Calcium in PDB 5wnz: Dna Polymerase Beta Substrate Complex with Incoming 5-Fodctp

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with Incoming 5-Fodctp:
2.7.7.7;

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fodctp, PDB code: 5wnz 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)	24.96 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.607, 79.627, 55.624, 90.00, 107.24, 90.00
R / Rfree (%)	19.3 / 25.4

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fodctp 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 5-Fodctp (pdb code 5wnz). 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 5-Fodctp, PDB code: 5wnz:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fodctp


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 5-Fodctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:31.9 occ:1.00 OD2 A:ASP192 2.2 32.1 1.0 O22 A:B7J406 2.3 32.5 1.0 O15 A:B7J406 2.3 26.7 1.0 O A:HOH509 2.3 32.2 1.0 OD1 A:ASP190 2.4 31.9 1.0 O18 A:B7J406 2.4 30.2 1.0 O A:ASP190 3.1 31.7 1.0 CG A:ASP192 3.2 26.0 1.0 P17 A:B7J406 3.5 31.4 1.0 OD1 A:ASP192 3.5 33.8 1.0 P13 A:B7J406 3.6 32.7 1.0 CG A:ASP190 3.6 37.5 1.0 CA A:CA405 3.6 44.6 1.0 P21 A:B7J406 3.7 32.2 1.0 C A:ASP190 3.7 37.7 1.0 N A:ASP190 3.8 26.8 1.0 O A:HOH517 3.9 30.0 1.0 O16 A:B7J406 3.9 36.4 1.0 O20 A:B7J406 4.0 38.3 1.0 CA A:ASP190 4.2 33.3 1.0 C11 A:B7J406 4.3 27.1 1.0 O23 A:B7J406 4.4 30.9 1.0 OD2 A:ASP190 4.4 43.1 1.0 O12 A:B7J406 4.4 32.7 1.0 CB A:ASP190 4.5 35.7 1.0 N A:MET191 4.6 25.1 1.0 CB A:ASP192 4.6 28.9 1.0 N A:SER180 4.6 30.3 1.0 OG A:SER180 4.6 27.1 1.0 CA A:GLY179 4.6 26.3 1.0 O14 A:B7J406 4.7 37.0 1.0 N A:ASP192 4.7 30.7 1.0 O24 A:B7J406 4.8 31.8 1.0 O19 A:B7J406 4.8 37.9 1.0 C A:MET191 4.9 31.3 1.0 O P:HOH103 4.9 35.0 1.0 C A:GLY189 4.9 35.4 1.0 CA A:MET191 4.9 29.6 1.0 N A:GLY189 5.0 31.5 1.0

Calcium binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fodctp


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 5-Fodctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:44.6 occ:1.00 OD1 A:ASP192 2.3 33.8 1.0 OD2 A:ASP256 2.5 35.1 1.0 O15 A:B7J406 2.6 26.7 1.0 O P:HOH103 2.6 35.0 1.0 OD2 A:ASP190 2.6 43.1 1.0 OD1 A:ASP190 2.6 31.9 1.0 O3' P:DC10 2.7 38.4 1.0 CG A:ASP190 3.0 37.5 1.0 C3' P:DC10 3.3 35.4 1.0 CG A:ASP192 3.3 26.0 1.0 CA A:CA404 3.6 31.9 1.0 P13 A:B7J406 3.6 32.7 1.0 OD2 A:ASP192 3.7 32.1 1.0 CG A:ASP256 3.7 42.5 1.0 O12 A:B7J406 3.8 32.7 1.0 O14 A:B7J406 3.9 37.0 1.0 C5' P:DC10 4.0 33.1 1.0 C4' P:DC10 4.0 35.9 1.0 C11 A:B7J406 4.2 27.1 1.0 CB A:ASP256 4.4 37.4 1.0 CB A:ASP190 4.5 35.7 1.0 OP1 P:DC10 4.6 46.8 1.0 CB A:ASP192 4.7 28.9 1.0 O A:MET191 4.7 32.5 1.0 O5' P:DC10 4.7 35.8 1.0 C2' P:DC10 4.7 38.2 1.0 OD1 A:ASP256 4.7 42.7 1.0 NH2 A:ARG254 5.0 43.2 1.0 O22 A:B7J406 5.0 32.5 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