Calcium in PDB 6mr7: Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog:
2.7.7.7;

The structure of Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog, PDB code: 6mr7 was solved by B.D.Freudenthal, M.R.Smith, 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)	24.71 / 2.14
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.032, 79.825, 55.518, 90.00, 110.60, 90.00
R / Rfree (%)	18.6 / 25.2

The structure of Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Calcium atom in the Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog (pdb code 6mr7). 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 Templating Adenine and Incoming Fapy-Dgtp Analog, PDB code: 6mr7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog


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 Templating Adenine and Incoming Fapy-Dgtp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:33.1 occ:1.00 O A:HOH515 2.3 37.9 1.0 OD2 A:ASP192 2.4 38.2 1.0 OD1 A:ASP190 2.4 31.6 1.0 O2G A:GKS401 2.4 42.8 0.3 O1A A:GKS401 2.4 44.0 0.3 O2G A:GKS401 2.5 42.8 0.7 O A:HOH603 2.6 35.2 1.0 O1A A:GKS401 2.6 44.2 0.7 O2B A:GKS401 2.7 39.9 0.7 O2B A:GKS401 2.7 40.0 0.3 CG A:ASP192 3.3 35.9 1.0 CG A:ASP190 3.3 36.6 1.0 O3A A:GKS401 3.3 43.9 0.7 PA A:GKS401 3.4 42.5 0.7 PA A:GKS401 3.4 43.0 0.3 PG A:GKS401 3.5 45.7 0.7 OD2 A:ASP190 3.5 46.2 1.0 O3A A:GKS401 3.5 43.8 0.3 PG A:GKS401 3.5 45.6 0.3 OD1 A:ASP192 3.6 44.0 1.0 O1G A:GKS401 3.6 41.5 0.7 PB A:GKS401 3.7 44.3 0.7 PB A:GKS401 3.7 44.4 0.3 O1G A:GKS401 3.8 41.4 0.3 NA A:NA406 4.0 52.4 1.0 O3B A:GKS401 4.0 43.9 0.3 O3B A:GKS401 4.0 44.0 0.7 N2 A:GKS401 4.1 41.8 0.7 O A:HOH501 4.1 47.6 1.0 O2A A:GKS401 4.1 44.8 0.3 O2A A:GKS401 4.2 44.9 0.7 O A:HOH560 4.3 35.7 1.0 O A:HOH523 4.3 40.9 1.0 O3' P:DC10 4.6 47.6 1.0 O A:ASP190 4.6 29.1 1.0 CB A:ASP192 4.7 33.3 1.0 CA A:GLY179 4.7 30.7 1.0 N2 A:GKS401 4.7 40.9 0.3 O5' A:GKS401 4.7 42.5 0.7 O5' A:GKS401 4.8 42.5 0.3 CB A:ASP190 4.8 28.1 1.0 O3G A:GKS401 4.8 46.9 0.7 O A:HOH572 4.8 32.5 1.0 O3G A:GKS401 4.9 46.8 0.3 C A:ASP190 4.9 29.2 1.0

Calcium binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog


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 Templating Adenine and Incoming Fapy-Dgtp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:35.2 occ:1.00 O A:HOH661 2.4 31.8 1.0 O A:HOH535 2.4 34.4 1.0 O A:HOH634 2.5 30.1 1.0 OD2 A:ASP145 2.6 26.6 1.0 OD1 A:ASP145 2.7 25.9 1.0 O A:HOH673 2.7 31.6 1.0 O A:HOH652 2.8 30.1 1.0 CG A:ASP145 3.0 32.9 1.0 OE1 A:GLU249 4.3 45.9 1.0 ND1 A:HIS252 4.5 32.5 1.0 O A:HOH561 4.5 41.0 1.0 O A:HOH614 4.5 26.3 1.0 CA A:PRO251 4.5 35.7 1.0 CB A:ASP145 4.5 23.5 1.0 O A:TYR250 4.7 31.7 1.0 N A:HIS252 4.8 31.8 1.0

M.R.Smith, D.D.Shock, W.A.Beard, M.M.Greenberg, B.D.Freudenthal, S.H.Wilson. A Guardian Residue Hinders Insertion of A Fapy•Dgtp Analog By Modulating the Open-Closed Dna Polymerase Transition. Nucleic Acids Res. V. 47 3197 2019.
ISSN: ESSN 1362-4962
PubMed: 30649431
DOI: 10.1093/NAR/GKZ002