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Sodium in PDB 4gxi: R283K Dna Polymerase Beta Binary Complex with A Templating 8OG

Enzymatic activity of R283K Dna Polymerase Beta Binary Complex with A Templating 8OG

All present enzymatic activity of R283K Dna Polymerase Beta Binary Complex with A Templating 8OG:
2.7.7.7;

Protein crystallography data

The structure of R283K Dna Polymerase Beta Binary Complex with A Templating 8OG, PDB code: 4gxi was solved by B.D.Freudenthal, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.10 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.797, 79.258, 54.365, 90.00, 105.62, 90.00
R / Rfree (%) 20.3 / 25.9

Sodium Binding Sites:

The binding sites of Sodium atom in the R283K Dna Polymerase Beta Binary Complex with A Templating 8OG (pdb code 4gxi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the R283K Dna Polymerase Beta Binary Complex with A Templating 8OG, PDB code: 4gxi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4gxi

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Sodium binding site 1 out of 4 in the R283K Dna Polymerase Beta Binary Complex with A Templating 8OG


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of R283K Dna Polymerase Beta Binary Complex with A Templating 8OG within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:30.0
occ:1.00
 O A:THR101 2.3 12.0 1.0
O A:ILE106 2.3 14.6 1.0
OP1 P:DG9 2.5 12.2 1.0
O A:VAL103 2.5 13.2 1.0
O P:HOH101 2.6 14.1 1.0
O A:HOH512 2.7 18.4 1.0
C A:THR101 3.3 12.1 1.0
NA A:NA402 3.3 30.0 1.0
C A:ILE106 3.4 13.0 1.0
C A:VAL103 3.4 14.4 1.0
P P:DG9 3.5 16.8 1.0
OP2 P:DG9 3.8 17.8 1.0
N A:ILE106 3.8 11.5 1.0
CA A:THR101 3.8 11.8 1.0
CA A:SER104 4.0 13.1 1.0
CA A:ILE106 4.1 11.8 1.0
N A:GLY105 4.1 13.4 1.0
N A:SER104 4.1 14.0 1.0
N A:VAL103 4.1 13.6 1.0
N A:GLY107 4.3 13.9 1.0
CB A:THR101 4.3 14.0 1.0
N A:ARG102 4.3 16.2 1.0
C A:ARG102 4.3 15.5 1.0
C A:SER104 4.4 10.3 1.0
CA A:VAL103 4.4 14.3 1.0
CB A:ILE106 4.4 12.2 1.0
O P:HOH122 4.5 32.3 1.0
O3' P:DC8 4.6 14.5 1.0
CA A:GLY107 4.6 16.5 1.0
CA A:ARG102 4.6 16.1 1.0
C A:GLY105 4.7 9.3 1.0
O5' P:DG9 4.7 16.0 1.0
O A:LEU100 4.8 13.9 1.0
O A:ARG102 4.9 12.8 1.0
CA A:GLY105 4.9 12.3 1.0

Sodium binding site 2 out of 4 in 4gxi

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Sodium binding site 2 out of 4 in the R283K Dna Polymerase Beta Binary Complex with A Templating 8OG


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of R283K Dna Polymerase Beta Binary Complex with A Templating 8OG within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:30.0
occ:1.00
 O A:HOH760 2.5 25.7 1.0
O A:THR101 2.5 12.0 1.0
O A:HOH535 2.5 20.3 1.0
O A:HOH512 2.7 18.4 1.0
O A:HOH743 2.7 35.0 1.0
O P:HOH101 2.7 14.1 1.0
NA A:NA401 3.3 30.0 1.0
C A:THR101 3.5 12.1 1.0
O P:HOH122 3.8 32.3 1.0
CA A:ARG102 3.9 16.1 1.0
N A:ARG102 4.1 16.2 1.0
CB A:THR101 4.4 14.0 1.0
C A:ARG102 4.5 15.5 1.0
CA A:THR101 4.5 11.8 1.0
O A:HOH755 4.6 28.2 1.0
OG1 A:THR101 4.6 17.7 1.0
O A:HOH580 4.6 25.4 1.0
O A:ARG102 4.8 12.8 1.0
OP1 P:DG9 4.9 12.2 1.0
O P:HOH124 5.0 26.9 1.0

Sodium binding site 3 out of 4 in 4gxi

Go back to Sodium Binding Sites List in 4gxi
Sodium binding site 3 out of 4 in the R283K Dna Polymerase Beta Binary Complex with A Templating 8OG


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of R283K Dna Polymerase Beta Binary Complex with A Templating 8OG within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:30.0
occ:1.00
 O A:HOH516 2.3 22.5 1.0
OG A:SER171 2.3 15.1 1.0
CB A:SER171 3.5 18.8 1.0
N A:SER171 3.8 17.3 1.0
O A:HOH587 4.2 21.8 1.0
CA A:SER171 4.2 15.8 1.0
OD1 A:ASP170 4.6 19.5 1.0
O A:HOH705 4.9 23.5 1.0
C A:SER171 4.9 20.3 1.0
C A:ASP170 5.0 17.8 1.0
N A:GLU172 5.0 13.9 1.0

Sodium binding site 4 out of 4 in 4gxi

Go back to Sodium Binding Sites List in 4gxi
Sodium binding site 4 out of 4 in the R283K Dna Polymerase Beta Binary Complex with A Templating 8OG


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of R283K Dna Polymerase Beta Binary Complex with A Templating 8OG within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:30.0
occ:1.00
 O A:VAL65 2.1 23.4 1.0
O A:LYS60 2.1 23.1 1.0
O D:HOH112 2.2 23.8 1.0
O A:LEU62 2.8 24.2 1.0
OP1 D:DC3 2.9 21.5 1.0
O A:HOH635 3.0 28.4 1.0
C A:VAL65 3.2 20.2 1.0
C A:LYS60 3.3 27.0 1.0
C A:LEU62 3.7 23.5 1.0
N A:VAL65 3.8 19.3 1.0
P D:DC3 3.8 19.9 1.0
CA A:VAL65 3.8 18.1 1.0
OP2 D:DC3 3.9 14.6 1.0
CG A:LYS60 3.9 27.4 1.0
CA A:LYS60 3.9 23.6 1.0
N A:LEU62 4.1 24.6 1.0
CB A:VAL65 4.1 18.3 1.0
C A:LYS61 4.2 29.0 1.0
N A:GLY66 4.2 18.8 1.0
N A:GLY64 4.3 25.3 1.0
N A:LYS61 4.3 28.7 1.0
CA A:PRO63 4.4 23.5 1.0
N A:PRO63 4.5 25.1 1.0
CA A:GLY66 4.5 17.5 1.0
O A:LYS61 4.5 30.8 1.0
CA A:LYS61 4.6 25.1 1.0
CB A:LYS60 4.6 22.1 1.0
CA A:LEU62 4.6 22.4 1.0
O3' D:DT2 4.7 20.0 1.0
O A:ALA59 4.7 21.9 1.0
C A:PRO63 4.7 24.1 1.0
C A:GLY64 4.8 20.2 1.0
CG1 A:VAL65 4.8 15.9 1.0

Reference:

B.D.Freudenthal, W.A.Beard, S.H.Wilson. Dna Polymerase Minor Groove Interactions Modulate Mutagenic Bypass of A Templating 8-Oxoguanine Lesion. Nucleic Acids Res. V. 41 1848 2013.
ISSN: ISSN 0305-1048
PubMed: 23267011
DOI: 10.1093/NAR/GKS1276
Page generated: Sun Aug 17 19:33:53 2025

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