Zinc in PDB 9k2w: Cryo-Em Structure of USP7:DNMT1 Complex; Closed Conformation

All present enzymatic activity of Cryo-Em Structure of USP7:DNMT1 Complex; Closed Conformation:
2.1.1.37; 3.4.19.12;

The binding sites of Zinc atom in the Cryo-Em Structure of USP7:DNMT1 Complex; Closed Conformation (pdb code 9k2w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of USP7:DNMT1 Complex; Closed Conformation, PDB code: 9k2w:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of USP7:DNMT1 Complex; Closed Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of USP7:DNMT1 Complex; Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1701 b:194.9 occ:1.00 NE2 B:HIS793 2.1 150.7 1.0 SG B:CYS820 2.3 131.5 1.0 SG B:CYS896 2.3 146.2 1.0 SG B:CYS893 2.3 157.8 1.0 CD2 B:HIS793 2.8 149.8 1.0 CB B:CYS820 3.0 131.8 1.0 CB B:CYS893 3.1 155.8 1.0 CE1 B:HIS793 3.3 148.5 1.0 CB B:CYS896 3.5 142.6 1.0 N B:CYS896 3.6 140.8 1.0 CA B:CYS896 4.0 140.2 1.0 CG B:HIS793 4.0 147.6 1.0 ND1 B:HIS793 4.2 146.7 1.0 CB B:SER895 4.4 139.9 1.0 CA B:CYS820 4.4 130.9 1.0 CA B:CYS893 4.5 154.8 1.0 C B:SER895 4.5 136.7 1.0 OG B:SER895 4.6 139.4 1.0 C B:CYS820 4.7 135.6 1.0 C B:CYS893 4.9 154.8 1.0 O B:CYS893 4.9 155.5 1.0 CA B:SER895 4.9 136.6 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of USP7:DNMT1 Complex; Closed Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of USP7:DNMT1 Complex; Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1702 b:174.3 occ:1.00 NE2 B:HIS1502 2.1 114.5 1.0 SG B:CYS1478 2.3 165.2 1.0 SG B:CYS1485 2.3 164.5 1.0 SG B:CYS1476 2.3 172.2 1.0 CB B:CYS1478 2.8 167.0 1.0 CD2 B:HIS1502 2.8 112.7 1.0 CB B:CYS1476 2.9 170.1 1.0 CE1 B:HIS1502 3.2 112.6 1.0 CB B:CYS1485 3.5 161.5 1.0 N B:CYS1478 3.7 165.8 1.0 CA B:CYS1478 3.9 167.6 1.0 CA B:CYS1485 4.0 162.4 1.0 CG B:HIS1502 4.0 108.7 1.0 ND1 B:HIS1502 4.1 110.3 1.0 CA B:CYS1476 4.2 169.8 1.0 C B:CYS1476 4.5 170.2 1.0 N B:SER1477 4.6 171.5 1.0 C B:SER1477 4.9 169.2 1.0 C B:CYS1478 4.9 168.9 1.0 N B:CYS1485 5.0 163.0 1.0 CH2 B:TRP1498 5.0 109.5 1.0 N B:ASP1486 5.0 177.0 1.0

N.Nakamura, S.Yoshimi, A.Kikuchi, S.Kori, H.Onoda, M.Nakanishi, A.Nishiyama, K.Arita. Cryo-Em Structure of Activation/Inactivation Forms of UPS7 Bound to DNMT1 To Be Published.