Zinc in PDB 8smz: 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 4)

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 4)

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 4):
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 4) (pdb code 8smz). 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 4), PDB code: 8smz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8smz

Go back to Zinc Binding Sites List in 8smz
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 4)


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 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn301

b:81.8
occ:1.00
ND1 K:HIS33 2.0 56.0 1.0
SG K:CYS31 2.3 54.6 1.0
SG K:CYS51 2.3 53.5 1.0
SG K:CYS54 2.3 59.6 1.0
CE1 K:HIS33 2.6 56.0 1.0
CG K:HIS33 3.2 56.0 1.0
CB K:CYS51 3.3 53.5 1.0
CB K:CYS31 3.5 54.6 1.0
CB K:CYS54 3.6 59.6 1.0
N K:CYS54 3.6 59.6 1.0
NE2 K:HIS33 3.9 56.0 1.0
CB K:HIS33 3.9 56.0 1.0
CA K:CYS54 4.1 59.6 1.0
CD2 K:HIS33 4.1 56.0 1.0
CB K:PHE53 4.2 56.6 1.0
CB K:ARG56 4.6 47.6 1.0
C K:PHE53 4.6 56.6 1.0
C K:CYS54 4.6 59.6 1.0
CA K:CYS51 4.7 53.5 1.0
N K:ARG55 4.8 62.1 1.0
O K:CYS31 4.8 54.6 1.0
CA K:PHE53 4.8 56.6 1.0
CA K:CYS31 4.8 54.6 1.0
N K:PHE53 4.8 56.6 1.0
N K:ARG56 4.9 47.6 1.0
CD1 K:LEU29 4.9 48.5 1.0
C K:CYS31 4.9 54.6 1.0

Zinc binding site 2 out of 2 in 8smz

Go back to Zinc Binding Sites List in 8smz
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 4)


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 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn302

b:117.7
occ:1.00
SG K:CYS16 2.3 61.1 1.0
SG K:CYS36 2.3 55.4 1.0
SG K:CYS19 2.3 66.1 1.0
SG K:CYS39 2.3 56.0 1.0
CB K:CYS36 3.0 55.4 1.0
CB K:CYS16 3.2 61.1 1.0
CB K:CYS19 3.3 66.1 1.0
N K:CYS19 3.8 66.1 1.0
N K:CYS36 3.8 55.4 1.0
CB K:CYS39 3.9 56.0 1.0
CA K:CYS36 4.0 55.4 1.0
CA K:CYS19 4.1 66.1 1.0
CB K:ILE18 4.4 59.6 1.0
CA K:CYS16 4.7 61.1 1.0
C K:ILE18 4.7 59.6 1.0
C K:CYS19 4.9 66.1 1.0
CA K:ILE18 5.0 59.6 1.0
N K:ILE18 5.0 59.6 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 4) To Be Published.
Page generated: Thu Oct 31 11:03:47 2024

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