (2007) "Structure of the Wilms tumor suppressor protein zinc finger domain bound to DNA." J.Mol.Biol., 372, 1227-1245. doi: 10.1016/j.jmb.2007.07.017. Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA. SNAP output
2pua transcription-DNA X-ray (2.9 Å) Schumacher MA, Choi KY, Zalkin H, Brennan RG (1994) "Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices." Science, 266, 763-770. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2pub transcription-DNA X-ray (2.7 Å) Schumacher MA, Choi KY, Zalkin H, Brennan RG (1994) "Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices." Science, 266, 763-770. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2puc transcription-DNA X-ray (2.6 Å) Schumacher MA, Choi KY, Zalkin H, Brennan RG (1994) "Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices." Science, 266, 763-770. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2pud transcription-DNA X-ray (2.6 Å) Schumacher MA, Choi KY, Zalkin H, Brennan RG (1994) "Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices." Science, 266, 763-770. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2pue transcription-DNA X-ray (2.7 Å) Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner BL, Zalkin H, Brennan RG (1998) "Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190." Biochemistry, 37, 971-982. doi: 10.1021/bi971942s. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2puf transcription-DNA X-ray (3.0 Å) Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner BL, Zalkin H, Brennan RG (1998) "Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190." Biochemistry, 37, 971-982. doi: 10.1021/bi971942s. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2pug transcription-DNA X-ray (2.7 Å) Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner BL, Zalkin H, Brennan RG (1998) "Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190." Biochemistry, 37, 971-982. doi: 10.1021/bi971942s. Crystal structure of the laci family member, purr, bound to DNA: minor groove binding by alpha helices. SNAP output
2pvi hydrolase-DNA X-ray (1.76 Å) Horton JR, Bonventre J, Cheng X (1998) "How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?." J.Biol.Chem., 379, 451-458. Pvuii endonuclease complexed to an iodinated cognate DNA. SNAP output
2pxi lyase, transferase-DNA X-ray (2.1 Å) McKenna CE, Kashemirov BA, Upton TG, Batra VK, Goodman MF, Pedersen LC, Beard WA, Wilson SH (2007) "(R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta." J.Am.Chem.Soc., 129, 15412-15413. doi: 10.1021/ja072127v. Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monofluoromethylene triphosphate. SNAP output
2py5 replication, transferase-DNA X-ray (1.6 Å) Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2007) "Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases." Embo J., 26, 3494-3505. doi: 10.1038/sj.emboj.7601780. Phi29 DNA polymerase complexed with single-stranded DNA. SNAP output
2pyj replication, transferase-DNA X-ray (2.03 Å) Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2007) "Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases." Embo J., 26, 3494-3505. doi: 10.1038/sj.emboj.7601780. Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex). SNAP output
2pyl replication, transferase-DNA X-ray (2.2 Å) Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2007) "Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases." Embo J., 26, 3494-3505. doi: 10.1038/sj.emboj.7601780. Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex). SNAP output
