Cobalt in PDB 4jbh: 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum
Enzymatic activity of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum
All present enzymatic activity of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum:
1.1.1.1;
Protein crystallography data
The structure of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum, PDB code: 4jbh
was solved by
S.Lovell,
K.P.Battaile,
A.Vitale,
N.Throne,
X.Hu,
M.Shen,
S.D'auria,
D.S.Auld,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.16 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.402,
125.336,
82.943,
90.00,
107.12,
90.00
|
R / Rfree (%)
|
15.1 /
19.5
|
Other elements in 4jbh:
The structure of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum also contains other interesting chemical elements:
Cobalt Binding Sites:
The binding sites of Cobalt atom in the 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum
(pdb code 4jbh). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the
2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum, PDB code: 4jbh:
Jump to Cobalt binding site number:
1;
2;
3;
4;
Cobalt binding site 1 out
of 4 in 4jbh
Go back to
Cobalt Binding Sites List in 4jbh
Cobalt binding site 1 out
of 4 in the 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co402
b:39.2
occ:0.50
|
ZN
|
A:ZN401
|
0.0
|
39.3
|
0.5
|
SG
|
A:CYS105
|
2.3
|
25.1
|
1.0
|
SG
|
A:CYS94
|
2.3
|
28.1
|
1.0
|
SG
|
A:CYS97
|
2.3
|
29.6
|
1.0
|
SG
|
A:CYS91
|
2.4
|
27.4
|
1.0
|
CB
|
A:CYS105
|
3.2
|
24.8
|
1.0
|
CB
|
A:CYS97
|
3.4
|
25.2
|
1.0
|
CB
|
A:CYS94
|
3.4
|
34.7
|
1.0
|
N
|
A:CYS91
|
3.5
|
30.5
|
1.0
|
CB
|
A:CYS91
|
3.5
|
26.9
|
1.0
|
CA
|
A:CYS105
|
3.5
|
25.5
|
1.0
|
N
|
A:CYS94
|
3.8
|
36.0
|
1.0
|
N
|
A:GLY92
|
3.9
|
33.9
|
1.0
|
CA
|
A:CYS91
|
4.0
|
35.0
|
1.0
|
N
|
A:GLU106
|
4.0
|
29.1
|
1.0
|
N
|
A:CYS97
|
4.1
|
25.7
|
1.0
|
C
|
A:CYS105
|
4.1
|
30.1
|
1.0
|
CA
|
A:CYS94
|
4.2
|
26.8
|
1.0
|
CA
|
A:CYS97
|
4.4
|
25.8
|
1.0
|
C
|
A:CYS91
|
4.4
|
35.6
|
1.0
|
N
|
A:HIS93
|
4.4
|
34.2
|
1.0
|
N
|
A:VAL107
|
4.5
|
34.6
|
1.0
|
C
|
A:TYR90
|
4.6
|
29.2
|
1.0
|
C
|
A:CYS94
|
4.8
|
31.4
|
1.0
|
CB
|
A:VAL107
|
4.8
|
39.4
|
1.0
|
N
|
A:CYS105
|
4.8
|
27.4
|
1.0
|
CA
|
A:GLY92
|
4.9
|
28.7
|
1.0
|
CA
|
