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Cadmium in PDB 2wxt: Clostridium Perfringens Alpha-Toxin Strain NCTC8237

Enzymatic activity of Clostridium Perfringens Alpha-Toxin Strain NCTC8237

All present enzymatic activity of Clostridium Perfringens Alpha-Toxin Strain NCTC8237:
3.1.4.3;

Protein crystallography data

The structure of Clostridium Perfringens Alpha-Toxin Strain NCTC8237, PDB code: 2wxt was solved by N.Justin, C.E.Naylor, A.K.Basak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.06 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 60.180, 174.370, 79.530, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 23.2

Other elements in 2wxt:

The structure of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 (pdb code 2wxt). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237, PDB code: 2wxt:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 2wxt

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Cadmium binding site 1 out of 8 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1372

b:25.3
occ:0.62
 ND1 A:HIS46 2.4 12.6 1.0
OE2 A:GLU47 2.4 34.1 1.0
CE1 A:HIS46 2.7 20.2 1.0
OE1 A:GLU47 3.0 39.6 1.0
CD A:GLU47 3.0 31.8 1.0
CG A:HIS46 3.1 34.7 1.0
NE2 A:HIS46 3.6 32.4 1.0
CD2 A:HIS46 3.8 33.5 1.0
CB A:HIS46 3.8 34.6 1.0
O A:HOH2043 4.1 34.1 1.0
CD1 A:LEU50 4.3 20.2 1.0
CG A:GLU47 4.5 29.4 1.0
O A:HOH2039 4.5 50.4 1.0
N A:GLU47 4.6 17.8 1.0
O A:HOH2098 4.7 35.1 1.0
O A:HOH2040 4.7 32.7 1.0
CD A:LYS115 4.8 23.4 0.5
C A:HIS46 4.8 18.8 1.0
O A:HOH2042 4.8 46.3 1.0
CA A:HIS46 5.0 21.5 1.0

Cadmium binding site 2 out of 8 in 2wxt

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Cadmium binding site 2 out of 8 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1373

b:21.8
occ:1.00
 O A:HOH2243 1.9 16.4 1.0
ND1 A:HIS68 2.2 19.9 1.0
OD1 A:ASP130 2.4 22.9 1.0
NE2 A:HIS126 2.4 17.4 1.0
OD1 A:ASP56 2.5 21.8 1.0
O A:HOH2065 2.5 24.3 1.0
CE1 A:HIS68 3.0 24.4 1.0
CE1 A:HIS126 3.2 19.2 1.0
CG A:ASP130 3.3 21.5 1.0
CG A:HIS68 3.3 23.2 1.0
CG A:ASP56 3.4 22.6 1.0
OD2 A:ASP130 3.5 19.5 1.0
CD2 A:HIS126 3.5 16.9 1.0
ZN A:ZN1371 3.6 21.4 1.0
OD2 A:ASP56 3.6 23.7 1.0
CB A:HIS68 3.7 22.4 1.0
NE2 A:HIS68 4.2 27.3 1.0
CD2 A:HIS68 4.3 26.4 1.0
CE1 A:HIS136 4.4 26.5 1.0
ND1 A:HIS126 4.4 15.8 1.0
CG A:HIS126 4.6 14.7 1.0
NE2 A:HIS11 4.6 19.3 1.0
CB A:ASP130 4.7 21.5 1.0
CB A:ASP56 4.8 21.8 1.0

Cadmium binding site 3 out of 8 in 2wxt

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Cadmium binding site 3 out of 8 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1374

b:27.5
occ:1.00
 OE1 A:GLU152 2.2 25.4 1.0
NE2 A:HIS136 2.3 24.9 1.0
NE2 A:HIS148 2.5 29.7 1.0
OE2 A:GLU152 2.7 27.7 1.0
CD A:GLU152 2.8 27.1 1.0
CD2 A:HIS136 3.3 23.2 1.0
CE1 A:HIS136 3.3 26.5 1.0
CD2 A:HIS148 3.4 29.4 1.0
CE1 A:HIS148 3.4 32.7 1.0
O A:HOH2065 3.9 24.3 1.0
CG A:GLU152 4.4 30.3 1.0
ND1 A:HIS136 4.4 24.4 1.0
O A:HOH2114 4.4 36.6 1.0
N A:TRP1 4.4 20.1 1.0
CG A:HIS136 4.4 23.9 1.0
O A:HOH2243 4.4 16.4 1.0
O A:HOH2002 4.5 37.4 1.0
ND1 A:HIS148 4.5 33.3 1.0
CG A:HIS148 4.6 33.2 1.0
O A:HOH2113 4.6 23.0 1.0
O A:HOH2001 4.7 31.8 1.0
ZN A:ZN1371 4.9 21.4 1.0
O A:HOH2107 4.9 37.5 1.0

