Sodium in PDB 5v1p: Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog

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

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog, PDB code: 5v1p 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)	24.68 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.676, 79.990, 55.706, 90.00, 107.50, 90.00
R / Rfree (%)	17.5 / 23.1

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

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog (pdb code 5v1p). 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 Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog, PDB code: 5v1p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog


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:C at the Primer Terminus and Incoming Dctp Analog within 5.0Å range: probe atom residue distance (Å) B Occ P:Na401 b:20.3 occ:1.00 OP1 P:DG9 2.2 19.3 0.3 O A:THR101 2.3 20.4 1.0 O A:ILE106 2.4 14.6 1.0 O A:VAL103 2.5 17.1 1.0 O P:HOH504 2.5 28.6 1.0 OP1 P:DG9 2.5 19.6 0.7 O A:HOH695 2.6 26.7 1.0 C A:THR101 3.3 17.2 1.0 P P:DG9 3.4 23.8 0.3 C A:VAL103 3.4 18.1 1.0 C A:ILE106 3.4 16.5 1.0 P P:DG9 3.5 24.1 0.7 OP2 P:DG9 3.6 19.3 0.7 N A:ILE106 3.7 17.6 1.0 OP2 P:DG9 3.8 19.5 0.3 O A:HOH687 3.9 41.0 1.0 CA A:THR101 3.9 18.1 1.0 N A:GLY105 3.9 16.8 1.0 CA A:SER104 4.0 17.4 1.0 CA A:ILE106 4.1 15.9 1.0 N A:SER104 4.1 14.5 1.0 N A:VAL103 4.1 18.7 1.0 C A:ARG102 4.3 23.3 1.0 C A:SER104 4.3 20.9 1.0 O5' P:DG9 4.3 20.6 0.3 N A:ARG102 4.3 16.2 1.0 N A:GLY107 4.4 17.1 1.0 CA A:VAL103 4.4 18.7 1.0 O3' P:DC8 4.5 18.7 1.0 CB A:THR101 4.5 21.4 1.0 CB A:ILE106 4.5 18.4 1.0 CA A:ARG102 4.6 24.7 1.0 C A:GLY105 4.6 21.5 1.0 O5' P:DG9 4.7 18.4 0.7 O A:ARG102 4.7 22.3 1.0 CA A:GLY107 4.7 16.8 1.0 CA A:GLY105 4.8 20.8 1.0 O A:LEU100 4.8 16.2 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog


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 Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:28.4 occ:1.00 O A:VAL65 2.3 26.7 1.0 O A:LEU62 2.4 30.2 1.0 O A:HOH688 2.5 35.9 1.0 O A:LYS60 2.6 36.4 1.0 OP1 D:DC3 2.6 27.1 1.0 O D:HOH203 2.6 43.3 1.0 C A:VAL65 3.4 29.4 1.0 C A:LEU62 3.4 31.1 1.0 P D:DC3 3.5 31.4 1.0 C A:LYS60 3.6 32.3 1.0 OP2 D:DC3 3.6 28.3 1.0 N A:VAL65 3.8 27.1 1.0 N A:GLY64 4.0 30.7 1.0 CA A:PRO63 4.0 25.3 1.0 CA A:VAL65 4.1 26.8 1.0 N A:LEU62 4.1 26.4 1.0 N A:PRO63 4.1 27.6 1.0 C A:LYS61 4.2 38.0 1.0 CA A:LYS60 4.3 27.9 1.0 O A:LYS61 4.4 31.7 1.0 CA A:LEU62 4.4 27.4 1.0 C A:PRO63 4.4 31.0 1.0 CB A:VAL65 4.4 25.4 1.0 N A:GLY66 4.4 28.0 1.0 O3' D:DT2 4.4 33.7 1.0 CG A:LYS60 4.5 32.2 1.0 N A:LYS61 4.6 28.0 1.0 C A:GLY64 4.7 33.5 1.0 CA A:LYS61 4.7 38.7 1.0 CA A:GLY66 4.7 27.0 1.0 O5' D:DC3 4.8 38.6 1.0 CA A:GLY64 4.9 37.4 1.0 O A:ALA59 4.9 28.5 1.0 CB A:LYS60 5.0 32.7 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