Cobalt in PDB 2d2j: Opda From Agrobacterium Radiobacter Without Inhibitor/Product Present at 1.75 A Resolution

All present enzymatic activity of Opda From Agrobacterium Radiobacter Without Inhibitor/Product Present at 1.75 A Resolution:
3.1.8.1;

The structure of Opda From Agrobacterium Radiobacter Without Inhibitor/Product Present at 1.75 A Resolution, PDB code: 2d2j 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)	30.00 / 1.75
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.242, 109.242, 63.221, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 19.5

The binding sites of Cobalt atom in the Opda From Agrobacterium Radiobacter Without Inhibitor/Product Present at 1.75 A Resolution (pdb code 2d2j). 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 Without Inhibitor/Product Present at 1.75 A Resolution, PDB code: 2d2j:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Opda From Agrobacterium Radiobacter Without Inhibitor/Product Present at 1.75 A Resolution


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 Without Inhibitor/Product Present at 1.75 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Co800 b:15.0 occ:1.00 O A:HOH1124 1.9 15.7 1.0 OQ2 A:KCX169 2.1 11.7 1.0 OD1 A:ASP301 2.1 11.4 1.0 NE2 A:HIS57 2.2 10.2 1.0 NE2 A:HIS55 2.3 10.8 1.0 O1 A:EDO701 2.6 31.4 1.0 CX A:KCX169 3.0 12.9 1.0 CG A:ASP301 3.0 11.9 1.0 CD2 A:HIS57 3.1 11.9 1.0 CE1 A:HIS57 3.2 13.9 1.0 CD2 A:HIS55 3.2 11.3 1.0 CE1 A:HIS55 3.3 9.8 1.0 OD2 A:ASP301 3.4 12.6 1.0 OQ1 A:KCX169 3.5 13.4 1.0 CO A:CO801 3.6 16.9 1.0 C1 A:EDO701 3.9 33.4 1.0 O A:HOH997 3.9 27.5 1.0 O A:HOH810 4.2 15.2 1.0 NZ A:KCX169 4.2 13.0 1.0 CE1 A:HIS230 4.3 13.3 1.0 ND1 A:HIS57 4.3 10.9 1.0 CG A:HIS57 4.3 11.9 1.0 CB A:ASP301 4.3 9.8 1.0 CG A:HIS55 4.4 11.2 1.0 ND1 A:HIS55 4.4 8.9 1.0 CG2 A:VAL101 4.4 11.7 1.0 NE2 A:HIS230 4.5 13.1 1.0 O2 A:EDO701 4.6 32.9 1.0 CA A:ASP301 4.8 10.3 1.0 C2 A:EDO701 4.9 33.5 1.0 O A:HOH1116 4.9 22.8 1.0

Cobalt binding site 2 out of 2 in the Opda From Agrobacterium Radiobacter Without Inhibitor/Product Present at 1.75 A Resolution


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 Without Inhibitor/Product Present at 1.75 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Co801 b:16.9 occ:1.00 OQ1 A:KCX169 2.1 13.4 1.0 O A:HOH1124 2.1 15.7 1.0 NE2 A:HIS230 2.1 13.1 1.0 ND1 A:HIS201 2.2 11.3 1.0 O A:HOH810 2.3 15.2 1.0 O A:HOH1116 2.5 22.8 1.0 CE1 A:HIS230 3.1 13.3 1.0 CE1 A:HIS201 3.1 13.5 1.0 CD2 A:HIS230 3.1 13.1 1.0 CX A:KCX169 3.2 12.9 1.0 CG A:HIS201 3.3 11.8 1.0 OQ2 A:KCX169 3.4 11.7 1.0 CO A:CO800 3.6 15.0 1.0 CB A:HIS201 3.7 12.1 1.0 NE1 A:TRP131 4.1 12.3 1.0 ND1 A:HIS230 4.2 13.3 1.0 CG A:HIS230 4.2 12.4 1.0 NE2 A:HIS201 4.2 13.7 1.0 OD2 A:ASP301 4.3 12.6 1.0 CE1 A:HIS55 4.3 9.8 1.0 NZ A:KCX169 4.3 13.0 1.0 NE2 A:HIS55 4.3 10.8 1.0 CD2 A:HIS201 4.3 11.3 1.0 O1 A:EDO701 4.4 31.4 1.0 O A:HOH1054 4.5 26.7 1.0 CA A:HIS201 4.5 11.8 1.0 O2 A:EDO701 4.7 32.9 1.0 CD1 A:TRP131 4.7 13.2 1.0 OD1 A:ASP301 4.9 11.4 1.0 O A:HOH1114 4.9 22.4 1.0 CG A:ASP301 4.9 11.9 1.0 CE A:KCX169 4.9 11.8 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