5mC-DNA-protein interactions for PDB entry 4gjr [5mC-protein List · SNAP web server]
Summary information and primary citation
- PDB-id
- 4gjr; SNAP-derived features in text and JSON formats; DNAproDB
- Class
- transcription-DNA
- Method
- X-ray (1.85 Å)
- Summary
- Crystal structure of the tal effector dhax3 bound to methylated dsDNA
- Reference
- Yan N, Deng D, Yan CY, Yin P, Pan XJ, Shi YG: "Crystal structure of a protein complex."
- Abstract
Cartoon-block schematics in six views (download the tarball)
List of 6 5mC-amino acid contacts
- The contacts include paired nucleotides (mostly a G in Watson-Crick G-C pairing), and amino-acids within a 4.5-A distance cutoff to base atoms of 5mC.
- The structure is oriented in the base reference frame of 5mC, allowing for easy comparison and direct superimposition between entries.
- The black sphere (•) denotes the 5-methyl carbon atom in 5mC.
No. 1 I.5CM8: hydrophobic-with-A.GLY437 hydrophobic-with-A.GLY438 is-WC-paired is-in-duplex [+]:TcT/AGA |
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No. 2 I.5CM11: stacking-with-A.ASP573 is-WC-paired is-in-duplex [+]:AcC/GGT |
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No. 3 I.5CM15: hydrophobic-with-A.GLY675 hydrophobic-with-A.GLY676 is-WC-paired is-in-duplex [+]:CcC/GGG |
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No. 4 G.5CM8: hydrophobic-with-B.GLY437 hydrophobic-with-B.GLY471 hydrophobic-with-B.GLY472 is-WC-paired is-in-duplex [+]:TcT/AGA |
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No. 5 G.5CM11: stacking-with-B.ASP573 is-WC-paired is-in-duplex [+]:AcC/GGT |
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No. 6 G.5CM15: hydrophobic-with-B.GLY675 hydrophobic-with-B.GLY676 is-WC-paired is-in-duplex [+]:CcC/GGG |
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