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Cadmium in PDB 2wy6: 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: 2wy6 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) 24.91 / 3.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.238, 107.238, 225.087, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 28.1

Other elements in 2wy6:

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

Calcium (Ca) 4 atoms
Zinc (Zn) 3 atoms

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Cadmium atom in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I (pdb code 2wy6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 15 binding sites of Cadmium where determined in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I, PDB code: 2wy6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 15 in 2wy6

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Cadmium binding site 1 out of 15 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:Cd1372

b:68.7
occ:1.00
 ND1 A:HIS68 2.3 54.9 1.0
OD2 A:ASP130 2.3 58.3 1.0
NE2 A:HIS126 2.4 58.1 1.0
OD1 A:ASP56 2.5 78.7 1.0
CE1 A:HIS68 3.0 61.0 1.0
CE1 A:HIS126 3.1 68.3 1.0
ZN A:ZN1371 3.3 61.4 1.0
CG A:ASP130 3.4 53.3 1.0
CG A:ASP56 3.5 82.2 1.0
CG A:HIS68 3.5 60.7 1.0
CD2 A:HIS126 3.6 74.2 1.0
OD1 A:ASP130 3.7 51.7 1.0
OD2 A:ASP56 3.8 85.3 1.0
CB A:HIS68 4.0 59.4 1.0
NE2 A:HIS68 4.2 58.3 1.0
ND1 A:HIS126 4.3 71.1 1.0
NE2 A:HIS11 4.4 65.7 1.0
CE1 A:HIS136 4.4 57.8 1.0
CD2 A:HIS68 4.5 59.0 1.0
CG A:HIS126 4.6 77.1 1.0
CB A:ASP130 4.7 54.7 1.0
CB A:ASP56 4.8 78.3 1.0
O A:TRP1 4.8 87.3 1.0
CA A:ASP56 5.0 77.4 1.0

Cadmium binding site 2 out of 15 in 2wy6

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Cadmium binding site 2 out of 15 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:Cd1373

b:80.4
occ:1.00
 OE2 A:GLU152 2.1 70.5 1.0
NE2 A:HIS148 2.2 77.3 1.0
NE2 A:HIS136 2.3 56.8 1.0
OE1 A:GLU152 2.6 74.5 1.0
CD A:GLU152 2.6 72.6 1.0
CE1 A:HIS136 3.1 57.8 1.0
CE1 A:HIS148 3.2 85.4 1.0
CD2 A:HIS148 3.3 84.8 1.0
CD2 A:HIS136 3.5 63.4 1.0
CG A:GLU152 4.1 69.6 1.0
ND1 A:HIS136 4.3 59.3 1.0
ND1 A:HIS148 4.3 78.5 1.0
CG A:HIS148 4.4 82.6 1.0
N A:TRP1 4.4 82.9 1.0
CG A:HIS136 4.5 61.1 1.0
ZN A:ZN1371 4.7 61.4 1.0
O A:TRP1 5.0 87.3 1.0

Cadmium binding site 3 out of 15 in 2wy6

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Cadmium binding site 3 out of 15 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:Cd1374

b:96.7
occ:1.00
 OD2 A:ASP215 2.5 0.7 1.0
CG A:ASP215 3.1 0.2 1.0
OD1 A:ASP215 3.6 0.4 1.0
CB A:ASP215 3.9 95.2 1.0

Cadmium binding site 4 out of 15 in 2wy6

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Cadmium binding site 4 out of 15 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
B:Cd1371

b:92.6
occ:1.00
 OE2 A:GLU291 2.3 94.7 1.0
OE1 A:GLU291 2.6 78.8 1.0
OE2 B:GLU47 2.7 0.4 1.0
CD A:GLU291 2.8 86.0 1.0
OE1 B:GLU47 2.8 0.0 1.0
ND1 B:HIS46 3.0 83.3 1.0
CD B:GLU47 3.1 0.1 1.0
CB B:HIS46 3.6 79.6 1.0
CG B:HIS46 3.7 82.3 1.0
OD2 A:ASP293 3.7 0.9 1.0
OH A:TYR88 3.9 89.2 1.0
CE1 B:HIS46 4.1 88.3 1.0
CG A:GLU291 4.3 83.9 1.0
CE2 A:TYR88 4.4 80.3 1.0
CG A:ASP293 4.6 0.3 1.0
CZ A:TYR88 4.6 80.7 1.0
CG B:GLU47 4.6 97.5 1.0
CD1 A:TYR275 4.8 0.8 1.0
CA B:HIS46 4.8 77.5 1.0
CE1 A:TYR275 4.9 0.9 1.0
N B:GLU47 4.9 98.2 1.0
CD2 B:HIS46 4.9 84.6 1.0

