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:
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 Sites List in 2wxu
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 Sites List in 2wxu
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 Sites List in 2wxu
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 Sites List in 2wxu
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 Sites List in 2wxu
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 Sites List in 2wxu
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
Go back to
Cadmium Binding Sites List in 2wxu
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
|