Zinc in PDB 8sn5: Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with RNF168 and UBCH5C~Ub (UBCH5C Chemically Conjugated to Histone H2A) (Class 3)

All present enzymatic activity of Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with RNF168 and UBCH5C~Ub (UBCH5C Chemically Conjugated to Histone H2A) (Class 3):
2.3.2.23; 2.3.2.24; 2.3.2.27;

The binding sites of Zinc atom in the Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with RNF168 and UBCH5C~Ub (UBCH5C Chemically Conjugated to Histone H2A) (Class 3) (pdb code 8sn5). 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 the Human Nucleosome Core Particle in Complex with RNF168 and UBCH5C~Ub (UBCH5C Chemically Conjugated to Histone H2A) (Class 3), PDB code: 8sn5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with RNF168 and UBCH5C~Ub (UBCH5C Chemically Conjugated to Histone H2A) (Class 3)


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 the Human Nucleosome Core Particle in Complex with RNF168 and UBCH5C~Ub (UBCH5C Chemically Conjugated to Histone H2A) (Class 3) within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn301 b:158.8 occ:1.00 ND1 K:HIS33 2.1 90.0 1.0 CE1 K:HIS33 2.2 90.0 1.0 SG K:CYS54 2.3 100.3 1.0 SG K:CYS31 2.3 92.0 1.0 SG K:CYS51 2.3 78.3 1.0 CB K:CYS51 2.9 78.3 1.0 CB K:CYS31 3.2 92.0 1.0 CG K:HIS33 3.4 90.0 1.0 NE2 K:HIS33 3.4 90.0 1.0 N K:CYS54 3.5 100.3 1.0 CB K:CYS54 3.8 100.3 1.0 CD2 K:HIS33 4.0 90.0 1.0 CA K:CYS54 4.1 100.3 1.0 CB K:HIS33 4.3 90.0 1.0 CA K:CYS51 4.3 78.3 1.0 N K:ARG55 4.4 82.5 1.0 C K:CYS54 4.4 100.3 1.0 CB K:PHE53 4.4 91.5 1.0 CD2 K:PHE53 4.5 91.5 1.0 CA K:CYS31 4.6 92.0 1.0 O K:CYS31 4.6 92.0 1.0 N K:PHE53 4.6 91.5 1.0 C K:CYS51 4.6 78.3 1.0 C K:PHE53 4.6 91.5 1.0 O K:CYS51 4.7 78.3 1.0 CA K:PHE53 4.8 91.5 1.0 C K:CYS31 4.9 92.0 1.0 N K:ARG56 4.9 76.2 1.0 CD2 K:LEU29 5.0 85.9 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with RNF168 and UBCH5C~Ub (UBCH5C Chemically Conjugated to Histone H2A) (Class 3)


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 the Human Nucleosome Core Particle in Complex with RNF168 and UBCH5C~Ub (UBCH5C Chemically Conjugated to Histone H2A) (Class 3) within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn302 b:168.9 occ:1.00 SG K:CYS36 2.3 94.7 1.0 SG K:CYS39 2.3 92.2 1.0 SG K:CYS16 2.3 109.6 1.0 SG K:CYS19 2.3 105.2 1.0 CB K:CYS16 3.3 109.6 1.0 CB K:CYS39 3.4 92.2 1.0 CB K:CYS19 3.4 105.2 1.0 CB K:CYS36 3.7 94.7 1.0 N K:CYS19 3.7 105.2 1.0 CA K:CYS19 4.2 105.2 1.0 N K:CYS36 4.3 94.7 1.0 CB K:ILE18 4.3 96.9 1.0 CA K:CYS36 4.5 94.7 1.0 CA K:CYS39 4.5 92.2 1.0 N K:CYS39 4.5 92.2 1.0 O K:CYS36 4.7 94.7 1.0 CA K:CYS16 4.7 109.6 1.0 C K:ILE18 4.7 96.9 1.0 N K:ILE18 4.8 96.9 1.0 CA K:ILE18 4.9 96.9 1.0 C K:CYS36 4.9 94.7 1.0 CG2 K:ILE18 5.0 96.9 1.0 C K:CYS19 5.0 105.2 1.0

Q.Hu, M.V.Botuyan, D.Zhao, G.Cui, G.Mer. Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with RNF168 and UBCH5C~Ub (UBCH5C Chemically Conjugated to Histone H2A) (Class 3) To Be Published.