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Sodium in PDB 5v1n: Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp

Enzymatic activity of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp, PDB code: 5v1n was solved by B.D.Freudenthal, M.A.Schaich, A.M.Whitaker, M.R.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.61 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.546, 79.225, 55.536, 90.00, 107.32, 90.00
R / Rfree (%) 18.1 / 23.7

Other elements in 5v1n:

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp (pdb code 5v1n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp, PDB code: 5v1n:

Sodium binding site 1 out of 1 in 5v1n

Go back to Sodium Binding Sites List in 5v1n
Sodium binding site 1 out of 1 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:20.5
occ:1.00
 O A:THR101 2.3 19.2 1.0
OP1 P:DG9 2.4 18.5 1.0
O A:ILE106 2.4 14.5 1.0
O A:VAL103 2.4 17.9 1.0
O P:HOH103 2.6 27.8 1.0
O A:HOH697 2.7 22.8 1.0
C A:THR101 3.3 14.4 1.0
C A:VAL103 3.4 18.2 1.0
P P:DG9 3.4 18.9 1.0
C A:ILE106 3.4 16.7 1.0
OP2 P:DG9 3.6 19.8 1.0
N A:ILE106 3.7 19.6 1.0
CA A:THR101 3.9 21.6 1.0
N A:GLY105 3.9 15.6 1.0
CA A:SER104 3.9 16.8 1.0
N A:SER104 4.0 13.7 1.0
CA A:ILE106 4.1 17.8 1.0
N A:VAL103 4.1 20.0 1.0
O P:HOH120 4.2 33.1 1.0
O A:HOH701 4.2 33.9 1.0
C A:SER104 4.2 17.3 1.0
C A:ARG102 4.3 19.2 1.0
O3' P:DC8 4.3 16.0 1.0
N A:ARG102 4.3 17.5 1.0
CA A:VAL103 4.4 23.8 1.0
N A:GLY107 4.4 18.4 1.0
CB A:THR101 4.5 16.8 1.0
CB A:ILE106 4.5 22.0 1.0
C A:GLY105 4.5 19.0 1.0
CA A:ARG102 4.5 20.5 1.0
O5' P:DG9 4.6 18.9 1.0
O A:ARG102 4.7 17.3 1.0
CA A:GLY107 4.7 15.7 1.0
CA A:GLY105 4.8 20.9 1.0
O A:LEU100 4.8 16.9 1.0

Reference:

A.M.Whitaker, M.R.Smith, M.A.Schaich, B.D.Freudenthal. Capturing A Mammalian Dna Polymerase Extending From An Oxidized Nucleotide. Nucleic Acids Res. V. 45 6934 2017.
ISSN: ESSN 1362-4962
PubMed: 28449123
DOI: 10.1093/NAR/GKX293
Page generated: Mon Aug 18 02:42:37 2025

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