Cobalt in PDB 4lem: Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis
Enzymatic activity of Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis
All present enzymatic activity of Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis:
1.5.1.12;
Protein crystallography data
The structure of Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis, PDB code: 4lem
was solved by
T.Lagautriere,
G.Bashiri,
E.N.Baker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.01 /
2.27
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
164.299,
164.299,
259.114,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
14.8 /
20.4
|
Other elements in 4lem:
The structure of Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis also contains other interesting chemical elements:
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis
(pdb code 4lem). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the
Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis, PDB code: 4lem:
Jump to Cobalt binding site number:
1;
2;
3;
4;
Cobalt binding site 1 out
of 4 in 4lem
Go back to
Cobalt Binding Sites List in 4lem
Cobalt binding site 1 out
of 4 in the Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis
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 Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co601
b:21.2
occ:1.00
|
CO
|
A:B12601
|
0.0
|
21.2
|
1.0
|
N21
|
A:B12601
|
1.8
|
21.9
|
1.0
|
N23
|
A:B12601
|
1.9
|
22.2
|
1.0
|
N22
|
A:B12601
|
1.9
|
22.4
|
1.0
|
N24
|
A:B12601
|
1.9
|
23.0
|
1.0
|
N3B
|
A:B12601
|
2.2
|
22.6
|
1.0
|
C19
|
A:B12601
|
2.8
|
20.9
|
1.0
|
C4
|
A:B12601
|
2.8
|
22.1
|
1.0
|
C1
|
A:B12601
|
2.8
|
20.4
|
1.0
|
C14
|
A:B12601
|
2.8
|
21.1
|
1.0
|
C6
|
A:B12601
|
2.9
|
21.2
|
1.0
|
C9
|
A:B12601
|
2.9
|
22.0
|
1.0
|
C11
|
A:B12601
|
2.9
|
22.2
|
1.0
|
C16
|
A:B12601
|
3.0
|
20.4
|
1.0
|
C2B
|
A:B12601
|
3.1
|
23.1
|
1.0
|
C5
|
A:B12601
|
3.2
|
21.8
|
1.0
|
C9B
|
A:B12601
|
3.3
|
23.1
|
1.0
|
C15
|
A:B12601
|
3.3
|
20.6
|
1.0
|
C10
|
A:B12601
|
3.3
|
23.1
|
1.0
|
C20
|
A:B12601
|
3.5
|
19.0
|
1.0
|
C4B
|
A:B12601
|
3.9
|
24.5
|
1.0
|
C2
|
A:B12601
|
4.0
|
22.3
|
1.0
|
C18
|
A:B12601
|
4.1
|
22.0
|
1.0
|
C3
|
A:B12601
|
4.1
|
21.2
|
1.0
|
N29
|
A:B12601
|
4.1
|
21.8
|
1.0
|
C17
|
A:B12601
|
4.2
|
21.6
|
1.0
|
C13
|
A:B12601
|
4.2
|
23.2
|
1.0
|
C8
|
A:B12601
|
4.2
|
24.4
|
1.0
|
C7
|
A:B12601
|
4.2
|
23.1
|
1.0
|
C12
|
A:B12601
|
4.3
|
22.0
|
1.0
|
N1B
|
A:B12601
|
4.3
|
22.6
|
1.0
|
O39
|
A:B12601
|
4.4
|
18.7
|
1.0
|
C27
|
A:B12601
|
4.4
|
22.7
|
1.0
|
C8B
|
A:B12601
|
4.5
|
24.3
|
1.0
|
O
|
A:HOH785
|
4.5
|
28.0
|
1.0
|
C35
|
A:B12601
|
4.7
|
22.8
|
1.0
|
C38
|
A:B12601
|
4.7
|
21.1
|
1.0
|
C26
|
A:B12601
|
4.7
|
22.8
|
1.0
|
C54
|
A:B12601
|
4.9
|
19.3
|
1.0
|
C53
|
A:B12601
|
4.9
|
20.4
|
1.0
|
C41
|
A:B12601
|
4.9
|
28.4
|
1.0
|
O28
|
A:B12601
|
4.9
|
23.5
|
1.0
|
|
Cobalt binding site 2 out
of 4 in 4lem
Go back to
Cobalt Binding Sites List in 4lem
Cobalt binding site 2 out
of 4 in the Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis
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 Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co601
b:25.3
occ:1.00
|
CO
|
B:B12601
|
0.0
|
25.3
|
1.0
|
N21
|
B:B12601
|
1.8
|
24.8
|
1.0
|
N23
|
B:B12601
|
1.9
|
26.8
|
1.0
|
N24
|
B:B12601
|
1.9
|
22.1
|
1.0
|
N22
|
B:B12601
|
1.9
|
24.6
|
1.0
