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Sodium in PDB 8uq8: Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker

Enzymatic activity of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker

All present enzymatic activity of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker:
2.3.2.23; 2.3.2.24;

Protein crystallography data

The structure of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker, PDB code: 8uq8 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) 36.06 / 2.34
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 107.539, 107.539, 113.985, 90, 90, 120
R / Rfree (%) 19.6 / 23.6

Other elements in 8uq8:

The structure of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 21 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker (pdb code 8uq8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker, PDB code: 8uq8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 8uq8

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Sodium binding site 1 out of 5 in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- 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 2- Residue Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4009

b:33.0
occ:1.00
 OG A:SER1083 2.9 32.1 1.0
O A:HOH5029 3.0 31.6 1.0
HA A:SER1083 3.1 38.4 1.0
HG A:SER1083 3.2 38.5 1.0
HB3 A:SER1083 3.3 46.4 1.0
HB2 A:ALA1068 3.4 41.6 1.0
CB A:SER1083 3.5 38.6 1.0
CA A:SER1083 3.8 32.0 1.0
HH21 A:ARG1090 4.1 51.1 1.0
HH22 A:ARG1090 4.2 51.1 1.0
H A:ILE1084 4.3 36.9 1.0
CB A:ALA1068 4.3 34.7 1.0
HB1 A:ALA1068 4.4 41.6 1.0
HB2 A:SER1083 4.4 46.4 1.0
NH2 A:ARG1090 4.5 42.6 1.0
N A:SER1083 4.6 36.3 1.0
O A:VAL1067 4.7 38.7 1.0
O A:HOH5061 4.8 31.8 1.0
HB3 A:ALA1068 4.8 41.6 1.0
H A:SER1083 4.8 43.6 1.0
N A:ILE1084 4.9 30.8 1.0
C A:SER1083 4.9 31.7 1.0

Sodium binding site 2 out of 5 in 8uq8

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Sodium binding site 2 out of 5 in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- 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 2- Residue Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4011

b:48.5
occ:1.00
 O A:LEU2102 2.3 40.8 1.0
O A:HOH5008 2.3 43.2 1.0
O A:ARG2099 2.3 36.9 1.0
C A:LEU2102 3.4 42.3 1.0
C A:ARG2099 3.5 34.0 1.0
H A:LEU2102 3.5 47.2 1.0
O A:LEU2100 3.8 38.5 1.0
N A:LEU2102 3.8 39.3 1.0
HA A:PRO2103 3.8 48.6 1.0
C A:LEU2100 3.8 36.2 1.0
HA A:LEU2100 3.9 36.7 1.0
HA A:ARG2099 4.1 46.4 1.0
CA A:LEU2102 4.2 40.3 1.0
N A:LEU2101 4.2 41.6 1.0
HB2 A:ALA2107 4.2 48.0 1.0
CA A:LEU2100 4.3 30.6 1.0
N A:PRO2103 4.3 44.1 1.0
N A:LEU2100 4.3 33.4 1.0
C A:LEU2101 4.4 37.4 1.0
CA A:PRO2103 4.4 40.5 1.0
CA A:ARG2099 4.5 38.7 1.0
H A:LEU2101 4.5 49.9 1.0
C A:PRO2103 4.7 45.0 1.0
O A:VAL2098 4.8 33.9 1.0
CA A:LEU2101 4.8 35.6 1.0
HA A:LEU2102 4.9 48.3 1.0
HB2 A:LEU2102 4.9 50.0 1.0
N A:GLY2104 4.9 44.4 1.0
CB A:ALA2107 4.9 40.0 1.0
HB3 A:ALA2107 4.9 48.0 1.0
HB3 A:ARG2099 4.9 44.8 1.0
HA2 A:GLY2104 4.9 59.0 1.0
H A:GLY2104 5.0 53.3 1.0

Sodium binding site 3 out of 5 in 8uq8

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Sodium binding site 3 out of 5 in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- 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 2- Residue Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4012

