5mC-DNA-protein interactions for PDB entry 6c2f [5mC-protein List · SNAP web server]
Summary information and primary citation
- PDB-id
- 6c2f; SNAP-derived features in text and JSON formats; DNAproDB
- Class
- DNA binding protein-DNA
- Method
- X-ray (2.65 Å)
- Summary
- Mbd2 in complex with methylated DNA
- Reference
- Liu K, Xu C, Tempel W, Arrowsmith CH, Bountra C, Edwards AM, Min J, Structural Genomics Consortium: "MBD2 in complex with methylated DNA."
- 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 B.5CM6: stacking-with-A.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG |
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No. 2 E.5CM6: stacking-with-D.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG |
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No. 3 H.5CM6: stacking-with-G.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG |
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No. 4 K.5CM6: stacking-with-J.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG |
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No. 5 N.5CM6: stacking-with-M.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG |
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No. 6 Q.5CM6: stacking-with-P.ARG188 is-WC-paired is-in-duplex [+]:CcG/CGG |
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