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 . ➥(1) [+]:GcC/GGC, hydrophobic-with-AA, is-WC-paired, is-in-duplex
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 . ➥(2) [+]:Acg/cgT, [-]:cgT/Acg, is-WC-paired, is-in-duplex, other-contacts
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 . ➥(2) [-]:GGC/GcC, hydrophobic-with-AA, is-WC-paired, is-in-duplex, stacking-with-AA
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 . ➥(2) [+]:CcG/cGG, [-]:cGG/CcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex, other-contacts
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 . ➥(1) [+]:GcC/gGC, hydrophobic-with-AA, is-WC-paired, is-in-duplex
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 . ➥(1) [+]:GcC/GGC, hydrophobic-with-AA, is-WC-paired, is-in-duplex
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 . ➥(1) [+]:GcC/GGC, hydrophobic-with-AA, is-WC-paired, is-in-duplex
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 . ➥(1) [+]:GcC/GGC, hydrophobic-with-AA, is-WC-paired, is-in-duplex
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 . ➥(2) [+]:TcG/cGA, [-]:cGG/CcG, is-WC-paired, is-in-duplex, stacking-with-AA
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 . ➥(1) [-]:cGG/CcG, is-WC-paired, is-in-duplex, other-contacts
2uyc transferase X-ray (2.0 Å) Daujotyte D, Grazulis S "HhaI DNA Methyltransferase R163N Mutant Complex with 13mer Gcgc-Gmgc Oligonucleotide and Sah." Hhai DNA methyltransferase r163n mutant complex with 13mer gcgc-gmgc oligonucleotide and sah . ➥(1) [+]:GcC/GGC, hydrophobic-with-AA, is-WC-paired, is-in-duplex
2uyh transferase X-ray (2.63 Å) Daujotyte D, Grazulis S "HhaI DNA Methyltransferase S87Q-Q237S Mutant Complex with 13mer Gcgc-Gmgc Oligonucleotide and Sah." Hhai DNA methyltransferase s87q-q237s mutant complex with 13mer gcgc- gmgc oligonucleotide and sah . ➥(1) [+]:GcC/GGC, hydrophobic-with-AA, is-WC-paired, is-in-duplex
2uz4 transferase X-ray (2.1 Å) Daujotyte D, Leinartaite L, Grazulis S "DNA Methyltransferase R165N Mutant." Hhai DNA methyltransferase r165n mutant complex with 13mer gcgc-gmgc oligonucleotide and sah . ➥(1) [+]:GcC/GGC, hydrophobic-with-AA, is-WC-paired, is-in-duplex
2zkd ligase X-ray (1.6 Å) Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M (2008) "Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism." Nature, 455, 818-821. doi: 10.1038/nature07249. Crystal structure of the sra domain of mouse np95 in complex with hemi-methylated cpg DNA . ➥(2) not-WC-paired, not-in-duplex, stacking-with-AA
2zke ligase X-ray (2.6 Å) Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M (2008) "Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism." Nature, 455, 818-821. doi: 10.1038/nature07249. Crystal structure of the sra domain of mouse np95 in complex with hemi-methylated cpg DNA . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
2zkf ligase X-ray (2.55 Å) Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M (2008) "Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism." Nature, 455, 818-821. doi: 10.1038/nature07249. Crystal structure of the sra domain of mouse np95 in complex with hemi-methylated cpg DNA . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
2zo0 ligase-DNA X-ray (2.19 Å) Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, Cheng X (2008) "The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix." Nature, 455, 826-829. doi: 10.1038/nature07280. Mouse np95 sra domain DNA specific complex 1 . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
2zo1 ligase-DNA X-ray (1.96 Å) Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, Cheng X (2008) "The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix." Nature, 455, 826-829. doi: 10.1038/nature07280. Mouse np95 sra domain DNA specific complex 2 . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
3c2i transcription regulator X-ray (2.5 Å) Ho KL, McNae IW, Schmiedeberg L, Klose RJ, Bird AP, Walkinshaw MD (2008) "MeCP2 binding to DNA depends upon hydration at methyl-CpG." Mol.Cell, 29, 525-531. doi: 10.1016/j.molcel.2007.12.028. The crystal structure of methyl-cpg binding domain of human mecp2 in complex with a methylated DNA sequence from bdnf . ➥(2) [+]:AcG/cGT, [-]:cGG/CcG, is-WC-paired, is-in-duplex, stacking-with-AA
3clz ligase X-ray (2.2 Å) Avvakumov GV, Walker JR, Xue S, Li Y, Duan S, Bronner C, Arrowsmith CH, Dhe-Paganon S (2008) "Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1." Nature, 455, 822-825. doi: 10.1038/nature07273. The set and ring associated (sra) domain of uhrf1 bound to methylated DNA . ➥(4) not-WC-paired, not-in-duplex, stacking-with-AA
3f8i ligase-DNA X-ray (2.29 Å) Hashimoto H, Horton JR, Zhang X, Cheng X (2009) "UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications." Epigenetics, 4, 8-14. Mouse uhrf1 sra domain bound with hemi-methylated cpg, crystal structure in space group p21 . ➥(2) not-WC-paired, not-in-duplex, stacking-with-AA
3f8j ligase-DNA X-ray (1.99 Å) Hashimoto H, Horton JR, Zhang X, Cheng X (2009) "UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications." Epigenetics, 4, 8-14. Mouse uhrf1 sra domain bound with hemi-methylated cpg, crystal structure in space group c222(1) . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
3fde ligase X-ray (1.41 Å) Hashimoto H, Horton JR, Zhang X, Cheng X (2009) "UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications." Epigenetics, 4, 8-14. Mouse uhrf1 sra domain bound with hemi-methylated cpg DNA, crystal structure in space group c222(1) at 1.4 Å resolution . ➥(2) not-WC-paired, not-in-duplex, stacking-with-AA
3q0b transferase-DNA X-ray (2.2 Å) Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, Reinberg D, Patel DJ, Jacobsen SE (2011) "A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo." Genes Dev., 25, 137-152. doi: 10.1101/gad.1980311. Crystal structure of suvh5 sra- fully methylated cg DNA complex in space group p42212 . ➥(2) not-WC-paired, not-in-duplex, stacking-with-AA
3q0c transferase-DNA X-ray (2.66 Å) Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, Reinberg D, Patel DJ, Jacobsen SE (2011) "A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo." Genes Dev., 25, 137-152. doi: 10.1101/gad.1980311. Crystal structure of suvh5 sra-fully methylated cg DNA complex in space group p6122 . ➥(2) not-WC-paired, not-in-duplex, stacking-with-AA
3q0d transferase-DNA X-ray (2.37 Å) Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, Reinberg D, Patel DJ, Jacobsen SE (2011) "A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo." Genes Dev., 25, 137-152. doi: 10.1101/gad.1980311. Crystal structure of suvh5 sra- hemi methylated cg DNA complex . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
3q0f transferase-DNA X-ray (2.75 Å) Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, Reinberg D, Patel DJ, Jacobsen SE (2011) "A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo." Genes Dev., 25, 137-152. doi: 10.1101/gad.1980311. Crystal structure of suvh5 sra- methylated chh DNA complex . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
3ssc DNA binding protein-DNA X-ray (2.1 Å) Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V (2012) "The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine." Nucleic Acids Res., 40, 7552-7562. doi: 10.1093/nar/gks332. DNA binding domain of restriction endonuclease bound to DNA . ➥(2) not-WC-paired, not-in-duplex, stacking-with-AA