b:49.2
occ:1.00
 OH A:TYR2121 2.4 37.9 1.0
HE1 A:TYR2121 2.8 40.5 1.0
HB1 A:ALA3045 2.9 50.7 1.0
O A:HOH5069 3.0 48.6 1.0
HH A:TYR2121 3.0 45.5 1.0
CZ A:TYR2121 3.3 31.2 1.0
CE1 A:TYR2121 3.4 33.7 1.0
CB A:ALA3045 3.6 42.3 1.0
HB2 A:ALA3045 3.6 50.7 1.0
HH21 A:ARG3017 3.6 50.1 1.0
NH2 A:ARG3017 3.8 41.7 1.0
HB3 A:ALA3045 3.9 50.7 1.0
HE A:ARG3017 4.0 66.2 1.0
CZ A:ARG3017 4.1 54.2 1.0
HH22 A:ARG3017 4.1 50.1 1.0
NE A:ARG3017 4.2 55.2 1.0
HH12 A:ARG3020 4.6 40.1 1.0
CE2 A:TYR2121 4.7 27.8 1.0
HH11 A:ARG3020 4.7 40.1 1.0
NH1 A:ARG3020 4.7 33.4 1.0
CD1 A:TYR2121 4.7 25.7 1.0
NH1 A:ARG3017 4.8 47.5 1.0
HD2 A:ARG3017 4.8 45.1 1.0
CA A:ALA3045 4.9 40.8 1.0
HE2 A:TYR2121 5.0 33.3 1.0

Sodium binding site 4 out of 5 in 8uq8

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Sodium binding site 4 out of 5 in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- 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 2- Residue Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Na4016

b:50.5
occ:1.00
 HH a:TYR2121 1.7 49.5 1.0
OH a:TYR2121 2.6 41.2 1.0
HE1 a:TYR2121 2.9 40.6 1.0
O a:HOH5076 2.9 46.1 1.0
HB1 a:ALA3045 3.0 51.0 1.0
CZ a:TYR2121 3.4 35.5 1.0
CE1 a:TYR2121 3.5 33.9 1.0
CB a:ALA3045 3.6 42.5 1.0
HB2 a:ALA3045 3.6 51.0 1.0
HB3 a:ALA3045 3.8 51.0 1.0
O a:HOH5025 3.9 33.8 1.0
HH21 a:ARG3017 4.0 52.7 1.0
NH2 a:ARG3017 4.2 43.9 1.0
HE a:ARG3017 4.3 64.9 1.0
HH12 a:ARG3020 4.4 42.8 1.0
HH11 a:ARG3020 4.5 42.8 1.0
CZ a:ARG3017 4.5 53.6 1.0
HH22 a:ARG3017 4.5 52.7 1.0
NE a:ARG3017 4.5 54.1 1.0
NH1 a:ARG3020 4.6 35.6 1.0
CE2 a:TYR2121 4.8 29.0 1.0
CD1 a:TYR2121 4.8 29.0 1.0
CA a:ALA3045 5.0 42.0 1.0

Sodium binding site 5 out of 5 in 8uq8

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Sodium binding site 5 out of 5 in the Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2- Residue Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Na4017

b:54.8
occ:1.00
 O a:ARG2099 2.1 39.7 1.0
O a:LEU2102 2.2 44.8 1.0
O a:HOH5005 2.5 45.2 1.0
C a:ARG2099 3.3 32.1 1.0
C a:LEU2102 3.4 41.1 1.0
H a:LEU2102 3.5 48.5 1.0
HA a:ARG2099 3.7 42.3 1.0
HB2 a:ALA2107 3.8 45.7 1.0
N a:LEU2102 3.8 40.5 1.0
C a:LEU2100 4.0 36.2 1.0
HA a:PRO2103 4.0 56.2 1.0
O a:LEU2100 4.1 38.8 1.0
HA a:LEU2100 4.1 38.7 1.0
CA a:ARG2099 4.1 35.3 1.0
CA a:LEU2102 4.2 43.2 1.0
N a:LEU2100 4.2 32.6 1.0
CA a:LEU2100 4.3 32.2 1.0
N a:PRO2103 4.3 46.3 1.0
N a:LEU2101 4.4 41.4 1.0
HB3 a:ALA2107 4.4 45.7 1.0
CB a:ALA2107 4.4 38.1 1.0
CA a:PRO2103 4.5 46.8 1.0
C a:PRO2103 4.5 48.9 1.0
O a:VAL2098 4.5 33.4 1.0
HB1 a:ALA2107 4.5 45.7 1.0
H a:LEU2101 4.5 49.7 1.0
HA2 a:GLY2104 4.5 55.9 1.0
HB3 a:ARG2099 4.5 40.4 1.0
C a:LEU2101 4.6 38.6 1.0
HB2 a:LEU2102 4.7 49.7 1.0
N a:GLY2104 4.7 49.3 1.0
O a:PRO2103 4.8 46.7 1.0
CB a:ARG2099 4.9 33.6 1.0
H a:GLY2104 5.0 59.1 1.0
CB a:LEU2102 5.0 41.4 1.0
HA a:LEU2102 5.0 51.9 1.0

Reference:

Q.Hu, M.V.Botuyan, G.Mer. Crystal Structure of RNF168 (Ring)-UBCH5C Fused to H2A-H2B Via A 2-Residue Linker To Be Published.
Page generated: Wed Oct 9 13:54:19 2024

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