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Cadmium in PDB 2wxu: Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I

Enzymatic activity of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I

All present enzymatic activity of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I:
3.1.4.3;

Protein crystallography data

The structure of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I, PDB code: 2wxu was solved by S.G.Vachieri, 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) 24.64 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 59.861, 173.643, 78.564, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.6

Other elements in 2wxu:

The structure of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I also contains other interesting chemical elements:

Calcium (Ca) 5 atoms
Zinc (Zn) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I (pdb code 2wxu). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I, PDB code: 2wxu:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 2wxu

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Cadmium binding site 1 out of 7 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


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 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1371

b:29.1
occ:1.00
 OE2 A:GLU47 2.3 17.0 1.0
ND1 A:HIS46 2.5 10.9 1.0
O A:HOH2062 2.5 26.9 1.0
O A:HOH2067 2.5 28.6 1.0
O A:HOH2065 2.7 38.3 1.0
CE1 A:HIS46 3.2 31.2 1.0
CG A:HIS46 3.3 21.8 1.0
CD A:GLU47 3.6 32.7 1.0
CB A:HIS46 3.8 25.8 1.0
O A:HOH2064 4.1 36.6 1.0
NE2 A:HIS46 4.2 24.4 1.0
CD2 A:HIS46 4.3 20.3 1.0
OE1 A:GLU47 4.4 37.5 1.0
CD1 A:LEU50 4.4 25.1 1.0
CG A:GLU47 4.5 34.5 1.0
N A:GLU47 4.6 18.9 1.0
NZ A:LYS115 4.7 28.7 1.0
CD A:LYS115 4.7 25.5 1.0
C A:HIS46 4.8 22.5 1.0
CA A:HIS46 4.9 22.6 1.0
O A:HOH2066 5.0 43.8 1.0

Cadmium binding site 2 out of 7 in 2wxu

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Cadmium binding site 2 out of 7 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


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 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1372

b:19.3
occ:1.00
 O A:HOH2402 2.2 16.0 1.0
OD2 A:ASP130 2.3 16.1 1.0
ND1 A:HIS68 2.4 16.2 1.0
NE2 A:HIS126 2.4 15.9 1.0
OD1 A:ASP56 2.5 18.8 1.0
O A:HOH2107 2.6 22.2 1.0
CE1 A:HIS68 3.1 21.2 1.0
CG A:ASP130 3.2 19.5 1.0
CE1 A:HIS126 3.3 18.2 1.0
CD2 A:HIS126 3.4 12.1 1.0
CG A:ASP56 3.5 20.0 1.0
CG A:HIS68 3.5 17.6 1.0
OD1 A:ASP130 3.5 16.1 1.0
ZN A:ZN1375 3.6 19.3 1.0
OD2 A:ASP56 3.7 20.9 1.0
CB A:HIS68 3.9 15.1 1.0
NE2 A:HIS68 4.3 16.3 1.0
CE1 A:HIS136 4.4 20.4 1.0
O A:HOH2190 4.4 28.5 1.0
ND1 A:HIS126 4.4 14.2 1.0
CD2 A:HIS68 4.5 16.9 1.0
CG A:HIS126 4.6 13.4 1.0
CB A:ASP130 4.6 19.8 1.0
NE2 A:HIS11 4.6 18.6 1.0
CB A:ASP56 4.8 22.6 1.0
O A:HOH2176 4.8 24.1 1.0

Cadmium binding site 3 out of 7 in 2wxu

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Cadmium binding site 3 out of 7 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


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 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1373

b:23.7
occ:1.00
 O A:HOH2190 2.3 28.5 1.0
NE2 A:HIS136 2.4 17.3 1.0
NE2 A:HIS148 2.4 24.6 1.0
OE2 A:GLU152 2.5 23.9 1.0
OE1 A:GLU152 2.6 31.2 1.0
O A:HOH2176 2.6 24.1 1.0
CD A:GLU152 2.9 26.4 1.0
CD2 A:HIS148 3.3 24.3 1.0
CE1 A:HIS136 3.3 20.4 1.0
CD2 A:HIS136 3.4 17.4 1.0
CE1 A:HIS148 3.4 24.2 1.0
O A:HOH2107 3.7 22.2 1.0
O A:HOH2402 4.3 16.0 1.0
CG A:GLU152 4.4 25.4 1.0
N A:TRP1 4.4 19.9 1.0
ND1 A:HIS136 4.4 19.2 1.0
O A:HOH2188 4.5 35.9 1.0
CG A:HIS148 4.5 26.5 1.0
CG A:HIS136 4.5 17.0 1.0
ND1 A:HIS148 4.5 24.6 1.0
O A:HOH2006 4.5 33.1 1.0
O A:HOH2001 4.8 25.3 1.0
O A:HOH2191 4.8 23.3 1.0
ZN A:ZN1375 4.8 19.3 1.0
O A:HOH2178 4.8 38.2 1.0

