Cobalt in PDB 2d2g: Opda From Agrobacterium Radiobacter with Bound Product Dimethylthiophosphate

All present enzymatic activity of Opda From Agrobacterium Radiobacter with Bound Product Dimethylthiophosphate:
3.1.8.1;

The structure of Opda From Agrobacterium Radiobacter with Bound Product Dimethylthiophosphate, PDB code: 2d2g was solved by C.Jackson, H.K.Kim, P.D.Carr, J.W.Liu, D.L.Ollis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.956, 108.956, 62.672, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 19.4

The binding sites of Cobalt atom in the Opda From Agrobacterium Radiobacter with Bound Product Dimethylthiophosphate (pdb code 2d2g). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Opda From Agrobacterium Radiobacter with Bound Product Dimethylthiophosphate, PDB code: 2d2g:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Opda From Agrobacterium Radiobacter with Bound Product Dimethylthiophosphate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Opda From Agrobacterium Radiobacter with Bound Product Dimethylthiophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Co800 b:13.4 occ:1.00 O4 A:DZZ901 2.0 16.0 0.7 OQ2 A:KCX169 2.1 11.4 1.0 NE2 A:HIS57 2.1 8.8 1.0 OD1 A:ASP301 2.2 11.5 1.0 NE2 A:HIS55 2.3 11.4 1.0 CX A:KCX169 3.0 12.1 1.0 CG A:ASP301 3.1 11.0 1.0 CE1 A:HIS57 3.1 11.9 1.0 CD2 A:HIS57 3.2 9.4 1.0 CD2 A:HIS55 3.2 10.3 1.0 CE1 A:HIS55 3.3 10.6 1.0 OD2 A:ASP301 3.4 9.8 1.0 OQ1 A:KCX169 3.4 12.5 1.0 P1 A:DZZ901 3.5 18.7 0.7 CO A:CO801 3.6 15.4 1.0 O A:HOH1213 3.8 32.2 1.0 O2 A:DZZ901 4.1 17.0 0.7 NZ A:KCX169 4.2 10.4 1.0 S1 A:DZZ901 4.2 13.9 0.7 ND1 A:HIS57 4.2 10.2 1.0 CG A:HIS57 4.3 10.4 1.0 CE1 A:HIS230 4.3 9.1 1.0 CG2 A:VAL101 4.3 9.7 1.0 CG A:HIS55 4.4 9.3 1.0 ND1 A:HIS55 4.4 9.6 1.0 CB A:ASP301 4.4 8.5 1.0 NE2 A:HIS230 4.5 10.1 1.0 O1 A:DZZ901 4.8 17.1 0.7 CA A:ASP301 4.8 9.3 1.0 C1 A:DZZ901 4.9 17.7 0.7 C2 A:DZZ901 4.9 16.6 0.7

Cobalt binding site 2 out of 2 in the Opda From Agrobacterium Radiobacter with Bound Product Dimethylthiophosphate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Opda From Agrobacterium Radiobacter with Bound Product Dimethylthiophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Co801 b:15.4 occ:1.00 OQ1 A:KCX169 2.1 12.5 1.0 NE2 A:HIS230 2.1 10.1 1.0 ND1 A:HIS201 2.2 8.9 1.0 S1 A:DZZ901 2.4 13.9 0.7 CE1 A:HIS201 3.0 10.9 1.0 CE1 A:HIS230 3.0 9.1 1.0 CD2 A:HIS230 3.1 11.0 1.0 CX A:KCX169 3.2 12.1 1.0 CG A:HIS201 3.3 11.4 1.0 OQ2 A:KCX169 3.5 11.4 1.0 CO A:CO800 3.6 13.4 1.0 CB A:HIS201 3.7 10.4 1.0 P1 A:DZZ901 3.7 18.7 0.7 NH2 A:ARG254 3.8 19.7 1.0 O4 A:DZZ901 3.9 16.0 0.7 NE1 A:TRP131 4.1 12.6 1.0 ND1 A:HIS230 4.2 10.0 1.0 CE1 A:HIS55 4.2 10.6 1.0 NE2 A:HIS201 4.2 10.2 1.0 NE2 A:HIS55 4.2 11.4 1.0 CG A:HIS230 4.2 10.5 1.0 NZ A:KCX169 4.2 10.4 1.0 O2 A:DZZ901 4.3 17.0 0.7 OD2 A:ASP301 4.3 9.8 1.0 CD2 A:HIS201 4.3 10.5 1.0 CA A:HIS201 4.4 10.3 1.0 CZ A:ARG254 4.5 18.4 1.0 CD1 A:TRP131 4.7 12.4 1.0 CE A:KCX169 4.9 10.2 1.0 OD1 A:ASP301 4.9 11.5 1.0 CG A:ASP301 4.9 11.0 1.0

C.Jackson, H.K.Kim, P.D.Carr, J.W.Liu, D.L.Ollis. The Structure of An Enzyme-Product Complex Reveals the Critical Role of A Terminal Hydroxide Nucleophile in the Bacterial Phosphotriesterase Mechanism Biochim.Biophys.Acta V.1752 56 2005.
ISSN: ISSN 0006-3002
PubMed: 16054447
DOI: 10.1016/J.BBAPAP.2005.06.008