5mC interactions in PDB entry 4GJP 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

4GJP

Class

transcription-DNA

Method

X-ray (1.94 Å)

Summary

Crystal structure of the tal effector dhax3 bound to dsDNA containing repetitive methyl-cpg
List of 4 5mC-amino acid contacts:

I.5CM6: stacking-with-A.ASN505 is-WC-paired is-in-duplex [+]:TcG/CGA

I.5CM8: stacking-with-A.ASN573 is-WC-paired is-in-duplex [+]:GcG/CGC

G.5CM6: stacking-with-B.ASN505 is-WC-paired is-in-duplex [+]:TcG/CGA

G.5CM8: stacking-with-B.ASN573 is-WC-paired is-in-duplex [+]:GcG/CGC

Reference

Yan, N., Deng, D., Yan, C.Y., Yin, P., Pan, X.J., Shi, Y.G.: "Crystal structure of a protein complex." To be Published

Abstract

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.

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 I.5CM6: download PDB file for the 5mC entry stacking-with-A.ASN505 is-WC-paired is-in-duplex [+]:TcG/CGA
	No. 2 I.5CM8: download PDB file for the 5mC entry stacking-with-A.ASN573 is-WC-paired is-in-duplex [+]:GcG/CGC
	No. 3 G.5CM6: download PDB file for the 5mC entry stacking-with-B.ASN505 is-WC-paired is-in-duplex [+]:TcG/CGA
	No. 4 G.5CM8: download PDB file for the 5mC entry stacking-with-B.ASN573 is-WC-paired is-in-duplex [+]:GcG/CGC