Cobalt in PDB 9icb: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and COCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and COCL2, PDB code: 9icb was solved by H.Pelletier, M.R.Sawaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.884, 57.712, 48.421, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / n/a

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and COCL2 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Cobalt atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and COCL2 (pdb code 9icb). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and COCL2, PDB code: 9icb:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and COCL2


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and COCL2 within 5.0Å range: probe atom residue distance (Å) B Occ P:Co340 b:30.0 occ:0.44 O3' P:DG7 2.4 0.0 1.0 OD2 A:ASP192 2.8 32.4 1.0 O1A A:DTP338 3.3 85.3 0.5 OD1 A:ASP192 3.3 43.2 1.0 CG A:ASP192 3.4 36.3 1.0 OD1 A:ASP190 3.4 24.1 1.0 OD2 A:ASP190 3.5 34.7 1.0 CO A:CO339 3.5 30.0 0.5 C3' P:DG7 3.6 0.0 1.0 OD2 A:ASP256 3.7 34.8 1.0 CG A:ASP190 3.8 27.1 1.0 O A:HOH631 3.8 30.6 1.0 PA A:DTP338 3.8 91.3 0.5 O2A A:DTP338 3.9 89.1 0.5 C4' P:DG7 3.9 0.0 1.0 O5' A:DTP338 4.0 71.7 0.5 C5' A:DTP338 4.5 87.1 0.5 C5' P:DG7 4.6 0.0 1.0 CG A:ASP256 4.6 29.5 1.0 CB A:ASP192 4.7 23.5 1.0 C2' P:DG7 4.7 0.0 1.0

Cobalt binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and COCL2


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2'- Deoxyadenosine-5'-Triphosphate, Soaked in the Presence of Datp and COCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co339 b:30.0 occ:0.48 O1A A:DTP338 1.4 85.3 0.5 OD1 A:ASP190 2.3 24.1 1.0 PA A:DTP338 2.8 91.3 0.5 O1G A:DTP338 2.9 23.6 0.5 O3G A:DTP338 3.0 60.1 0.5 PG A:DTP338 3.4 37.5 0.5 O2B A:DTP338 3.4 0.0 0.5 O A:HOH631 3.5 30.6 1.0 CG A:ASP190 3.5 27.1 1.0 CO P:CO340 3.5 30.0 0.4 O3A A:DTP338 3.6 84.7 0.5 OD2 A:ASP192 3.6 32.4 1.0 O A:ASP190 3.6 18.4 1.0 O3B A:DTP338 3.8 71.1 0.5 O5' A:DTP338 3.8 71.7 0.5 O2A A:DTP338 3.8 89.1 0.5 N A:ASP190 3.8 21.1 1.0 PB A:DTP338 3.9 87.0 0.5 C A:ASP190 4.2 12.1 1.0 OD2 A:ASP190 4.4 34.7 1.0 CA A:ASP190 4.4 16.6 1.0 O A:HOH502 4.5 1.0 1.0 CB A:ASP190 4.5 22.4 1.0 C A:GLY189 4.8 27.8 1.0 CG A:ASP192 4.8 36.3 1.0 N A:GLY189 4.9 16.3 1.0 O2G A:DTP338 4.9 72.3 0.5 CA A:GLY189 4.9 22.4 1.0

H.Pelletier, M.R.Sawaya. Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human Dna Polymerase Beta By X-Ray Structural Analysis. Biochemistry V. 35 12778 1996.
ISSN: ISSN 0006-2960
PubMed: 8841120
DOI: 10.1021/BI960790I