A:TYR90
|
4.9
|
31.6
|
1.0
|
O
|
A:CYS94
|
4.9
|
28.4
|
1.0
|
CG2
|
A:VAL107
|
4.9
|
36.1
|
1.0
|
C
|
A:HIS93
|
5.0
|
31.7
|
1.0
|
CB
|
A:TYR90
|
5.0
|
26.0
|
1.0
|
|
Cobalt binding site 2 out
of 4 in 4jbh
Go back to
Cobalt Binding Sites List in 4jbh
Cobalt binding site 2 out
of 4 in the 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co403
b:38.0
occ:0.50
|
ZN
|
B:ZN402
|
0.1
|
38.1
|
0.5
|
SG
|
B:CYS91
|
2.3
|
28.5
|
1.0
|
SG
|
B:CYS97
|
2.3
|
26.4
|
1.0
|
SG
|
B:CYS105
|
2.3
|
27.8
|
1.0
|
SG
|
B:CYS94
|
2.4
|
26.9
|
1.0
|
CB
|
B:CYS105
|
3.3
|
29.2
|
1.0
|
CB
|
B:CYS97
|
3.4
|
25.9
|
1.0
|
CB
|
B:CYS91
|
3.4
|
29.8
|
1.0
|
N
|
B:CYS91
|
3.4
|
27.3
|
1.0
|
CB
|
B:CYS94
|
3.6
|
36.3
|
1.0
|
CA
|
B:CYS105
|
3.7
|
28.8
|
1.0
|
N
|
B:GLY92
|
3.8
|
30.6
|
1.0
|
CA
|
B:CYS91
|
3.8
|
31.4
|
1.0
|
N
|
B:CYS94
|
3.9
|
34.2
|
1.0
|
N
|
B:GLU106
|
4.1
|
28.4
|
1.0
|
C
|
B:CYS91
|
4.2
|
37.1
|
1.0
|
N
|
B:CYS97
|
4.3
|
26.3
|
1.0
|
CA
|
B:CYS94
|
4.3
|
33.2
|
1.0
|
C
|
B:CYS105
|
4.3
|
32.1
|
1.0
|
N
|
B:HIS93
|
4.3
|
32.2
|
1.0
|
CA
|
B:CYS97
|
4.5
|
28.6
|
1.0
|
N
|
B:VAL107
|
4.5
|
34.6
|
1.0
|
C
|
B:TYR90
|
4.6
|
31.2
|
1.0
|
CB
|
B:VAL107
|
4.7
|
33.3
|
1.0
|
CA
|
B:GLY92
|
4.8
|
33.1
|
1.0
|
CA
|
B:TYR90
|
4.8
|
32.2
|
1.0
|
CB
|
B:TYR90
|
4.9
|
27.8
|
1.0
|
C
|
B:CYS94
|
4.9
|
29.3
|
1.0
|
C
|
B:HIS93
|
5.0
|
37.4
|
1.0
|
C
|
B:GLY92
|
5.0
|
35.4
|
1.0
|
N
|
B:CYS105
|
5.0
|
28.1
|
1.0
|
O
|
B:CYS94
|
5.0
|
26.2
|
1.0
|
|
Cobalt binding site 3 out
of 4 in 4jbh
Go back to
Cobalt Binding Sites List in 4jbh
Cobalt binding site 3 out
of 4 in the 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co403
b:40.8
occ:0.50
|
ZN
|
C:ZN402
|
0.1
|
40.8
|
0.5
|
SG
|
C:CYS105
|
2.2
|
27.1
|
1.0
|
SG
|
C:CYS97
|
2.3
|
32.4
|
1.0
|
SG
|
C:CYS91
|
2.4
|
31.4
|
1.0
|
SG
|
C:CYS94
|
2.4
|
28.4
|
1.0
|
CB
|
C:CYS105
|
3.2
|
30.3
|
1.0
|
CB
|
C:CYS97
|
3.4
|
34.9
|
1.0
|
N
|
C:CYS91
|
3.5
|
29.1
|
1.0
|
CB
|
C:CYS91
|
3.5
|
30.2
|
1.0
|
CB
|
C:CYS94
|
3.6
|
33.1
|
1.0
|
CA
|
C:CYS105
|
3.6
|
32.6
|
1.0
|
N
|
C:GLY92
|
3.8
|
39.6
|
1.0
|
CA
|
C:CYS91
|
3.9
|
33.7
|
1.0
|
N
|
C:CYS94
|
3.9
|
40.0
|
1.0
|
N
|
C:GLU106
|
4.1
|
29.2
|
1.0
|
C
|
C:CYS105
|
4.2
|
30.4
|
1.0
|
N
|
C:CYS97
|
4.2
|
28.0
|
1.0
|
C
