Sodium in PDB 5v1r: Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp

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

The structure of Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp, PDB code: 5v1r was solved by B.D.Freudenthal, M.R.Smith, A.M.Whitaker, M.A.Schaich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.98 / 2.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.596, 79.730, 55.647, 90.00, 107.53, 90.00
R / Rfree (%)	18 / 23.7

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

Magnesium	(Mg)	3 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp (pdb code 5v1r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp, PDB code: 5v1r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C 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 Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:26.6 occ:1.00 OP1 P:DG9 2.3 29.6 1.0 O A:ILE106 2.3 24.4 1.0 O A:THR101 2.3 30.2 1.0 O P:HOH202 2.5 32.4 1.0 O A:VAL103 2.5 25.3 1.0 O A:HOH654 2.7 30.4 1.0 C A:ILE106 3.3 27.6 1.0 C A:THR101 3.3 28.3 1.0 P P:DG9 3.3 30.7 1.0 C A:VAL103 3.5 26.0 1.0 OP2 P:DG9 3.5 26.6 1.0 N A:ILE106 3.6 26.6 1.0 CA A:THR101 3.8 28.6 1.0 N A:GLY105 3.9 27.8 1.0 CA A:ILE106 4.0 26.1 1.0 CA A:SER104 4.0 29.9 1.0 O A:HOH638 4.1 40.9 1.0 N A:SER104 4.1 20.1 1.0 N A:VAL103 4.2 29.4 1.0 N A:GLY107 4.2 26.4 1.0 C A:SER104 4.3 27.7 1.0 N A:ARG102 4.3 25.9 1.0 C A:ARG102 4.4 28.6 1.0 O3' P:DC8 4.4 25.2 1.0 CB A:ILE106 4.4 25.3 1.0 CB A:THR101 4.4 29.1 1.0 CA A:VAL103 4.5 32.0 1.0 C A:GLY105 4.5 28.4 1.0 O5' P:DG9 4.5 29.1 1.0 CA A:GLY107 4.5 25.7 1.0 CA A:ARG102 4.6 30.6 1.0 O A:LEU100 4.7 25.6 1.0 CA A:GLY105 4.7 29.5 1.0 O A:ARG102 4.8 26.7 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C 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 2 of Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:39.0 occ:1.00 O A:VAL65 2.3 38.3 1.0 O A:LEU62 2.3 40.6 1.0 O A:LYS60 2.4 41.8 1.0 O D:HOH106 2.5 41.2 1.0 OP1 D:DC3 2.5 37.9 1.0 C A:LEU62 3.3 37.6 1.0 C A:VAL65 3.4 35.3 1.0 C A:LYS60 3.5 38.1 1.0 P D:DC3 3.7 40.8 1.0 N A:VAL65 3.8 35.4 1.0 OP2 D:DC3 3.9 40.2 1.0 CA A:PRO63 3.9 36.6 1.0 N A:LEU62 4.0 37.8 1.0 N A:PRO63 4.0 39.9 1.0 CA A:VAL65 4.0 35.3 1.0 N A:GLY64 4.1 38.3 1.0 C A:LYS61 4.1 43.8 1.0 CA A:LYS60 4.2 37.3 1.0 CA A:LEU62 4.3 37.1 1.0 CB A:VAL65 4.3 33.1 1.0 C A:PRO63 4.4 43.5 1.0 CG A:LYS60 4.4 44.1 1.0 N A:LYS61 4.4 35.6 1.0 N A:GLY66 4.5 33.6 1.0 O A:LYS61 4.5 43.2 1.0 CA A:LYS61 4.6 39.4 1.0 O3' D:DT2 4.6 42.0 1.0 C A:GLY64 4.7 38.7 1.0 CA A:GLY66 4.8 38.3 1.0 O A:ALA59 4.8 37.7 1.0 O5' D:DC3 4.9 44.3 1.0 CB A:LYS60 4.9 36.3 1.0

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