Atomistry » Cadmium » PDB 1gyn-1jre » 1jgm
Atomistry »
  Cadmium »
    PDB 1gyn-1jre »
      1jgm »

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

Go back to Cadmium Binding Sites List in 1jgm
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: Sat Dec 12 08:09:50 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy