Calcium in PDB 5ugo: Dna Polymerase Beta Nick Complex with Imidodiphosphate

All present enzymatic activity of Dna Polymerase Beta Nick Complex with Imidodiphosphate:
2.7.7.7;

The structure of Dna Polymerase Beta Nick Complex with Imidodiphosphate, PDB code: 5ugo was solved by B.D.Freudenthal, S.H.Wilson, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.81 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.596, 79.312, 55.194, 90.00, 107.55, 90.00
R / Rfree (%)	17.9 / 23.6

The binding sites of Calcium atom in the Dna Polymerase Beta Nick Complex with Imidodiphosphate (pdb code 5ugo). 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 Nick Complex with Imidodiphosphate, PDB code: 5ugo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Dna Polymerase Beta Nick Complex with Imidodiphosphate


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 Nick Complex with Imidodiphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:16.9 occ:1.00 OD2 A:ASP192 2.2 14.4 1.0 OD1 A:ASP190 2.3 17.5 1.0 OP1 P:DC11 2.3 13.7 1.0 O2 A:2PN401 2.4 22.2 0.7 O6 A:2PN401 2.4 12.0 0.7 O A:HOH643 2.6 16.3 1.0 O5 A:2PN401 3.0 42.9 0.7 P2 A:2PN401 3.2 28.0 0.7 CG A:ASP192 3.2 14.6 1.0 OD1 A:ASP192 3.5 18.6 1.0 CG A:ASP190 3.5 19.4 1.0 CA A:CA403 3.6 22.3 1.0 P1 A:2PN401 3.6 39.2 0.7 P P:DC11 3.7 20.1 1.0 N1 A:2PN401 3.8 23.8 0.7 O A:ASP190 4.0 19.7 1.0 C5' P:DC11 4.2 17.9 1.0 O5' P:DC11 4.2 20.7 1.0 OD2 A:ASP190 4.2 28.3 1.0 C A:ASP190 4.2 14.8 1.0 N A:ASP190 4.3 12.4 1.0 O4 A:2PN401 4.5 12.8 0.7 CB A:ASP192 4.5 13.6 1.0 O1 A:2PN401 4.5 12.2 0.7 O A:HOH646 4.6 16.7 1.0 CA A:ASP190 4.6 11.6 1.0 CB A:ASP190 4.6 14.1 1.0 O3 A:2PN401 4.6 44.0 0.7 CA A:GLY179 4.6 14.0 1.0 OP2 P:DC11 4.7 16.4 1.0 O3' P:DC10 4.7 16.6 1.0 N A:SER180 4.7 15.3 1.0 O A:HOH564 4.7 25.5 1.0 OG A:SER180 4.8 20.5 1.0 N A:MET191 4.8 12.8 1.0 O P:HOH126 4.9 29.1 1.0 N A:ASP192 4.9 14.5 1.0

Calcium binding site 2 out of 2 in the Dna Polymerase Beta Nick Complex with Imidodiphosphate


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 Nick Complex with Imidodiphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:22.3 occ:1.00 OD2 A:ASP190 2.3 28.3 1.0 OD2 A:ASP256 2.3 17.7 1.0 OD1 A:ASP192 2.3 18.6 1.0 OP1 P:DC11 2.5 13.7 1.0 O A:HOH564 2.5 25.5 1.0 O3' P:DC10 2.6 16.6 1.0 OD1 A:ASP190 2.8 17.5 1.0 CG A:ASP190 2.9 19.4 1.0 P P:DC11 3.1 20.1 1.0 CG A:ASP192 3.3 14.6 1.0 CG A:ASP256 3.4 15.6 1.0 CA A:CA402 3.6 16.9 1.0 OD2 A:ASP192 3.7 14.4 1.0 C3' P:DC10 3.9 14.9 1.0 CB A:ASP256 4.0 13.4 1.0 C4' P:DC10 4.1 20.7 1.0 OP2 P:DC11 4.2 16.4 1.0 C5' P:DC10 4.2 15.6 1.0 O5' P:DC11 4.3 20.7 1.0 CB A:ASP190 4.4 14.1 1.0 OD1 A:ASP256 4.4 15.9 1.0 C5' P:DC11 4.4 17.9 1.0 O A:MET191 4.5 16.7 1.0 CB A:ASP192 4.6 13.6 1.0 NH2 A:ARG254 4.7 16.4 1.0 O P:HOH126 4.8 29.1 1.0 C A:MET191 4.8 14.0 1.0 N A:ASP256 4.8 14.8 1.0 O5' P:DC10 4.9 19.2 1.0 C2' P:DC10 4.9 15.4 1.0 CA A:ASP192 4.9 13.4 1.0 OP1 P:DC10 4.9 16.8 1.0

D.D.Shock, B.D.Freudenthal, W.A.Beard, S.H.Wilson. Modulating the Dna Polymerase Beta Reaction Equilibrium to Dissect the Reverse Reaction. Nat. Chem. Biol. V. 13 1074 2017.
ISSN: ESSN 1552-4469
PubMed: 28759020
DOI: 10.1038/NCHEMBIO.2450