5mC interactions in PDB entry 4GZN 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]

X-ray (0.99 Å)
Mouse zfp57 zinc fingers in complex with methylated DNA
List of 2 5mC-amino acid contacts:
  1. A.5CM7: other-contacts is-WC-paired is-in-duplex [+]:CcG/cGG
  2. B.5CM5: stacking-with-C.ARG178 is-WC-paired is-in-duplex [-]:cGC/GcG
direct SNAP output · DNAproDB 2.0
Liu, Y., Toh, H., Sasaki, H., Zhang, X., Cheng, X.: (2012) "An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence." Genes Dev., 26, 2374-2379.
Zinc finger transcription factor Zfp57 recognizes the methylated CpG within the TGCCGC element. We determined the structure of the DNA-binding domain of Zfp57, consisting of two adjacent zinc fingers, in complex with fully methylated DNA at 1.0 Å resolution. The first zinc finger contacts the 5' half (TGC), and the second recognizes the 3' half (CGC) of the recognition sequence. Zfp57 recognizes the two 5-methylcytosines (5mCs) asymmetrically: One involves hydrophobic interactions with Arg178, which also interacts with the neighboring 3' guanine and forms a 5mC-Arg-G interaction, while the other involves a layer of ordered water molecules. Two point mutations in patients with transient neonatal diabetes abolish DNA-binding activity. Zfp57 has reduced binding affinity for unmodified DNA and the oxidative products of 5mC.

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

List of 2 5mC-amino acid contacts [summary · schematics · top · homepage · tutorial]

No. 1 A.5CM7: download PDB file for the 5mC entry
other-contacts is-WC-paired is-in-duplex [+]:CcG/cGG
No. 2 B.5CM5: download PDB file for the 5mC entry
stacking-with-C.ARG178 is-WC-paired is-in-duplex [-]:cGC/GcG