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Zinc in PDB 8smy: Cryo-Em Structure of the Human Nucleosome Core Particle in Complex with RNF168 and UBCH5C~Ub (UBCH5C Chemically Conjugated to Histone H2A. No Density For Ub.) (Class 3)

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. No Density For Ub.) (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. No Density For Ub.) (Class 3):
2.3.2.23; 2.3.2.24; 2.3.2.27;

Zinc Binding Sites:

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. No Density For Ub.) (Class 3) (pdb code 8smy). 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. No Density For Ub.) (Class 3), PDB code: 8smy:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8smy

Go back to Zinc Binding Sites List in 8smy
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. No Density For Ub.) (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. No Density For Ub.) (Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn301

b:75.3
occ:1.00
ND1 K:HIS33 2.1 46.6 1.0
SG K:CYS31 2.3 46.5 1.0
SG K:CYS54 2.3 46.0 1.0
SG K:CYS51 2.3 38.5 1.0
CG K:HIS33 2.4 46.6 1.0
CE1 K:HIS33 2.8 46.6 1.0
CB K:CYS54 2.9 46.0 1.0
CB K:HIS33 2.9 46.6 1.0
CD2 K:HIS33 3.2 46.6 1.0
CB K:CYS31 3.3 46.5 1.0
NE2 K:HIS33 3.4 46.6 1.0
CB K:CYS51 3.5 38.5 1.0
N K:CYS54 3.5 46.0 1.0
CA K:CYS54 3.8 46.0 1.0
CA K:HIS33 4.3 46.6 1.0
CB K:PHE53 4.4 40.0 1.0
O K:CYS31 4.4 46.5 1.0
N K:HIS33 4.5 46.6 1.0
CA K:CYS31 4.6 46.5 1.0
C K:PHE53 4.6 40.0 1.0
C K:CYS31 4.6 46.5 1.0
CD2 K:PHE53 4.7 40.0 1.0
CD1 K:LEU29 4.8 41.2 1.0
CA K:CYS51 4.9 38.5 1.0
CA K:PHE53 4.9 40.0 1.0
C K:CYS54 5.0 46.0 1.0

Zinc binding site 2 out of 2 in 8smy

Go back to Zinc Binding Sites List in 8smy
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. No Density For Ub.) (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. No Density For Ub.) (Class 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn302

b:102.8
occ:1.00
SG K:CYS36 2.3 49.2 1.0
SG K:CYS19 2.3 60.2 1.0
SG K:CYS39 2.3 47.5 1.0
SG K:CYS16 2.3 62.1 1.0
CB K:CYS19 3.3 60.2 1.0
CB K:CYS16 3.3 62.1 1.0
CB K:CYS39 3.4 47.5 1.0
N K:CYS19 3.5 60.2 1.0
CA K:CYS19 4.0 60.2 1.0
CB K:CYS36 4.0 49.2 1.0
CB K:ILE18 4.3 53.4 1.0
N K:CYS36 4.5 49.2 1.0
C K:ILE18 4.6 53.4 1.0
CA K:CYS39 4.6 47.5 1.0
N K:CYS39 4.7 47.5 1.0
N K:ILE18 4.7 53.4 1.0
CA K:CYS16 4.8 62.1 1.0
CA K:ILE18 4.8 53.4 1.0
C K:CYS19 4.8 60.2 1.0
CA K:CYS36 4.8 49.2 1.0
N K:MET20 4.9 65.9 1.0

Reference:

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. No Density For Ub.) (Class 3) To Be Published.
Page generated: Thu Oct 31 11:03:44 2024

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