Zinc in PDB 4yoc: Crystal Structure of Human DNMT1 and USP7/Hausp Complex

All present enzymatic activity of Crystal Structure of Human DNMT1 and USP7/Hausp Complex:
2.1.1.37; 3.4.19.12;

The structure of Crystal Structure of Human DNMT1 and USP7/Hausp Complex, PDB code: 4yoc was solved by J.Cheng, H.Yang, J.Fang, R.Gong, P.Wang, Z.Li, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.42 / 2.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	110.231, 111.619, 163.868, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.8

The binding sites of Zinc atom in the Crystal Structure of Human DNMT1 and USP7/Hausp Complex (pdb code 4yoc). 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 Human DNMT1 and USP7/Hausp Complex, PDB code: 4yoc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human DNMT1 and USP7/Hausp Complex


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 Human DNMT1 and USP7/Hausp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:76.6 occ:1.00 NE2 A:HIS1502 2.2 99.2 1.0 SG A:CYS1478 2.4 0.8 1.0 SG A:CYS1476 2.5 78.1 1.0 SG A:CYS1485 2.5 98.5 1.0 CB A:CYS1478 3.0 82.2 1.0 CD2 A:HIS1502 3.1 71.0 1.0 CE1 A:HIS1502 3.3 73.1 1.0 CB A:CYS1476 3.4 70.8 1.0 CB A:CYS1485 3.6 0.4 1.0 CA A:CYS1485 3.7 98.0 1.0 N A:CYS1478 4.0 94.2 1.0 CA A:CYS1478 4.2 87.6 1.0 CG A:HIS1502 4.3 72.1 1.0 ND1 A:HIS1502 4.3 66.0 1.0 N A:CYS1485 4.4 0.9 1.0 CA A:CYS1476 4.7 85.7 1.0 CH2 A:TRP1498 4.8 59.6 1.0 C A:CYS1485 4.8 90.3 1.0 N A:SER1477 4.8 91.1 1.0 C A:CYS1476 5.0 90.4 1.0 CZ2 A:TRP1498 5.0 66.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human DNMT1 and USP7/Hausp Complex


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 Human DNMT1 and USP7/Hausp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:59.0 occ:1.00 NE2 A:HIS793 2.1 87.9 1.0 SG A:CYS893 2.3 63.8 1.0 SG A:CYS820 2.3 69.5 1.0 SG A:CYS896 2.4 66.7 1.0 CB A:CYS820 2.7 54.7 1.0 CE1 A:HIS793 3.0 73.0 1.0 CD2 A:HIS793 3.1 86.0 1.0 CB A:CYS893 3.3 59.4 1.0 N A:CYS896 3.5 72.5 1.0 CB A:CYS896 3.5 67.6 1.0 CA A:CYS896 3.9 76.0 1.0 CB A:SER895 4.0 49.6 1.0 ND1 A:HIS793 4.1 72.6 1.0 CG A:HIS793 4.2 87.5 1.0 CA A:CYS820 4.2 69.5 1.0 C A:SER895 4.3 66.3 1.0 OG A:SER895 4.4 61.5 1.0 CA A:SER895 4.5 55.8 1.0 CA A:CYS893 4.7 72.2 1.0 C A:CYS820 4.7 70.1 1.0 N A:SER895 4.7 58.9 1.0 C A:CYS893 5.0 79.7 1.0

J.Cheng, H.Yang, J.Fang, L.Ma, R.Gong, P.Wang, Z.Li, Y.Xu. Molecular Mechanism For USP7-Mediated DNMT1 Stabilization By Acetylation. Nat Commun V. 6 7023 2015.
ISSN: ESSN 2041-1723
PubMed: 25960197
DOI: 10.1038/NCOMMS8023