Sodium in PDB 4ub5: Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S:
2.7.7.7;

The structure of Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S, PDB code: 4ub5 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)	21.09 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.066, 77.713, 55.112, 90.00, 114.24, 90.00
R / Rfree (%)	22.6 / 29

The structure of Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S also contains other interesting chemical elements:

Manganese

(Mn)

5 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S (pdb code 4ub5). 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 Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S, PDB code: 4ub5:
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 Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 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 Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:20.9 occ:1.00 O A:THR101 2.3 28.9 1.0 O P:HOH204 2.4 23.0 1.0 O A:HOH576 2.4 33.9 1.0 O A:VAL103 2.5 22.8 1.0 OP1 P:DG9 2.5 22.2 1.0 O A:ILE106 2.5 22.8 1.0 C A:THR101 3.3 23.5 1.0 C A:VAL103 3.3 24.1 1.0 C A:ILE106 3.5 18.9 1.0 P P:DG9 3.5 27.1 1.0 OP2 P:DG9 3.6 24.5 1.0 N A:ILE106 3.8 23.1 1.0 CA A:THR101 3.9 25.3 1.0 CA A:SER104 4.0 24.7 1.0 N A:SER104 4.0 21.9 1.0 N A:GLY105 4.0 16.9 1.0 N A:VAL103 4.1 19.2 1.0 CA A:ILE106 4.1 21.9 1.0 CA A:VAL103 4.3 20.5 1.0 C A:ARG102 4.3 20.1 1.0 C A:SER104 4.4 22.0 1.0 N A:GLY107 4.4 19.0 1.0 N A:ARG102 4.4 23.1 1.0 CB A:THR101 4.4 25.0 1.0 O3' P:DC8 4.5 23.9 1.0 CB A:ILE106 4.5 12.7 1.0 CA A:GLY107 4.6 18.6 1.0 C A:GLY105 4.7 21.9 1.0 CA A:ARG102 4.7 19.5 1.0 O5' P:DG9 4.7 23.5 1.0 O A:ARG102 4.8 26.5 1.0 O A:LEU100 4.8 21.0 1.0 CA A:GLY105 5.0 18.9 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 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 Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:49.0 occ:1.00 O A:LYS60 2.4 36.5 1.0 O D:HOH102 2.4 36.5 1.0 O A:LEU62 2.5 34.5 1.0 O A:VAL65 2.5 38.6 1.0 OP1 D:DC3 2.6 30.6 1.0 C A:LEU62 3.3 34.6 1.0 C A:LYS60 3.6 44.9 1.0 C A:VAL65 3.7 33.6 1.0 P D:DC3 3.8 38.9 1.0 N A:PRO63 3.9 34.5 1.0 C A:LYS61 4.0 47.1 1.0 CA A:PRO63 4.0 36.8 1.0 N A:LEU62 4.0 44.3 1.0 OP2 D:DC3 4.1 30.0 1.0 O A:LYS61 4.1 47.9 1.0 N A:VAL65 4.2 33.8 1.0 CA A:LEU62 4.3 30.4 1.0 CA A:LYS60 4.4 42.8 1.0 CA A:VAL65 4.4 29.5 1.0 N A:GLY64 4.4 36.9 1.0 N A:LYS61 4.5 48.9 1.0 CA A:LYS61 4.5 48.0 1.0 CG A:LYS60 4.6 47.6 1.0 C A:PRO63 4.6 42.1 1.0 CB A:VAL65 4.7 41.6 1.0 N A:GLY66 4.7 37.6 1.0 O5' D:DC3 4.8 30.6 1.0 O3' D:DT2 4.9 35.2 1.0 CA A:GLY66 4.9 31.1 1.0 O A:ALA59 5.0 36.8 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