Sodium 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:

Cobalt

(Co)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Organophoshatedegrading Enzyme (Opda)-Phosphate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:38.6 occ:1.00 O4 A:PO4362 2.0 33.3 0.8 NA A:NA2 2.8 50.7 1.0 O2 A:PO4362 2.8 32.2 0.8 P A:PO4362 2.9 37.0 0.8 O1 A:PO4362 3.9 27.6 0.8 O3 A:PO4362 4.0 33.6 0.8 CZ2 A:TRP131 4.2 20.6 1.0 CE1 A:PHE306 4.2 22.2 1.0 NE2 A:HIS57 4.3 15.5 1.0 CO A:CO800 4.4 28.8 1.0 CD2 A:LEU303 4.4 20.7 1.0 O A:HOH525 4.4 34.3 1.0 O A:HOH23 4.4 22.2 1.0 CZ A:PHE306 4.5 23.5 1.0 CE1 A:HIS57 4.6 14.2 1.0 CD2 A:HIS57 4.7 16.0 1.0 CH2 A:TRP131 4.8 20.2 1.0 CE2 A:TRP131 4.8 21.5 1.0 OQ1 A:KCX169 4.9 19.2 0.8 CA A:GLY60 5.0 20.2 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Organophoshatedegrading Enzyme (Opda)-Phosphate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2 b:50.7 occ:1.00 O2 A:PO4362 1.9 32.2 0.8 NA A:NA1 2.8 38.6 1.0 P A:PO4362 3.1 37.0 0.8 O4 A:PO4362 3.3 33.3 0.8 OH A:TYR257 3.3 29.9 1.0 O3 A:PO4362 3.6 33.6 0.8 OD2 A:ASP301 3.7 20.7 1.0 O A:HOH525 4.1 34.3 1.0 NH1 A:ARG254 4.2 32.8 1.0 CG A:ASP301 4.2 19.8 1.0 OD1 A:ASP301 4.3 20.7 1.0 CZ A:TYR257 4.3 30.6 1.0 O1 A:PO4362 4.3 27.6 0.8 CZ A:PHE306 4.4 23.5 1.0 CE2 A:TYR257 4.4 30.5 1.0 O A:ASP301 4.6 18.9 1.0 CO A:CO800 4.7 28.8 1.0 CE2 A:PHE306 4.8 24.2 1.0 CD1 A:LEU271 4.9 33.8 1.0 CD2 A:LEU271 4.9 28.0 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