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

Enzymatic activity of High Resolution Structure of the Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta

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

Protein crystallography data

The structure of High Resolution Structure of the Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1jgm was solved by M.M.Benning, H.Shim, F.M.Raushel, H.M.Holden, 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 (°) 128.450, 90.030, 68.390, 90.00, 91.72, 90.00
R / Rfree (%) 20.2 / 23.6

Other elements in 1jgm:

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

Sodium (Na) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the High Resolution Structure of the Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta (pdb code 1jgm). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the High Resolution Structure of the Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1jgm:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 1jgm

Go back to Cadmium Binding Sites List in 1jgm
Cadmium binding site 1 out of 4 in the High Resolution Structure of the 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 Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1

b:14.2
occ:1.00
 NE2 A:HIS55 2.0 11.3 1.0
O A:HOH590 2.1 11.5 1.0
NE2 A:HIS57 2.2 12.4 1.0
OQ1 A:KCX169 2.2 12.5 1.0
OD2 A:ASP301 2.3 14.7 1.0
CD2 A:HIS55 3.0 13.1 1.0
CX A:KCX169 3.0 9.7 1.0
CE1 A:HIS55 3.1 12.1 1.0
CG A:ASP301 3.1 21.2 1.0
CD2 A:HIS57 3.2 13.4 1.0
CE1 A:HIS57 3.2 13.0 1.0
OD1 A:ASP301 3.2 16.1 1.0
OQ2 A:KCX169 3.5 15.4 1.0
O2 A:EDO8 3.5 23.8 1.0
CD A:CD2 3.7 16.2 1.0
O A:HOH648 3.8 31.6 1.0
C2 A:EDO8 3.9 19.7 1.0
O A:HOH699 4.0 11.3 1.0
CG2 A:VAL101 4.1 13.7 1.0
O A:HOH709 4.1 30.8 1.0
NZ A:KCX169 4.2 13.1 1.0
CG A:HIS55 4.2 9.4 1.0
CE1 A:HIS230 4.2 17.9 1.0
ND1 A:HIS55 4.2 11.6 1.0
CG A:HIS57 4.4 13.1 1.0
ND1 A:HIS57 4.4 12.3 1.0
CB A:ASP301 4.4 12.6 1.0
NE2 A:HIS230 4.4 18.2 1.0
O A:HOH696 4.8 39.5 1.0

Cadmium binding site 2 out of 4 in 1jgm

Go back to Cadmium Binding Sites List in 1jgm
Cadmium binding site 2 out of 4 in the High Resolution Structure of the 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 Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2

b:16.2
occ:1.00
 O A:HOH699 1.5 11.3 1.0
NE2 A:HIS230 2.1 18.2 1.0
OQ2 A:KCX169 2.2 15.4 1.0
O A:HOH590 2.3 11.5 1.0
ND1 A:HIS201 2.3 15.5 1.0
O A:HOH646 2.5 19.5 1.0
CD2 A:HIS230 3.1 20.1 1.0
CE1 A:HIS230 3.1 17.9 1.0
CE1 A:HIS201 3.2 17.6 1.0
CX A:KCX169 3.2 9.7 1.0
CG A:HIS201 3.3 18.1 1.0
O A:HOH709 3.4 30.8 1.0
OQ1 A:KCX169 3.6 12.5 1.0
CB A:HIS201 3.7 12.9 1.0
CD A:CD1 3.7 14.2 1.0
O2 A:EDO8 3.9 23.8 1.0
O A:HOH648 4.2 31.6 1.0
NE2 A:HIS55 4.2 11.3 1.0
CE1 A:HIS55 4.3 12.1 1.0
CG A:HIS230 4.3 22.2 1.0
ND1 A:HIS230 4.3 15.9 1.0
OD1 A:ASP301 4.3 16.1 1.0
NE1 A:TRP131 4.3 13.7 1.0
NE2 A:HIS201 4.3 22.0 1.0
O A:HOH597 4.4 30.4 1.0
CD2 A:HIS201 4.5 19.4 1.0
NZ A:KCX169 4.5 13.1 1.0
CA A:HIS201 4.6 12.1 1.0
NE2 A:HIS254 4.9 16.3 1.0
CE A:KCX169 4.9 14.5 1.0
O A:HOH645 5.0 36.7 1.0

