Cobalt in PDB 4ur3: Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form
Enzymatic activity of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form
All present enzymatic activity of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form:
1.97.1.8;
Protein crystallography data
The structure of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form, PDB code: 4ur3
was solved by
M.Bommer,
C.Kunze,
J.Fesseler,
T.Schubert,
G.Diekert,
H.Dobbek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.763 /
2.24
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.315,
110.601,
178.792,
90.00,
95.91,
90.00
|
R / Rfree (%)
|
17.93 /
21.77
|
Other elements in 4ur3:
The structure of Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form also contains other interesting chemical elements:
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form
(pdb code 4ur3). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the
Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form, PDB code: 4ur3:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
Cobalt binding site 1 out
of 6 in 4ur3
Go back to
Cobalt Binding Sites List in 4ur3
Cobalt binding site 1 out
of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form
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 Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co503
b:34.1
occ:1.00
|
CO
|
A:BVQ503
|
0.0
|
34.1
|
1.0
|
N21
|
A:BVQ503
|
1.9
|
30.0
|
1.0
|
N24
|
A:BVQ503
|
1.9
|
33.0
|
1.0
|
N22
|
A:BVQ503
|
1.9
|
33.4
|
1.0
|
N23
|
A:BVQ503
|
1.9
|
36.7
|
1.0
|
O
|
A:HOH2132
|
2.2
|
39.8
|
1.0
|
C19
|
A:BVQ503
|
2.8
|
27.7
|
1.0
|
C9
|
A:BVQ503
|
2.8
|
36.1
|
1.0
|
C4
|
A:BVQ503
|
2.9
|
29.7
|
1.0
|
C1
|
A:BVQ503
|
2.9
|
30.4
|
1.0
|
C11
|
A:BVQ503
|
2.9
|
37.7
|
1.0
|
C6
|
A:BVQ503
|
3.0
|
31.8
|
1.0
|
C16
|
A:BVQ503
|
3.0
|
26.2
|
1.0
|
C14
|
A:BVQ503
|
3.0
|
30.9
|
1.0
|
C10
|
A:BVQ503
|
3.2
|
32.5
|
1.0
|
C5
|
A:BVQ503
|
3.3
|
32.0
|
1.0
|
C15
|
A:BVQ503
|
3.4
|
28.8
|
1.0
|
C20
|
A:BVQ503
|
3.5
|
26.5
|
1.0
|
O
|
A:HOH2191
|
3.7
|
33.3
|
1.0
|
C18
|
A:BVQ503
|
4.1
|
28.4
|
1.0
|
C2
|
A:BVQ503
|
4.1
|
28.8
|
1.0
|
C3
|
A:BVQ503
|
4.2
|
23.9
|
1.0
|
C8
|
A:BVQ503
|
4.2
|
37.2
|
1.0
|
C7
|
A:BVQ503
|
4.2
|
33.3
|
1.0
|
C17
|
A:BVQ503
|
4.3
|
31.4
|
1.0
|
C12
|
A:BVQ503
|
4.3
|
34.1
|
1.0
|
C13
|
A:BVQ503
|
4.3
|
35.0
|
1.0
|
C26
|
A:BVQ503
|
4.6
|
25.6
|
1.0
|
C37
|
A:BVQ503
|
4.7
|
29.6
|
1.0
|
C35
|
A:BVQ503
|
4.8
|
31.5
|
1.0
|
C41
|
A:BVQ503
|
4.8
|
27.9
|
1.0
|
CE2
|
A:PHE38
|
4.9
|
30.0
|
1.0
|
C53
|
A:BVQ503
|
4.9
|
30.3
|
1.0
|
|
Cobalt binding site 2 out
of 6 in 4ur3
Go back to
Cobalt Binding Sites List in 4ur3
Cobalt binding site 2 out
of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form
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 Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co503
b:26.4
occ:1.00
|
CO
|
B:BVQ503
|
0.0
|
26.4
|
1.0
|
N21
|
B:BVQ503
|
1.9
|
25.5
|
1.0
|
N24
|
B:BVQ503
|
1.9
|
19.7
|
1.0
|
N22
|
B:BVQ503
|
1.9
|
18.8
|
1.0
|
N23
|
B:BVQ503
|
1.9
|
22.9
|
1.0
|
O
|
B:HOH2135
|
2.3
|
22.9
|
1.0
|
C19
|
B:BVQ503
|
2.8
|
19.7
|
1.0
|
C9
|
B:BVQ503
|
2.8
|
23.3
|
1.0
|
C1
|
B:BVQ503
|
2.9
|
20.9
|
1.0
|
C4
|
B:BVQ503
|
2.9
|
19.4
|
1.0
|
C11
|
B:BVQ503
|
2.9
|
18.3
|
1.0
|
C6
|
B:BVQ503
|
3.0
|
22.0
|
1.0
|
C16
|
B:BVQ503
|
3.0
|
22.1
|
1.0
|
C14
|
B:BVQ503
|
3.0
|
21.2
|
1.0
|
C10
|
B:BVQ503
|
3.2
|
23.4
|
1.0
|
C5
|
B:BVQ503
|
3.3
|
20.9
|
1.0
|
C15
|
B:BVQ503
|
3.4
|
24.4
|
1.0
|
C20
|
B:BVQ503
|
3.5
|
18.1
|
1.0
|
O
|
B:HOH2196
|
3.7
|
19.4
|
1.0
|
C18
|
B:BVQ503
|
4.1
|
18.5
|
1.0
|
C2
|
B:BVQ503
|
4.1
|
19.3
|
1.0
|
C8
|
B:BVQ503
|
4.2
|
22.7
|
1.0
|
C3
|
B:BVQ503
|
4.2
|
21.1
|
1.0
|
C7
|
B:BVQ503
|
4.2
|
22.8
|
1.0
|
C17
|
B:BVQ503
|
4.3
|
24.5
|
1.0
|
C12
|
B:BVQ503
|
4.3
|
29.6
|
1.0
|
C13
|
B:BVQ503
|
4.3
|
23.6
|
1.0
|
C42
|
B:BVQ503
|
4.5
|
29.6
|
1.0
|
C26
|
B:BVQ503
|
4.6
|
20.4
|
1.0
|
C37
|
B:BVQ503
|
4.7
|
24.3
|
1.0
|
C35
|
B:BVQ503
|
4.8
|
18.3
|
1.0
|
C53
|
B:BVQ503
|
4.9
|
23.9
|
1.0
|
C41
|
B:BVQ503
|
5.0
|
22.3
|
1.0
|
C54
|
B:BVQ503
|
5.0
|
17.4
|
1.0
|
|
Cobalt binding site 3 out
of 6 in 4ur3
Go back to
Cobalt Binding Sites List in 4ur3
Cobalt binding site 3 out
of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form
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 Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co503
b:28.5
occ:1.00
|
CO
|
C:BVQ503
|
0.0
|
28.5
|
1.0
|
N21
|
C:BVQ503
|
1.9
|
21.6
|
1.0
|
N24
|
C:BVQ503
|
1.9
|
22.9
|
1.0
|
N22
|
C:BVQ503
|
1.9
|
24.6
|
1.0
|
N23
|
C:BVQ503
|
1.9
|
27.0
|
1.0
|
C19
|
C:BVQ503
|
2.8
|
14.7
|
1.0
|
C9
|
C:BVQ503
|
2.8
|
23.6
|
1.0
|
C1
|
C:BVQ503
|
2.9
|
20.0
|
1.0
|
C4
|
C:BVQ503
|
2.9
|
22.0
|
1.0
|
C11
|
C:BVQ503
|
2.9
|
22.3
|
1.0
|
C6
|
C:BVQ503
|
3.0
|
23.0
|
1.0
|
C16
|
C:BVQ503
|
3.0
|
22.1
|
1.0
|
C14
|
C:BVQ503
|
3.0
|
20.1
|
1.0
|
O
|
C:HOH2176
|
3.1
|
24.9
|
1.0
|
C10
|
C:BVQ503
|
3.2
|
17.7
|
1.0
|
C5
|
C:BVQ503
|
3.3
|
22.8
|
1.0
|
C15
|
C:BVQ503
|
3.4
|
21.5
|
1.0
|
O
|
C:HOH2252
|
3.5
|
23.8
|
1.0
|
C20
|
C:BVQ503
|
3.5
|
15.6
|
1.0
|
C18
|
C:BVQ503
|
4.1
|
20.9
|
1.0
|
C2
|
C:BVQ503
|
4.1
|
15.3
|
1.0
|
C3
|
C:BVQ503
|
4.2
|
16.9
|
1.0
|
C8
|
C:BVQ503
|
4.2
|
21.1
