Sodium in PDB 4uaw: Dna Polymerase Beta Substrate Complex with A Templating Adenine and Incoming 8-Oxodgtp, 0 S

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with A Templating Adenine and Incoming 8-Oxodgtp, 0 S:
2.7.7.7;

The structure of Dna Polymerase Beta Substrate Complex with A Templating Adenine and Incoming 8-Oxodgtp, 0 S, PDB code: 4uaw was solved by B.D.Freudenthal, S.H.Wilson, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.73 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.932, 79.929, 55.515, 90.00, 107.59, 90.00
R / Rfree (%)	18.3 / 24

The structure of Dna Polymerase Beta Substrate Complex with A Templating Adenine and Incoming 8-Oxodgtp, 0 S also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Substrate Complex with A Templating Adenine and Incoming 8-Oxodgtp, 0 S (pdb code 4uaw). 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 A Templating Adenine and Incoming 8-Oxodgtp, 0 S, PDB code: 4uaw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Substrate Complex with A Templating Adenine and Incoming 8-Oxodgtp, 0 S


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 A Templating Adenine and Incoming 8-Oxodgtp, 0 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:19.4 occ:1.00 O A:THR101 2.5 21.6 1.0 OP1 P:DG9 2.6 17.4 1.0 O A:VAL103 2.6 15.2 1.0 O P:HOH108 2.6 22.8 1.0 O A:ILE106 2.6 14.7 1.0 O A:HOH626 2.7 24.5 1.0 C A:THR101 3.4 17.8 1.0 C A:VAL103 3.4 13.8 1.0 P P:DG9 3.5 20.1 1.0 OP2 P:DG9 3.7 19.1 1.0 C A:ILE106 3.7 16.5 1.0 O A:HOH700 3.7 36.8 1.0 N A:ILE106 3.9 13.4 1.0 CA A:SER104 3.9 15.3 1.0 N A:GLY105 4.0 15.5 1.0 CA A:THR101 4.0 18.8 1.0 N A:SER104 4.0 14.5 1.0 N A:VAL103 4.1 13.7 1.0 O P:HOH128 4.1 39.9 1.0 CA A:ILE106 4.3 14.1 1.0 C A:ARG102 4.3 20.2 1.0 C A:SER104 4.3 15.3 1.0 N A:ARG102 4.4 17.5 1.0 CA A:VAL103 4.4 15.9 1.0 O3' P:DC8 4.5 18.9 1.0 CB A:THR101 4.5 17.9 1.0 CA A:ARG102 4.6 18.6 1.0 CB A:ILE106 4.6 18.4 1.0 N A:GLY107 4.7 15.6 1.0 O A:ARG102 4.7 19.6 1.0 C A:GLY105 4.8 17.0 1.0 O A:HOH713 4.8 36.3 1.0 O5' P:DG9 4.8 23.1 1.0 CA A:GLY107 4.9 17.6 1.0 CA A:GLY105 4.9 18.0 1.0 O A:LEU100 4.9 17.5 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with A Templating Adenine and Incoming 8-Oxodgtp, 0 S


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 A Templating Adenine and Incoming 8-Oxodgtp, 0 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:28.4 occ:1.00 O A:LYS60 2.6 28.3 1.0 O A:LEU62 2.6 27.0 1.0 O A:VAL65 2.7 27.1 1.0 OP1 D:DC3 2.7 29.0 1.0 O A:HOH689 2.9 35.7 1.0 O D:HOH104 3.0 34.7 1.0 C A:LEU62 3.4 26.6 1.0 C A:LYS60 3.6 30.2 1.0 C A:VAL65 3.8 28.3 1.0 P D:DC3 3.8 29.2 1.0 N A:LEU62 3.9 26.4 1.0 OP2 D:DC3 3.9 26.9 1.0 C A:LYS61 4.0 35.1 1.0 N A:PRO63 4.0 31.0 1.0 CA A:PRO63 4.1 29.7 1.0 N A:VAL65 4.1 25.2 1.0 O A:LYS61 4.2 32.7 1.0 CA A:LEU62 4.2 27.0 1.0 N A:GLY64 4.3 23.4 1.0 CA A:LYS60 4.3 27.5 1.0 CA A:VAL65 4.4 24.6 1.0 N A:LYS61 4.4 28.6 1.0 CA A:LYS61 4.5 25.5 1.0 CG A:LYS60 4.5 32.6 1.0 CB A:VAL65 4.5 23.7 1.0 C A:PRO63 4.6 26.9 1.0 O3' D:DT2 4.7 30.5 1.0 N A:GLY66 4.8 27.5 1.0 O A:ALA59 4.9 24.4 1.0 O5' D:DC3 5.0 34.2 1.0

B.D.Freudenthal, W.A.Beard, L.Perera, D.D.Shock, T.Kim, T.Schlick, S.H.Wilson. Uncovering the Polymerase-Induced Cytotoxicty of An Oxidized Nucleotide Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13886