Cadmium in PDB 1i0d: High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta

All present enzymatic activity of High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta:
3.1.8.1;

The structure of High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1i0d was solved by H.M.Holden, M.M.Benning, F.M.Raushel, H.Shim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.444, 90.034, 68.385, 90.00, 91.72, 90.00
R / Rfree (%)	n/a / n/a

The structure of High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Cadmium atom in the High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta (pdb code 1i0d). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1i0d:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:21.6 occ:1.00 O A:HOH1054 2.1 13.4 1.0 O2 A:FMT369 2.2 13.1 1.0 ND1 A:HIS201 2.2 14.1 1.0 NE2 A:HIS230 2.2 16.0 1.0 O A:HOH1056 2.4 16.6 1.0 O A:HOH876 2.8 32.2 1.0 CE1 A:HIS201 3.1 18.5 1.0 C A:FMT369 3.1 13.0 1.0 CE1 A:HIS230 3.2 17.6 1.0 CD2 A:HIS230 3.2 16.7 1.0 CG A:HIS201 3.3 16.7 1.0 O1 A:FMT369 3.4 11.4 1.0 ZN A:ZN401 3.5 11.0 1.0 CB A:HIS201 3.7 11.6 1.0 O2 A:EDO406 3.8 11.8 0.5 CE1 A:HIS55 4.0 12.2 1.0 NE2 A:HIS55 4.0 9.9 1.0 OD1 A:ASP301 4.1 15.9 1.0 NE1 A:TRP131 4.1 13.8 1.0 NE2 A:HIS201 4.2 20.3 1.0 ND1 A:HIS230 4.3 15.2 1.0 CG A:HIS230 4.3 18.6 1.0 CD2 A:HIS201 4.3 19.1 1.0 NZ A:LYS169 4.4 12.8 1.0 CA A:HIS201 4.5 12.6 1.0 O A:HOH980 4.5 32.3 1.0 O2 A:EDO406 4.5 26.3 0.5 CD1 A:TRP131 4.8 12.4 1.0 CE A:LYS169 4.8 13.5 1.0 CG A:ASP301 4.9 18.3 1.0 C2 A:EDO406 4.9 19.8 1.0 OD2 A:ASP301 5.0 13.9 1.0

Cadmium binding site 2 out of 2 in the High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd402 b:17.6 occ:1.00 O B:HOH1053 2.1 13.0 1.0 ND1 B:HIS201 2.2 11.6 1.0 O2 B:FMT369 2.2 10.6 1.0 NE2 B:HIS230 2.2 10.0 1.0 O B:HOH1055 2.5 14.8 1.0 O B:HOH1059 2.7 26.1 1.0 CE1 B:HIS201 3.1 13.2 1.0 C B:FMT369 3.1 12.0 1.0 CD2 B:HIS230 3.1 12.2 1.0 CE1 B:HIS230 3.2 10.8 1.0 CG B:HIS201 3.3 12.4 1.0 O1 B:FMT369 3.4 10.2 1.0 ZN B:ZN401 3.6 9.1 1.0 CB B:HIS201 3.7 12.3 1.0 O1 B:EDO405 3.9 9.2 0.5 OD1 B:ASP301 4.1 11.8 1.0 CE1 B:HIS55 4.2 11.1 1.0 NE1 B:TRP131 4.2 11.6 1.0 NE2 B:HIS55 4.2 9.4 1.0 NE2 B:HIS201 4.2 12.5 1.0 CG B:HIS230 4.3 12.1 1.0 ND1 B:HIS230 4.3 11.3 1.0 O B:HOH1061 4.4 28.8 1.0 NZ B:LYS169 4.4 12.1 1.0 CD2 B:HIS201 4.4 11.7 1.0 O2 B:EDO420 4.4 37.8 1.0 CA B:HIS201 4.5 9.4 1.0 O1 B:EDO405 4.6 16.8 0.5 O B:HOH1064 4.8 34.2 1.0 CD1 B:TRP131 4.8 11.7 1.0 C1 B:EDO405 4.9 21.0 1.0 CE B:LYS169 4.9 9.3 1.0 CG B:ASP301 4.9 13.8 1.0 NE2 B:HIS254 5.0 10.4 1.0

M.M.Benning, H.Shim, F.M.Raushel, H.M.Holden. High Resolution X-Ray Structures of Different Metal-Substituted Forms of Phosphotriesterase From Pseudomonas Diminuta. Biochemistry V. 40 2712 2001.
ISSN: ISSN 0006-2960
PubMed: 11258882
DOI: 10.1021/BI002661E