Zinc in PDB 5ydr: Structure of DNMT1 Rfts Domain in Complex with Ubiquitin

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

The structure of Structure of DNMT1 Rfts Domain in Complex with Ubiquitin, PDB code: 5ydr was solved by C.Qian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.77 / 2.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	131.760, 131.760, 61.025, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 23.3

The binding sites of Zinc atom in the Structure of DNMT1 Rfts Domain in Complex with Ubiquitin (pdb code 5ydr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of DNMT1 Rfts Domain in Complex with Ubiquitin, PDB code: 5ydr:

Zinc binding site 1 out of 1 in the Structure of DNMT1 Rfts Domain in Complex with Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of DNMT1 Rfts Domain in Complex with Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:31.7 occ:1.00 ND1 B:HIS418 2.1 25.2 1.0 SG B:CYS356 2.3 22.6 1.0 SG B:CYS414 2.3 23.0 1.0 SG B:CYS353 2.4 24.9 1.0 CE1 B:HIS418 3.0 31.2 1.0 CB B:CYS353 3.1 23.9 1.0 CG B:HIS418 3.2 25.7 1.0 CB B:CYS356 3.3 21.6 1.0 CB B:CYS414 3.5 22.7 1.0 CB B:HIS418 3.5 20.5 1.0 N B:CYS356 3.7 25.1 1.0 CA B:CYS356 4.1 21.4 1.0 NE2 B:HIS418 4.2 32.1 1.0 CD2 B:HIS418 4.3 26.9 1.0 CB B:HIS416 4.4 29.6 1.0 N B:HIS418 4.5 23.1 1.0 CB B:GLN355 4.5 24.4 1.0 CA B:CYS353 4.6 25.4 1.0 CA B:HIS418 4.6 21.8 1.0 C B:GLN355 4.8 25.6 1.0 SG B:CYS420 4.8 23.0 0.5 CA B:CYS414 4.8 23.7 1.0 C B:CYS356 4.9 24.8 1.0

T.Li, L.Wang, Y.Du, S.Xie, X.Yang, F.Lian, Z.Zhou, C.Qian. Structural and Mechanistic Insights Into UHRF1-Mediated DNMT1 Activation in the Maintenance Dna Methylation. Nucleic Acids Res. V. 46 3218 2018.
ISSN: ESSN 1362-4962
PubMed: 29471350
DOI: 10.1093/NAR/GKY104