Cadmium binding site 4 out of 7 in 2wxu

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Cadmium binding site 4 out of 7 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


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 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1374

b:22.3
occ:1.00
 OE2 A:GLU173 2.2 22.9 1.0
OE1 A:GLU173 2.5 21.6 1.0
SG A:CYS169 2.6 21.4 1.0
CD A:GLU173 2.7 25.0 1.0
CB A:CYS169 3.6 19.2 1.0
CA A:CYS169 3.9 21.4 1.0
O A:HOH2208 4.0 20.6 1.0
CG A:GLU173 4.2 24.9 1.0
O A:GLY168 4.2 19.1 1.0
O A:HOH2211 4.4 25.1 1.0
N A:LYS170 4.6 25.1 1.0
CB A:GLU173 4.8 21.5 1.0
C A:CYS169 4.9 23.1 1.0
N A:CYS169 4.9 19.5 1.0
C A:GLY168 5.0 21.5 1.0

Cadmium binding site 5 out of 7 in 2wxu

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Cadmium binding site 5 out of 7 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


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 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1376

b:29.3
occ:0.92
 O A:HOH2279 2.3 27.6 1.0
O A:HOH2130 2.3 49.5 1.0
ND1 A:HIS241 2.4 22.5 1.0
OE1 A:GLU245 2.4 54.5 1.0
O A:HOH2274 2.5 38.7 1.0
OE2 A:GLU245 2.5 65.7 1.0
O A:HOH2281 2.7 38.8 1.0
CD A:GLU245 2.7 58.4 1.0
CE1 A:HIS241 3.2 23.8 1.0
CG A:HIS241 3.5 22.4 1.0
CB A:HIS241 3.9 22.0 1.0
CG A:GLU245 4.1 52.6 1.0
O A:HOH2093 4.1 38.1 1.0
NE2 A:HIS241 4.4 23.1 1.0
CD1 A:LEU180 4.4 19.8 1.0
O A:HOH2092 4.4 48.0 1.0
CD2 A:HIS241 4.5 22.0 1.0
CA A:HIS241 4.6 20.1 1.0
O A:HOH2278 4.6 41.8 1.0
O A:HIS241 4.7 21.3 1.0
ND2 A:ASN247 4.8 57.5 1.0
O A:HOH2275 4.8 37.8 1.0
C A:HIS241 4.9 20.7 1.0

Cadmium binding site 6 out of 7 in 2wxu

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Cadmium binding site 6 out of 7 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


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 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1378

b:25.1
occ:1.00
 OD2 A:ASP216 2.3 23.5 1.0
ND1 A:HIS212 2.4 26.3 1.0
O A:HOH2262 2.4 25.4 1.0
O A:HOH2249 2.4 18.0 1.0
O A:HOH2254 2.5 25.8 1.0
CG A:ASP216 3.3 23.2 1.0
CE1 A:HIS212 3.3 27.9 1.0
CG A:HIS212 3.4 27.5 1.0
CB A:HIS212 3.7 26.4 1.0
OD1 A:ASP216 3.8 20.4 1.0
CA A:HIS212 4.0 28.7 1.0
O A:SER206 4.3 23.9 1.0
CB A:ASP216 4.4 22.6 1.0
N A:SER213 4.4 25.8 1.0
NE2 A:HIS212 4.4 24.0 1.0
CD2 A:HIS212 4.5 26.7 1.0
O A:HOH2255 4.7 19.8 1.0
C A:HIS212 4.8 27.4 1.0
O A:HOH2253 4.9 35.8 1.0
O A:SER211 4.9 33.9 1.0

Cadmium binding site 7 out of 7 in 2wxu

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Cadmium binding site 7 out of 7 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


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 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1379

b:23.3
occ:1.00
 NE2 A:HIS207 2.4 23.8 1.0
O A:HOH2251 2.5 30.5 1.0
CD2 A:HIS207 3.2 23.4 1.0
CE1 A:HIS207 3.5 24.0 1.0
O A:HOH2261 4.0 21.2 1.0
OD1 A:ASP216 4.2 20.4 1.0
O A:HOH2114 4.4 45.3 1.0
CG A:HIS207 4.4 21.1 1.0
ND1 A:HIS207 4.5 24.3 1.0
CD2 A:TYR219 4.6 20.4 1.0
CG A:TYR219 4.8 20.1 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: Fri Jul 19 15:21:41 2024

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