5mC-DNA-protein interactions for PDB entry 8yv8

Summary information and primary citation

PDB-id: 8yv8; SNAP-derived features in text and JSON formats; DNAproDB
Class: DNA binding protein
Method: cryo-EM (3.0 Å)
Summary: cryo-EM structure of cdca7 bound to nucleosome including hemimethylated cpg site in widom601 positioning sequence.
Reference: Wassing I, Nishiyama A, Arita K, Funabiki H: "CDCA7 is a hemimethylated DNA adaptor for the nucleosome remodeler HELLS."
Abstract

Cartoon-block schematics in six views (download the tarball)

PyMOL session file	Download PDB file	View in 3Dmol.js

List of 1 5mC-amino acid contact

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.5CM-58: `stacking-with-K.ARG274 is-WC-paired is-in-duplex [+]:TcG/CGA`