2pyo structural protein-DNA X-ray (2.43 Å) Clapier CR, Chakravarthy S, Petosa C, Fernandez-Tornero C, Luger K, Muller CW (2007) "Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer." Proteins, 71, 1-7. doi: 10.1002/prot.21720. Drosophila nucleosome core. SNAP output
2pzs replication, transferase-DNA X-ray (2.6 Å) Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA (2007) "Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases." Embo J., 26, 3494-3505. doi: 10.1038/sj.emboj.7601780. Phi29 DNA polymerase complexed with primer-template DNA (post-translocation binary complex). SNAP output
2q10 hydrolase-DNA X-ray (1.75 Å) Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M (2007) "Monomeric Restriction Endonuclease BcnI in the Apo Form and in an Asymmetric Complex with Target DNA." J.Mol.Biol., 369, 722-734. doi: 10.1016/j.jmb.2007.03.018. Restriction endonuclease bcni (wild type)-cognate DNA substrate complex. SNAP output
2q2k DNA binding protein-DNA X-ray (3.0 Å) Schumacher MA, Glover TC, Brzoska AJ, Jensen SO, Dunham TD, Skurray RA, Firth N (2007) "Segrosome structure revealed by a complex of ParR with centromere DNA." Nature, 450, 1268-1271. doi: 10.1038/nature06392. Structure of nucleic-acid binding protein. SNAP output
2q2t ligase-DNA X-ray (2.3 Å) Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S (2007) "Structural basis for nick recognition by a minimal pluripotent DNA ligase." Nat.Struct.Mol.Biol., 14, 770-778. doi: 10.1038/nsmb1266. Structure of chlorella virus DNA ligase-adenylate bound to a 5' phosphorylated nick. SNAP output
2q2u ligase-DNA X-ray (3.0 Å) Nair PA, Nandakumar J, Smith P, Odell M, Lima CD, Shuman S (2007) "Structural basis for nick recognition by a minimal pluripotent DNA ligase." Nat.Struct.Mol.Biol., 14, 770-778. doi: 10.1038/nsmb1266. Structure of chlorella virus DNA ligase-product DNA complex. SNAP output
2qby replication-DNA X-ray (3.35 Å) Dueber EL, Corn JE, Bell SD, Berger JM (2007) "Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex." Science, 317, 1210-1213. doi: 10.1126/science.1143690. Crystal structure of a heterodimer of cdc6-orc1 initiators bound to origin DNA (from s. solfataricus). SNAP output
2qfj transcription repressor-DNA X-ray (2.1 Å) Crichlow GV, Zhou H, Hsiao H-H, Frederick KB, Debrosse M, Yang Y, Folta-Stogniew EJ, Chung H-J, Fan C, De La Cruz EM, Levens D, Lolis E, Braddock D (2007) "Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition." EMBO J., 27, 277-289. doi: 10.1038/sj.emboj.7601936. Crystal structure of first two rrm domains of fir bound to ssDNA from a portion of fuse. SNAP output
2qhb DNA binding protein-DNA X-ray (2.4 Å) Cho H-S, Byun J-S, Jun S-H, Han W, Lee W "Complex structure of plant telomere bindig protein, NgTRF and telomere DNA." Crystal structure of ngtrf complexed with telomeric DNA. SNAP output
2qk9 hydrolase-DNA-RNA X-ray (2.55 Å) Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, Yang W (2007) "Structure of Human RNase H1 Complexed with an RNA/DNA Hybrid: Insight into HIV Reverse Transcription." Mol.Cell, 28, 264-276. doi: 10.1016/j.molcel.2007.08.015. Human rnase h catalytic domain mutant d210n in complex with 18-mer RNA-DNA hybrid. SNAP output
2qkb hydrolase-DNA-RNA X-ray (2.4 Å) Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, Yang W (2007) "Structure of Human RNase H1 Complexed with an RNA/DNA Hybrid: Insight into HIV Reverse Transcription." Mol.Cell, 28, 264-276. doi: 10.1016/j.molcel.2007.08.015. Human rnase h catalytic domain mutant d210n in complex with 20-mer RNA-DNA hybrid. SNAP output