3ssd DNA binding protein-DNA X-ray (2.2 Å) Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V (2012) "The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine." Nucleic Acids Res., 40, 7552-7562. doi: 10.1093/nar/gks332. DNA binding domain of restriction endonuclease bound to DNA . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
3vxv hydrolase-DNA X-ray (2.0 Å) Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M (2013) "Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4." J.Biol.Chem., 288, 6351-6362. doi: 10.1074/jbc.M112.431098. Crystal structure of methyl cpg binding domain of mbd4 in complex with the 5mcg-tg sequence . ➥(1) [+]:CcG/TGG, is-WC-paired, is-in-duplex, stacking-with-AA
3vxx hydrolase-DNA X-ray (2.204 Å) Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M (2013) "Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4." J.Biol.Chem., 288, 6351-6362. doi: 10.1074/jbc.M112.431098. Crystal structure of methyl cpg binding domain of mbd4 in complex with the 5mcg-5mcg sequence . ➥(2) [+]:CcG/cGG, [-]:cGG/CcG, is-WC-paired, is-in-duplex, stacking-with-AA
3vyb hydrolase-DNA X-ray (2.4 Å) Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M (2013) "Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4." J.Biol.Chem., 288, 6351-6362. doi: 10.1074/jbc.M112.431098. Crystal structure of methyl cpg binding domain of mbd4 in complex with the 5mcg-hmcg sequence . ➥(1) [+]:CcG/cGG, is-WC-paired, is-in-duplex, stacking-with-AA
3vyq hydrolase-DNA X-ray (2.525 Å) Otani J, Arita K, Kato T, Kinoshita M, Kimura H, Suetake I, Tajima S, Ariyoshi M, Shirakawa M (2013) "Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4." J.Biol.Chem., 288, 6351-6362. doi: 10.1074/jbc.M112.431098. Crystal structure of the methyl cpg binding domain of mbd4 in complex with the 5mcg-tg sequence in space group p1 . ➥(1) [+]:CcG/TGG, is-WC-paired, is-in-duplex, stacking-with-AA
4aqu hydrolase X-ray (2.3 Å) Valton J, Daboussi F, Leduc S, Molina R, Redondo P, Macmaster R, Montoya G, Duchateau P (2012) "5'-Cytosine-Phosphoguanine (Cpg) Methylation Impacts the Activity of Natural and Engineered Meganucleases." J.Biol.Chem., 287, 30139. doi: 10.1074/JBC.M112.379966. Crystal structure of i-crei complexed with its target methylated at position plus 2 (in the b strand) in the presence of calcium . ➥(1) [-]:CGT/AcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex
4aqx hydrolase X-ray (2.2 Å) Valton J, Daboussi F, Leduc S, Molina R, Redondo P, Macmaster R, Montoya G, Duchateau P (2012) "5'-Cytosine-Phosphoguanine (Cpg) Methylation Impacts the Activity of Natural and Engineered Meganucleases." J.Biol.Chem., 287, 30139. doi: 10.1074/JBC.M112.379966. Crystal structure of i-crei complexed with its target methylated at position plus 2 (in the b strand) in the presence of magnesium . ➥(1) [-]:CGT/AcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex
4da4 transferase-DNA X-ray (2.6 Å) Song J, Teplova M, Ishibe-Murakami S, Patel DJ (2012) "Structure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation." Science, 335, 709-712. doi: 10.1126/science.1214453. Structure of mouse dnmt1 (731-1602) bound to hemimethylated cpg DNA . ➥(2) [+]:CcG/GGG, is-WC-paired, is-in-duplex, stacking-with-AA
4dkj transferase-DNA X-ray (2.15 Å) Wojciechowski M, Czapinska H, Bochtler M (2013) "CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI." Proc.Natl.Acad.Sci.USA, 110, 105-110. doi: 10.1073/pnas.1207986110. Cpg specific methyltransferase in complex with target DNA . ➥(1) [-]:GGC/GcC, is-WC-paired, is-in-duplex, stacking-with-AA
4f6n DNA binding protein-DNA X-ray (2.8 Å) 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. Crystal structure of kaiso zinc finger DNA binding protein in complex with methylated cpg site DNA . ➥(4) [+]:CcG/cGG, [+]:GcG/cGc, [-]:cGT/AcG, [-]:cGc/GcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
4gjp transcription-DNA X-ray (1.94 Å) Yan N, Deng D, Yan CY, Yin P, Pan XJ, Shi YG "Crystal structure of a protein complex." Crystal structure of the tal effector dhax3 bound to dsDNA containing repetitive methyl-cpg . ➥(4) [+]:GcG/CGC, [+]:TcG/CGA, is-WC-paired, is-in-duplex, stacking-with-AA
4gjr transcription-DNA X-ray (1.85 Å) Yan N, Deng D, Yan CY, Yin P, Pan XJ, Shi YG "Crystal structure of a protein complex." Crystal structure of the tal effector dhax3 bound to methylated dsDNA . ➥(6) [+]:AcC/GGT, [+]:CcC/GGG, [+]:TcT/AGA, hydrophobic-with-AA, is-WC-paired, is-in-duplex, stacking-with-AA
4gzn transcription-DNA X-ray (0.99 Å) Liu Y, Toh H, Sasaki H, Zhang X, Cheng X (2012) "An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence." Genes Dev., 26, 2374-2379. doi: 10.1101/gad.202200.112. Mouse zfp57 zinc fingers in complex with methylated DNA . ➥(2) [+]:CcG/cGG, [-]:cGC/GcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
4hp1 DNA binding protein-DNA X-ray (2.25 Å) Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y, Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q, Clark E, Ma C, Barbara A, Veenstra GJ, Xu G, Kaiser UB, Liu XS, Sugrue SP, He X, Min J, Kato Y, Shi YG (2012) "Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development." Cell(Cambridge,Mass.), 151, 1200-1213. doi: 10.1016/j.cell.2012.11.014. Crystal structure of tet3 in complex with a non-cpg dsDNA . ➥(2) [+]:CcG/cGG, [-]:cGG/CcG, is-WC-paired, is-in-duplex, other-contacts
4lg7 hydrolase-DNA X-ray (2.5 Å) Xu C, Tempel W, Wernimont AK, Bountra C, Arrowsmith CH, Edwards AM, Min J "Crystal structure MBD4 MBD domain in complex with methylated CpG DNA." Crystal structure mbd4 mbd domain in complex with methylated cpg DNA . ➥(2) [+]:AcG/cGT, [-]:cGT/AcG, is-WC-paired, is-in-duplex, stacking-with-AA
4lt5 oxidoreductase-DNA X-ray (2.893 Å) Hashimoto H, Pais JE, Zhang X, Saleh L, Fu ZQ, Dai N, Correa IR, Zheng Y, Cheng X (2014) "Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA." Nature, 506, 391-395. doi: 10.1038/nature12905. Structure of a naegleria tet-like dioxygenase in complex with 5-methylcytosine DNA . ➥(2) [+]:GcT/AGC, hydrophobic-with-AA, is-WC-paired, is-in-duplex, not-WC-paired, not-in-duplex, stacking-with-AA
4m9e transcription-DNA X-ray (1.851 Å) Liu Y, Olanrewaju YO, Zheng Y, Hashimoto H, Blumenthal RM, Zhang X, Cheng X (2014) "Structural basis for Klf4 recognition of methylated DNA." Nucleic Acids Res., 42, 4859-4867. doi: 10.1093/nar/gku134. Structure of klf4 zinc finger DNA binding domain in complex with methylated DNA . ➥(2) [+]:GcG/cGC, [-]:cGT/AcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
4m9v transcription-DNA X-ray (0.969 Å) Liu Y, Olanrewaju YO, Zhang X, Cheng X (2013) "DNA recognition of 5-carboxylcytosine by a zfp57 mutant at an atomic resolution of 0.97 angstrom." Biochemistry, 52, 9310-9317. doi: 10.1021/bi401360n. Zfp57 mutant (e182q) in complex with 5-carboxylcytosine DNA . ➥(2) [+]:CcG/cGG, is-WC-paired, is-in-duplex, other-contacts
4mht transferase-DNA X-ray (2.7 Å) O'Gara M, Klimasauskas S, Roberts RJ, Cheng X (1996) "Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes." J.Mol.Biol., 261, 634-645. doi: 10.1006/jmbi.1996.0489. Ternary structure of hhai methyltransferase with native DNA and adohcy . ➥(2) [+]:GcC/GGC, hydrophobic-with-AA, is-WC-paired, is-in-duplex, not-WC-paired, not-in-duplex, stacking-with-AA
4nm6 oxidoreductase-DNA X-ray (2.026 Å) Hu L, Li Z, Cheng J, Rao Q, Gong W, Liu M, Shi YG, Zhu J, Wang P, Xu Y (2013) "Crystal Structure of TET2-DNA Complex: Insight into TET-Mediated 5mC Oxidation." Cell(Cambridge,Mass.), 155, 1545-1555. doi: 10.1016/j.cell.2013.11.020. Crystal structure of tet2-DNA complex . ➥(2) [-]:.GG/Cc., is-WC-paired, is-in-duplex, not-WC-paired, not-in-duplex, stacking-with-AA
