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Sodium 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:

Chlorine (Cl) 36 atoms
Zinc (Zn) 4 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 4 in 8uq9

Go back to Sodium Binding Sites List in 8uq9
Sodium 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 Sodium with other atoms in the Na 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:Na4023

b:50.0
occ:1.00
 OH A:TYR2040 2.5 37.8 1.0
O A:HOH5033 2.5 41.3 1.0
CE2 A:TYR2040 3.2 36.5 1.0
CZ A:TYR2040 3.3 35.3 1.0
CE A:MET1038 3.7 44.0 1.0
CG A:ARG3029 4.2 40.9 1.0
OE2 A:GLU2035 4.3 41.2 1.0
CG A:PRO3026 4.4 37.0 1.0
O A:SER2036 4.5 34.1 1.0
CD2 A:TYR2040 4.5 34.3 1.0
CD A:ARG3029 4.6 46.1 1.0
CB A:ARG3029 4.6 36.9 1.0
OD1 A:ASN1041 4.6 47.7 1.0
CE1 A:TYR2040 4.6 33.0 1.0
SD A:MET1038 4.6 59.7 1.0
CB A:PRO3026 4.6 39.9 1.0
NE A:ARG3029 4.9 46.5 1.0

Sodium binding site 2 out of 4 in 8uq9

Go back to Sodium Binding Sites List in 8uq9
Sodium 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 Sodium with other atoms in the Na 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:Na4009

b:35.9
occ:1.00
 OG a:SER59 2.6 35.1 1.0
OG a:SER60 2.9 37.7 1.0
NH1 a:ARG63 3.1 30.8 1.0
N a:SER60 3.2 28.0 1.0
CB a:SER59 3.5 33.9 1.0
NH2 a:ARG63 3.6 33.9 1.0
O a:HOH5161 3.7 33.6 1.0
CA a:SER60 3.7 34.3 1.0
CB a:SER60 3.7 35.5 1.0
CZ a:ARG63 3.8 30.0 1.0
C a:SER59 3.8 30.7 1.0
CA a:SER59 4.3 33.0 1.0
O a:SER59 4.5 34.8 1.0
O a:HOH5027 4.7 37.6 1.0
N a:SER59 4.9 33.9 1.0
NH2 a:ARG57 4.9 41.6 1.0

Sodium binding site 3 out of 4 in 8uq9

Go back to Sodium Binding Sites List in 8uq9
Sodium 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 Sodium with other atoms in the Na 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:Na4019

b:43.5
occ:1.00
 OD1 a:ASP1117 2.4 57.3 1.0
OD2 a:ASP1117 2.4 54.5 1.0
CG a:ASP1117 2.7 55.2 1.0
SG a:CYS1085 3.5 44.4 1.0
O a:HOH5172 4.1 47.0 1.0
CB a:ASP1117 4.3 44.7 1.0
O a:HOH5066 4.4 47.6 1.0
O a:ASP1117 4.8 43.2 1.0

Sodium binding site 4 out of 4 in 8uq9

Go back to Sodium Binding Sites List in 8uq9
Sodium 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 Sodium with other atoms in the Na 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:Na4023

b:44.2
occ:1.00
 O a:HOH5092 2.3 41.3 1.0
O a:ARG2099 2.3 36.0 1.0
O a:LEU2102 2.3 41.0 1.0
C a:LEU2102 3.4 40.1 1.0
C a:ARG2099 3.5 31.8 1.0
N a:LEU2102 3.8 36.4 1.0
O a:LEU2100 3.9 33.2 1.0
C a:LEU2100 3.9 33.6 1.0
CA a:LEU2102 4.2 40.5 1.0
N a:LEU2101 4.3 37.7 1.0
CA a:LEU2100 4.3 30.7 1.0
N a:PRO2103 4.3 46.7 1.0
C a:LEU2101 4.4 37.0 1.0
O a:HOH5208 4.4 51.4 1.0
N a:LEU2100 4.4 32.0 1.0
CA a:PRO2103 4.5 44.9 1.0
CA a:ARG2099 4.5 34.3 1.0
C a:PRO2103 4.6 45.1 1.0
O a:VAL2098 4.7 34.4 1.0
CA a:LEU2101 4.8 32.6 1.0
CB a:ALA2107 4.9 38.1 1.0
N a:GLY2104 4.9 44.1 1.0
O a:LEU2101 5.0 36.4 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: Wed Oct 9 13:54:19 2024

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