Cadmium binding site 4 out of 8 in 2wxt

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Cadmium binding site 4 out of 8 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1375

b:35.8
occ:0.68
 OE1 A:GLU157 2.4 35.7 1.0
OE2 A:GLU157 2.5 31.7 1.0
CD A:GLU157 2.7 32.9 1.0
O A:HOH2118 3.0 39.6 1.0
CG A:GLU157 4.1 32.3 1.0
O A:HOH2112 4.5 36.6 1.0
CB A:GLU157 4.8 29.6 1.0

Cadmium binding site 5 out of 8 in 2wxt

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Cadmium binding site 5 out of 8 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1376

b:31.7
occ:0.78
 SG A:CYS169 2.6 40.5 1.0
O A:HOH2124 2.7 33.0 1.0
O A:GLY168 2.7 31.2 1.0
C A:GLY168 3.3 30.2 1.0
CB A:CYS169 3.6 34.8 1.0
N A:CYS169 4.0 31.2 1.0
CA A:GLY168 4.0 27.2 1.0
O A:HOH2054 4.0 43.3 1.0
CA A:CYS169 4.1 32.9 1.0
CD A:CD1377 4.2 32.0 0.9
O A:HOH2053 4.5 50.9 1.0
O A:HOH2125 5.0 47.0 1.0

Cadmium binding site 6 out of 8 in 2wxt

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Cadmium binding site 6 out of 8 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1377

b:32.0
occ:0.91
 OE2 A:GLU173 2.3 36.9 1.0
OE1 A:GLU173 2.5 36.5 1.0
CD A:GLU173 2.7 37.9 1.0
O A:HOH2125 2.8 47.0 1.0
SG A:CYS169 2.9 40.5 1.0
CD A:CD1378 4.0 34.2 1.0
CB A:CYS169 4.1 34.8 1.0
CG A:GLU173 4.2 38.1 1.0
CA A:CYS169 4.2 32.9 1.0
CD A:CD1376 4.2 31.7 0.8
O A:HOH2124 4.2 33.0 1.0
O A:GLY168 4.3 31.2 1.0
O A:HOH2129 4.4 38.8 1.0
O A:HOH2055 4.5 47.2 1.0
N A:LYS170 4.7 29.0 1.0
CB A:GLU173 4.8 36.4 1.0

Cadmium binding site 7 out of 8 in 2wxt

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Cadmium binding site 7 out of 8 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1378

b:34.2
occ:0.99
 OE2 A:GLU173 2.2 36.9 1.0
CD A:GLU173 3.3 37.9 1.0
CG A:GLU173 3.6 38.1 1.0
CD A:CD1377 4.0 32.0 0.9
CB A:GLU173 4.1 36.4 1.0
O A:HOH2129 4.3 38.8 1.0
OE1 A:GLU173 4.4 36.5 1.0
O A:HOH2130 4.5 33.3 1.0
SG A:CYS169 4.8 40.5 1.0

Cadmium binding site 8 out of 8 in 2wxt

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Cadmium binding site 8 out of 8 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1379

b:38.1
occ:1.00
 OE1 A:GLU245 2.3 53.0 1.0
OE2 A:GLU245 2.4 57.1 1.0
ND1 A:HIS241 2.4 28.4 1.0
CD A:GLU245 2.6 54.1 1.0
CG A:HIS241 3.4 25.8 1.0
CE1 A:HIS241 3.4 30.6 1.0
CB A:HIS241 3.6 27.1 1.0
CG A:GLU245 4.0 53.0 1.0
CD1 A:LEU180 4.4 26.3 1.0
CA A:HIS241 4.4 26.6 1.0
NE2 A:HIS241 4.5 31.5 1.0
CD2 A:HIS241 4.5 28.2 1.0
O A:HIS241 4.6 23.1 1.0
O A:HOH2136 4.8 45.4 1.0
C A:HIS241 4.8 23.9 1.0
ND2 A:ASN247 4.9 60.7 1.0
CB A:GLU245 4.9 49.3 1.0
NZ A:LYS183 4.9 62.0 1.0

Reference:

S.G.Vachieri, G.C.Clark, A.Alape-Giron, M.Flores-Diaz, N.Justin, C.E.Naylor, R.W.Titball, A.K.Basak. Comparison of A Nontoxic Variant of Clostridium Perfringens [Alpha]-Toxin with the Toxic Wild-Type Strain Acta Crystallogr.,Sect.D V. 66 1067 2010.
ISSN: ISSN 0907-4449
PubMed: 20944240
DOI: 10.1107/S090744491003369X
Page generated: Thu Jul 10 12:09:43 2025

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