Calcium in PDB 5wo0: Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp

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

The structure of Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp, PDB code: 5wo0 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)	31.79 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.728, 79.637, 55.289, 90.00, 107.28, 90.00
R / Rfree (%)	20 / 23.1

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

Chlorine	(Cl)	3 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Dna Polymerase Beta Substrate Complex with Incoming 5-Fodutp (pdb code 5wo0). 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-Fodutp, PDB code: 5wo0:
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-Fodutp


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-Fodutp within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca402 b:21.1 occ:1.00 OD1 A:ASP192 2.3 17.0 1.0 OD2 A:ASP256 2.3 21.6 1.0 OD2 A:ASP190 2.4 20.4 1.0 O3' P:DC10 2.4 22.6 1.0 O A:HOH564 2.5 21.0 1.0 O14 A:B7A405 2.5 16.9 1.0 OD1 A:ASP190 2.6 20.5 1.0 CG A:ASP190 2.8 23.4 1.0 CG A:ASP192 3.4 14.3 1.0 C3' P:DC10 3.5 21.3 1.0 CG A:ASP256 3.5 19.9 1.0 P13 A:B7A405 3.5 18.9 1.0 CA A:CA406 3.7 20.2 1.0 OD2 A:ASP192 3.8 16.3 1.0 O15 A:B7A405 3.9 21.3 1.0 O12 A:B7A405 3.9 18.7 1.0 C4' P:DC10 4.1 23.6 1.0 C5' P:DC10 4.1 21.4 1.0 C11 A:B7A405 4.2 15.9 1.0 CB A:ASP256 4.2 14.2 1.0 O A:HOH705 4.3 24.6 1.0 CB A:ASP190 4.3 16.6 1.0 O A:HOH579 4.5 27.7 1.0 OD1 A:ASP256 4.5 18.7 1.0 O A:MET191 4.6 14.3 1.0 CB A:ASP192 4.6 14.1 1.0 O5' P:DC10 4.7 21.6 1.0 C2' P:DC10 4.8 22.9 1.0 OP1 P:DC10 4.8 21.1 1.0 NH2 A:ARG254 4.9 17.8 1.0 C A:MET191 4.9 14.2 1.0 O24 A:B7A405 5.0 19.5 1.0

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


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-Fodutp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:20.2 occ:1.00 OD2 A:ASP192 2.2 16.3 1.0 OD1 A:ASP190 2.3 20.5 1.0 O14 A:B7A405 2.3 16.9 1.0 O24 A:B7A405 2.3 19.5 1.0 O19 A:B7A405 2.3 16.6 1.0 O A:HOH558 2.5 16.6 1.0 O A:ASP190 2.8 17.9 1.0 CG A:ASP192 3.2 14.3 1.0 P17 A:B7A405 3.4 18.2 1.0 CG A:ASP190 3.5 23.4 1.0 OD1 A:ASP192 3.5 17.0 1.0 C A:ASP190 3.5 17.4 1.0 P21 A:B7A405 3.6 18.4 1.0 P13 A:B7A405 3.6 18.9 1.0 CA P:CA402 3.7 21.1 1.0 O16 A:B7A405 3.8 19.0 1.0 N A:ASP190 3.8 15.9 1.0 O20 A:B7A405 3.8 16.9 1.0 CA A:ASP190 4.1 13.0 1.0 O A:HOH632 4.1 16.3 1.0 O A:HOH705 4.2 24.6 1.0 O23 A:B7A405 4.2 17.3 1.0 OD2 A:ASP190 4.3 20.4 1.0 CB A:ASP190 4.4 16.6 1.0 N A:MET191 4.4 16.1 1.0 C11 A:B7A405 4.4 15.9 1.0 OG A:SER180 4.5 18.3 1.0 CB A:ASP192 4.6 14.1 1.0 O12 A:B7A405 4.6 18.7 1.0 CA A:GLY179 4.6 13.6 1.0 N A:ASP192 4.6 12.3 1.0 N A:SER180 4.6 12.4 1.0 O15 A:B7A405 4.7 21.3 1.0 C A:MET191 4.7 14.2 1.0 O18 A:B7A405 4.7 17.9 1.0 CA A:MET191 4.7 15.5 1.0 O22 A:B7A405 4.8 22.2 1.0 C A:GLY189 4.9 15.7 1.0 O A:HOH564 5.0 21.0 1.0 N A:GLY189 5.0 16.2 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