Calcium in PDB 5v1n: Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp:
2.7.7.7;

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp, PDB code: 5v1n was solved by B.D.Freudenthal, M.A.Schaich, A.M.Whitaker, M.R.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.61 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.546, 79.225, 55.536, 90.00, 107.32, 90.00
R / Rfree (%)	18.1 / 23.7

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp (pdb code 5v1n). 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 8-Oxog:A at the Primer Terminus and Incoming Dctp, PDB code: 5v1n:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp


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 8-Oxog:A at the Primer Terminus and Incoming Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:18.7 occ:1.00 O3G A:DCP406 2.2 15.8 1.0 O2A A:DCP406 2.2 14.7 1.0 OD2 A:ASP192 2.3 22.8 1.0 O2B A:DCP406 2.3 13.2 1.0 OD1 A:ASP190 2.3 16.8 1.0 O A:HOH547 2.4 15.2 1.0 O A:ASP190 3.1 19.2 1.0 CG A:ASP192 3.3 14.8 1.0 PB A:DCP406 3.4 17.5 1.0 CG A:ASP190 3.5 14.9 1.0 PG A:DCP406 3.5 18.2 1.0 PA A:DCP406 3.5 18.0 1.0 OD1 A:ASP192 3.6 23.7 1.0 O3A A:DCP406 3.6 19.3 1.0 O A:HOH524 3.6 17.2 1.0 O A:HOH502 3.7 25.0 1.0 C A:ASP190 3.7 19.8 1.0 O3B A:DCP406 3.9 22.0 1.0 N A:ASP190 3.9 15.3 1.0 O A:HOH609 4.1 15.6 1.0 O1G A:DCP406 4.2 14.3 1.0 C5' A:DCP406 4.2 13.8 1.0 CA A:ASP190 4.2 14.1 1.0 OD2 A:ASP190 4.3 27.1 1.0 CB A:ASP190 4.5 15.8 1.0 O5' A:DCP406 4.5 17.5 1.0 N A:MET191 4.6 14.4 1.0 OG A:SER180 4.6 17.4 1.0 N A:SER180 4.6 15.7 1.0 CA A:GLY179 4.6 9.7 1.0 CB A:ASP192 4.6 17.2 1.0 O1A A:DCP406 4.6 17.6 1.0 O1B A:DCP406 4.7 17.0 1.0 N A:ASP192 4.8 19.7 1.0 O2G A:DCP406 4.8 19.4 1.0 C A:MET191 4.9 16.4 1.0 C A:GLY189 4.9 20.2 1.0 CA A:MET191 5.0 17.4 1.0 N A:GLY189 5.0 19.5 1.0

Calcium binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp


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 8-Oxog:A at the Primer Terminus and Incoming Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:36.6 occ:1.00 O A:HOH732 2.4 44.6 1.0 O A:HOH704 2.4 38.8 1.0 O A:HOH524 2.5 17.2 1.0 O A:HOH509 2.5 28.0 1.0 O A:HOH621 2.5 27.5 1.0 O P:HOH109 3.0 28.2 1.0 O2G A:DCP406 4.3 19.4 1.0 O1A A:DCP406 4.3 17.6 1.0 O A:HOH710 4.5 47.1 1.0 OP2 P:8OG10 4.6 19.4 1.0 OD2 A:ASP190 4.6 27.1 1.0 OP1 P:8OG10 4.6 20.4 1.0 O3G A:DCP406 4.7 15.8 1.0 O A:HOH592 4.7 31.1 1.0 O A:HOH730 4.8 21.8 1.0 CG A:ASP190 4.9 14.9 1.0 CA A:GLY189 5.0 14.2 1.0

A.M.Whitaker, M.R.Smith, M.A.Schaich, B.D.Freudenthal. Capturing A Mammalian Dna Polymerase Extending From An Oxidized Nucleotide. Nucleic Acids Res. V. 45 6934 2017.
ISSN: ESSN 1362-4962
PubMed: 28449123
DOI: 10.1093/NAR/GKX293