Calcium in PDB 4ubc: Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 0 S

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

The structure of Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 0 S, PDB code: 4ubc 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)	29.19 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.775, 79.783, 55.539, 90.00, 107.47, 90.00
R / Rfree (%)	18.6 / 26

The binding sites of Calcium atom in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 0 S (pdb code 4ubc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 0 S, PDB code: 4ubc:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine 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 Cytosine and Incoming 8-Oxodgtp, 0 S within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca101 b:46.0 occ:1.00 O A:HOH632 2.4 40.4 1.0 O A:HOH670 2.4 25.2 1.0 O1A A:8DG401 2.4 15.1 1.0 O A:HOH624 2.5 25.7 1.0 O A:HOH732 2.5 41.1 1.0 O A:HOH740 3.0 46.2 1.0 PA A:8DG401 3.6 18.4 1.0 O3A A:8DG401 3.8 22.7 1.0 O A:HOH640 4.3 36.1 1.0 O A:HOH574 4.4 18.7 1.0 O8 A:8DG401 4.4 23.3 1.0 O5' A:8DG401 4.5 17.2 1.0 O A:HOH693 4.5 28.4 1.0 O2G A:8DG401 4.5 19.3 1.0 OP2 P:DC10 4.6 31.6 1.0 O2A A:8DG401 4.8 15.6 1.0 O A:HOH580 4.9 17.6 1.0 O3B A:8DG401 4.9 19.6 1.0

Calcium binding site 2 out of 3 in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine 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 Cytosine and Incoming 8-Oxodgtp, 0 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:15.0 occ:1.00 OD2 A:ASP256 2.3 17.6 1.0 OD1 A:ASP192 2.3 13.1 1.0 O2A A:8DG401 2.3 15.6 1.0 O A:HOH574 2.4 18.7 1.0 O3' P:DC10 2.4 19.9 1.0 OD2 A:ASP190 2.5 18.3 1.0 OD1 A:ASP190 2.6 14.3 1.0 CG A:ASP190 2.9 17.7 1.0 CG A:ASP192 3.4 14.5 1.0 CG A:ASP256 3.5 21.9 1.0 PA A:8DG401 3.5 18.4 1.0 C3' P:DC10 3.6 21.4 1.0 CA A:CA403 3.7 15.2 1.0 O1A A:8DG401 3.8 15.1 1.0 OD2 A:ASP192 3.9 16.7 1.0 O5' A:8DG401 3.9 17.2 1.0 CB A:ASP256 4.1 18.1 1.0 C4' P:DC10 4.2 26.3 1.0 C5' A:8DG401 4.2 16.9 1.0 C5' P:DC10 4.3 17.1 1.0 O A:HOH693 4.4 28.4 1.0 CB A:ASP190 4.4 16.2 1.0 O A:MET191 4.4 14.8 1.0 OD1 A:ASP256 4.4 17.3 1.0 CB A:ASP192 4.6 14.1 1.0 O A:HOH677 4.6 30.1 1.0 OP1 P:DC10 4.8 25.3 1.0 O5' P:DC10 4.8 20.6 1.0 NH2 A:ARG254 4.8 19.8 1.0 C2' P:DC10 4.8 27.5 1.0 C A:MET191 4.9 14.6 1.0 O3A A:8DG401 4.9 22.7 1.0 O3G A:8DG401 4.9 17.1 1.0 C A:ASP190 5.0 18.5 1.0

Calcium binding site 3 out of 3 in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine 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 3 of Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 0 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:15.2 occ:1.00 O3G A:8DG401 2.3 17.1 1.0 OD1 A:ASP190 2.3 14.3 1.0 OD2 A:ASP192 2.3 16.7 1.0 O2A A:8DG401 2.3 15.6 1.0 O2B A:8DG401 2.4 14.2 1.0 O A:HOH575 2.5 16.1 1.0 O A:ASP190 2.6 17.3 1.0 CG A:ASP192 3.2 14.5 1.0 C A:ASP190 3.4 18.5 1.0 OD1 A:ASP192 3.4 13.1 1.0 PB A:8DG401 3.4 15.9 1.0 CG A:ASP190 3.5 17.7 1.0 PG A:8DG401 3.6 18.6 1.0 PA A:8DG401 3.6 18.4 1.0 CA A:CA402 3.7 15.0 1.0 N A:ASP190 3.7 17.2 1.0 O3A A:8DG401 3.8 22.7 1.0 O3B A:8DG401 3.8 19.6 1.0 CA A:ASP190 4.0 13.6 1.0 O A:HOH693 4.1 28.4 1.0 O A:HOH585 4.2 16.0 1.0 O1G A:8DG401 4.3 14.0 1.0 CB A:ASP190 4.4 16.2 1.0 N A:MET191 4.4 15.2 1.0 OD2 A:ASP190 4.4 18.3 1.0 OG A:SER180 4.5 22.7 1.0 O1A A:8DG401 4.6 15.1 1.0 CB A:ASP192 4.6 14.1 1.0 O5' A:8DG401 4.6 17.2 1.0 N A:SER180 4.6 20.4 1.0 C5' A:8DG401 4.6 16.9 1.0 CA A:GLY179 4.6 11.5 1.0 C A:MET191 4.7 14.6 1.0 CA A:MET191 4.7 18.9 1.0 N A:ASP192 4.7 18.4 1.0 O2G A:8DG401 4.8 19.3 1.0 O1B A:8DG401 4.8 15.3 1.0 C A:GLY189 4.9 25.2 1.0 O A:HOH574 4.9 18.7 1.0 N A:GLY189 4.9 20.1 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