Zinc in PDB 6pzv: Crystal Structure of Bovine DNMT1 Rfts Domain in Complex with H3K9ME3 and Ubiquitin

All present enzymatic activity of Crystal Structure of Bovine DNMT1 Rfts Domain in Complex with H3K9ME3 and Ubiquitin:
2.1.1.37;

The structure of Crystal Structure of Bovine DNMT1 Rfts Domain in Complex with H3K9ME3 and Ubiquitin, PDB code: 6pzv was solved by W.Ren, J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.11 / 3.01
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.322, 196.445, 67.703, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 27.2

The binding sites of Zinc atom in the Crystal Structure of Bovine DNMT1 Rfts Domain in Complex with H3K9ME3 and Ubiquitin (pdb code 6pzv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Bovine DNMT1 Rfts Domain in Complex with H3K9ME3 and Ubiquitin, PDB code: 6pzv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Bovine DNMT1 Rfts Domain in Complex with H3K9ME3 and Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Bovine DNMT1 Rfts Domain in Complex with H3K9ME3 and Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn602 b:88.1 occ:1.00 SG C:CYS351 2.0 0.3 1.0 ND1 C:HIS416 2.1 91.1 1.0 SG C:CYS354 2.2 60.0 1.0 CB C:CYS351 2.3 0.9 1.0 CE1 C:HIS416 2.8 92.0 1.0 SG C:CYS412 2.9 69.3 1.0 CG C:HIS416 3.2 80.2 1.0 CB C:HIS416 3.7 70.2 1.0 N C:CYS354 3.7 77.2 1.0 CB C:CYS354 3.8 78.4 1.0 CA C:CYS351 3.8 91.6 1.0 NE2 C:HIS416 4.0 86.2 1.0 CB C:ARG414 4.1 69.2 1.0 CD2 C:HIS416 4.2 84.5 1.0 CA C:CYS354 4.3 56.0 1.0 CB C:CYS412 4.4 57.7 1.0 CG C:ARG414 4.5 67.9 1.0 CB C:GLU353 4.5 96.9 1.0 C C:CYS351 4.5 87.0 1.0 N C:GLU353 4.6 91.0 1.0 C C:GLU353 4.7 80.7 1.0 N C:CYS351 4.8 80.8 1.0 C C:CYS354 4.8 83.0 1.0 CA C:GLU353 4.8 91.5 1.0 CB C:GLN356 4.9 64.4 1.0 N C:LEU355 5.0 82.5 1.0 CA C:HIS416 5.0 65.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Bovine DNMT1 Rfts Domain in Complex with H3K9ME3 and Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Bovine DNMT1 Rfts Domain in Complex with H3K9ME3 and Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn601 b:74.4 occ:1.00 ND1 G:HIS416 2.0 80.5 1.0 SG G:CYS354 2.3 63.6 1.0 SG G:CYS412 2.4 61.0 1.0 SG G:CYS351 2.5 90.5 1.0 CG G:HIS416 2.9 71.8 1.0 CE1 G:HIS416 3.1 76.0 1.0 CB G:HIS416 3.2 60.9 1.0 CB G:CYS351 3.4 89.7 1.0 CB G:CYS412 3.6 48.8 1.0 CB G:CYS354 3.8 65.4 1.0 CD2 G:HIS416 4.1 73.3 1.0 NE2 G:HIS416 4.1 74.5 1.0 N G:CYS354 4.1 81.9 1.0 CB G:ARG414 4.2 60.4 1.0 N G:HIS416 4.3 54.8 1.0 CA G:HIS416 4.3 45.9 1.0 CB G:GLU353 4.4 73.1 1.0 CA G:CYS354 4.6 86.7 1.0 O G:HIS416 4.9 47.5 1.0 N G:ARG414 4.9 61.5 1.0 SG G:CYS418 4.9 76.6 1.0 CA G:CYS351 4.9 98.5 1.0 CG G:ARG414 4.9 53.8 1.0 CA G:ARG414 4.9 60.4 1.0 CA G:CYS412 5.0 42.9 1.0 C G:ARG414 5.0 63.1 1.0

W.Ren, H.Fan, S.A.Grimm, Y.Guo, J.J.Kim, J.Yin, L.Li, C.J.Petell, X.F.Tan, Z.M.Zhang, J.P.Coan, L.Gao, L.Cai, B.Detrick, B.Cetin, Q.Cui, B.D.Strahl, O.Gozani, Y.Wang, K.M.Miller, S.E.O'leary, P.A.Wade, D.J.Patel, G.G.Wang, J.Song. Direct Readout of Heterochromatic H3K9ME3 Regulates DNMT1-Mediated Maintenance Dna Methylation. Proc.Natl.Acad.Sci.Usa V. 117 18439 2020.
ISSN: ESSN 1091-6490
PubMed: 32675241
DOI: 10.1073/PNAS.2009316117