Cobalt in PDB 2d2h: Opda From Agrobacterium Radiobacter with Bound Inhibitor Trimethyl Phosphate at 1.8 A Resolution

All present enzymatic activity of Opda From Agrobacterium Radiobacter with Bound Inhibitor Trimethyl Phosphate at 1.8 A Resolution:
3.1.8.1;

The structure of Opda From Agrobacterium Radiobacter with Bound Inhibitor Trimethyl Phosphate at 1.8 A Resolution, PDB code: 2d2h 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)	19.60 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.926, 108.926, 62.345, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 21.4

The binding sites of Cobalt atom in the Opda From Agrobacterium Radiobacter with Bound Inhibitor Trimethyl Phosphate at 1.8 A Resolution (pdb code 2d2h). 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 Inhibitor Trimethyl Phosphate at 1.8 A Resolution, PDB code: 2d2h:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Opda From Agrobacterium Radiobacter with Bound Inhibitor Trimethyl Phosphate at 1.8 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 with Bound Inhibitor Trimethyl Phosphate at 1.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Co800 b:12.7 occ:1.00 O A:HOH1130 1.8 11.1 1.0 OQ2 A:KCX169 2.1 12.0 1.0 OD1 A:ASP301 2.1 10.4 1.0 NE2 A:HIS57 2.2 10.7 1.0 NE2 A:HIS55 2.3 9.2 1.0 O A:TZZ901 2.3 41.1 1.0 CG A:ASP301 3.0 9.9 1.0 CX A:KCX169 3.1 10.9 1.0 CD2 A:HIS55 3.1 9.4 1.0 CE1 A:HIS57 3.1 12.2 1.0 CD2 A:HIS57 3.2 9.3 1.0 OD2 A:ASP301 3.3 10.6 1.0 CE1 A:HIS55 3.3 9.3 1.0 OQ1 A:KCX169 3.4 11.0 1.0 CO A:CO801 3.6 15.1 1.0 P A:TZZ901 3.9 41.7 1.0 O A:HOH934 4.2 12.9 1.0 NZ A:KCX169 4.2 13.6 1.0 CE1 A:HIS230 4.2 10.8 1.0 ND1 A:HIS57 4.3 10.7 1.0 CB A:ASP301 4.3 8.1 1.0 CG A:HIS57 4.3 8.7 1.0 C2 A:TZZ901 4.3 38.3 1.0 CG A:HIS55 4.3 7.7 1.0 CG2 A:VAL101 4.3 10.3 1.0 ND1 A:HIS55 4.4 8.5 1.0 NE2 A:HIS230 4.4 11.3 1.0 O3 A:TZZ901 4.7 41.2 1.0 C1 A:TZZ901 4.7 42.5 1.0 CA A:ASP301 4.8 8.4 1.0 O2 A:TZZ901 4.8 42.2 1.0 O1 A:TZZ901 4.9 41.8 1.0 O A:HOH1131 4.9 21.7 1.0

Cobalt binding site 2 out of 2 in the Opda From Agrobacterium Radiobacter with Bound Inhibitor Trimethyl Phosphate at 1.8 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 with Bound Inhibitor Trimethyl Phosphate at 1.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Co801 b:15.1 occ:1.00 O A:HOH1130 2.0 11.1 1.0 OQ1 A:KCX169 2.1 11.0 1.0 NE2 A:HIS230 2.1 11.3 1.0 ND1 A:HIS201 2.2 8.1 1.0 O A:HOH934 2.2 12.9 1.0 O A:HOH1131 2.6 21.7 1.0 CE1 A:HIS230 3.0 10.8 1.0 CE1 A:HIS201 3.0 10.7 1.0 CD2 A:HIS230 3.1 10.4 1.0 CX A:KCX169 3.2 10.9 1.0 CG A:HIS201 3.3 10.2 1.0 OQ2 A:KCX169 3.4 12.0 1.0 CO A:CO800 3.6 12.7 1.0 CB A:HIS201 3.7 9.2 1.0 O A:TZZ901 4.0 41.1 1.0 NE1 A:TRP131 4.1 10.7 1.0 ND1 A:HIS230 4.1 11.4 1.0 CG A:HIS230 4.2 10.2 1.0 NE2 A:HIS55 4.2 9.2 1.0 NE2 A:HIS201 4.2 10.4 1.0 OD2 A:ASP301 4.2 10.6 1.0 NZ A:KCX169 4.2 13.6 1.0 CE1 A:HIS55 4.3 9.3 1.0 O A:HOH1013 4.3 28.8 1.0 CD2 A:HIS201 4.4 8.0 1.0 CA A:HIS201 4.4 9.3 1.0 CD1 A:TRP131 4.8 10.7 1.0 CG A:ASP301 4.9 9.9 1.0 O1 A:TZZ901 4.9 41.8 1.0 O A:HOH1127 4.9 16.3 1.0 OD1 A:ASP301 4.9 10.4 1.0 CE A:KCX169 4.9 13.6 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