Calcium in PDB 5wnx: Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp:
2.7.7.7;

The structure of Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp, PDB code: 5wnx was solved by M.A.Schaich, M.R.Smith, A.S.Cloud, S.M.Holloran, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.02 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.243, 79.203, 55.625, 90.00, 107.36, 90.00
R / Rfree (%)	20.6 / 29

The structure of Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp (pdb code 5wnx). 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 Incoming 6-Tdgtp, PDB code: 5wnx:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp


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 Incoming 6-Tdgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:37.3 occ:1.00 OD1 A:ASP192 2.3 35.0 1.0 OD2 A:ASP190 2.4 33.2 1.0 O A:HOH504 2.4 32.8 1.0 OD2 A:ASP256 2.5 28.3 1.0 O3' P:DC10 2.5 36.1 1.0 OD1 A:ASP190 2.7 42.0 1.0 O1A A:SGT404 2.8 35.0 1.0 CG A:ASP190 2.9 30.6 1.0 CG A:ASP192 3.3 30.2 1.0 OD2 A:ASP192 3.5 31.7 1.0 C3' P:DC10 3.6 42.0 1.0 CG A:ASP256 3.6 33.0 1.0 PA A:SGT404 3.7 35.3 1.0 CA A:CA406 3.8 36.7 1.0 O2A A:SGT404 3.9 36.1 1.0 C5' P:DC10 4.0 43.0 1.0 O5' A:SGT404 4.1 31.8 1.0 C4' P:DC10 4.1 38.5 1.0 CB A:ASP256 4.1 32.9 1.0 C5' A:SGT404 4.2 26.1 1.0 O A:MET191 4.3 25.4 1.0 CB A:ASP190 4.4 31.3 1.0 OP1 P:DC10 4.6 53.0 1.0 O5' P:DC10 4.6 46.8 1.0 OD1 A:ASP256 4.6 31.5 1.0 CB A:ASP192 4.7 23.5 1.0 NH2 A:ARG254 4.8 41.5 1.0 C A:MET191 4.9 27.8 1.0 C2' P:DC10 4.9 37.4 1.0

Calcium binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with Incoming 6-Tdgtp


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 Incoming 6-Tdgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:36.7 occ:1.00 O3G A:SGT404 2.3 34.6 1.0 O1A A:SGT404 2.3 35.0 1.0 OD2 A:ASP192 2.3 31.7 1.0 OD1 A:ASP190 2.5 42.0 1.0 O2B A:SGT404 2.5 25.4 1.0 O A:HOH505 2.6 31.5 1.0 O A:ASP190 2.8 34.5 1.0 CG A:ASP192 3.4 30.2 1.0 C A:ASP190 3.5 38.1 1.0 CG A:ASP190 3.6 30.6 1.0 PG A:SGT404 3.6 34.7 1.0 PB A:SGT404 3.6 33.1 1.0 PA A:SGT404 3.7 35.3 1.0 CA A:CA405 3.8 37.3 1.0 N A:ASP190 3.8 24.7 1.0 OD1 A:ASP192 3.8 35.0 1.0 O3A A:SGT404 4.0 31.2 1.0 O2G A:SGT404 4.0 36.4 1.0 O3B A:SGT404 4.0 40.2 1.0 CA A:ASP190 4.1 33.5 1.0 N A:MET191 4.3 33.6 1.0 OD2 A:ASP190 4.3 33.2 1.0 CA A:GLY179 4.4 25.8 1.0 CB A:ASP190 4.4 31.3 1.0 C5' A:SGT404 4.4 26.1 1.0 OG A:SER180 4.5 33.2 1.0 N A:SER180 4.5 32.3 1.0 CB A:ASP192 4.6 23.5 1.0 CA A:MET191 4.6 33.6 1.0 O5' A:SGT404 4.6 31.8 1.0 C A:MET191 4.6 27.8 1.0 O2A A:SGT404 4.7 36.1 1.0 O1G A:SGT404 4.7 34.4 1.0 N A:ASP192 4.8 36.3 1.0 C A:GLY189 4.9 35.4 1.0 O1B A:SGT404 4.9 47.5 1.0 O A:HOH504 4.9 32.8 1.0 O A:MET191 5.0 25.4 1.0

M.A.Schaich, M.R.Smith, A.S.Cloud, S.M.Holloran, B.D.Freudenthal. Structures of A Dna Polymerase Inserting Therapeutic Nucleotide Analogues. Chem. Res. Toxicol. V. 30 1993 2017.
ISSN: ISSN 1520-5010
PubMed: 28862449
DOI: 10.1021/ACS.CHEMRESTOX.7B00173