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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 1i0d:

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

Cadmium (Cd) 2 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the High Resolution Structure of the Zinc/Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1i0d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1i0d

Go back to Zinc Binding Sites List in 1i0d
Zinc 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 Zinc with other atoms in the Zn 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:Zn401

b:11.0
occ:1.00
NE2 A:HIS55 1.9 9.9 1.0
O A:HOH1054 2.0 13.4 1.0
NE2 A:HIS57 2.1 12.2 1.0
O1 A:FMT369 2.1 11.4 1.0
OD2 A:ASP301 2.3 13.9 1.0
C A:FMT369 2.9 13.0 1.0
CD2 A:HIS55 2.9 12.1 1.0
O2 A:EDO406 2.9 26.3 0.5
CE1 A:HIS55 3.0 12.2 1.0
CE1 A:HIS57 3.1 12.4 1.0
CG A:ASP301 3.1 18.3 1.0
CD2 A:HIS57 3.1 12.7 1.0
OD1 A:ASP301 3.3 15.9 1.0
O2 A:FMT369 3.4 13.1 1.0
O2 A:EDO406 3.4 11.8 0.5
CD A:CD402 3.5 21.6 1.0
C2 A:EDO406 3.7 19.8 1.0
NZ A:LYS169 4.1 12.8 1.0
CG A:HIS55 4.1 10.8 1.0
ND1 A:HIS55 4.1 10.1 1.0
CG2 A:VAL101 4.2 12.2 1.0
ND1 A:HIS57 4.2 11.6 1.0
CG A:HIS57 4.3 12.5 1.0
CE1 A:HIS230 4.3 17.6 1.0
O A:HOH1056 4.3 16.6 1.0
NE2 A:HIS230 4.4 16.0 1.0
CB A:ASP301 4.4 12.7 1.0
O A:HOH877 4.9 39.9 1.0

Zinc binding site 2 out of 2 in 1i0d

Go back to Zinc Binding Sites List in 1i0d
Zinc 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 Zinc with other atoms in the Zn 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:Zn401

b:9.1
occ:1.00
O B:HOH1053 2.0 13.0 1.0
NE2 B:HIS55 2.1 9.4 1.0
NE2 B:HIS57 2.1 10.8 1.0
O1 B:FMT369 2.2 10.2 1.0
OD2 B:ASP301 2.3 11.2 1.0
O1 B:EDO405 2.9 16.8 0.5
C B:FMT369 3.0 12.0 1.0
CE1 B:HIS57 3.1 10.2 1.0
CD2 B:HIS55 3.1 9.9 1.0
CG B:ASP301 3.1 13.8 1.0
CD2 B:HIS57 3.1 8.7 1.0
CE1 B:HIS55 3.1 11.1 1.0
OD1 B:ASP301 3.3 11.8 1.0
O2 B:FMT369 3.5 10.6 1.0
O1 B:EDO405 3.5 9.2 0.5
CD B:CD402 3.6 17.6 1.0
C1 B:EDO405 3.6 21.0 1.0
O2 B:EDO420 4.0 37.8 1.0
NZ B:LYS169 4.1 12.1 1.0
CG2 B:VAL101 4.1 10.3 1.0
ND1 B:HIS57 4.2 9.4 1.0
CG B:HIS57 4.2 10.9 1.0
CG B:HIS55 4.3 8.6 1.0
ND1 B:HIS55 4.3 8.4 1.0
CE1 B:HIS230 4.3 10.8 1.0
NE2 B:HIS230 4.4 10.0 1.0
CB B:ASP301 4.4 11.0 1.0
O B:HOH1055 4.4 14.8 1.0
O1 B:EDO420 4.8 43.0 1.0
O B:HOH1059 4.9 26.1 1.0
C2 B:EDO405 5.0 31.9 1.0
CA B:ASP301 5.0 10.4 1.0

Reference:

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
Page generated: Wed Dec 16 02:52:10 2020

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