|
1.0
|
C7
|
C:BVQ503
|
4.2
|
20.1
|
1.0
|
C17
|
C:BVQ503
|
4.3
|
23.8
|
1.0
|
C12
|
C:BVQ503
|
4.3
|
23.3
|
1.0
|
C13
|
C:BVQ503
|
4.3
|
24.7
|
1.0
|
C42
|
C:BVQ503
|
4.5
|
32.9
|
1.0
|
C26
|
C:BVQ503
|
4.6
|
14.7
|
1.0
|
C37
|
C:BVQ503
|
4.7
|
23.6
|
1.0
|
C35
|
C:BVQ503
|
4.8
|
18.4
|
1.0
|
C53
|
C:BVQ503
|
4.9
|
24.1
|
1.0
|
CE2
|
C:PHE38
|
4.9
|
24.4
|
1.0
|
C41
|
C:BVQ503
|
4.9
|
23.5
|
1.0
|
|
Cobalt binding site 4 out
of 6 in 4ur3
Go back to
Cobalt Binding Sites List in 4ur3
Cobalt binding site 4 out
of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form
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 Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co503
b:26.1
occ:1.00
|
CO
|
D:BVQ503
|
0.0
|
26.1
|
1.0
|
N21
|
D:BVQ503
|
1.9
|
20.7
|
1.0
|
N24
|
D:BVQ503
|
1.9
|
20.1
|
1.0
|
N22
|
D:BVQ503
|
1.9
|
20.0
|
1.0
|
N23
|
D:BVQ503
|
1.9
|
23.8
|
1.0
|
O
|
D:HOH2134
|
2.2
|
27.8
|
1.0
|
C19
|
D:BVQ503
|
2.8
|
20.2
|
1.0
|
C9
|
D:BVQ503
|
2.8
|
20.6
|
1.0
|
C1
|
D:BVQ503
|
2.9
|
22.3
|
1.0
|
C4
|
D:BVQ503
|
2.9
|
17.1
|
1.0
|
C11
|
D:BVQ503
|
2.9
|
20.1
|
1.0
|
C6
|
D:BVQ503
|
3.0
|
20.4
|
1.0
|
C16
|
D:BVQ503
|
3.0
|
21.5
|
1.0
|
C14
|
D:BVQ503
|
3.0
|
22.9
|
1.0
|
C10
|
D:BVQ503
|
3.2
|
23.0
|
1.0
|
C5
|
D:BVQ503
|
3.3
|
19.0
|
1.0
|
C15
|
D:BVQ503
|
3.4
|
19.1
|
1.0
|
C20
|
D:BVQ503
|
3.5
|
18.8
|
1.0
|
O
|
D:HOH2197
|
3.7
|
19.4
|
1.0
|
C18
|
D:BVQ503
|
4.1
|
18.2
|
1.0
|
C2
|
D:BVQ503
|
4.1
|
18.9
|
1.0
|
C8
|
D:BVQ503
|
4.2
|
25.8
|
1.0
|
C3
|
D:BVQ503
|
4.2
|
18.8
|
1.0
|
C7
|
D:BVQ503
|
4.2
|
21.8
|
1.0
|
C17
|
D:BVQ503
|
4.3
|
20.0
|
1.0
|
C12
|
D:BVQ503
|
4.3
|
22.4
|
1.0
|
C13
|
D:BVQ503
|
4.3
|
21.7
|
1.0
|
C26
|
D:BVQ503
|
4.6
|
19.0
|
1.0
|
C37
|
D:BVQ503
|
4.6
|
19.4
|
1.0
|
CE2
|
D:PHE38
|
4.8
|
24.5
|
1.0
|
C35
|
D:BVQ503
|
4.8
|
17.3
|
1.0
|
C41
|
D:BVQ503
|
4.8
|
21.5
|
1.0
|
C53
|
D:BVQ503
|
4.9
|
19.2
|
1.0
|
|
Cobalt binding site 5 out
of 6 in 4ur3
Go back to
Cobalt Binding Sites List in 4ur3
Cobalt binding site 5 out
of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form
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 Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Co503
b:46.1
occ:1.00
|
CO
|
E:BVQ503
|
0.0
|
46.1
|
1.0
|
N21
|
E:BVQ503
|
1.9
|
42.0
|
1.0
|
N24
|
E:BVQ503
|
1.9
|
39.5
|
1.0
|
N22
|
E:BVQ503
|
1.9
|
42.2
|
1.0
|
N23
|
E:BVQ503
|
1.9
|
43.7
|
1.0
|
O
|
E:HOH2098
|
2.2
|
40.8
|
1.0
|
C19
|
E:BVQ503
|
2.8
|
38.4
|
1.0
|
C9
|
E:BVQ503
|
2.8
|
43.4
|
1.0
|
C4
|
E:BVQ503
|
2.9
|
38.1
|
1.0
|
C1
|
E:BVQ503
|
2.9
|
39.8
|
1.0
|
C11
|
E:BVQ503
|
2.9
|
42.3
|
1.0
|
C6
|
