Cobalt in PDB 2j3z: Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1
Protein crystallography data
The structure of Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1, PDB code: 2j3z
was solved by
C.Schleberger,
H.Hochmann,
H.Barth,
K.Aktories,
G.E.Schulz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
2.30
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.421,
272.898,
246.290,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20 /
25.8
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1
(pdb code 2j3z). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the
Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1, PDB code: 2j3z:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
Cobalt binding site 1 out
of 7 in 2j3z
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Cobalt Binding Sites List in 2j3z
Cobalt binding site 1 out
of 7 in the Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co1432
b:69.1
occ:1.00
|
N
|
A:ILE115
|
3.6
|
35.1
|
1.0
|
N
|
A:ARG116
|
3.8
|
36.2
|
1.0
|
CG
|
A:PRO161
|
3.8
|
31.5
|
1.0
|
CA
|
A:SER114
|
4.2
|
37.7
|
1.0
|
OD1
|
A:ASP121
|
4.3
|
45.6
|
1.0
|
CA
|
A:ILE115
|
4.3
|
34.1
|
1.0
|
C
|
A:SER114
|
4.4
|
36.6
|
1.0
|
CB
|
A:ILE115
|
4.4
|
32.9
|
1.0
|
CB
|
A:PRO161
|
4.5
|
31.6
|
1.0
|
CB
|
A:ARG116
|
4.5
|
38.2
|
1.0
|
C
|
A:ILE115
|
4.6
|
35.5
|
1.0
|
CB
|
A:SER114
|
4.6
|
39.4
|
1.0
|
CA
|
A:ARG116
|
4.6
|
38.1
|
1.0
|
CD
|
A:PRO161
|
4.7
|
31.1
|
1.0
|
O
|
A:ARG116
|
4.7
|
39.8
|
1.0
|
|
Cobalt binding site 2 out
of 7 in 2j3z
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Cobalt Binding Sites List in 2j3z
Cobalt binding site 2 out
of 7 in the Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co1432
b:46.7
occ:1.00
|
NE2
|
B:HIS243
|
1.9
|
59.9
|
1.0
|
NE2
|
A:HIS243
|
2.1
|
58.0
|
1.0
|
CE1
|
C:HIS243
|
2.2
|
53.3
|
1.0
|
NE2
|
C:HIS243
|
2.3
|
54.9
|
1.0
|
O
|
B:HOH2095
|
2.3
|
45.5
|
1.0
|
CE1
|
B:HIS243
|
2.4
|
62.1
|
1.0
|
CE1
|
A:HIS243
|
2.9
|
59.5
|
1.0
|
CD2
|
B:HIS243
|
3.2
|
56.2
|
1.0
|
CD2
|
A:HIS243
|
3.3
|
53.8
|
1.0
|
ND1
|
C:HIS243
|
3.5
|
49.9
|
1.0
|
CD2
|
C:HIS243
|
3.6
|
52.9
|
1.0
|
ND1
|
B:HIS243
|
3.7
|
60.5
|
1.0
|
ND1
|
A:HIS243
|
4.1
|
58.0
|
1.0
|
CG
|
B:HIS243
|
4.1
|
55.7
|
1.0
|
CG
|
C:HIS243
|
4.2
|
49.2
|
1.0
|
CG
|
A:HIS243
|
4.3
|
53.0
|
1.0
|
|
Cobalt binding site 3 out
of 7 in 2j3z