Cadmium binding site 3 out of 4 in 1jgm

Go back to Cadmium Binding Sites List in 1jgm
Cadmium binding site 3 out of 4 in the High Resolution Structure of the 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 3 of High Resolution Structure of the Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3

b:12.1
occ:1.00
 O B:HOH721 2.2 11.3 1.0
NE2 B:HIS55 2.2 10.6 1.0
NE2 B:HIS57 2.2 12.1 1.0
OQ1 B:KCX169 2.2 11.7 1.0
OD2 B:ASP301 2.4 11.6 1.0
O1 B:EDO7 3.0 35.0 0.5
CX B:KCX169 3.0 11.4 1.0
CD2 B:HIS55 3.1 9.0 1.0
CG B:ASP301 3.1 11.6 1.0
CD2 B:HIS57 3.2 9.6 1.0
CE1 B:HIS57 3.2 9.9 1.0
OD1 B:ASP301 3.2 12.8 1.0
CE1 B:HIS55 3.3 10.2 1.0
OQ2 B:KCX169 3.5 12.3 1.0
O1 B:EDO7 3.6 8.2 0.5
CD B:CD4 3.8 12.3 1.0
O2 B:EDO20 3.9 24.3 1.0
C1 B:EDO7 4.0 23.9 1.0
CG2 B:VAL101 4.1 11.2 1.0
NZ B:KCX169 4.2 11.2 1.0
CE1 B:HIS230 4.3 10.7 1.0
CG B:HIS55 4.3 9.6 1.0
O B:HOH742 4.3 24.5 1.0
CG B:HIS57 4.3 11.6 1.0
ND1 B:HIS57 4.3 10.4 1.0
ND1 B:HIS55 4.4 9.4 1.0
CB B:ASP301 4.5 10.7 1.0
NE2 B:HIS230 4.5 9.7 1.0
O B:HOH606 4.7 12.5 1.0
O1 B:EDO20 4.9 55.1 1.0

Cadmium binding site 4 out of 4 in 1jgm

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Cadmium binding site 4 out of 4 in the High Resolution Structure of the 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 4 of High Resolution Structure of the Cadmium-Containing Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd4

b:12.3
occ:1.00
 O B:HOH721 2.2 11.3 1.0
NE2 B:HIS230 2.2 9.7 1.0
OQ2 B:KCX169 2.3 12.3 1.0
ND1 B:HIS201 2.3 12.7 1.0
O B:HOH606 2.4 12.5 1.0
O B:HOH681 2.5 15.1 1.0
CE1 B:HIS201 3.2 11.9 1.0
CD2 B:HIS230 3.2 12.1 1.0
CE1 B:HIS230 3.3 10.7 1.0
CX B:KCX169 3.3 11.4 1.0
CG B:HIS201 3.4 13.4 1.0
OQ1 B:KCX169 3.6 11.7 1.0
O B:HOH742 3.6 24.5 1.0
CD B:CD3 3.8 12.1 1.0
CB B:HIS201 3.8 14.4 1.0
O1 B:EDO7 3.9 8.2 0.5
O B:HOH607 4.2 22.0 1.0
O2 B:EDO20 4.2 24.3 1.0
NE1 B:TRP131 4.3 12.7 1.0
OD1 B:ASP301 4.3 12.8 1.0
O1 B:EDO7 4.3 35.0 0.5
CG B:HIS230 4.4 9.7 1.0
ND1 B:HIS230 4.4 10.4 1.0
NE2 B:HIS201 4.4 10.2 1.0
NE2 B:HIS55 4.4 10.6 1.0
CE1 B:HIS55 4.5 10.2 1.0
CD2 B:HIS201 4.5 11.4 1.0
NZ B:KCX169 4.5 11.2 1.0
CA B:HIS201 4.7 10.0 1.0
O B:HOH680 4.9 26.6 1.0
CD1 B:TRP131 5.0 11.5 1.0
NE2 B:HIS254 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: Fri Jul 19 13:38:09 2024

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