Zinc in PDB 8u14: Cryo-Em Structure of the Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 2)

Enzymatic activity of Cryo-Em Structure of the Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 2)

All present enzymatic activity of Cryo-Em Structure of the Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 2):
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 Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 2) (pdb code 8u14). 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 Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 2), PDB code: 8u14:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8u14

Go back to Zinc Binding Sites List in 8u14
Zinc binding site 1 out of 2 in the Cryo-Em Structure of the Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (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 Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn301

b:188.0
occ:1.00
ND1 K:HIS33 2.1 157.4 1.0
SG K:CYS51 2.3 157.2 1.0
SG K:CYS54 2.3 157.7 1.0
SG K:CYS31 2.3 156.0 1.0
CE1 K:HIS33 2.4 157.4 1.0
CB K:CYS54 3.3 157.7 1.0
CB K:CYS51 3.3 157.2 1.0
CG K:HIS33 3.4 157.4 1.0
CB K:CYS31 3.5 156.0 1.0
N K:CYS54 3.5 157.7 1.0
NE2 K:HIS33 3.7 157.4 1.0
CA K:CYS54 3.9 157.7 1.0
CD2 K:HIS33 4.2 157.4 1.0
CB K:PHE53 4.2 157.2 1.0
NH2 K:ARG56 4.2 147.6 1.0
CB K:HIS33 4.2 157.4 1.0
C K:PHE53 4.4 157.2 1.0
C K:CYS54 4.7 157.7 1.0
CA K:PHE53 4.7 157.2 1.0
CZ K:ARG56 4.7 147.6 1.0
CD1 K:LEU29 4.7 151.8 1.0
CA K:CYS51 4.7 157.2 1.0
N K:PHE53 4.8 157.2 1.0
CD2 K:PHE53 4.8 157.2 1.0
NE K:ARG56 4.8 147.6 1.0
CA K:CYS31 4.9 156.0 1.0
N K:ARG55 5.0 158.2 1.0

Zinc binding site 2 out of 2 in 8u14

Go back to Zinc Binding Sites List in 8u14
Zinc binding site 2 out of 2 in the Cryo-Em Structure of the Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (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 Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn302

b:242.6
occ:1.00
SG K:CYS36 2.3 192.6 1.0
SG K:CYS16 2.3 201.5 1.0
SG K:CYS39 2.3 199.4 1.0
SG K:CYS19 2.3 219.5 1.0
CB K:CYS19 3.4 219.5 1.0
CB K:CYS16 3.6 201.5 1.0
N K:CYS19 3.7 219.5 1.0
CB K:CYS39 3.8 199.4 1.0
CB K:CYS36 3.8 192.6 1.0
CA K:CYS19 4.1 219.5 1.0
CD1 K:LEU35 4.5 182.1 1.0
NH1 K:ARG91 4.5 209.0 1.0
C K:CYS19 4.6 219.5 1.0
N K:CYS36 4.7 192.6 1.0
O K:GLU21 4.7 205.0 1.0
CA K:CYS36 4.7 192.6 1.0
N K:GLU21 4.7 205.0 1.0
O K:CYS36 4.7 192.6 1.0
N K:CYS39 4.7 199.4 1.0
CB K:GLU21 4.8 205.0 1.0
N K:MET20 4.8 213.7 1.0
CB K:ILE18 4.8 212.8 1.0
CA K:CYS39 4.8 199.4 1.0
C K:ILE18 4.9 212.8 1.0
CA K:CYS16 4.9 201.5 1.0

Reference:

Q.Hu, M.V.Botuyan, D.Zhao, G.Cui, G.Mer. Cryo-Em Structure of the Human Nucleosome Core Particle Ubiquitylated at Histone H2A Lysine 15 in Complex with RNF168-UBCH5C (Class 2) To Be Published.
Page generated: Thu Oct 31 12:01:08 2024

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