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Cadmium in PDB 1psc: Phosphotriesterase From Pseudomonas Diminuta

Protein crystallography data

The structure of Phosphotriesterase From Pseudomonas Diminuta, PDB code: 1psc was solved by M.M.Benning, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 129.500, 91.400, 69.400, 90.00, 91.90, 90.00
R / Rfree (%) n/a / n/a

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 4 in 1psc

Go back to Cadmium Binding Sites List in 1psc
Cadmium binding site 1 out of 4 in the 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 Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd801

b:17.3
occ:1.00
NE2 A:HIS55 2.0 6.6 1.0
NE2 A:HIS57 2.2 18.7 1.0
O2 A:FMT901 2.4 12.9 1.0
OD1 A:ASP301 2.5 15.7 1.0
O A:HOH912 2.6 36.8 1.0
CD2 A:HIS55 3.0 17.4 1.0
CE1 A:HIS57 3.1 21.9 1.0
CG A:ASP301 3.2 30.4 1.0
C A:FMT901 3.2 13.2 1.0
CD2 A:HIS57 3.2 15.8 1.0
CE1 A:HIS55 3.2 14.8 1.0
OD2 A:ASP301 3.2 24.7 1.0
O1 A:FMT901 3.4 24.9 1.0
CD A:CD802 3.8 19.8 1.0
CG2 A:VAL101 4.1 8.1 1.0
CG A:HIS55 4.2 11.5 1.0
ND1 A:HIS57 4.3 15.6 1.0
ND1 A:HIS55 4.3 9.3 1.0
CE1 A:HIS230 4.3 17.8 1.0
CG A:HIS57 4.3 14.9 1.0
NZ A:LYS169 4.4 17.5 1.0
O A:HOH1007 4.4 37.4 1.0
CB A:ASP301 4.5 20.0 1.0
NE2 A:HIS230 4.6 13.3 1.0
O A:HOH922 4.7 40.7 1.0
O A:HOH905 4.9 38.9 1.0

Cadmium binding site 2 out of 4 in 1psc

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Cadmium binding site 2 out of 4 in the 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 Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd802

b:19.8
occ:1.00
NE2 A:HIS230 2.1 13.3 1.0
O1 A:FMT901 2.3 24.9 1.0
ND1 A:HIS201 2.4 17.1 1.0
O A:HOH905 2.6 38.9 1.0
O A:HOH985 2.7 17.7 1.0
O A:HOH912 2.7 36.8 1.0
CE1 A:HIS230 3.1 17.8 1.0
C A:FMT901 3.2 13.2 1.0
CD2 A:HIS230 3.2 22.8 1.0
CE1 A:HIS201 3.4 28.4 1.0
CG A:HIS201 3.4 24.6 1.0
O2 A:FMT901 3.5 12.9 1.0
CB A:HIS201 3.7 10.5 1.0
CD A:CD801 3.8 17.3 1.0
NE1 A:TRP131 4.3 9.8 1.0
ND1 A:HIS230 4.3 17.9 1.0
OD2 A:ASP301 4.3 24.7 1.0
CG A:HIS230 4.3 16.8 1.0
O A:HOH1020 4.3 38.5 1.0
NE2 A:HIS55 4.4 6.6 1.0
CE1 A:HIS55 4.4 14.8 1.0
O A:HOH1007 4.4 37.4 1.0
NE2 A:HIS201 4.5 22.1 1.0
NZ A:LYS169 4.5 17.5 1.0
CD2 A:HIS201 4.5 26.6 1.0
CA A:HIS201 4.7 15.2 1.0
CE A:LYS169 5.0 8.8 1.0

Cadmium binding site 3 out of 4 in 1psc

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Cadmium binding site 3 out of 4 in the 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 Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd803

b:15.2
occ:1.00
NE2 B:HIS55 2.0 6.9 1.0
NE2 B:HIS57 2.2 14.7 1.0
O1 B:FMT902 2.3 11.6 1.0
OD1 B:ASP301 2.4 11.2 1.0
O B:HOH1004 2.7 28.9 1.0
CE1 B:HIS55 3.0 12.2 1.0
CD2 B:HIS55 3.0 14.4 1.0
C B:FMT902 3.1 14.1 1.0
CG B:ASP301 3.1 15.7 1.0
CE1 B:HIS57 3.2 15.8 1.0
OD2 B:ASP301 3.2 14.3 1.0
CD2 B:HIS57 3.2 10.9 1.0
O2 B:FMT902 3.5 17.1 1.0
CD B:CD804 3.8 16.6 1.0
CG2 B:VAL101 4.1 8.3 1.0
ND1 B:HIS55 4.1 9.7 1.0
CG B:HIS55 4.2 3.7 1.0
NZ B:LYS169 4.3 17.1 1.0
CE1 B:HIS230 4.3 9.9 1.0
ND1 B:HIS57 4.3 10.4 1.0
CG B:HIS57 4.4 14.1 1.0
NE2 B:HIS230 4.5 14.7 1.0
CB B:ASP301 4.5 11.1 1.0
O B:HOH1003 4.7 37.6 1.0
O B:HOH1039 4.8 30.4 1.0
O B:HOH1035 4.9 40.1 1.0
O B:HOH1019 5.0 38.7 1.0

Cadmium binding site 4 out of 4 in 1psc

Go back to Cadmium Binding Sites List in 1psc
Cadmium binding site 4 out of 4 in the 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 Phosphotriesterase From Pseudomonas Diminuta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd804

b:16.6
occ:1.00
NE2 B:HIS230 2.1 14.7 1.0
O2 B:FMT902 2.2 17.1 1.0
ND1 B:HIS201 2.2 16.4 1.0
O B:HOH1002 2.7 16.9 1.0
O B:HOH1003 2.7 37.6 1.0
O B:HOH1004 2.7 28.9 1.0
CD2 B:HIS230 3.1 19.3 1.0
CE1 B:HIS201 3.2 28.5 1.0
CE1 B:HIS230 3.2 9.9 1.0
C B:FMT902 3.2 14.1 1.0
CG B:HIS201 3.3 25.1 1.0
O1 B:FMT902 3.5 11.6 1.0
CB B:HIS201 3.6 12.1 1.0
CD B:CD803 3.8 15.2 1.0
CG B:HIS230 4.3 19.6 1.0
ND1 B:HIS230 4.3 18.5 1.0
NE2 B:HIS201 4.3 20.4 1.0
OD2 B:ASP301 4.4 14.3 1.0
CE1 B:HIS55 4.4 12.2 1.0
CD2 B:HIS201 4.4 15.5 1.0
NE1 B:TRP131 4.4 11.9 1.0
NE2 B:HIS55 4.4 6.9 1.0
NZ B:LYS169 4.5 17.1 1.0
CA B:HIS201 4.5 14.6 1.0
O B:HOH1047 4.6 49.0 1.0
O B:HOH1039 4.7 30.4 1.0
CZ B:PHE132 4.9 0.0 1.0
NE2 B:HIS254 4.9 19.9 1.0

Reference:

M.M.Benning, J.M.Kuo, F.M.Raushel, H.M.Holden. Three-Dimensional Structure of the Binuclear Metal Center of Phosphotriesterase. Biochemistry V. 34 7973 1995.
ISSN: ISSN 0006-2960
PubMed: 7794910
DOI: 10.1021/BI00025A002
Page generated: Fri Aug 28 12:19:46 2020
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