Calcium in PDB 5v1f: Dna Polymerase Beta Substrate Complex with 8-Oxog at the Primer Terminus and Incoming Dctp

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

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog at the Primer Terminus and Incoming Dctp, PDB code: 5v1f was solved by B.D.Freudenthal, M.R.Smith, M.A.Schaich, A.M.Whitaker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.41 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.218, 79.016, 55.626, 90.00, 107.01, 90.00
R / Rfree (%)	22.6 / 29.7

The binding sites of Calcium atom in the Dna Polymerase Beta Substrate Complex with 8-Oxog at the Primer Terminus and Incoming Dctp (pdb code 5v1f). 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 at the Primer Terminus and Incoming Dctp, PDB code: 5v1f:
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 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 at the Primer Terminus and Incoming Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:33.8 occ:1.00 O2G A:DCP403 2.1 37.5 1.0 O2A A:DCP403 2.2 30.9 1.0 OD2 A:ASP190 2.3 34.2 1.0 OD2 A:ASP192 2.4 46.6 1.0 O2B A:DCP403 2.5 26.8 1.0 O A:ASP190 2.9 39.8 1.0 CG A:ASP192 3.4 39.1 1.0 PB A:DCP403 3.5 36.0 1.0 PG A:DCP403 3.5 35.6 1.0 C A:ASP190 3.5 40.2 1.0 CG A:ASP190 3.6 47.9 1.0 CA A:CA402 3.6 42.6 1.0 PA A:DCP403 3.6 35.2 1.0 N A:ASP190 3.6 34.9 1.0 OD1 A:ASP192 3.8 39.2 1.0 O3B A:DCP403 3.9 45.1 1.0 O3A A:DCP403 4.0 37.0 1.0 CA A:ASP190 4.0 35.9 1.0 O A:HOH529 4.3 30.8 1.0 O1G A:DCP403 4.3 40.1 1.0 CB A:ASP190 4.4 43.8 1.0 N A:MET191 4.4 38.8 1.0 OD1 A:ASP190 4.4 49.2 1.0 C5' A:DCP403 4.5 34.4 1.0 N A:SER180 4.5 47.1 1.0 O1A A:DCP403 4.6 31.7 1.0 OG A:SER180 4.6 40.0 1.0 O3G A:DCP403 4.6 39.9 1.0 CA A:GLY179 4.7 34.5 1.0 O5' A:DCP403 4.7 41.0 1.0 CB A:ASP192 4.7 38.4 1.0 C A:GLY189 4.7 44.6 1.0 N A:GLY189 4.7 50.2 1.0 C A:MET191 4.8 38.4 1.0 CA A:MET191 4.9 35.1 1.0 O1B A:DCP403 4.9 45.6 1.0 N A:ASP192 5.0 30.4 1.0 CA A:GLY189 5.0 36.7 1.0

Calcium binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with 8-Oxog 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 at the Primer Terminus and Incoming Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:42.6 occ:1.00 OD1 A:ASP192 2.2 39.2 1.0 O3' P:8OG10 2.4 43.7 0.9 OD2 A:ASP256 2.5 49.8 1.0 O2A A:DCP403 2.5 30.9 1.0 OD2 A:ASP190 2.7 34.2 1.0 OD1 A:ASP190 2.8 49.2 1.0 CG A:ASP190 3.0 47.9 1.0 CG A:ASP192 3.2 39.1 1.0 OD2 A:ASP192 3.3 46.6 1.0 PA A:DCP403 3.5 35.2 1.0 CA A:CA401 3.6 33.8 1.0 C3' P:8OG10 3.6 49.8 0.9 O5' A:DCP403 3.7 41.0 1.0 CG A:ASP256 3.7 53.7 1.0 C5' A:DCP403 3.9 34.4 1.0 O1A A:DCP403 3.9 31.7 1.0 O5' P:8OG10 4.3 53.8 0.9 O A:MET191 4.5 37.6 1.0 CB A:ASP190 4.5 43.8 1.0 C4' P:8OG10 4.5 50.7 0.9 OD1 A:ASP256 4.5 60.6 1.0 CB A:ASP192 4.6 38.4 1.0 CB A:ASP256 4.6 48.5 1.0 C2' P:8OG10 4.7 47.9 0.9 OP1 P:8OG10 4.7 58.4 0.9 C5' P:8OG10 4.9 53.3 0.9 C A:MET191 5.0 38.4 1.0 O3A A:DCP403 5.0 37.0 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