E:BVQ503
|
3.0
|
41.0
|
1.0
|
C16
|
E:BVQ503
|
3.0
|
42.4
|
1.0
|
C14
|
E:BVQ503
|
3.0
|
44.7
|
1.0
|
C10
|
E:BVQ503
|
3.2
|
40.5
|
1.0
|
C5
|
E:BVQ503
|
3.3
|
40.0
|
1.0
|
C15
|
E:BVQ503
|
3.4
|
45.7
|
1.0
|
C20
|
E:BVQ503
|
3.5
|
37.3
|
1.0
|
C18
|
E:BVQ503
|
4.1
|
40.0
|
1.0
|
C2
|
E:BVQ503
|
4.1
|
35.4
|
1.0
|
C3
|
E:BVQ503
|
4.2
|
39.0
|
1.0
|
C7
|
E:BVQ503
|
4.2
|
37.1
|
1.0
|
C8
|
E:BVQ503
|
4.2
|
40.8
|
1.0
|
C17
|
E:BVQ503
|
4.2
|
40.1
|
1.0
|
C12
|
E:BVQ503
|
4.2
|
48.3
|
1.0
|
C13
|
E:BVQ503
|
4.3
|
43.7
|
1.0
|
C26
|
E:BVQ503
|
4.6
|
35.8
|
1.0
|
C37
|
E:BVQ503
|
4.6
|
37.1
|
1.0
|
C42
|
E:BVQ503
|
4.7
|
46.7
|
1.0
|
C35
|
E:BVQ503
|
4.8
|
39.7
|
1.0
|
C53
|
E:BVQ503
|
4.9
|
47.5
|
1.0
|
|
Cobalt binding site 6 out
of 6 in 4ur3
Go back to
Cobalt Binding Sites List in 4ur3
Cobalt binding site 6 out
of 6 in the Crystal Structure of the Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form
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 Pce Reductive Dehalogenase From S. Multivorans P2(1) Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Co503
b:35.0
occ:1.00
|
CO
|
F:BVQ503
|
0.0
|
35.0
|
1.0
|
N21
|
F:BVQ503
|
1.9
|
24.5
|
1.0
|
N24
|
F:BVQ503
|
1.9
|
24.9
|
1.0
|
N22
|
F:BVQ503
|
1.9
|
28.1
|
1.0
|
N23
|
F:BVQ503
|
1.9
|
27.2
|
1.0
|
C19
|
F:BVQ503
|
2.8
|
22.4
|
1.0
|
C9
|
F:BVQ503
|
2.8
|
32.1
|
1.0
|
C1
|
F:BVQ503
|
2.9
|
24.4
|
1.0
|
C4
|
F:BVQ503
|
2.9
|
23.3
|
1.0
|
C11
|
F:BVQ503
|
2.9
|
29.6
|
1.0
|
C6
|
F:BVQ503
|
3.0
|
29.1
|
1.0
|
C16
|
F:BVQ503
|
3.0
|
26.9
|
1.0
|
C14
|
F:BVQ503
|
3.0
|
27.6
|
1.0
|
O
|
F:HOH2096
|
3.1
|
28.1
|
1.0
|
C10
|
F:BVQ503
|
3.2
|
30.2
|
1.0
|
C5
|
F:BVQ503
|
3.3
|
26.4
|
1.0
|
C15
|
F:BVQ503
|
3.4
|
28.4
|
1.0
|
C20
|
F:BVQ503
|
3.5
|
28.1
|
1.0
|
O
|
F:HOH2132
|
3.7
|
30.1
|
1.0
|
C18
|
F:BVQ503
|
4.1
|
26.4
|
1.0
|
C2
|
F:BVQ503
|
4.1
|
23.9
|
1.0
|
C3
|
F:BVQ503
|
4.2
|
25.7
|
1.0
|
C8
|
F:BVQ503
|
4.2
|
28.5
|
1.0
|
C7
|
F:BVQ503
|
4.2
|
29.1
|
1.0
|
C12
|
F:BVQ503
|
4.3
|
28.7
|
1.0
|
C17
|
F:BVQ503
|
4.3
|
28.4
|
1.0
|
C13
|
F:BVQ503
|
4.3
|
30.2
|
1.0
|
C26
|
F:BVQ503
|
4.6
|
23.4
|
1.0
|
C37
|
F:BVQ503
|
4.7
|
29.8
|
1.0
|
C42
|
F:BVQ503
|
4.7
|
37.3
|
1.0
|
C35
|
F:BVQ503
|
4.8
|
25.4
|
1.0
|
C53
|
F:BVQ503
|
4.9
|
32.3
|
1.0
|
CE2
|
F:PHE38
|
4.9
|
26.3
|
1.0
|
|
Reference:
M.Bommer,
C.Kunze,
J.Fesseler,
T.Schubert,
G.Diekert,
H.Dobbek.
Structural Basis For Organohalide Respiration. Science V. 346 455 2014.
ISSN: ISSN 0036-8075
PubMed: 25278505
DOI: 10.1126/SCIENCE.1258118
Page generated: Tue Jul 30 17:34:31 2024
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