Cobalt in PDB 3so7: Organophoshatedegrading Enzyme (Opda)-Phosphate Complex

The structure of Organophoshatedegrading Enzyme (Opda)-Phosphate Complex, PDB code: 3so7 was solved by F.Ely, M.Pedroso, L.R.Gahan, D.L.Ollis, L.W.Guddat, G.Schenk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.24 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.189, 109.189, 62.932, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 23.3

The structure of Organophoshatedegrading Enzyme (Opda)-Phosphate Complex also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Cobalt atom in the Organophoshatedegrading Enzyme (Opda)-Phosphate Complex (pdb code 3so7). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Organophoshatedegrading Enzyme (Opda)-Phosphate Complex, PDB code: 3so7:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Organophoshatedegrading Enzyme (Opda)-Phosphate Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Organophoshatedegrading Enzyme (Opda)-Phosphate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co800 b:28.8 occ:1.00 NE2 A:HIS57 2.1 15.5 1.0 NE2 A:HIS55 2.2 18.5 1.0 OD1 A:ASP301 2.2 20.7 1.0 O3 A:PO4362 2.3 33.6 0.8 OQ1 A:KCX169 2.3 19.2 0.8 O4 A:PO4362 2.8 33.3 0.8 CE1 A:HIS57 3.0 14.2 1.0 CG A:ASP301 3.1 19.8 1.0 P A:PO4362 3.1 37.0 0.8 CD2 A:HIS55 3.1 20.2 1.0 CE1 A:HIS55 3.2 17.5 1.0 CX A:KCX169 3.2 21.8 0.8 CD2 A:HIS57 3.2 16.0 1.0 OD2 A:ASP301 3.3 20.7 1.0 OQ2 A:KCX169 3.5 23.1 0.8 CO A:CO801 3.7 30.9 1.0 O1 A:PO4362 4.1 27.6 0.8 CE1 A:HIS230 4.2 16.5 1.0 O2 A:PO4362 4.2 32.2 0.8 CG2 A:VAL101 4.2 17.2 1.0 ND1 A:HIS57 4.2 14.5 1.0 ND1 A:HIS55 4.2 18.9 1.0 CG A:HIS55 4.3 18.8 1.0 NZ A:KCX169 4.3 20.4 1.0 CG A:HIS57 4.3 16.7 1.0 NA A:NA1 4.4 38.6 1.0 NE2 A:HIS230 4.4 16.8 1.0 CB A:ASP301 4.4 18.8 1.0 NA A:NA2 4.7 50.7 1.0 CA A:ASP301 4.9 19.4 1.0

Cobalt binding site 2 out of 2 in the Organophoshatedegrading Enzyme (Opda)-Phosphate Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Organophoshatedegrading Enzyme (Opda)-Phosphate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co801 b:30.9 occ:1.00 NE2 A:HIS230 2.1 16.8 1.0 ND1 A:HIS201 2.1 17.7 1.0 OQ2 A:KCX169 2.2 23.1 0.8 O3 A:PO4362 2.2 33.6 0.8 O1 A:PO4362 2.2 27.6 0.8 P A:PO4362 2.7 37.0 0.8 CD2 A:HIS230 3.0 19.4 1.0 CE1 A:HIS201 3.0 17.3 1.0 CE1 A:HIS230 3.1 16.5 1.0 CX A:KCX169 3.1 21.8 0.8 CG A:HIS201 3.1 18.3 1.0 OQ1 A:KCX169 3.3 19.2 0.8 CB A:HIS201 3.4 16.2 1.0 CO A:CO800 3.7 28.8 1.0 O4 A:PO4362 3.8 33.3 0.8 NE1 A:TRP131 3.9 20.9 1.0 O2 A:PO4362 4.0 32.2 0.8 NH1 A:ARG254 4.0 32.8 1.0 CE1 A:HIS55 4.1 17.5 1.0 ND1 A:HIS230 4.2 19.2 1.0 NE2 A:HIS201 4.2 19.8 1.0 CA A:HIS201 4.2 17.3 1.0 CG A:HIS230 4.2 18.9 1.0 NE2 A:HIS55 4.2 18.5 1.0 CD2 A:HIS201 4.2 15.3 1.0 NZ A:KCX169 4.2 20.4 1.0 OD2 A:ASP301 4.4 20.7 1.0 O A:HOH525 4.5 34.3 1.0 CD1 A:TRP131 4.6 22.3 1.0 CE A:KCX169 4.6 19.9 1.0

F.Ely, M.M.Pedroso, L.R.Gahan, D.L.Ollis, L.W.Guddat, G.Schenk. Phosphate-Bound Structure of An Organophosphate-Degrading Enzyme From Agrobacterium Radiobacter. J.Inorg.Biochem. V. 106 19 2011.
ISSN: ISSN 0162-0134
PubMed: 22112835
DOI: 10.1016/J.JINORGBIO.2011.09.015