|
C:CYS91
|
4.3
|
41.8
|
1.0
|
CA
|
C:CYS94
|
4.3
|
28.4
|
1.0
|
N
|
C:HIS93
|
4.3
|
31.9
|
1.0
|
CA
|
C:CYS97
|
4.4
|
34.6
|
1.0
|
N
|
C:VAL107
|
4.5
|
32.8
|
1.0
|
C
|
C:TYR90
|
4.6
|
36.2
|
1.0
|
CB
|
C:VAL107
|
4.7
|
39.8
|
1.0
|
CA
|
C:GLY92
|
4.7
|
34.7
|
1.0
|
CA
|
C:TYR90
|
4.8
|
29.2
|
1.0
|
CG2
|
C:VAL107
|
4.8
|
42.0
|
1.0
|
CB
|
C:TYR90
|
4.8
|
25.4
|
1.0
|
N
|
C:CYS105
|
4.9
|
29.9
|
1.0
|
C
|
C:CYS94
|
4.9
|
32.6
|
1.0
|
O
|
C:CYS94
|
4.9
|
30.1
|
1.0
|
C
|
C:GLY92
|
4.9
|
36.0
|
1.0
|
|
Cobalt binding site 4 out
of 4 in 4jbh
Go back to
Cobalt Binding Sites List in 4jbh
Cobalt binding site 4 out
of 4 in the 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of 2.2A Resolution Structure of Cobalt and Zinc Bound Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co403
b:47.2
occ:0.50
|
ZN
|
D:ZN402
|
0.1
|
47.2
|
0.5
|
SG
|
D:CYS97
|
2.3
|
32.7
|
1.0
|
SG
|
D:CYS94
|
2.3
|
30.7
|
1.0
|
SG
|
D:CYS91
|
2.3
|
36.6
|
1.0
|
SG
|
D:CYS105
|
2.4
|
29.9
|
1.0
|
CB
|
D:CYS97
|
3.3
|
37.6
|
1.0
|
CB
|
D:CYS105
|
3.4
|
33.1
|
1.0
|
CB
|
D:CYS94
|
3.4
|
35.6
|
1.0
|
N
|
D:CYS91
|
3.4
|
31.6
|
1.0
|
CB
|
D:CYS91
|
3.5
|
32.0
|
1.0
|
CA
|
D:CYS105
|
3.7
|
30.9
|
1.0
|
N
|
D:GLY92
|
3.8
|
34.5
|
1.0
|
N
|
D:CYS94
|
3.8
|
35.4
|
1.0
|
CA
|
D:CYS91
|
3.9
|
35.5
|
1.0
|
N
|
D:GLU106
|
4.1
|
35.4
|
1.0
|
CA
|
D:CYS94
|
4.2
|
35.5
|
1.0
|
N
|
D:CYS97
|
4.2
|
31.4
|
1.0
|
C
|
D:CYS91
|
4.2
|
39.6
|
1.0
|
C
|
D:CYS105
|
4.3
|
35.8
|
1.0
|
N
|
D:HIS93
|
4.3
|
34.8
|
1.0
|
CA
|
D:CYS97
|
4.4
|
34.8
|
1.0
|
N
|
D:VAL107
|
4.6
|
38.4
|
1.0
|
C
|
D:TYR90
|
4.6
|
33.6
|
1.0
|
CA
|
D:GLY92
|
4.7
|
37.8
|
1.0
|
CB
|
D:VAL107
|
4.8
|
41.9
|
1.0
|
C
|
D:CYS94
|
4.8
|
34.6
|
1.0
|
CA
|
D:TYR90
|
4.8
|
33.1
|
1.0
|
O
|
D:CYS94
|
4.9
|
35.6
|
1.0
|
CB
|
D:TYR90
|
4.9
|
30.7
|
1.0
|
C
|
D:HIS93
|
4.9
|
40.8
|
1.0
|
C
|
D:GLY92
|
5.0
|
37.0
|
1.0
|
N
|
D:CYS105
|
5.0
|
29.9
|
1.0
|
|
Reference:
A.Vitale,
N.Thorne,
S.Lovell,
K.P.Battaile,
X.Hu,
M.Shen,
S.D'auria,
D.S.Auld.
Physicochemical Characterization of A Thermostable Alcohol Dehydrogenase From Pyrobaculum Aerophilum. Plos One V. 8 63828 2013.
ISSN: ESSN 1932-6203
PubMed: 23755111
DOI: 10.1371/JOURNAL.PONE.0063828
Page generated: Tue Jul 30 17:14:14 2024
|