4pw7 ligase-DNA X-ray (2.001 Å) Zhou T, Xiong J, Wang M, Yang N, Wong J, Zhu B, Xu RM (2014) "Structural Basis for Hydroxymethylcytosine Recognition by the SRA Domain of UHRF2." Mol.Cell, 54, 879-886. doi: 10.1016/j.molcel.2014.04.003. Structure of uhrf2-sra in complex with a 5mc-containing DNA . ➥(2) not-WC-paired, not-in-duplex, stacking-with-AA
4qen transcription-DNA X-ray (2.002 Å) Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S, Vashisht AA, Gallego-Bartolome J, Wohlschlegel JA, Patel DJ, Jacobsen SE (2014) "Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE." Mol.Cell, 55, 495-504. doi: 10.1016/j.molcel.2014.06.009. Crystal structure of kryptonite in complex with mchh DNA and sah . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
4qeo transcription-DNA X-ray (2.0 Å) Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S, Vashisht AA, Gallego-Bartolome J, Wohlschlegel JA, Patel DJ, Jacobsen SE (2014) "Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE." Mol.Cell, 55, 495-504. doi: 10.1016/j.molcel.2014.06.009. Crystal structure of kryptonite in complex with mchh DNA, h3(1-15) peptide and sah . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
4qep transcription-DNA X-ray (3.1 Å) Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S, Vashisht AA, Gallego-Bartolome J, Wohlschlegel JA, Patel DJ, Jacobsen SE (2014) "Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE." Mol.Cell, 55, 495-504. doi: 10.1016/j.molcel.2014.06.009. Crystal structure of kryptonite in complex with mchg DNA and sah . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
4r28 hydrolase-DNA X-ray (3.055 Å) Horton JR, Wang H, Mabuchi MY, Zhang X, Roberts RJ, Zheng Y, Wilson GG, Cheng X (2014) "Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix." Nucleic Acids Res., 42, 12092-12101. doi: 10.1093/nar/gku871. Mspji restriction endonuclease in complex with 27-mer oligonucleotide . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
4r2a DNA binding protein-DNA X-ray (1.591 Å) Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence." Genes Dev., 28, 2304-2313. doi: 10.1101/gad.250746.114. Egr1-zif268 zinc fingers in complex with methylated DNA . ➥(2) [+]:GcG/cGC, [-]:cGT/AcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
4r2e DNA binding protein-DNA X-ray (1.84 Å) Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence." Genes Dev., 28, 2304-2313. doi: 10.1101/gad.250746.114. Wilms tumor protein (wt1) zinc fingers in complex with methylated DNA . ➥(2) [+]:GcG/cGC, [-]:cGT/AcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
4r2r DNA binding protein-DNA X-ray (2.089 Å) Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence." Genes Dev., 28, 2304-2313. doi: 10.1101/gad.250746.114. Wilms tumor protein (wt1) zinc fingers in complex with carboxylated DNA . ➥(1) [-]:cGT/AcG, is-WC-paired, is-in-duplex, other-contacts
4r2s DNA binding protein-DNA X-ray (2.489 Å) Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X (2014) "Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence." Genes Dev., 28, 2304-2313. doi: 10.1101/gad.250746.114. Wilms tumor protein (wt1) q369p zinc fingers in complex with methylated DNA . ➥(2) [+]:GcG/cGC, [-]:cGT/AcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
4x9j transcription regulator-DNA X-ray (1.412 Å) Zandarashvili L, White MA, Esadze A, Iwahara J (2015) "Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1." Febs Lett., 589, 1748-1753. doi: 10.1016/j.febslet.2015.05.022. Egr-1 with doubly methylated DNA . ➥(4) [+]:GcG/cGC, [-]:cGT/AcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
5bt2 DNA binding protein-DNA X-ray (2.2 Å) Chia JY, Tan WS, Ng CL, Hu NJ, Foo HL, Ho KL (2016) "A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence." Sci Rep, 6, 31210. doi: 10.1038/srep31210. Mecp2 mbd domain (a140v) in complex with methylated DNA . ➥(2) [+]:AcG/cGT, [-]:cGG/CcG, is-WC-paired, is-in-duplex, stacking-with-AA
5cg9 oxidoreductase-DNA X-ray (2.693 Å) Hashimoto H, Pais JE, Dai N, Correa IR, Zhang X, Zheng Y, Cheng X (2015) "Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA." Nucleic Acids Res., 43, 10713-10721. doi: 10.1093/nar/gkv870. Ngtet1 in complex with 5mc DNA in space group p3221 . ➥(2) not-WC-paired, not-in-duplex, stacking-with-AA
5cpj "structural protein-DNA X-ray (3.15 Å) Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H (2015) "Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA." Open Biology, 5. doi: 10.1098/rsob.150128. Nucleosome containing methylated sat2r DNA . ➥(2) [+]:TcG/cGA, [-]:cGA/TcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex, other-contacts
5cpk structural protein-DNA X-ray (2.632 Å) Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H (2015) "Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA." Open Biology, 5. doi: 10.1098/rsob.150128. Nucleosome containing methylated sat2l DNA . ➥(1) [+]:TcG/cGA, is-WC-paired, is-in-duplex, other-contacts
5ef6 transcription X-ray (3.0 Å) Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J (2017) "Impact of cytosine methylation on DNA binding specificities of human transcription factors." Science, 356. doi: 10.1126/science.aaj2239. Structure of hoxb13 complex with methylated DNA . ➥(8) [+]:AcG/cGT, [-]:cGA/TcG, [-]:cGG/CcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex
5ego transcription X-ray (2.54 Å) Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J (2017) "Impact of cytosine methylation on DNA binding specificities of human transcription factors." Science, 356. doi: 10.1126/science.aaj2239. Hoxb13-meis1 heterodimer bound to methylated DNA . ➥(2) [+]:AcG/cGT, [-]:cGA/TcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex
5emc transcription-DNA X-ray (2.3 Å) Jin J, Lian T, SU XD "The effects of cytosine methylation on general transcription factors." Transcription factor grdbd and smgre complex . ➥(1) [-]:TGT/AcA, is-WC-paired, is-in-duplex, other-contacts
5gse structural protein-DNA X-ray (3.14 Å) Kato D, Osakabe A, Arimura Y, Mizukami Y, Horikoshi N, Saikusa K, Akashi S, Nishimura Y, Park SY, Nogami J, Maehara K, Ohkawa Y, Matsumoto A, Kono H, Inoue R, Sugiyama M, Kurumizaka H (2017) "Crystal structure of the overlapping dinucleosome composed of hexasome and octasome." Science, 356, 205-208. doi: 10.1126/science.aak9867. Crystal structure of unusual nucleosome . ➥(1) [+]:CcT/AGG, is-WC-paired, is-in-duplex, other-contacts
5ke7 transcription-DNA X-ray (2.06 Å) Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X (2016) "Distinctive Klf4 mutants determine preference for DNA methylation status." Nucleic Acids Res., 44, 10177-10185. doi: 10.1093/nar/gkw774. Mouse klf4 znf1-3 and tpg-mpa sequence DNA complex structure . ➥(1) [-]:TGT/AcA, is-WC-paired, is-in-duplex, other-contacts
5ke8 transcription-DNA X-ray (2.45 Å) Hashimoto H, Wang D, Steves AN, Jin P, Blumenthal RM, Zhang X, Cheng X (2016) "Distinctive Klf4 mutants determine preference for DNA methylation status." Nucleic Acids Res., 44, 10177-10185. doi: 10.1093/nar/gkw774. Mouse klf4 e446p znf1-3 and mpg-mpg sequence DNA complex structure . ➥(2) [+]:GcG/cGC, [-]:cGT/AcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
5kl4 transcription-DNA X-ray (1.783 Å) Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X (2016) "Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications." Nucleic Acids Res., 44, 10165-10176. doi: 10.1093/nar/gkw766. Wilms tumor protein (wt1) znf2-4 q369h in complex with formylated DNA . ➥(2) [-]:cGT/AcG, is-WC-paired, is-in-duplex, other-contacts
