Zinc in PDB 8sn4: Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with RNF168 and UBCH5C~Ub (UBCH5C Chemically Conjugated to Histone H2A) (Class 2)

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 2):
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 2) (pdb code 8sn4). 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 2), PDB code: 8sn4:
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 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn301 b:128.0 occ:1.00 ND1 K:HIS33 2.1 91.2 1.0 CE1 K:HIS33 2.3 91.2 1.0 SG K:CYS54 2.3 91.3 1.0 SG K:CYS31 2.3 86.2 1.0 SG K:CYS51 2.3 81.4 1.0 CB K:CYS51 3.2 81.4 1.0 CB K:CYS31 3.2 86.2 1.0 CG K:HIS33 3.3 91.2 1.0 NE2 K:HIS33 3.4 91.2 1.0 N K:CYS54 3.7 91.3 1.0 CB K:CYS54 3.8 91.3 1.0 CD2 K:HIS33 3.9 91.2 1.0 CA K:CYS54 4.2 91.3 1.0 CB K:HIS33 4.2 91.2 1.0 CG K:ARG56 4.4 73.9 1.0 N K:ARG55 4.4 83.2 1.0 CA K:CYS51 4.5 81.4 1.0 CD2 K:PHE53 4.5 89.7 1.0 C K:CYS54 4.5 91.3 1.0 CB K:PHE53 4.6 89.7 1.0 CA K:CYS31 4.7 86.2 1.0 NE K:ARG56 4.7 73.9 1.0 O K:CYS51 4.7 81.4 1.0 CD K:ARG56 4.7 73.9 1.0 C K:CYS51 4.7 81.4 1.0 C K:PHE53 4.8 89.7 1.0 N K:PHE53 4.8 89.7 1.0 CA K:PHE53 5.0 89.7 1.0 O K:CYS31 5.0 86.2 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 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn302 b:161.2 occ:1.00 SG K:CYS39 2.3 91.8 1.0 SG K:CYS19 2.3 109.2 1.0 SG K:CYS36 2.3 99.4 1.0 SG K:CYS16 2.3 107.4 1.0 CB K:CYS19 3.2 109.2 1.0 CB K:CYS16 3.3 107.4 1.0 CB K:CYS39 3.4 91.8 1.0 CB K:CYS36 3.6 99.4 1.0 N K:CYS19 3.7 109.2 1.0 CA K:CYS19 4.1 109.2 1.0 N K:CYS36 4.2 99.4 1.0 CA K:CYS36 4.4 99.4 1.0 N K:CYS39 4.5 91.8 1.0 CA K:CYS39 4.5 91.8 1.0 CB K:ILE18 4.5 99.4 1.0 O K:CYS36 4.6 99.4 1.0 CA K:CYS16 4.7 107.4 1.0 C K:ILE18 4.8 99.4 1.0 C K:CYS36 4.9 99.4 1.0 N K:ILE18 4.9 99.4 1.0 C K:CYS19 4.9 109.2 1.0 CA K:ILE18 5.0 99.4 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 2) To Be Published.