Sodium in PDB 6uom: Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp

Enzymatic activity of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp

All present enzymatic activity of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp:
2.7.7.7;

Protein crystallography data

The structure of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp, PDB code: 6uom was solved by M.R.Smith, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.800, 80.400, 55.500, 90.00, 107.90, 90.00
R / Rfree (%) 19.4 / 24.4

Other elements in 6uom:

The structure of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp (pdb code 6uom). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp, PDB code: 6uom:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6uom

Go back to Sodium Binding Sites List in 6uom
Sodium binding site 1 out of 4 in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:21.6
occ:1.00
 O A:THR101 2.3 23.1 1.0
OP1 P:DG9 2.3 19.1 1.0
O A:ILE106 2.5 16.7 1.0
O P:HOH208 2.5 24.4 1.0
O A:HOH645 2.6 23.9 1.0
O A:VAL103 2.6 18.1 1.0
C A:THR101 3.3 22.8 1.0
P P:DG9 3.4 21.3 1.0
C A:ILE106 3.5 19.9 1.0
C A:VAL103 3.5 22.0 1.0
OP2 P:DG9 3.5 22.9 1.0
N A:ILE106 3.9 19.5 1.0
CA A:THR101 3.9 18.7 1.0
CA A:SER104 4.0 21.2 1.0
N A:GLY105 4.1 20.3 1.0
N A:VAL103 4.1 20.9 1.0
N A:SER104 4.1 17.3 1.0
CA A:ILE106 4.2 13.9 1.0
C A:ARG102 4.3 21.1 1.0
N A:ARG102 4.4 18.2 1.0
C A:SER104 4.4 21.1 1.0
N A:GLY107 4.4 20.4 1.0
O5' P:DG9 4.5 24.8 1.0
CA A:VAL103 4.5 21.2 1.0
O3' P:DC8 4.5 18.6 1.0
CB A:THR101 4.5 21.8 1.0
CB A:ILE106 4.6 16.6 1.0
CA A:ARG102 4.6 22.5 0.5
CA A:ARG102 4.6 22.6 0.5
CA A:GLY107 4.7 21.4 1.0
C A:GLY105 4.7 21.5 1.0
O A:ARG102 4.8 23.0 1.0
O A:LEU100 4.9 19.7 1.0
CA A:GLY105 4.9 22.2 1.0

Sodium binding site 2 out of 4 in 6uom

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Sodium binding site 2 out of 4 in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:27.9
occ:1.00
 O A:LYS60 2.4 32.3 1.0
O A:VAL65 2.4 27.9 1.0
O A:LEU62 2.4 31.7 1.0
O D:HOH212 2.5 35.6 1.0
OP1 D:DC3 2.5 24.1 1.0
O D:HOH205 2.6 37.7 1.0
C A:LEU62 3.4 26.3 1.0
C A:LYS60 3.5 35.4 1.0
C A:VAL65 3.5 23.7 1.0
P D:DC3 3.6 30.5 1.0
OP2 D:DC3 3.8 34.4 1.0
N A:VAL65 3.9 25.4 1.0
CA A:PRO63 4.0 31.9 1.0
N A:LEU62 4.1 28.0 1.0
N A:PRO63 4.1 32.8 1.0
N A:GLY64 4.2 28.7 1.0
CA A:VAL65 4.2 21.7 1.0
CA A:LYS60 4.2 30.6 1.0
C A:LYS61 4.2 34.7 1.0
CG A:LYS60 4.2 30.6 1.0
CA A:LEU62 4.4 24.8 1.0
N A:LYS61 4.5 31.2 1.0
CB A:VAL65 4.5 28.9 1.0
C A:PRO63 4.5 29.6 1.0
O A:LYS61 4.5 32.8 1.0
O3' D:DT2 4.6 27.9 1.0
N A:GLY66 4.6 24.3 1.0
CA A:LYS61 4.6 31.1 1.0
NZ A:LYS60 4.8 39.5 1.0
CB A:LYS60 4.8 33.8 1.0
C A:GLY64 4.8 29.7 1.0
O5' D:DC3 4.8 31.2 1.0
CA A:GLY66 4.9 26.3 1.0
O A:ALA59 5.0 25.5 1.0

Sodium binding site 3 out of 4 in 6uom

Go back to Sodium Binding Sites List in 6uom
Sodium binding site 3 out of 4 in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:12.5
occ:1.00
 OD2 A:ASP145 2.1 24.8 1.0
O A:HOH586 2.2 28.5 1.0
O A:HOH594 2.3 25.5 1.0
O A:HOH649 2.4 33.0 1.0
ND1 A:HIS252 2.4 20.9 1.0
CE1 A:HIS252 3.1 20.9 1.0
CG A:ASP145 3.2 28.4 1.0
CG A:HIS252 3.6 24.1 1.0
OD1 A:ASP145 3.7 31.3 1.0
N A:HIS252 4.1 20.9 1.0
CB A:HIS252 4.1 20.3 1.0
NE2 A:HIS252 4.3 19.9 1.0
CD1 A:TYR142 4.4 20.4 1.0
CB A:ASP145 4.5 27.8 1.0
CD2 A:HIS252 4.6 21.3 1.0
CE1 A:TYR142 4.7 20.9 1.0
O A:HOH512 4.7 36.4 1.0
OE1 A:GLU249 4.8 37.9 1.0
CA A:HIS252 4.8 22.7 1.0
O A:TYR250 4.8 25.6 1.0
C A:PRO251 5.0 22.3 1.0
CA A:PRO251 5.0 23.8 1.0

Sodium binding site 4 out of 4 in 6uom

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Sodium binding site 4 out of 4 in the Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Y271G Dna Polymerase Beta Ternary Complex with Templating Adenine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:37.8
occ:1.00
 O A:HOH653 2.4 39.6 1.0
O A:HOH648 2.4 31.9 1.0
O2G A:8GT407 2.4 35.1 1.0
PG A:8GT407 3.7 27.8 1.0
O A:HOH654 4.0 30.5 1.0
O1G A:8GT407 4.0 28.6 1.0
O1A A:8GT407 4.2 30.2 1.0
O3B A:8GT407 4.3 27.6 1.0
CA A:GLY189 4.6 19.9 1.0
O2A A:8GT407 4.8 27.0 1.0
O3G A:8GT407 4.9 21.2 1.0

Reference:

M.R.Smith, K.S.Alnajjar, N.M.Hoitsma, J.B.Sweasy, B.D.Freudenthal. Molecular Characterization of Oxidized Ribonucleotide Insertion By Human Dna Polymerase Beta J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
Page generated: Tue Dec 15 14:32:58 2020

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