5kl5 transcription-DNA X-ray (2.289 Å) Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X (2016) "Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications." Nucleic Acids Res., 44, 10165-10176. doi: 10.1093/nar/gkw766. Wilms tumor protein (wt1) znf2-4 q369h in complex with carboxylated DNA . ➥(1) [-]:cGT/AcG, is-WC-paired, is-in-duplex, other-contacts
5kl7 transcription-DNA X-ray (1.579 Å) Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X (2016) "Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications." Nucleic Acids Res., 44, 10165-10176. doi: 10.1093/nar/gkw766. Wilms tumor protein (wt1) znf2-4q369r in complex with carboxylated DNA . ➥(1) [-]:cGT/AcG, is-WC-paired, is-in-duplex, other-contacts
5lty transcription X-ray (2.66 Å) Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J (2017) "Impact of cytosine methylation on DNA binding specificities of human transcription factors." Science, 356. doi: 10.1126/science.aaj2239. Homeobox transcription factor cdx2 bound to methylated DNA . ➥(2) [+]:AcG/cGT, hydrophobic-with-AA, is-WC-paired, is-in-duplex
5lux transcription X-ray (3.23 Å) Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J (2017) "Impact of cytosine methylation on DNA binding specificities of human transcription factors." Science, 356. doi: 10.1126/science.aaj2239. Homeobox transcription factor cdx1 bound to methylated DNA . ➥(4) [+]:AcG/cGT, [-]:cGA/TcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex
5mcv transcription X-ray (1.6 Å) Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg H, Shakked Z (2018) "New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins." Structure, 26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006. New insights into the role of DNA shape on its recognition by p53 proteins (complex p53dbd-lwc1) . ➥(4) [+]:gcG/Cgc, [-]:Cgc/gcG, is-WC-paired, is-in-duplex, stacking-with-AA
5mcw transcription X-ray (1.897 Å) Golovenko D, Brauning B, Vyas P, Haran TE, Rozenberg H, Shakked Z (2018) "New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins." Structure, 26, 1237-1250.e6. doi: 10.1016/j.str.2018.06.006. New insights into the role of DNA shape on its recognition by p53 proteins (complex p53dbd-lwc2) . ➥(4) [+]:gcG/Cgc, [-]:Cgc/gcG, is-WC-paired, is-in-duplex, stacking-with-AA
5mht transferase-DNA X-ray (2.7 Å) O'Gara M, Roberts RJ, Cheng X (1996) "A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase." J.Mol.Biol., 263, 597-606. doi: 10.1006/jmbi.1996.0601. Ternary structure of hhai methyltransferase with hemimethylated DNA and adohcy . ➥(1) [+]:GcC/GGC, hydrophobic-with-AA, is-WC-paired, is-in-duplex
5szx transcription regulator-DNA X-ray (2.251 Å) Hong S, Wang D, Horton JR, Zhang X, Speck SH, Blumenthal RM, Cheng X (2017) "Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta." Nucleic Acids Res., 45, 2503-2515. doi: 10.1093/nar/gkx057. Epstein-barr virus zta DNA binding domain homodimer in complex with methylated DNA . ➥(2) [+]:TcG/cGA, [-]:cGC/GcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
5t00 transcription regulator-DNA X-ray (2.19 Å) Hashimoto H, Wang D, Horton JR, Zhang X, Corces VG, Cheng X (2017) "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA." Mol. Cell, 66, 711-720.e3. doi: 10.1016/j.molcel.2017.05.004. Human ctcf znf3-7 and methylated DNA complex . ➥(4) [+]:GcG/cGC, [-]:cGC/GcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
5t01 transcription regulator-DNA X-ray (1.89 Å) Hong S, Wang D, Horton JR, Zhang X, Speck SH, Blumenthal RM, Cheng X (2017) "Methyl-dependent and spatial-specific DNA recognition by the orthologous transcription factors human AP-1 and Epstein-Barr virus Zta." Nucleic Acids Res., 45, 2503-2515. doi: 10.1093/nar/gkx057. Human c-jun DNA binding domain homodimer in complex with methylated DNA . ➥(1) [-]:CGT/AcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex
5vmu transcription-DNA X-ray (2.346 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2018) "CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso." Biochemistry, 57, 2109-2120. doi: 10.1021/acs.biochem.8b00065. Kaiso (zbtb33) zinc finger DNA binding domain in complex with a double cpg-methylated DNA resembling the specific kaiso binding sequence (kbs) . ➥(4) [+]:CcG/cGG, [+]:GcG/cGc, [-]:cGA/TcG, [-]:cGc/GcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
5vmv transcription-DNA X-ray (2.313 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2018) "CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso." Biochemistry, 57, 2109-2120. doi: 10.1021/acs.biochem.8b00065. Kaiso (zbtb33) zinc finger DNA binding domain in complex with its double cpg-methylated DNA consensus binding site . ➥(4) [+]:GcG/cGc, [+]:TcG/cGA, [-]:cGA/TcG, [-]:cGc/GcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
5vmw transcription-DNA X-ray (2.397 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2018) "CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso." Biochemistry, 57, 2109-2120. doi: 10.1021/acs.biochem.8b00065. Kaiso (zbtb33) zinc finger DNA binding domain in complex with a double cpg-methylated DNA resembling the specific kaiso binding sequence (kbs) . ➥(4) [+]:CcG/cGG, [+]:GcG/cGc, [-]:cGA/TcG, [-]:cGc/GcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
5vmx transcription-DNA X-ray (2.05 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2018) "CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso." Biochemistry, 57, 2109-2120. doi: 10.1021/acs.biochem.8b00065. Kaiso (zbtb33) zinc finger DNA binding domain in complex with a hemi cpg-methylated DNA resembling the specific kaiso binding sequence (kbs) . ➥(2) [+]:CcG/CGG, [+]:GcG/CGC, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
5vmy transcription-DNA X-ray (2.002 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2018) "CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso." Biochemistry, 57, 2109-2120. doi: 10.1021/acs.biochem.8b00065. Kaiso (zbtb33) zinc finger DNA binding domain in complex with a hemi cpg-methylated DNA resembling the specific kaiso binding sequence (kbs) . ➥(2) [+]:CcG/CGG, [+]:GcG/CGC, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
5vmz transcription-DNA X-ray (2.319 Å) Nikolova EN, Stanfield RL, Dyson HJ, Wright PE (2018) "CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso." Biochemistry, 57, 2109-2120. doi: 10.1021/acs.biochem.8b00065. Kaiso (zbtb33) e535q mutant zinc finger DNA binding domain in complex with a double cpg-methylated DNA resembling the specific kaiso binding sequence (kbs) . ➥(4) [+]:CcG/cGG, [+]:GcG/cGc, [-]:cGA/TcG, [-]:cGc/GcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
6a5n gene regulation-DNA X-ray (2.4 Å) Li X, Harris CJ, Zhong Z, Chen W, Liu R, Jia B, Wang Z, Li S, Jacobsen SE, Du J (2018) "Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation." Proc. Natl. Acad. Sci. U.S.A., 115, E8793-E8802. doi: 10.1073/pnas.1809841115. Crystal structure of arabidopsis thaliana suvh6 in complex with methylated DNA . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
6c1a DNA binding protein-DNA X-ray (2.05 Å) Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J (2018) "Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA." J. Biol. Chem., 293, 7344-7354. doi: 10.1074/jbc.RA118.001785. Mbd2 in complex with methylated DNA . ➥(2) [-]:TGT/AcA, is-WC-paired, is-in-duplex, other-contacts
6c1t DNA binding protein-DNA X-ray (1.84 Å) Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J (2018) "Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA." J. Biol. Chem., 293, 7344-7354. doi: 10.1074/jbc.RA118.001785. Mbd2 in complex with a partially methylated DNA . ➥(1) [+]:AcA/TGT, is-WC-paired, is-in-duplex, other-contacts
