Calcium in PDB 5wny: Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp

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

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp, PDB code: 5wny 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)	24.65 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.480, 79.747, 55.570, 90.00, 107.23, 90.00
R / Rfree (%)	18.1 / 23.7

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Chlorine	(Cl)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fdutp (pdb code 5wny). 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-Fdutp, PDB code: 5wny:
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-Fdutp


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-Fdutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:24.4 occ:1.00 O11 A:B7P409 2.2 23.9 1.0 OD1 A:ASP190 2.3 27.3 1.0 O20 A:B7P409 2.3 26.5 1.0 OD2 A:ASP192 2.4 27.2 1.0 O14 A:B7P409 2.4 18.2 1.0 O A:HOH527 2.4 28.8 1.0 CG A:ASP192 3.3 22.1 1.0 O A:ASP190 3.3 32.3 1.0 P13 A:B7P409 3.4 24.4 1.0 P09 A:B7P409 3.4 30.2 1.0 OD1 A:ASP192 3.5 28.5 1.0 CG A:ASP190 3.5 30.1 1.0 P17 A:B7P409 3.6 24.9 1.0 CA A:CA408 3.6 37.7 1.0 O12 A:B7P409 3.7 24.4 1.0 O16 A:B7P409 3.8 35.8 1.0 C A:ASP190 3.8 30.1 1.0 N A:ASP190 4.0 25.3 1.0 O A:HOH661 4.2 34.0 1.0 O A:HOH574 4.2 25.6 1.0 C07 A:B7P409 4.3 24.5 1.0 O19 A:B7P409 4.3 24.4 1.0 CA A:ASP190 4.3 24.2 1.0 OD2 A:ASP190 4.3 49.4 1.0 O08 A:B7P409 4.4 22.8 1.0 OG A:SER180 4.5 27.4 1.0 CB A:ASP190 4.5 24.4 1.0 O10 A:B7P409 4.5 28.4 1.0 N A:SER180 4.6 24.2 1.0 N A:MET191 4.6 24.1 1.0 CA A:GLY179 4.7 19.9 1.0 CB A:ASP192 4.7 26.0 1.0 O18 A:B7P409 4.7 38.2 1.0 O A:HOH614 4.7 40.3 1.0 O15 A:B7P409 4.8 31.7 1.0 N A:ASP192 4.8 21.1 1.0 C A:MET191 4.9 24.8 1.0 C A:GLY189 5.0 27.2 1.0

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


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-Fdutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:37.7 occ:1.00 OD1 A:ASP192 2.2 28.5 1.0 OD2 A:ASP190 2.3 49.4 1.0 OD2 A:ASP256 2.5 30.1 1.0 O3' P:DC10 2.6 35.6 1.0 O11 A:B7P409 2.6 23.9 1.0 OD1 A:ASP190 2.6 27.3 1.0 O A:HOH614 2.7 40.3 1.0 CG A:ASP190 2.8 30.1 1.0 CG A:ASP192 3.3 22.1 1.0 C3' P:DC10 3.3 28.1 1.0 CA A:CA407 3.6 24.4 1.0 CG A:ASP256 3.6 29.3 1.0 P09 A:B7P409 3.7 30.2 1.0 OD2 A:ASP192 3.7 27.2 1.0 O08 A:B7P409 4.0 22.8 1.0 O10 A:B7P409 4.0 28.4 1.0 C4' P:DC10 4.1 39.2 1.0 CB A:ASP256 4.1 26.7 1.0 C07 A:B7P409 4.2 24.5 1.0 C5' P:DC10 4.2 26.1 1.0 CB A:ASP190 4.3 24.4 1.0 O A:HOH661 4.5 34.0 1.0 O A:MET191 4.5 24.5 1.0 CB A:ASP192 4.6 26.0 1.0 OD1 A:ASP256 4.6 24.9 1.0 C2' P:DC10 4.6 40.5 1.0 O5' P:DC10 4.8 29.5 1.0 C A:MET191 4.8 24.8 1.0 NH2 A:ARG254 4.9 32.4 1.0 OP1 P:DC10 5.0 43.4 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