Zinc in PDB 8uq9: Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker

Enzymatic activity of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker

All present enzymatic activity of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker:
2.3.2.23; 2.3.2.24; 2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker, PDB code: 8uq9 was solved by Q.Hu, M.V.Botuyan, G.Mer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.18 / 2.30
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 108.135, 108.135, 114.01, 90, 90, 120
R / Rfree (%) 18.3 / 20.6

Other elements in 8uq9:

The structure of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker also contains other interesting chemical elements:

Sodium (Na) 4 atoms
Chlorine (Cl) 36 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker (pdb code 8uq9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker, PDB code: 8uq9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8uq9

Go back to Zinc Binding Sites List in 8uq9
Zinc binding site 1 out of 4 in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4010

b:32.5
occ:1.00
 ND1 A:HIS33 2.0 36.2 1.0
SG A:CYS31 2.3 28.8 1.0
SG A:CYS51 2.3 30.7 1.0
SG A:CYS54 2.3 32.8 1.0
CE1 A:HIS33 3.0 40.6 1.0
CG A:HIS33 3.0 35.1 1.0
CB A:CYS51 3.2 35.0 1.0
CB A:CYS31 3.2 34.3 1.0
CB A:HIS33 3.4 30.2 1.0
CB A:CYS54 3.4 34.3 1.0
N A:CYS54 3.7 40.1 1.0
CA A:CYS54 4.1 36.0 1.0
NE2 A:HIS33 4.1 44.7 1.0
CD2 A:HIS33 4.2 36.5 1.0
CB A:PHE53 4.4 34.0 1.0
CA A:CYS31 4.5 32.2 1.0
N A:HIS33 4.5 33.4 1.0
O A:HOH5231 4.6 48.4 1.0
CA A:HIS33 4.6 29.8 1.0
CA A:CYS51 4.6 34.0 1.0
C A:PHE53 4.7 39.9 1.0
C A:CYS31 4.7 33.2 1.0
O A:CYS31 4.7 31.4 1.0
C A:CYS54 4.8 34.8 1.0
N A:PHE53 4.9 37.6 1.0
CA A:PHE53 4.9 34.3 1.0

Zinc binding site 2 out of 4 in 8uq9

Go back to Zinc Binding Sites List in 8uq9
Zinc binding site 2 out of 4 in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4011

b:31.0
occ:1.00
 SG A:CYS39 2.2 32.5 1.0
SG A:CYS19 2.3 25.0 1.0
SG A:CYS16 2.3 26.3 1.0
SG A:CYS36 2.3 25.2 1.0
CB A:CYS16 3.1 28.7 1.0
CB A:CYS39 3.2 29.2 1.0
CB A:CYS19 3.2 26.1 1.0
CB A:CYS36 3.6 27.6 1.0
N A:CYS19 3.6 30.9 1.0
OG A:SER99 3.8 48.2 1.0
CA A:CYS19 4.0 27.2 1.0
N A:CYS36 4.1 27.0 1.0
CA A:CYS39 4.3 33.8 1.0
N A:CYS39 4.4 30.9 1.0
CA A:CYS36 4.4 27.5 1.0
CB A:ILE18 4.5 29.6 1.0
NH1 A:ARG91 4.6 35.0 1.0
CA A:CYS16 4.6 27.6 1.0
C A:ILE18 4.7 31.6 1.0
O A:CYS36 4.7 27.9 1.0
NH2 A:ARG91 4.7 41.0 1.0
N A:ILE18 4.9 31.3 1.0
C A:CYS36 4.9 28.7 1.0
C A:CYS19 4.9 32.1 1.0
CA A:ILE18 4.9 31.0 1.0
C A:CYS16 5.0 28.8 1.0

Zinc binding site 3 out of 4 in 8uq9

Go back to Zinc Binding Sites List in 8uq9
Zinc binding site 3 out of 4 in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Zn4012

b:32.6
occ:1.00
 ND1 a:HIS33 2.0 36.5 1.0
SG a:CYS31 2.2 30.5 1.0
SG a:CYS51 2.3 31.0 1.0
SG a:CYS54 2.4 35.2 1.0
CE1 a:HIS33 2.9 38.0 1.0
CG a:HIS33 3.0 36.3 1.0
CB a:CYS51 3.2 35.5 1.0
CB a:CYS31 3.3 34.5 1.0
CB a:HIS33 3.4 30.1 1.0
CB a:CYS54 3.5 37.8 1.0
N a:CYS54 3.8 41.0 1.0
NE2 a:HIS33 4.1 45.9 1.0
CD2 a:HIS33 4.1 37.3 1.0
CA a:CYS54 4.2 37.8 1.0
CB a:PHE53 4.4 34.7 1.0
N a:HIS33 4.6 33.8 1.0
CA a:CYS31 4.6 32.2 1.0
CA a:HIS33 4.6 30.7 1.0
O a:HOH5244 4.6 49.5 1.0
CA a:CYS51 4.6 35.9 1.0
C a:CYS31 4.7 33.1 1.0
O a:CYS31 4.8 33.1 1.0
C a:PHE53 4.8 41.2 1.0
C a:CYS54 4.9 36.5 1.0
N a:PHE53 4.9 38.4 1.0
CD1 a:LEU29 5.0 28.9 1.0
CA a:PHE53 5.0 35.7 1.0
CB a:ARG56 5.0 38.6 1.0

Zinc binding site 4 out of 4 in 8uq9

Go back to Zinc Binding Sites List in 8uq9
Zinc binding site 4 out of 4 in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4- Residue Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Zn4013

b:30.5
occ:1.00
 SG a:CYS39 2.3 31.6 1.0
SG a:CYS19 2.3 25.7 1.0
SG a:CYS16 2.3 24.7 1.0
SG a:CYS36 2.3 25.6 1.0
CB a:CYS16 3.1 29.6 1.0
CB a:CYS39 3.1 28.9 1.0
CB a:CYS19 3.3 28.5 1.0
CB a:CYS36 3.5 28.9 1.0
N a:CYS19 3.6 30.8 1.0
OG a:SER99 3.8 47.7 1.0
CA a:CYS19 4.1 28.8 1.0
N a:CYS36 4.1 26.7 1.0
CA a:CYS39 4.3 33.4 1.0
N a:CYS39 4.3 30.3 1.0
CA a:CYS36 4.3 27.7 1.0
CB a:ILE18 4.4 31.0 1.0
NH1 a:ARG91 4.5 38.4 1.0
CA a:CYS16 4.6 28.0 1.0
O a:CYS36 4.7 28.2 1.0
C a:ILE18 4.7 31.4 1.0
NH2 a:ARG91 4.7 45.1 1.0
N a:ILE18 4.9 30.0 1.0
C a:CYS36 4.9 28.6 1.0
CA a:ILE18 4.9 30.5 1.0
C a:CYS19 4.9 31.5 1.0
C a:CYS16 5.0 29.4 1.0

Reference:

Q.Hu, M.V.Botuyan, G.Mer. Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 4-Residue Linker To Be Published.
Page generated: Thu Oct 31 12:26:07 2024

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