6c1u DNA binding protein-DNA X-ray (2.3 Å) Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J (2018) "Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA." J. Biol. Chem., 293, 7344-7354. doi: 10.1074/jbc.RA118.001785. Mbd2 in complex with a deoxy-oligonucleotide . ➥(2) [-]:TGT/AcA, is-WC-paired, is-in-duplex, other-contacts
6c1y DNA binding protein-DNA X-ray (2.3 Å) Lei M, Tempel W, Chen S, Liu K, Min J (2019) "Plasticity at the DNA recognition site of the MeCP2 mCG-binding domain." Biochim Biophys Acta Gene Regul Mech, 1862, 194409. doi: 10.1016/j.bbagrm.2019.194409. Mbd of human mecp2 in complex with methylated DNA . ➥(4) [+]:CcG/cGG, [-]:cGG/CcG, is-WC-paired, is-in-duplex, stacking-with-AA
6c2f DNA binding protein-DNA X-ray (2.65 Å) Liu K, Xu C, Tempel W, Arrowsmith CH, Bountra C, Edwards AM, Min J, Structural Genomics Consortium "MBD2 in complex with methylated DNA." Mbd2 in complex with methylated DNA . ➥(6) [+]:CcG/CGG, is-WC-paired, is-in-duplex, stacking-with-AA
6cc8 DNA binding protein-DNA X-ray (1.95 Å) Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J (2019) "Structural analyses reveal that MBD3 is a methylated CG binder." Febs J., 286, 3240-3254. doi: 10.1111/febs.14850. Crystal structure mbd3 mbd domain in complex with methylated cpg DNA . ➥(4) [+]:AcG/cGT, [-]:cGT/AcG, is-WC-paired, is-in-duplex, stacking-with-AA
6ccg transcription X-ray (1.9 Å) Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J (2019) "Structural analyses reveal that MBD3 is a methylated CG binder." Febs J., 286, 3240-3254. doi: 10.1111/febs.14850. Crystal structure mbd3 mbd domain in complex with methylated cpg DNA . ➥(4) [+]:GcG/cGC, [-]:cGC/GcG, is-WC-paired, is-in-duplex, stacking-with-AA
6ceu transcription-DNA X-ray (2.005 Å) Liu K, Lei M, Wu Z, Gan B, Cheng H, Li Y, Min J (2019) "Structural analyses reveal that MBD3 is a methylated CG binder." Febs J., 286, 3240-3254. doi: 10.1111/febs.14850. Mbd3 mbd in complex with methylated, non-palindromic cpg DNA: alternative interpretation of crystallographic data . ➥(4) [+]:GcG/cGC, [-]:cGT/AcG, is-WC-paired, is-in-duplex, stacking-with-AA
6cnp transcription-DNA X-ray (2.1 Å) Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J (2018) "Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA." J. Biol. Chem., 293, 7344-7354. doi: 10.1074/jbc.RA118.001785. Crystal structure of mbd2 complex with methylated cpg island . ➥(4) [+]:CcG/cGG, [-]:cGG/CcG, is-WC-paired, is-in-duplex, stacking-with-AA
6cnq transcription-DNA X-ray (2.151 Å) Liu K, Xu C, Lei M, Yang A, Loppnau P, Hughes TR, Min J (2018) "Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA." J. Biol. Chem., 293, 7344-7354. doi: 10.1074/jbc.RA118.001785. Mbd2 in complex with methylated DNA . ➥(4) [+]:AcG/cGT, [-]:cGT/AcG, is-WC-paired, is-in-duplex, stacking-with-AA
6d1t DNA binding protein-DNA X-ray (2.25 Å) Liu K, Xu C, Tempel W, Arrowsmith CH, Bountra C, Edwards AM, Min J, Structural Genomics Consortium "Complex of MBD1-MBD and methylated DNA." Complex of mbd1-mbd and methylated DNA . ➥(2) [+]:AcG/cGT, [-]:cGT/AcG, is-WC-paired, is-in-duplex, stacking-with-AA
6e93 DNA binding protein-DNA X-ray (1.747 Å) Hudson NO, Whitby FG, Buck-Koehntop BA (2018) "Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38." J. Biol. Chem., 293, 19835-19843. doi: 10.1074/jbc.RA118.005147. Crystal structure of zbtb38 c-terminal zinc fingers 6-9 in complex with methylated DNA . ➥(3) [+]:CcG/cGG, [+]:GcG/cGC, [-]:cGA/TcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex, other-contacts
6e94 DNA binding protein-DNA X-ray (1.594 Å) Hudson NO, Whitby FG, Buck-Koehntop BA (2018) "Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38." J. Biol. Chem., 293, 19835-19843. doi: 10.1074/jbc.RA118.005147. Crystal structure of zbtb38 c-terminal zinc fingers 6-9 k1055r in complex with methylated DNA . ➥(3) [+]:CcG/cGG, [+]:GcG/cGC, [-]:cGA/TcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
6jnm DNA binding protein-DNA X-ray (2.05 Å) Qiu Q, Mei H, Deng X, He K, Wu B, Yao Q, Zhang J, Lu F, Ma J, Cao X (2019) "DNA methylation repels targeting of Arabidopsis REF6." Nat Commun, 10, 2063. doi: 10.1038/s41467-019-10026-1. Ref6 znf2-4-nac004-mc3 complex . ➥(2) [+]:TcT/AGA, [-]:AGA/TcT, is-WC-paired, is-in-duplex, other-contacts
6jnn DNA binding protein-DNA X-ray (2.6 Å) Qiu Q, Mei H, Deng X, He K, Wu B, Yao Q, Zhang J, Lu F, Ma J, Cao X (2019) "DNA methylation repels targeting of Arabidopsis REF6." Nat Commun, 10, 2063. doi: 10.1038/s41467-019-10026-1. Ref6 znf2-4-nac004-mc1 complex . ➥(4) [+]:TcT/AGA, [-]:AGA/TcT, is-WC-paired, is-in-duplex, other-contacts
6jtq DNA binding protein-DNA X-ray (2.48 Å) Liu L, Yi C "RVD HA specifically contacts 5mC through van der Waals interactions." Rvd ha specifically contacts 5mc through van der waals interactions . ➥(2) [+]:TcG/CGA, is-WC-paired, is-in-duplex, stacking-with-AA
6jvz DNA binding protein-DNA X-ray (2.48 Å) Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J (2020) "Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors." J.Mol.Biol., 432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023. Rvd ha specifically contacts 5mc through van der waals interactions . ➥(2) [+]:TcG/CGA, is-WC-paired, is-in-duplex, stacking-with-AA
6jw1 DNA binding protein-DNA X-ray (2.49 Å) Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J (2020) "Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors." J.Mol.Biol., 432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023. Universal rvd r* accommodates 5mc via water-mediated interactions . ➥(2) [+]:TcG/CGA, is-WC-paired, is-in-duplex, stacking-with-AA
6jw3 DNA binding protein-DNA X-ray (3.1 Å) Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J (2020) "Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors." J.Mol.Biol., 432, 1035-1047. doi: 10.1016/j.jmb.2019.11.023. Degenerate rvd rg forms a distinct loop conformation . ➥(4) [+]:TcG/CGA, is-WC-paired, is-in-duplex, stacking-with-AA
6lew DNA binding protein-DNA X-ray (2.48 Å) Liu L, Yi C "RVD HA specifically contacts 5mC through van der Waals interactions." Rvd ha specifically contacts 5mc through van der waals interactions . ➥(2) [+]:TcG/CGA, is-WC-paired, is-in-duplex, stacking-with-AA
6m2v DNA binding protein-DNA X-ray (3.0 Å) Abhishek S, Nakarakanti NK, Deeksha W, Rajakumara E (2021) "Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA." Int.J.Biol.Macromol., 170, 514-522. doi: 10.1016/j.ijbiomac.2020.12.149. Crystal structure of uhrf1 sra complexed with fully-mchg DNA. . ➥(2) not-WC-paired, not-in-duplex, stacking-with-AA
6mg1 transcription-DNA X-ray (1.75 Å) Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal RM, Cheng X (2019) "Structural basis for effects of CpA modifications on C/EBP beta binding of DNA." Nucleic Acids Res., 47, 1774-1785. doi: 10.1093/nar/gky1264. C-terminal bzip domain of human c-ebpbeta with 16bp methylated oligonucleotide containing consensus recognition sequence-c2 crystal form . ➥(4) [+]:GcA/TGc, [+]:GcG/cGc, [-]:TGc/GcA, [-]:cGc/GcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex, stacking-with-AA
6mg2 transcription-DNA X-ray (1.928 Å) Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal RM, Cheng X (2019) "Structural basis for effects of CpA modifications on C/EBP beta binding of DNA." Nucleic Acids Res., 47, 1774-1785. doi: 10.1093/nar/gky1264. C-terminal bzip domain of human c-ebpbeta with 16bp methylated oligonucleotide containing consensus recognition sequence-c2221 crystal form . ➥(4) [+]:GcA/TGc, [+]:GcG/cGc, [-]:TGc/GcA, [-]:cGc/GcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