2qkk hydrolase-DNA-RNA X-ray (3.2 Å) Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, Yang W (2007) "Structure of Human RNase H1 Complexed with an RNA/DNA Hybrid: Insight into HIV Reverse Transcription." Mol.Cell, 28, 264-276. doi: 10.1016/j.molcel.2007.08.015. Human rnase h catalytic domain mutant d210n in complex with 14-mer RNA-DNA hybrid. SNAP output
2ql2 transcription-DNA X-ray (2.5 Å) Longo A, Guanga GP, Rose RB (2008) "Crystal structure of E47-NeuroD1/beta2 bHLH domain-DNA complex: heterodimer selectivity and DNA recognition." Biochemistry, 47, 218-229. doi: 10.1021/bi701527r. Crystal structure of the basic-helix-loop-helix domains of the heterodimer e47-neurod1 bound to DNA. SNAP output
2qnc hydrolase-DNA X-ray (3.1 Å) Biertumpfel C, Yang W, Suck D (2007) "Crystal structure of T4 endonuclease VII resolving a Holliday junction." Nature, 449, 616-620. doi: 10.1038/nature06152. Crystal structure of t4 endonuclease vii n62d mutant in complex with a DNA holliday junction. SNAP output
2qnf hydrolase-DNA X-ray (3.0 Å) Biertumpfel C, Yang W, Suck D (2007) "Crystal structure of T4 endonuclease VII resolving a Holliday junction." Nature, 449, 616-620. doi: 10.1038/nature06152. Crystal structure of t4 endonuclease vii h43n mutant in complex with heteroduplex DNA containing base mismatches. SNAP output
2qoj hydrolase-DNA X-ray (2.4 Å) Scalley-Kim M, McConnell-Smith A, Stoddard BL (2007) "Coevolution of a homing endonuclease and its host target sequence." J.Mol.Biol., 372, 1305-1319. doi: 10.1016/j.jmb.2007.07.052. Coevolution of a homing endonuclease and its host target sequence. SNAP output
2qsg DNA binding protein-DNA X-ray (3.1 Å) Min J-H, Pavletich NP (2007) "Recognition of DNA damage by the Rad4 nucleotide excision repair protein." Nature, 449, 570-575. doi: 10.1038/nature06155. Crystal structure of rad4-rad23 bound to a uv-damaged DNA. SNAP output
2qsh DNA binding protein-DNA X-ray (2.805 Å) Min J-H, Pavletich NP (2007) "Recognition of DNA damage by the Rad4 nucleotide excision repair protein." Nature, 449, 570-575. doi: 10.1038/nature06155. Crystal structure of rad4-rad23 bound to a mismatch DNA. SNAP output
2r0q recombination-DNA X-ray (3.2 Å) Mouw KW, Rowland SJ, Gajjar MM, Boocock MR, Stark WM, Rice PA (2008) "Architecture of a serine recombinase-DNA regulatory complex." Mol.Cell, 30, 145-155. doi: 10.1016/j.molcel.2008.02.023. Crystal structure of a serine recombinase- DNA regulatory complex. SNAP output
2r1j transcription-DNA X-ray (1.53 Å) Watkins D, Hsiao C, Woods KK, Koudelka GB, Williams LD (2008) "P22 c2 repressor-operator complex: mechanisms of direct and indirect readout." Biochemistry, 47, 2325-2338. doi: 10.1021/bi701826f. Crystal structure of the p22 c2 repressor protein in complex with the synthetic operator 9t. SNAP output
2r2r transferase-DNA X-ray (2.1 Å) Goodwin KD, Lewis MA, Long EC, Georgiadis MM (2008) "Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding." Proc.Natl.Acad.Sci.Usa, 105, 5052-5056. doi: 10.1073/pnas.0708143105. D(attagttataactaat) complexed with mmlv rt catalytic fragment. SNAP output
2r2s transferase-DNA X-ray (2.8 Å) Goodwin KD, Lewis MA, Long EC, Georgiadis MM (2008) "Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding." Proc.Natl.Acad.Sci.Usa, 105, 5052-5056. doi: 10.1073/pnas.0708143105. Co(iii)bleomycinb2 bound to d(attagttataactaat) complexed with mmlv rt catalytic fragment. SNAP output
2r2t transferase-DNA X-ray (2.0 Å) Goodwin KD, Lewis MA, Long EC, Georgiadis MM (2008) "Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding." Proc.Natl.Acad.Sci.Usa, 105, 5052-5056. doi: 10.1073/pnas.0708143105. D(atttagttaactaaat) complexed with mmlv rt catalytic fragment. SNAP output