Cadmium binding site 5 out of 15 in 2wy6

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Cadmium binding site 5 out of 15 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
B:Cd1373

b:70.2
occ:1.00
 ND1 B:HIS68 2.1 95.1 1.0
NE2 B:HIS126 2.4 39.7 1.0
OD2 B:ASP130 2.4 76.7 1.0
OD1 B:ASP56 2.5 67.7 1.0
CE1 B:HIS68 2.8 90.7 1.0
CE1 B:HIS126 3.1 49.4 1.0
CG B:HIS68 3.3 93.5 1.0
CG B:ASP130 3.5 70.9 1.0
CD2 B:HIS126 3.5 47.4 1.0
CG B:ASP56 3.5 73.9 1.0
ZN B:ZN1372 3.6 74.5 1.0
CB B:HIS68 3.9 91.5 1.0
OD1 B:ASP130 3.9 73.1 1.0
OD2 B:ASP56 3.9 79.5 1.0
NE2 B:HIS68 4.0 84.0 1.0
CD2 B:HIS68 4.3 90.5 1.0
ND1 B:HIS126 4.3 46.9 1.0
CE1 B:HIS136 4.4 74.1 1.0
CG B:HIS126 4.5 49.8 1.0
NE2 B:HIS11 4.6 55.9 1.0
CB B:ASP130 4.7 67.9 1.0
CB B:ASP56 4.8 71.0 1.0
CA B:ASP56 4.9 67.6 1.0
O B:TRP1 5.0 98.2 1.0

Cadmium binding site 6 out of 15 in 2wy6

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Cadmium binding site 6 out of 15 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
B:Cd1374

b:81.2
occ:1.00
 OE2 B:GLU152 2.1 94.9 1.0
NE2 B:HIS136 2.3 77.7 1.0
NE2 B:HIS148 2.4 49.1 1.0
OE1 B:GLU152 2.7 0.9 1.0
CD B:GLU152 2.7 94.1 1.0
CE1 B:HIS136 3.0 74.1 1.0
CE1 B:HIS148 3.2 63.4 1.0
CD2 B:HIS148 3.4 65.4 1.0
CD2 B:HIS136 3.5 81.7 1.0
CG B:GLU152 4.2 86.8 1.0
N B:TRP1 4.2 96.1 1.0
ND1 B:HIS136 4.3 69.2 1.0
ND1 B:HIS148 4.4 60.5 1.0
CG B:HIS136 4.5 73.2 1.0
CG B:HIS148 4.5 61.9 1.0
ZN B:ZN1372 4.7 74.5 1.0
O B:TRP1 4.8 98.2 1.0

Cadmium binding site 7 out of 15 in 2wy6

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Cadmium binding site 7 out of 15 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
B:Cd1375

b:0.5
occ:1.00
 OD2 B:ASP216 2.2 91.2 1.0
N B:SER213 3.2 0.6 1.0
CG B:ASP216 3.2 90.3 1.0
CA B:HIS212 3.4 1.0 1.0
CB B:HIS212 3.7 98.8 1.0
C B:HIS212 3.8 0.6 1.0
OD1 B:ASP216 3.9 87.3 1.0
CB B:SER213 4.1 0.1 1.0
CA B:SER213 4.2 0.5 1.0
CB B:ASP216 4.3 82.8 1.0
ND1 B:HIS212 4.4 0.1 1.0
CG B:HIS212 4.4 0.2 1.0
O B:SER206 4.6 74.0 1.0
N B:HIS212 4.6 0.4 1.0
OG B:SER213 4.9 1.0 1.0
O B:HIS212 5.0 0.1 1.0

Cadmium binding site 8 out of 15 in 2wy6

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Cadmium binding site 8 out of 15 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 8 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1376

b:69.2
occ:1.00
 OE2 B:GLU291 2.1 69.8 1.0
OD2 B:ASP293 2.5 73.9 1.0
CD B:GLU291 2.8 67.8 1.0
OE1 B:GLU291 3.1 67.2 1.0
CG B:ASP293 3.3 73.2 1.0
OD1 B:ASP293 3.8 83.4 1.0
CG B:GLU291 4.1 67.6 1.0
CB B:ASP293 4.1 67.5 1.0
CE2 B:TYR88 4.2 72.2 1.0
OH B:TYR88 4.3 77.2 1.0
CZ B:TYR88 4.8 70.6 1.0

Cadmium binding site 9 out of 15 in 2wy6

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Cadmium binding site 9 out of 15 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 9 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1379

b:0.6
occ:1.00
 OD2 B:ASP63 2.2 52.3 1.0
CG B:ASP63 2.9 66.6 1.0
OD1 B:ASP63 3.1 81.4 1.0
NE2 B:GLN66 3.9 75.8 1.0
CD1 B:LEU64 4.0 74.2 1.0
CB B:ASP63 4.1 69.7 1.0
CG B:LEU64 4.2 68.3 1.0
CB B:LEU64 4.9 74.5 1.0

Cadmium binding site 10 out of 15 in 2wy6

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Cadmium binding site 10 out of 15 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 10 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1380

b:0.6
occ:1.00
 ND1 B:HIS241 2.5 0.8 1.0
CE1 B:HIS241 3.3 0.7 1.0
CG B:HIS241 3.5 1.0 1.0
CB B:HIS241 3.9 0.7 1.0
NE2 B:HIS241 4.5 0.5 1.0
CA B:HIS241 4.6 1.0 1.0
CD2 B:HIS241 4.6 0.4 1.0
O B:HIS241 4.6 0.8 1.0
CD1 B:LEU180 4.7 80.3 1.0
C B:HIS241 4.8 0.8 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 2011.
ISSN: ISSN 0907-4449
PubMed: 20944240
DOI: 10.1107/S090744491003369X
Page generated: Fri Jul 19 15:21:41 2024

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