6mg3 transcription-DNA X-ray (2.05 Å) Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal RM, Cheng X (2019) "Structural basis for effects of CpA modifications on C/EBP beta binding of DNA." Nucleic Acids Res., 47, 1774-1785. doi: 10.1093/nar/gky1264. V285a mutant of the c-terminal bzip domain of human c-ebpbeta with 16bp methylated oligonucleotide containing consensus recognition sequence . ➥(4) [+]:GcA/TGc, [+]:GcG/cGc, [-]:TGc/GcA, [-]:cGc/GcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
6mht transferase-DNA X-ray (2.05 Å) Kumar S, Horton JR, Jones GD, Walker RT, Roberts RJ, Cheng X (1997) "DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase." Nucleic Acids Res., 25, 2773-2783. doi: 10.1093/nar/25.14.2773. Ternary structure of hhai methyltransferase with adohcy and DNA containing 4'-thio-2'deoxycytidine at the target . ➥(1) [+]:GcC/GGC, hydrophobic-with-AA, is-WC-paired, is-in-duplex
6ml6 transcription-DNA X-ray (1.54 Å) Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X (2019) "Structural basis of specific DNA binding by the transcription factor ZBTB24." Nucleic Acids Res., 47, 8388-8398. doi: 10.1093/nar/gkz557. Zbtb24 zinc fingers 4-8 with 19+1mer DNA oligonucleotide (sequence 4 with a cpa 5mc modification) . ➥(1) [+]:GcA/TGC, is-WC-paired, is-in-duplex, stacking-with-AA
6ml7 transcription-DNA X-ray (1.75 Å) Ren R, Hardikar S, Horton JR, Lu Y, Zeng Y, Singh AK, Lin K, Coletta LD, Shen J, Lin Kong CS, Hashimoto H, Zhang X, Chen T, Cheng X (2019) "Structural basis of specific DNA binding by the transcription factor ZBTB24." Nucleic Acids Res., 47, 8388-8398. doi: 10.1093/nar/gkz557. Zbtb24 zinc fingers 4-8 with 19+1mer DNA oligonucleotide (sequence 4 with a cpg 5mc modification) . ➥(1) [+]:AcG/CGT, is-WC-paired, is-in-duplex, other-contacts
6ogk DNA binding protein-DNA X-ray (1.65 Å) Lei M, Tempel W, Chen S, Liu K, Min J (2019) "Plasticity at the DNA recognition site of the MeCP2 mCG-binding domain." Biochim Biophys Acta Gene Regul Mech, 1862, 194409. doi: 10.1016/j.bbagrm.2019.194409. Mecp2 mbd in complex with DNA . ➥(1) [+]:AcA/TGT, is-WC-paired, is-in-duplex, other-contacts
6r64 hydrolase X-ray (2.64 Å) Slyvka A, Zagorskaite E, Czapinska H, Sasnauskas G, Bochtler M (2019) "Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping." Nucleic Acids Res., 47, 11943-11955. doi: 10.1093/nar/gkz1017. N-terminal domain of modification dependent ecokmcra restriction endonuclease (neco) in complex with c5mcgg target sequence . ➥(4) [+]:CcG/cGG, [-]:cGG/CcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex, stacking-with-AA
6t21 hydrolase X-ray (2.07 Å) Slyvka A, Zagorskaite E, Czapinska H, Sasnauskas G, Bochtler M (2019) "Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping." Nucleic Acids Res., 47, 11943-11955. doi: 10.1093/nar/gkz1017. N-terminal domain of ecokmcra restriction endonuclease (neco) in complex with t5mcga target sequence . ➥(4) [+]:TcG/cGA, [-]:cGA/TcG, hydrophobic-with-AA, is-WC-paired, is-in-duplex, stacking-with-AA
6w8v transferase-DNA X-ray (3.12 Å) Adam S, Anteneh H, Hornisch M, Wagner V, Lu J, Radde NE, Bashtrykov P, Song J, Jeltsch A (2020) "DNMT1 activity, base flipping mechanism and genome-wide DNA methylation are regulated by the DNA sequence context." Nat Commun. Crystal structure of mouse dnmt1 in complex with acg DNA . ➥(2) [+]:Cc./.GG, is-WC-paired, is-in-duplex, stacking-with-AA
6w8w transferase-DNA X-ray (3.0 Å) Adam S, Anteneh H, Hornisch M, Wagner V, Lu J, Radde NE, Bashtrykov P, Song J, Jeltsch A (2020) "DNMT1 activity, base flipping mechanism and genome-wide DNA methylation are regulated by the DNA sequence context." Nat Commun. Crystal structure of mouse dnmt1 in complex with ccg DNA . ➥(2) [+]:Ac./.GT, is-WC-paired, is-in-duplex, stacking-with-AA
6x6e DNA binding protein X-ray (2.0 Å) Liu X, Weikum ER, Tilo D, Vinson C, Ortlund EA (2021) "Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element." Nucleic Acids Res., 49, 8923-8933. doi: 10.1093/nar/gkab605. Glucocorticoid receptor DNA binding domain in complex with methylated precursor for a modern recognition element (methylated pre-gbs) . ➥(2) [+]:GcG/CGC, [-]:CGG/CcG, is-WC-paired, is-in-duplex, stacking-with-AA
6x9i transferase X-ray (2.2 Å) Pappalardi MB, Keenan K, Cockerill M, Kellner WA, Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE, Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW, Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X, Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG, Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM, Waddell I, Kruger RG, McCabe MT (2021) "Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia." Nat Cancer, 2, 1002-1017. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA . ➥(1) [+]:CcC/GGG, is-WC-paired, is-in-duplex, stacking-with-AA
6x9j transferase-transferase inhibitor-DNA X-ray (1.79 Å) Pappalardi MB, Keenan K, Cockerill M, Kellner WA, Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE, Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW, Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X, Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG, Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM, Waddell I, Kruger RG, McCabe MT (2021) "Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia." Nat Cancer, 2, 1002-1017. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA and inhibitor gsk3830052 . ➥(1) [+]:CcG/uGG, is-WC-paired, is-in-duplex, stacking-with-AA
6x9k transferase-transferase inhibitor-DNA X-ray (2.65 Å) Pappalardi MB, Keenan K, Cockerill M, Kellner WA, Stowell A, Sherk C, Wong K, Pathuri S, Briand J, Steidel M, Chapman P, Groy A, Wiseman AK, McHugh CF, Campobasso N, Graves AP, Fairweather E, Werner T, Raoof A, Butlin RJ, Rueda L, Horton JR, Fosbenner DT, Zhang C, Handler JL, Muliaditan M, Mebrahtu M, Jaworski JP, McNulty DE, Burt C, Eberl HC, Taylor AN, Ho T, Merrihew S, Foley SW, Rutkowska A, Li M, Romeril SP, Goldberg K, Zhang X, Kershaw CS, Bantscheff M, Jurewicz AJ, Minthorn E, Grandi P, Patel M, Benowitz AB, Mohammad HP, Gilmartin AG, Prinjha RK, Ogilvie D, Carpenter C, Heerding D, Baylin SB, Jones PA, Cheng X, King BW, Luengo JI, Jordan AM, Waddell I, Kruger RG, McCabe MT (2021) "Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia." Nat Cancer, 2, 1002-1017. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA and inhibitor gsk3685032a . ➥(1) [+]:CcG/uGG, is-WC-paired, is-in-duplex, stacking-with-AA
6ykf hydrolase X-ray (1.48 Å) Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz T, Xu SY, Bochtler M (2021) "Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA." Nucleic Acids Res., 49, 1708-1723. doi: 10.1093/nar/gkaa1218. Vcam4i restriction endonuclease in the presence of 5mc-modified ssDNA . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
6ymg hydrolase X-ray (3.14 Å) Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz T, Xu SY, Bochtler M (2021) "Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA." Nucleic Acids Res., 49, 1708-1723. doi: 10.1093/nar/gkaa1218. Vcam4i restriction endonuclease in complex with 5mc-modified dsDNA . ➥(2) not-WC-paired, not-in-duplex, stacking-with-AA
7cy6 transferase X-ray (2.1 Å) Li W, Zhang T, Sun M, Shi Y, Zhang XJ, Xu GL, Ding J (2021) "Molecular mechanism for vitamin C-derived C 5 -glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1." Nat Commun, 12, 744. doi: 10.1038/s41467-021-21061-2. Crystal structure of cmd1 in complex with 5mc-DNA . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
