Calcium in PDB 4ub4: Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Dgtp, 0 S

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

The structure of Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Dgtp, 0 S, PDB code: 4ub4 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)	25.43 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.594, 79.372, 55.465, 90.00, 107.50, 90.00
R / Rfree (%)	18.8 / 23.5

The binding sites of Calcium atom in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Dgtp, 0 S (pdb code 4ub4). 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 Cytosine and Incoming Dgtp, 0 S, PDB code: 4ub4:
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 Cytosine and Incoming Dgtp, 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 Dgtp, 0 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:27.8 occ:1.00 OD1 A:ASP192 2.2 26.2 1.0 OD2 A:ASP256 2.2 28.2 1.0 O3' P:DC10 2.4 32.5 1.0 O P:HOH105 2.4 33.6 1.0 OD2 A:ASP190 2.5 33.6 1.0 O1A A:DGT403 2.5 21.7 1.0 OD1 A:ASP190 2.6 22.9 1.0 CG A:ASP190 2.9 29.6 1.0 CG A:ASP192 3.3 21.1 1.0 CG A:ASP256 3.5 32.4 1.0 C3' P:DC10 3.5 29.3 1.0 OD2 A:ASP192 3.6 28.6 1.0 PA A:DGT403 3.7 28.1 1.0 CA A:CA402 3.8 24.1 1.0 O5' A:DGT403 4.1 25.9 1.0 O2A A:DGT403 4.1 26.0 1.0 C4' P:DC10 4.2 31.8 1.0 CB A:ASP256 4.2 25.9 1.0 C5' P:DC10 4.3 31.0 1.0 C5' A:DGT403 4.3 25.1 1.0 OD1 A:ASP256 4.4 25.9 1.0 O A:HOH648 4.4 35.3 1.0 CB A:ASP190 4.4 28.6 1.0 O A:MET191 4.5 23.1 1.0 CB A:ASP192 4.6 23.3 1.0 O5' P:DC10 4.7 27.2 1.0 OP1 P:DC10 4.7 32.3 1.0 C2' P:DC10 4.7 31.9 1.0 NH2 A:ARG254 4.8 29.8 1.0 C A:MET191 4.9 21.6 1.0 C A:ASP190 5.0 21.2 1.0 O A:ASP190 5.0 29.0 1.0

Calcium binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Dgtp, 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 Dgtp, 0 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:24.1 occ:1.00 OD2 A:ASP192 2.2 28.6 1.0 O A:HOH551 2.3 27.2 1.0 O1B A:DGT403 2.3 21.7 1.0 O1G A:DGT403 2.4 25.0 1.0 OD1 A:ASP190 2.4 22.9 1.0 O1A A:DGT403 2.5 21.7 1.0 O A:ASP190 2.7 29.0 1.0 CG A:ASP192 3.3 21.1 1.0 PB A:DGT403 3.4 26.2 1.0 C A:ASP190 3.6 21.2 1.0 PG A:DGT403 3.6 27.4 1.0 CG A:ASP190 3.6 29.6 1.0 PA A:DGT403 3.6 28.1 1.0 OD1 A:ASP192 3.6 26.2 1.0 O3A A:DGT403 3.7 28.1 1.0 CA A:CA401 3.8 27.8 1.0 O3B A:DGT403 3.8 29.5 1.0 N A:ASP190 3.8 25.6 1.0 CA A:ASP190 4.1 21.6 1.0 O A:HOH648 4.2 35.3 1.0 O3G A:DGT403 4.3 24.0 1.0 O A:HOH562 4.3 25.6 1.0 C5' A:DGT403 4.4 25.1 1.0 CB A:ASP190 4.5 28.6 1.0 N A:SER180 4.5 25.8 1.0 OG A:SER180 4.5 25.7 1.0 OD2 A:ASP190 4.5 33.6 1.0 N A:MET191 4.5 22.5 1.0 CA A:GLY179 4.5 21.3 1.0 CB A:ASP192 4.6 23.3 1.0 O5' A:DGT403 4.6 25.9 1.0 O2B A:DGT403 4.8 28.5 1.0 N A:ASP192 4.8 22.5 1.0 O2A A:DGT403 4.8 26.0 1.0 O2G A:DGT403 4.8 30.4 1.0 C A:MET191 4.9 21.6 1.0 N A:GLY189 4.9 26.6 1.0 CA A:MET191 4.9 24.4 1.0 C A:GLY189 4.9 28.1 1.0 O P:HOH105 5.0 33.6 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