2r2u transferase-DNA X-ray (2.3 Å) Goodwin KD, Lewis MA, Long EC, Georgiadis MM (2008) "Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding." Proc.Natl.Acad.Sci.Usa, 105, 5052-5056. doi: 10.1073/pnas.0708143105. Co(iii)bleomycinb2 bithiazole-c-terminal tail domain bound to d(atttagttaactaaat) complexed with mmlv rt catalytic fragment. SNAP output
2r5y transcription-DNA X-ray (2.6 Å) Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS (2007) "Functional specificity of a Hox protein mediated by the recognition of minor groove structure." Cell(Cambridge,Mass.), 131, 530-543. doi: 10.1016/j.cell.2007.09.024. Structure of scr-exd complex bound to a consensus hox-exd site. SNAP output
2r5z transcription-DNA X-ray (2.6 Å) Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS (2007) "Functional specificity of a Hox protein mediated by the recognition of minor groove structure." Cell(Cambridge,Mass.), 131, 530-543. doi: 10.1016/j.cell.2007.09.024. Structure of scr-exd complex bound to a DNA sequence derived from the fkh gene. SNAP output
2r7y hydrolase-RNA-DNA X-ray (1.8 Å) Jiang J-S, Gerlits O, Huang Z "Selenium Derivatized RNA/DNA Hybrid in complex with RNase H CATALYTIC DOMAIN MUTANT D132N." Selenium derivatized RNA-DNA hybrid in complex with rnase h catalytic domain mutant d132n. SNAP output
2r7z transcription-DNA-RNA hybrid X-ray (3.8 Å) Damsma GE, Alt A, Brueckner F, Carell T, Cramer P (2007) "Mechanism of transcriptional stalling at cisplatin-damaged DNA." Nat.Struct.Mol.Biol., 14, 1127-1133. doi: 10.1038/nsmb1314. Cisplatin lesion containing RNA polymerase ii elongation complex. SNAP output
2r8g replication, transferase-DNA X-ray (2.7 Å) Wang Y, Musser SK, Saleh S, Marnett LJ, Egli M, Stone MP (2008) "Insertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV." Biochemistry, 47, 7322-7334. doi: 10.1021/bi800152j. Selectivity of nucleoside triphosphate incorporation opposite 1,n2-propanodeoxyguanosine (pdg) by the sulfolobus solfataricus DNA polymerase dpo4 polymerase. SNAP output
2r8h replication, transferase-DNA X-ray (2.48 Å) Wang Y, Musser SK, Saleh S, Marnett LJ, Egli M, Stone MP (2008) "Insertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV." Biochemistry, 47, 7322-7334. doi: 10.1021/bi800152j. Selectivity of nucleoside triphosphate incorporation opposite 1,n2-propanodeoxyguanosine (pdg) by the sulfolobus solfataricus DNA polymerase dpo4 polymerase. SNAP output
2r8i replication, transferase-DNA X-ray (2.38 Å) Wang Y, Musser SK, Saleh S, Marnett LJ, Egli M, Stone MP (2008) "Insertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV." Biochemistry, 47, 7322-7334. doi: 10.1021/bi800152j. Selectivity of nucleoside triphosphate incorporation opposite 1,n2-propanodeoxyguanosine (pdg) by the sulfolobus solfataricus DNA polymerase dpo4 polymerase. SNAP output
2r8j replication, transferase-DNA X-ray (3.1 Å) Alt A, Lammens K, Chiocchini C, Lammens A, Pieck JC, Kuch D, Hopfner KP, Carell T (2007) "Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta." Science, 318, 967-970. doi: 10.1126/science.1148242. Structure of the eukaryotic DNA polymerase eta in complex with 1,2-d(gpg)-cisplatin containing DNA. SNAP output
2r8k replication, transferase-DNA X-ray (3.3 Å) Alt A, Lammens K, Chiocchini C, Lammens A, Pieck JC, Kuch D, Hopfner KP, Carell T (2007) "Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta." Science, 318, 967-970. doi: 10.1126/science.1148242.