7cy8 transferase X-ray (2.4 Å) Li W, Zhang T, Sun M, Shi Y, Zhang XJ, Xu GL, Ding J (2021) "Molecular mechanism for vitamin C-derived C 5 -glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1." Nat Commun, 12, 744. doi: 10.1038/s41467-021-21061-2. Crystal structure of cmd1 in complex with 5mc-DNA and vitamin c . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
7fef DNA binding protein-DNA X-ray (2.39 Å) Wu Z, Chen S, Zhou M, Jia L, Li Z, Zhang X, Min J, Liu K (2022) "Family-wide Characterization of Methylated DNA Binding Ability of Arabidopsis MBDs." J.Mol.Biol., 434, 167404. doi: 10.1016/j.jmb.2021.167404. Crystal structure of atmbd6 with DNA . ➥(2) [+]:AcG/cGT, [-]:cGT/AcG, is-WC-paired, is-in-duplex, stacking-with-AA
7mwk DNA binding protein-DNA X-ray (2.453 Å) Liu K, Dong A, Edwards AM, Arrowsmith CH, Min J, Structural Genomics Consortium (SGC) "Crystal structure of MBD2 with DNA." Crystal structure of mbd2 with DNA . ➥(4) [+]:AcG/cGT, [-]:cGT/AcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
7mwm DNA binding protein-DNA X-ray (1.601 Å) Liu K, Dong A, Edwards AM, Arrowsmith CH, Min J, Structural Genomics Consortium (SGC) "Crystal structure of MBD2 with DNA." Crystal structure of mbd2 with DNA . ➥(4) [+]:AcG/cGT, [-]:cGT/AcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
7ne3 oxidoreductase X-ray (2.26 Å) Ravichandran M, Rafalski D, Davies CI, Ortega-Recalde O, Nan X, Glanfield CR, Kotter A, Misztal K, Wang AH, Wojciechowski M, Razew M, Mayyas IM, Kardailsky O, Schwartz U, Zembrzycki K, Morison IM, Helm M, Weichenhan D, Jurkowska RZ, Krueger F, Plass C, Zacharias M, Bochtler M, Hore TA, Jurkowski TP (2022) "Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function." Sci Adv, 8, eabm2427. doi: 10.1126/sciadv.abm2427. Human tet2 in complex with favourable DNA substrate. . ➥(2) [-]:.GT/Ac., is-WC-paired, is-in-duplex, not-WC-paired, not-in-duplex, stacking-with-AA
7ne6 oxidoreductase X-ray (2.3 Å) Ravichandran M, Rafalski D, Davies CI, Ortega-Recalde O, Nan X, Glanfield CR, Kotter A, Misztal K, Wang AH, Wojciechowski M, Razew M, Mayyas IM, Kardailsky O, Schwartz U, Zembrzycki K, Morison IM, Helm M, Weichenhan D, Jurkowska RZ, Krueger F, Plass C, Zacharias M, Bochtler M, Hore TA, Jurkowski TP (2022) "Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function." Sci Adv, 8, eabm2427. doi: 10.1126/sciadv.abm2427. Human tet2 in complex with unfavourable DNA substrate. . ➥(2) [-]:.GC/Gc., is-WC-paired, is-in-duplex, not-WC-paired, not-in-duplex, stacking-with-AA
7nx5 viral protein X-ray (2.5 Å) Bernaudat F, Gustems M, Gunther J, Oliva MF, Buschle A, Gobel C, Pagniez P, Lupo J, Signor L, Muller CW, Morand P, Sattler M, Hammerschmidt W, Petosa C (2022) "Structural basis of DNA methylation-dependent site selectivity of the Epstein-Barr virus lytic switch protein ZEBRA/Zta/BZLF1." Nucleic Acids Res., 50, 490-511. doi: 10.1093/nar/gkab1183. Crystal structure of the epstein-barr virus protein zebra (bzlf1, zta) bound to a methylated DNA duplex . ➥(3) [+]:TcG/cGA, [-]:cGC/GcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
7r77 transferase-DNA cryo-EM (3.0 Å) Wang J, Catania S, Wang C, de la Cruz MJ, Rao B, Madhani HD, Patel DJ (2022) "Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance." Mol.Cell, 82, 1186-1198.e6. doi: 10.1016/j.molcel.2022.01.028. cryo-EM structure of dnmt5 binary complex with hemimethylated DNA . ➥(1) [+]:GcC/GGC, is-WC-paired, is-in-duplex, other-contacts
7r78 transferase-DNA cryo-EM (3.5 Å) Wang J, Catania S, Wang C, de la Cruz MJ, Rao B, Madhani HD, Patel DJ (2022) "Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance." Mol.Cell, 82, 1186-1198.e6. doi: 10.1016/j.molcel.2022.01.028. cryo-EM structure of dnmt5 quaternary complex with hemimethylated DNA, amp-pnp and sah . ➥(1) [+]:Gc./.GC, is-WC-paired, is-in-duplex, other-contacts
7ray DNA binding protein-DNA X-ray (1.78 Å) Liu K, Dong A, Loppnau P, Edwards AM, Arrowsmith CH, Min J, Structural Genomics Consortium (SGC) "Crystal structure of MBD2 with DNA." Crystal structure of mbd2 with DNA . ➥(2) [+]:AcG/cGT, [-]:cGT/AcG, is-WC-paired, is-in-duplex, stacking-with-AA
7sfc transferase-transferase inhibitor X-ray (1.97 Å) Horton JR, Pathuri S, Wong K, Ren R, Rueda L, Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB, Zhang X, King BW, Cheng X (2022) "Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors." Structure, 30, 793-802.e5. doi: 10.1016/j.str.2022.03.009. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA and inhibitor gsk3735967a . ➥(1) [+]:CcG/uGG, is-WC-paired, is-in-duplex, stacking-with-AA
7sfd transferase-transferase inhibitor X-ray (2.09 Å) Horton JR, Pathuri S, Wong K, Ren R, Rueda L, Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB, Zhang X, King BW, Cheng X (2022) "Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors." Structure, 30, 793-802.e5. doi: 10.1016/j.str.2022.03.009. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA and inhibitor gsk3543105a . ➥(1) [+]:CcG/uGG, is-WC-paired, is-in-duplex, stacking-with-AA
7sfe transferase-transferase inhibitor X-ray (2.55 Å) Horton JR, Pathuri S, Wong K, Ren R, Rueda L, Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB, Zhang X, King BW, Cheng X (2022) "Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors." Structure, 30, 793-802.e5. doi: 10.1016/j.str.2022.03.009. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA and inhibitor gsk3830334a . ➥(1) [+]:CcG/uGG, is-WC-paired, is-in-duplex, stacking-with-AA
7sff transferase-transferase inhibitor X-ray (2.05 Å) Horton JR, Pathuri S, Wong K, Ren R, Rueda L, Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB, Zhang X, King BW, Cheng X (2022) "Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors." Structure, 30, 793-802.e5. doi: 10.1016/j.str.2022.03.009. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA and inhibitor gsk3852279b . ➥(1) [+]:CcG/uGG, is-WC-paired, is-in-duplex, stacking-with-AA
7sfg transferase-transferase inhibitor X-ray (2.43 Å) Horton JR, Pathuri S, Wong K, Ren R, Rueda L, Fosbenner DT, Heerding DA, McCabe MT, Pappalardi MB, Zhang X, King BW, Cheng X (2022) "Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors." Structure, 30, 793-802.e5. doi: 10.1016/j.str.2022.03.009. Human dnmt1(729-1600) bound to zebularine-containing 12mer dsDNA and cofactor sam . ➥(1) [+]:CcC/GGG, is-WC-paired, is-in-duplex, stacking-with-AA
7t02 transferase-DNA cryo-EM (3.8 Å) Wang J, Catania S, Wang C, de la Cruz MJ, Rao B, Madhani HD, Patel DJ (2022) "Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance." Mol.Cell, 82, 1186-1198.e6. doi: 10.1016/j.molcel.2022.01.028. cryo-EM structure of dnmt5 pseudo-ternary complex solved by incubation with hemimethylated DNA and sam . ➥(1) [+]:Gc./.GC, is-WC-paired, is-in-duplex, other-contacts
7xi9 transferase-DNA cryo-EM (2.52 Å) Kikuchi A, Onoda H, Yamaguchi K, Kori S, Matsuzawa S, Chiba Y, Tanimoto S, Yoshimi S, Sato H, Yamagata A, Shirouzu M, Adachi N, Sharif J, Koseki H, Nishiyama A, Nakanishi M, Defossez PA, Arita K (2022) "Structural basis for activation of DNMT1." Nat Commun, 13, 7130. doi: 10.1038/s41467-022-34779-4. cryo-EM structure of human dnmt1 (aa:351-1616) in complex with ubiquitinated h3 and hemimethylated DNA analog (cxxc-ordered form) . ➥(1) [+]:Ac./.GT, is-WC-paired, is-in-duplex, stacking-with-AA
