Calcium 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:

Sodium

(Na)

2 atoms

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

Calcium 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 Calcium with other atoms in the Ca 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:Ca402 b:17.0 occ:1.00 OD1 A:ASP192 2.3 13.8 1.0 OD2 A:ASP256 2.4 16.5 1.0 O2A A:8DG401 2.4 16.5 1.0 O3' P:DC10 2.5 17.6 1.0 O P:HOH105 2.5 20.7 1.0 OD1 A:ASP190 2.6 13.0 1.0 OD2 A:ASP190 2.7 23.2 1.0 CG A:ASP190 3.0 15.9 1.0 CG A:ASP192 3.4 11.6 1.0 PA A:8DG401 3.6 18.1 1.0 CG A:ASP256 3.6 17.4 1.0 C3' P:DC10 3.6 20.3 1.0 CA A:CA403 3.8 13.9 1.0 OD2 A:ASP192 3.8 15.2 1.0 H5'1 A:8DG401 3.9 21.0 1.0 O1A A:8DG401 3.9 17.7 1.0 O5' A:8DG401 3.9 18.4 1.0 C4' P:DC10 4.2 17.0 1.0 C5' P:DC10 4.2 18.8 1.0 CB A:ASP256 4.3 17.9 1.0 O A:HOH634 4.3 23.9 1.0 C5' A:8DG401 4.4 17.5 1.0 H5'2 A:8DG401 4.5 21.0 1.0 OD1 A:ASP256 4.5 16.8 1.0 CB A:ASP190 4.5 13.4 1.0 O A:MET191 4.6 13.9 1.0 CB A:ASP192 4.7 16.2 1.0 O A:HOH685 4.7 27.7 1.0 OP1 P:DC10 4.7 22.6 1.0 O5' P:DC10 4.8 17.5 1.0 C2' P:DC10 4.9 20.7 1.0 NH2 A:ARG254 4.9 15.8 1.0 O3A A:8DG401 5.0 20.1 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca403 b:13.9 occ:1.00 O3G A:8DG401 2.3 17.6 1.0 OD2 A:ASP192 2.3 15.2 1.0 O2A A:8DG401 2.4 16.5 1.0 O2B A:8DG401 2.4 15.1 1.0 OD1 A:ASP190 2.5 13.0 1.0 O A:HOH587 2.5 16.0 1.0 O A:ASP190 2.8 14.1 1.0 CG A:ASP192 3.3 11.6 1.0 PB A:8DG401 3.5 15.8 1.0 C A:ASP190 3.5 15.5 1.0 OD1 A:ASP192 3.6 13.8 1.0 PG A:8DG401 3.6 18.6 1.0 PA A:8DG401 3.7 18.1 1.0 CG A:ASP190 3.7 15.9 1.0 CA A:CA402 3.8 17.0 1.0 O3A A:8DG401 3.8 20.1 1.0 N A:ASP190 3.8 16.2 1.0 O3B A:8DG401 3.9 17.1 1.0 CA A:ASP190 4.1 14.2 1.0 H5'2 A:8DG401 4.1 21.0 1.0 O A:HOH591 4.1 15.2 1.0 O A:HOH634 4.2 23.9 1.0 O1G A:8DG401 4.3 17.2 1.0 OG A:SER180 4.4 17.5 1.0 N A:MET191 4.5 13.8 1.0 CB A:ASP190 4.5 13.4 1.0 N A:SER180 4.6 15.8 1.0 OD2 A:ASP190 4.6 23.2 1.0 CA A:GLY179 4.6 12.4 1.0 CB A:ASP192 4.6 16.2 1.0 O5' A:8DG401 4.7 18.4 1.0 O1A A:8DG401 4.7 17.7 1.0 N A:ASP192 4.7 14.2 1.0 C5' A:8DG401 4.7 17.5 1.0 O2G A:8DG401 4.8 14.7 1.0 C A:MET191 4.8 12.6 1.0 CA A:MET191 4.8 16.0 1.0 H5'1 A:8DG401 4.8 21.0 1.0 O1B A:8DG401 4.8 16.0 1.0 C A:GLY189 4.9 16.2 1.0 N A:GLY189 4.9 17.9 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