Sodium in PDB 4ub1: Dna Polymerase Beta Product Complex with A Templating Adenine and 8- Oxodgmp, 90 S

All present enzymatic activity of Dna Polymerase Beta Product Complex with A Templating Adenine and 8- Oxodgmp, 90 S:
2.7.7.7;

The structure of Dna Polymerase Beta Product Complex with A Templating Adenine and 8- Oxodgmp, 90 S, PDB code: 4ub1 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)	31.96 / 2.34
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.131, 80.800, 55.462, 90.00, 109.58, 90.00
R / Rfree (%)	22.2 / 27.7

The binding sites of Sodium atom in the Dna Polymerase Beta Product Complex with A Templating Adenine and 8- Oxodgmp, 90 S (pdb code 4ub1). 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 Product Complex with A Templating Adenine and 8- Oxodgmp, 90 S, PDB code: 4ub1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Product Complex with A Templating Adenine and 8- Oxodgmp, 90 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 Product Complex with A Templating Adenine and 8- Oxodgmp, 90 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:35.4 occ:1.00 O P:HOH104 3.1 47.2 1.0 O A:THR101 3.4 28.0 1.0 OP1 P:DG9 3.6 28.6 1.0 O A:ARG102 3.7 29.6 1.0 CA A:SER104 3.9 23.2 1.0 O P:HOH102 4.0 27.6 1.0 N A:SER104 4.0 26.0 1.0 C A:ARG102 4.1 25.6 1.0 C A:VAL103 4.1 24.7 1.0 O A:VAL103 4.2 25.4 1.0 CB A:SER104 4.5 24.5 1.0 CA A:ARG102 4.5 25.2 1.0 C A:THR101 4.5 23.2 1.0 P P:DG9 4.6 24.3 1.0 N A:VAL103 4.7 21.9 1.0 O5' P:DG9 4.7 29.1 1.0 OG A:SER104 4.8 26.4 1.0 CA A:VAL103 5.0 25.7 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Product Complex with A Templating Adenine and 8- Oxodgmp, 90 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 Product Complex with A Templating Adenine and 8- Oxodgmp, 90 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:55.3 occ:1.00 O D:HOH103 3.7 41.4 1.0 O A:LYS60 3.8 39.9 1.0 CA A:LYS61 4.0 41.6 1.0 C A:LYS60 4.4 36.2 1.0 O A:LYS61 4.5 46.0 1.0 N A:LYS61 4.6 35.6 1.0 C A:LYS61 4.6 40.2 1.0 CG A:LYS60 4.7 42.2 1.0 CB A:LYS61 5.0 39.2 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