7xib transferase-DNA cryo-EM (2.23 Å) Kikuchi A, Onoda H, Yamaguchi K, Kori S, Matsuzawa S, Chiba Y, Tanimoto S, Yoshimi S, Sato H, Yamagata A, Shirouzu M, Adachi N, Sharif J, Koseki H, Nishiyama A, Nakanishi M, Defossez PA, Arita K (2022) "Structural basis for activation of DNMT1." Nat Commun, 13, 7130. doi: 10.1038/s41467-022-34779-4. cryo-EM structure of human dnmt1 (aa:351-1616) in complex with ubiquitinated h3 and hemimethylated DNA analog (cxxc-disordered form) . ➥(1) [+]:Ac./.GT, is-WC-paired, is-in-duplex, stacking-with-AA
7yhp DNA binding protein-DNA cryo-EM (3.1 Å) Du X, Yang Z, Xie G, Wang C, Zhang L, Yan K, Yang M, Li S, Zhu JK, Du J (2023) "Molecular basis of the plant ROS1-mediated active DNA demethylation." Nat.Plants, 9, 271-279. doi: 10.1038/s41477-022-01322-8. Cryoem structure of arabidopsis ros1 in complex with 5mc-dsDNA at 3.1 angstroms resolution . ➥(1) hydrophobic-with-AA, not-WC-paired, not-in-duplex
7yun DNA binding protein X-ray (2.13 Å) Liu K, Zhang J, Xiao Y, Yang A, Song X, Li Y, Chen Y, Hughes TR, Min J (2023) "Structural insights into DNA recognition by the BEN domain of the transcription factor BANP." J.Biol.Chem., 299, 104734. doi: 10.1016/j.jbc.2023.104734. Crystal structure of human bend6 ben domain in complex with methylated DNA . ➥(2) [+]:GcG/CGc, [-]:CGc/GcG, is-WC-paired, is-in-duplex, other-contacts, stacking-with-AA
8c56 transferase X-ray (2.4 Å) Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D, Bochtler M (2024) "Cytosine analogues as DNA methyltransferase substrates." Nucleic Acids Res., 52, 9267-9281. doi: 10.1093/nar/gkae568. Cpg specific m.mpei methyltransferase crystallized in the presence of 2'-deoxy-5-methylzebularine (5mz) and 5-methylcytosine containing dsDNA . ➥(1) [-]:GGC/GcC, is-WC-paired, is-in-duplex, stacking-with-AA
8c57 transferase X-ray (1.95 Å) Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D, Bochtler M (2024) "Cytosine analogues as DNA methyltransferase substrates." Nucleic Acids Res., 52, 9267-9281. doi: 10.1093/nar/gkae568. Cpg specific m.mpei methyltransferase crystallized in the presence of 5,6-dihydro-5-azacytosine (converted to 5m-dhac) and 5-methylcytosine containing dsDNA . ➥(1) [-]:GGC/GcC, is-WC-paired, is-in-duplex, stacking-with-AA
8c58 transferase X-ray (1.85 Å) Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D, Bochtler M (2024) "Cytosine analogues as DNA methyltransferase substrates." Nucleic Acids Res., 52, 9267-9281. doi: 10.1093/nar/gkae568. Cpg specific m.mpei methyltransferase crystallized in the presence of 5-hydroxycytosine and 5-methylcytosine containing dsDNA . ➥(1) [-]:GGC/GcC, is-WC-paired, is-in-duplex, stacking-with-AA
8c59 transferase X-ray (1.7 Å) Wojciechowski M, Czapinska H, Krwawicz J, Rafalski D, Bochtler M (2024) "Cytosine analogues as DNA methyltransferase substrates." Nucleic Acids Res., 52, 9267-9281. doi: 10.1093/nar/gkae568. Cpg specific m.mpei methyltransferase crystallized in the presence of 5-bromocytosine (converted to 5mc) and 5-methylcytosine containing dsDNA . ➥(2) [-]:GGC/GcC, hydrophobic-with-AA, is-WC-paired, is-in-duplex, not-WC-paired, not-in-duplex, stacking-with-AA
8eng transcription-DNA X-ray (1.25 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataagcggaagtggg) with hemi-methylated cpg (forward strand) . ➥(1) [+]:GcG/CGC, is-WC-paired, is-in-duplex, other-contacts
8eo1 transcription-DNA X-ray (1.28 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataagcggaagtggg) with hemi-methylated cpg (reverse strand) . ➥(1) [-]:CGG/CcG, is-WC-paired, is-in-duplex, other-contacts
8eo4 transcription-DNA X-ray (1.24 Å) Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK (2023) "DNA selection by the master transcription factor PU.1." Cell Rep, 42, 112671. doi: 10.1016/j.celrep.2023.112671. Human pu.1 ets-domain (165-270) bound to d(aataagcggaagtggg) with di-methylated cpg sites . ➥(2) [+]:GcG/cGC, [-]:cGG/CcG, is-WC-paired, is-in-duplex, other-contacts
8htx DNA binding protein X-ray (2.8 Å) Liu K, Zhang J, Xiao Y, Yang A, Song X, Li Y, Chen Y, Hughes TR, Min J (2023) "Structural insights into DNA recognition by the BEN domain of the transcription factor BANP." J.Biol.Chem., 299, 104734. doi: 10.1016/j.jbc.2023.104734. Crystal structure of banp in complex with methylated DNA . ➥(4) [+]:TcG/CGA, [-]:CGA/TcG, is-WC-paired, is-in-duplex, other-contacts
8ik4 DNA binding protein X-ray (2.1 Å) Adhav VA, Saikrishnan K "Structural basis of target recognition by the DNA binding domain of McrBC." Structure of DNA binding domain of mcrbc endonuclease bound to hemimethylated DNA: l68f mutant . ➥(1) not-WC-paired, not-in-duplex, stacking-with-AA
8jkk DNA binding protein-DNA X-ray (2.3 Å) Zhang L, Mu Y, Li T, Hu J, Lin H, Zhang L (2024) "Molecular basis of an atypical dsDNA 5mC/6mA bifunctional dioxygenase CcTet from Coprinopsis cinerea in catalyzing dsDNA 5mC demethylation." Nucleic Acids Res., 52, 3886-3895. doi: 10.1093/nar/gkae066. Crystal structure of the dioxygenase cctet from coprinopsis cinerea bound to 12bp 5-methylcytosine (5mc) containing duplex DNA . ➥(4) not-WC-paired, not-in-duplex, stacking-with-AA
8q5o hydrolase X-ray (2.33 Å) Szafran K, Rafalski D, Skowronek K, Wojciechowski M, Kazrani AA, Gilski M, Xu SY, Bochtler M (2024) "Structural analysis of the BisI family of modification dependent restriction endonucleases." Nucleic Acids Res., 52, 9103-9118. doi: 10.1093/nar/gkae634. N-terminal domain of restriction endonuclease eco15i with tetra-methylated target DNA. . ➥(4) [+]:GcT/AGc, [-]:TGc/GcA, hydrophobic-with-AA, is-WC-paired, is-in-duplex, stacking-with-AA
8rpx hydrolase X-ray (1.81 Å) Szafran K, Rafalski D, Skowronek K, Wojciechowski M, Kazrani AA, Gilski M, Xu SY, Bochtler M (2024) "Structural analysis of the BisI family of modification dependent restriction endonucleases." Nucleic Acids Res., 52, 9103-9118. doi: 10.1093/nar/gkae634. Nhoi restriction endonuclease in complex with quadruply methylated DNA target . ➥(10) [+]:GcA/TGc, [+]:GcT/AGc, [-]:AGc/GcT, [-]:TGc/GcA, hydrophobic-with-AA, is-WC-paired, is-in-duplex, not-WC-paired, not-in-duplex, other-contacts, stacking-with-AA
8tlk DNA binding protein-DNA X-ray (2.99 Å) Hardikar S, Ren R, Ying Z, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Dan J, Zhang X, Cheng X, Chen T (2023) "The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA." Biorxiv. doi: 10.1101/2023.12.15.571946. Cdca7 (human) binds non-b-form 32-mer DNA oligo containing a 5mc . ➥(2) [+]:TcG/CGT, [-]:CGT/TcG, is-WC-paired, is-in-duplex, stacking-with-AA
8xp8 DNA-antibiotic X-ray (1.64 Å) Lin SM, Huang HT, Fang PJ, Chang CF, Satange R, Chang CK, Chou SH, Neidle S, Hou MH (2024) "Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation." Nucleic Acids Res., 52, 8566-8579. doi: 10.1093/nar/gkae594. Crystal structure of d(acgmccgt-acggcgt) in complex with echinomycin . ➥(1) [-]:GGC/GcC, is-WC-paired, is-in-duplex, other-contacts
8xqc transferase cryo-EM (3.25 Å) Hayashi G, Takahashi Y, Kikuchi A, Kori S, Arita K, Murakami H "Activation of DNMT1 by Chemically Synthesized Dual monoubiquitinated PAF15 Protein." cryo-EM structure of human dnmt1 (aa:351-1616) in complex with ubiquitinated paf15 and hemimethylated DNA analog . ➥(1) [+]:Ac./.GT, is-WC-paired, is-in-duplex, stacking-with-AA
8yv8 DNA binding protein cryo-EM (3.0 Å) Wassing I, Nishiyama A, Arita K, Funabiki H "CDCA7 is a hemimethylated DNA adaptor for the nucleosome remodeler HELLS." cryo-EM structure of cdca7 bound to nucleosome including hemimethylated cpg site in widom601 positioning sequence. . ➥(1) [+]:TcG/CGA, is-WC-paired, is-in-duplex, stacking-with-AA
pdb-id class method authors reference annotation