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Cobalt Binding Sites List in 2j3z
Cobalt binding site 3 out
of 7 in the Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co1433
b:64.9
occ:1.00
|
N
|
B:ILE115
|
3.6
|
42.7
|
1.0
|
CG
|
B:PRO161
|
3.6
|
35.8
|
1.0
|
N
|
B:ARG116
|
3.8
|
43.9
|
1.0
|
OD1
|
B:ASP121
|
3.8
|
52.3
|
1.0
|
OG
|
B:SER114
|
4.0
|
49.3
|
1.0
|
CA
|
B:ILE115
|
4.3
|
42.0
|
1.0
|
C
|
B:SER114
|
4.4
|
44.7
|
1.0
|
CB
|
B:PRO161
|
4.4
|
36.3
|
1.0
|
CA
|
B:SER114
|
4.5
|
45.6
|
1.0
|
CB
|
B:ILE115
|
4.5
|
40.0
|
1.0
|
CD
|
B:PRO161
|
4.5
|
33.8
|
1.0
|
C
|
B:ILE115
|
4.6
|
43.8
|
1.0
|
O
|
B:ARG116
|
4.6
|
48.5
|
1.0
|
CB
|
B:ARG116
|
4.7
|
46.1
|
1.0
|
CA
|
B:ARG116
|
4.7
|
46.6
|
1.0
|
CB
|
B:SER114
|
4.9
|
47.8
|
1.0
|
CG
|
B:ARG116
|
4.9
|
44.1
|
1.0
|
CG
|
B:ASP121
|
4.9
|
51.6
|
1.0
|
|
Cobalt binding site 4 out
of 7 in 2j3z
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Cobalt Binding Sites List in 2j3z
Cobalt binding site 4 out
of 7 in the Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co1430
b:51.9
occ:1.00
|
O
|
C:HOH2040
|
3.6
|
30.8
|
1.0
|
N
|
C:ILE115
|
3.7
|
34.9
|
1.0
|
CG
|
C:PRO161
|
3.9
|
29.0
|
1.0
|
N
|
C:ARG116
|
4.2
|
35.5
|
1.0
|
CA
|
C:SER114
|
4.2
|
36.8
|
1.0
|
C
|
C:SER114
|
4.5
|
36.1
|
1.0
|
CB
|
C:SER114
|
4.6
|
38.3
|
1.0
|
CA
|
C:ILE115
|
4.6
|
33.6
|
1.0
|
OD1
|
C:ASP121
|
4.6
|
43.5
|
1.0
|
CB
|
C:ILE115
|
4.7
|
32.5
|
1.0
|
CB
|
C:PRO161
|
4.8
|
29.3
|
1.0
|
CD
|
C:PRO161
|
4.8
|
28.1
|
1.0
|
CB
|
C:ARG116
|
4.8
|
37.0
|
1.0
|
C
|
C:ILE115
|
4.9
|
35.1
|
1.0
|
|
Cobalt binding site 5 out
of 7 in 2j3z
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Cobalt Binding Sites List in 2j3z
Cobalt binding site 5 out
of 7 in the Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 5 of Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co1427
b:56.2
occ:1.00
|
O
|
D:HOH2021
|
3.3
|
42.0
|
1.0
|
N
|
D:ILE115
|
3.7
|
40.6
|
1.0
|
N
|
D:ARG116
|
3.9
|
41.6
|
1.0
|
CG
|
D:PRO161
|
3.9
|
36.1
|
1.0
|
OD1
|
D:ASP121
|
4.4
|
53.1
|
1.0
|
CB
|
D:ILE115
|
4.4
|
37.3
|
1.0
|
CB
|
D:PRO161
|
4.4
|
36.5
|
1.0
|
CA
|
D:ILE115
|
4.4
|
39.4
|
1.0
|
CA
|
D:SER114
|
4.5
|
43.0
|
1.0
|
CB
|
D:ARG116
|
4.5
|
43.6
|
1.0
|
CD
|
D:PRO161
|
4.6
|
36.6
|
1.0
|
C
|
D:SER114
|
4.6
|
41.7
|
1.0
|
CG
|
D:ARG116
|
4.6
|
40.7
|
1.0
|
C
|
D:ILE115
