5mC interactions in PDB entry 6C1Y auto-curated with SNAP

Last updated on 2019-09-30 by Xiang-Jun Lu <xiangjun@x3dna.org>. The block schematics were created with DSSR and rendered using PyMOL.

Summary information and primary citation [schematics · contacts · top · homepage · tutorial]

PDB-id

6C1Y

Class

DNA binding protein-DNA

Method

X-ray (2.3 Å)

Summary

Mbd of human mecp2 in complex with methylated DNA
List of 4 5mC-amino acid contacts:

D.5CM6: stacking-with-A.ARG133 is-WC-paired is-in-duplex [+]:CcG/cGG

C.5CM6: stacking-with-A.ARG111 is-WC-paired is-in-duplex [-]:cGG/CcG

F.5CM6: stacking-with-B.ARG133 is-WC-paired is-in-duplex [+]:CcG/cGG

E.5CM6: stacking-with-B.ARG111 is-WC-paired is-in-duplex [-]:cGG/CcG

direct SNAP output · DNAproDB 2.0

Reference

Liu, K., Bian, C., Tempel, W., Wernimont, A.K., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium: "mbd of human mecp2 in complex with methylated DNA." to be published

Abstract

Base-block schematics in six views [summary · contacts · top · homepage · tutorial]

The 5-methylcytosine group (PDB ligand '5CM') is shown in space-filling model, with the methyl-carbon atom in black.
Watson-Crick base pairs are represented as long rectangular blocks with the minor-groove edge in black. Color code: A-T red, C-G yellow, G-C green, T-A blue.
Protein is shown as cartoon in purple. DNA backbones are shown ribbon, colored code by chain identifier.
The block schematics were created with 3DNA-DSSR, and images were rendered using PyMOL.
Download the PyMOL session file corresponding to the top-left image in the following panel.

List of 4 5mC-amino acid contacts [summary · schematics · top · homepage · tutorial]

The contacts include paired nucleotides (mostly a G in G-C pairing), and amino-acids within a 4.5-A distance cutoff to the base atoms of 5mC.
The structure is oriented in the 'standard' 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 D.5CM6: download PDB file for the 5mC entry stacking-with-A.ARG133 is-WC-paired is-in-duplex [+]:CcG/cGG
	No. 2 C.5CM6: download PDB file for the 5mC entry stacking-with-A.ARG111 is-WC-paired is-in-duplex [-]:cGG/CcG
	No. 3 F.5CM6: download PDB file for the 5mC entry stacking-with-B.ARG133 is-WC-paired is-in-duplex [+]:CcG/cGG
	No. 4 E.5CM6: download PDB file for the 5mC entry stacking-with-B.ARG111 is-WC-paired is-in-duplex [-]:cGG/CcG