Calcium in PDB 4kld: Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 S

All present enzymatic activity of Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 S:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 S, PDB code: 4kld was solved by B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.15 / 1.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.800, 80.400, 55.500, 90.00, 107.90, 90.00
R / Rfree (%)	19.7 / 25.1

The structure of Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 S also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 S (pdb code 4kld). 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 Matched Substrate Complex with CA2+, 0 S, PDB code: 4kld:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 S


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 Matched Substrate Complex with CA2+, 0 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:27.3 occ:1.00 O3G A:DCP401 2.2 26.0 1.0 OD1 A:ASP190 2.3 23.2 1.0 O2A A:DCP401 2.3 23.4 1.0 OD2 A:ASP192 2.4 25.9 1.0 O2B A:DCP401 2.5 24.5 1.0 O A:HOH529 2.7 25.7 1.0 O A:ASP190 3.1 24.9 1.0 CG A:ASP192 3.4 29.0 1.0 PB A:DCP401 3.5 25.7 1.0 CG A:ASP190 3.5 25.6 1.0 PG A:DCP401 3.6 28.9 1.0 PA A:DCP401 3.6 23.0 1.0 OD1 A:ASP192 3.6 19.9 1.0 CA A:CA403 3.7 23.8 1.0 C A:ASP190 3.7 24.1 1.0 N A:ASP190 3.7 27.5 1.0 O3A A:DCP401 3.9 26.7 1.0 O3B A:DCP401 4.0 26.3 1.0 CA A:ASP190 4.1 21.6 1.0 O1G A:DCP401 4.3 24.7 1.0 OD2 A:ASP190 4.3 21.4 1.0 CB A:ASP190 4.4 22.9 1.0 O A:HOH517 4.4 21.1 1.0 C5' A:DCP401 4.5 21.8 1.0 O1A A:DCP401 4.6 24.0 1.0 N A:MET191 4.6 22.9 1.0 N A:SER180 4.7 26.6 1.0 O5' A:DCP401 4.7 23.3 1.0 OG A:SER180 4.7 27.8 1.0 CB A:ASP192 4.7 23.6 1.0 O2G A:DCP401 4.7 28.7 1.0 C A:GLY189 4.8 28.3 1.0 CA A:GLY179 4.8 25.6 1.0 O1B A:DCP401 4.9 25.5 1.0 N A:ASP192 4.9 21.6 1.0 C A:MET191 4.9 25.6 1.0 O A:HOH528 4.9 20.9 1.0

Calcium binding site 2 out of 2 in the Dna Polymerase Beta Matched Substrate Complex with CA2+, 0 S


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 Matched Substrate Complex with CA2+, 0 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:23.8 occ:1.00 OD2 A:ASP256 2.4 21.5 1.0 OD1 A:ASP192 2.4 19.9 1.0 OD2 A:ASP190 2.5 21.4 1.0 O2A A:DCP401 2.5 23.4 1.0 OD1 A:ASP190 2.6 23.2 1.0 O3' P:DC10 2.6 21.0 1.0 O A:HOH528 2.7 20.9 1.0 CG A:ASP190 2.9 25.6 1.0 CG A:ASP192 3.4 29.0 1.0 CG A:ASP256 3.6 29.1 1.0 CA A:CA402 3.7 27.3 1.0 PA A:DCP401 3.7 23.0 1.0 C3' P:DC10 3.8 19.9 1.0 OD2 A:ASP192 3.8 25.9 1.0 O1A A:DCP401 4.0 24.0 1.0 O5' A:DCP401 4.1 23.3 1.0 C5' A:DCP401 4.2 21.8 1.0 CB A:ASP256 4.2 19.7 1.0 C5' P:DC10 4.3 21.6 1.0 C4' P:DC10 4.3 25.8 1.0 CB A:ASP190 4.4 22.9 1.0 OD1 A:ASP256 4.6 23.9 1.0 O A:MET191 4.6 24.2 1.0 OP1 P:DC10 4.7 21.1 1.0 CB A:ASP192 4.7 23.6 1.0 O A:HOH561 4.8 28.1 1.0 O5' P:DC10 4.8 25.6 1.0 NH2 A:ARG254 4.9 20.2 1.0 O3G A:DCP401 5.0 26.0 1.0

B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson. Observing A Dna Polymerase Choose Right From Wrong. Cell(Cambridge,Mass.) V. 154 157 2013.
ISSN: ISSN 0092-8674
PubMed: 23827680
DOI: 10.1016/J.CELL.2013.05.048