Zinc in PDB 8sn3: Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with RNF168 and UBCH5C~Ub (UBCH5C Chemically Conjugated to Histone H2A) (Class 1)

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 1):
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 1) (pdb code 8sn3). 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 1), PDB code: 8sn3:
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 1)


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 1) within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn301 b:102.2 occ:1.00 SG K:CYS31 2.3 55.6 1.0 SG K:CYS51 2.3 54.5 1.0 SG K:CYS54 2.3 65.7 1.0 CB K:CYS54 2.6 65.7 1.0 CB K:CYS51 2.6 54.5 1.0 CB K:CYS31 2.8 55.6 1.0 CA K:CYS54 3.8 65.7 1.0 N K:CYS54 3.8 65.7 1.0 ND1 K:HIS33 3.8 48.1 1.0 CA K:CYS51 4.2 54.5 1.0 CE1 K:HIS33 4.2 48.1 1.0 CA K:CYS31 4.3 55.6 1.0 NE K:ARG56 4.4 44.9 1.0 CG K:HIS33 4.6 48.1 1.0 C K:CYS54 4.7 65.7 1.0 CD2 K:LEU29 4.8 44.4 1.0 C K:CYS51 4.8 54.5 1.0 NH2 K:ARG56 4.8 44.9 1.0 CG K:ARG56 4.8 44.9 1.0 CZ K:ARG56 4.9 44.9 1.0 N K:CYS31 4.9 55.6 1.0 O K:CYS51 5.0 54.5 1.0 N K:CYS51 5.0 54.5 1.0 C K:PHE53 5.0 63.8 1.0 N K:ARG55 5.0 50.8 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 1)


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 1) within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn302 b:93.1 occ:1.00 SG K:CYS39 2.3 54.1 1.0 SG K:CYS36 2.3 50.0 1.0 SG K:CYS19 2.3 64.8 1.0 SG K:CYS16 2.3 64.7 1.0 CB K:CYS16 3.3 64.7 1.0 CB K:CYS39 3.4 54.1 1.0 CB K:CYS19 3.5 64.8 1.0 CB K:CYS36 3.6 50.0 1.0 N K:CYS19 3.8 64.8 1.0 N K:CYS36 4.2 50.0 1.0 CA K:CYS19 4.3 64.8 1.0 CA K:CYS36 4.4 50.0 1.0 CB K:ILE18 4.5 64.5 1.0 N K:CYS39 4.5 54.1 1.0 CA K:CYS39 4.6 54.1 1.0 O K:CYS36 4.6 50.0 1.0 CA K:CYS16 4.7 64.7 1.0 C K:CYS36 4.9 50.0 1.0 C K:ILE18 4.9 64.5 1.0 N K:ILE18 5.0 64.5 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 1) To Be Published.