|
4.7
|
40.8
|
1.0
|
CA
|
D:ARG116
|
4.7
|
43.4
|
1.0
|
CB
|
D:SER114
|
4.9
|
45.5
|
1.0
|
O
|
D:ARG116
|
4.9
|
46.6
|
1.0
|
|
Cobalt binding site 6 out
of 7 in 2j3z
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Cobalt Binding Sites List in 2j3z
Cobalt binding site 6 out
of 7 in the Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 6 of Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Co1429
b:57.2
occ:1.00
|
N
|
E:ILE115
|
3.5
|
43.9
|
1.0
|
O
|
E:HOH2026
|
3.7
|
34.7
|
1.0
|
CG
|
E:PRO161
|
3.8
|
39.1
|
1.0
|
N
|
E:ARG116
|
3.9
|
44.9
|
1.0
|
CB
|
E:ILE115
|
4.2
|
41.5
|
1.0
|
CA
|
E:ILE115
|
4.3
|
43.2
|
1.0
|
CB
|
E:PRO161
|
4.3
|
40.2
|
1.0
|
CA
|
E:SER114
|
4.4
|
45.6
|
1.0
|
C
|
E:SER114
|
4.5
|
45.1
|
1.0
|
OD1
|
E:ASP121
|
4.5
|
53.2
|
1.0
|
CD
|
E:PRO161
|
4.6
|
38.3
|
1.0
|
C
|
E:ILE115
|
4.6
|
44.5
|
1.0
|
CB
|
E:ARG116
|
4.6
|
46.4
|
1.0
|
OG
|
E:SER114
|
4.7
|
49.1
|
1.0
|
CB
|
E:SER114
|
4.8
|
47.7
|
1.0
|
CA
|
E:ARG116
|
4.8
|
46.8
|
1.0
|
CG
|
E:ARG116
|
4.8
|
44.7
|
1.0
|
O
|
E:ARG116
|
4.8
|
48.6
|
1.0
|
|
Cobalt binding site 7 out
of 7 in 2j3z
Go back to
Cobalt Binding Sites List in 2j3z
Cobalt binding site 7 out
of 7 in the Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 7 of Crystal Structure of the Enzymatic Component C2-I of the C2-Toxin From Clostridium Botulinum at pH 6.1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Co1427
b:55.0
occ:1.00
|
O
|
F:HOH2034
|
3.5
|
37.9
|
1.0
|
N
|
F:ILE115
|
3.5
|
44.9
|
1.0
|
N
|
F:ARG116
|
3.8
|
44.6
|
1.0
|
CG
|
F:PRO161
|
4.0
|
37.2
|
1.0
|
CB
|
F:ILE115
|
4.3
|
41.0
|
1.0
|
CA
|
F:ILE115
|
4.3
|
43.4
|
1.0
|
CA
|
F:SER114
|
4.4
|
48.3
|
1.0
|
C
|
F:SER114
|
4.5
|
46.7
|
1.0
|
OG
|
F:SER114
|
4.5
|
52.9
|
1.0
|
CB
|
F:PRO161
|
4.6
|
37.6
|
1.0
|
C
|
F:ILE115
|
4.6
|
44.4
|
1.0
|
CB
|
F:ARG116
|
4.6
|
45.5
|
1.0
|
OD1
|
F:ASP121
|
4.6
|
53.5
|
1.0
|
CB
|
F:SER114
|
4.7
|
51.2
|
1.0
|
CA
|
F:ARG116
|
4.7
|
46.1
|
1.0
|
O
|
F:ARG116
|
4.8
|
50.0
|
1.0
|
CD
|
F:PRO161
|
4.8
|
36.5
|
1.0
|
CG
|
F:ARG116
|
5.0
|
42.7
|
1.0
|
|
Reference:
C.Schleberger,
H.Hochmann,
H.Barth,
K.Aktories,
G.E.Schulz.
Structure and Action of the Binary C2 Toxin From Clostridium Botulinum. J.Mol.Biol. V. 364 705 2006.
ISSN: ISSN 0022-2836
PubMed: 17027031
DOI: 10.1016/J.JMB.2006.09.002
Page generated: Tue Jul 30 15:16:35 2024
|