|
N3B
|
B:B12601
|
2.3
|
26.2
|
1.0
|
C19
|
B:B12601
|
2.7
|
23.3
|
1.0
|
C1
|
B:B12601
|
2.8
|
26.2
|
1.0
|
C4
|
B:B12601
|
2.8
|
24.0
|
1.0
|
C14
|
B:B12601
|
2.9
|
26.9
|
1.0
|
C6
|
B:B12601
|
2.9
|
24.0
|
1.0
|
C11
|
B:B12601
|
2.9
|
26.3
|
1.0
|
C16
|
B:B12601
|
3.0
|
25.2
|
1.0
|
C9
|
B:B12601
|
3.0
|
25.4
|
1.0
|
C2B
|
B:B12601
|
3.2
|
27.8
|
1.0
|
C5
|
B:B12601
|
3.2
|
25.0
|
1.0
|
C15
|
B:B12601
|
3.3
|
27.2
|
1.0
|
C10
|
B:B12601
|
3.4
|
26.2
|
1.0
|
C9B
|
B:B12601
|
3.4
|
26.2
|
1.0
|
C20
|
B:B12601
|
3.4
|
24.7
|
1.0
|
O39
|
B:B12601
|
3.9
|
44.7
|
1.0
|
C4B
|
B:B12601
|
3.9
|
26.9
|
1.0
|
C2
|
B:B12601
|
4.0
|
26.7
|
1.0
|
C3
|
B:B12601
|
4.1
|
25.4
|
1.0
|
C18
|
B:B12601
|
4.1
|
25.4
|
1.0
|
C13
|
B:B12601
|
4.2
|
28.1
|
1.0
|
C12
|
B:B12601
|
4.2
|
29.6
|
1.0
|
C17
|
B:B12601
|
4.2
|
25.4
|
1.0
|
C8
|
B:B12601
|
4.3
|
25.4
|
1.0
|
C7
|
B:B12601
|
4.3
|
27.6
|
1.0
|
O
|
B:HOH828
|
4.4
|
37.1
|
1.0
|
N1B
|
B:B12601
|
4.4
|
28.1
|
1.0
|
C26
|
B:B12601
|
4.4
|
30.7
|
1.0
|
C8B
|
B:B12601
|
4.6
|
26.9
|
1.0
|
C38
|
B:B12601
|
4.6
|
38.0
|
1.0
|
C35
|
B:B12601
|
4.7
|
26.5
|
1.0
|
C53
|
B:B12601
|
4.8
|
28.6
|
1.0
|
C41
|
B:B12601
|
4.9
|
26.6
|
1.0
|
C46
|
B:B12601
|
4.9
|
30.5
|
1.0
|
C54
|
B:B12601
|
4.9
|
23.9
|
1.0
|
|
Cobalt binding site 3 out
of 4 in 4lem
Go back to
Cobalt Binding Sites List in 4lem
Cobalt binding site 3 out
of 4 in the Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis
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 Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co601
b:49.1
occ:1.00
|
CO
|
C:B12601
|
0.0
|
49.1
|
1.0
|
N21
|
C:B12601
|
1.8
|
54.5
|
1.0
|
N24
|
C:B12601
|
1.9
|
49.1
|
1.0
|
N23
|
C:B12601
|
1.9
|
51.4
|
1.0
|
N22
|
C:B12601
|
2.0
|
56.8
|
1.0
|
N3B
|
C:B12601
|
2.3
|
48.9
|
1.0
|
C19
|
C:B12601
|
2.7
|
48.6
|
1.0
|
C4
|
C:B12601
|
2.8
|
55.8
|
1.0
|
C1
|
C:B12601
|
2.8
|
53.0
|
1.0
|
C14
|
C:B12601
|
2.8
|
48.0
|
1.0
|
C6
|
C:B12601
|
2.9
|
57.6
|
1.0
|
C16
|
C:B12601
|
3.0
|
47.9
|
1.0
|
C11
|
C:B12601
|
3.0
|
57.6
|
1.0
|
C9
|
C:B12601
|
3.0
|
58.6
|
1.0
|
C2B
|
C:B12601
|
3.2
|
45.2
|
1.0
|
C5
|
C:B12601
|
3.2
|
56.7
|
1.0
|
C15
|
C:B12601
|
3.3
|
49.0
|
1.0
|
C9B
|
C:B12601
|
3.4
|
50.8
|
1.0
|
C10
|
C:B12601
|
3.4
|
55.4
|
1.0
|
C20
|
C:B12601
|
3.6
|
47.4
|
1.0
|
C4B
|
C:B12601
|
4.0
|
49.5
|
1.0
|
C18
|
C:B12601
|
4.0
|
44.6
|
1.0
|
C2
|
C:B12601
|
4.0
|
55.7
|
1.0
|
C3
|
C:B12601
|
4.1
|
55.1
|
1.0
|
C17
|
C:B12601
|
4.2
|
46.1
|
1.0
|
C13
|
C:B12601
|
4.2
|
52.8
|
1.0
|
C7
|
C:B12601
|
4.3
|
64.7
|
1.0
|
C12
|
C:B12601
|
4.3
|
54.4
|
1.0
|
C8
|
C:B12601
|
4.3
|
63.5
|
1.0
|
N1B
|
C:B12601
|
4.4
|
46.5
|
1.0
|
C26
|
C:B12601
|
4.5
|
62.2
|
1.0
|
C38
|
C:B12601
|
4.5
|
75.7
|
1.0
|
C8B
|
C:B12601
|
4.6
|
50.5
|
1.0
|
O39
|
C:B12601
|
4.6
|
78.7
|
1.0
|
N40
|
C:B12601
|
4.6
|
75.1
|
1.0
|
C35
|
C:B12601
|
4.7
|
58.7
|
1.0
|
C53
|
C:B12601
|
4.8
|
51.4
|
1.0
|
O28
|
C:B12601
|
4.9
|
69.0
|
1.0
|
C54
|
C:B12601
|
4.9
|
40.1
|
1.0
|
C42
|
C:B12601
|
5.0
|
69.5
|
1.0
|
|
Cobalt binding site 4 out
of 4 in 4lem
Go back to
Cobalt Binding Sites List in 4lem
Cobalt binding site 4 out
of 4 in the Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis
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 Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co601
b:29.5
occ:1.00
|
CO
|
D:B12601
|
0.0
|
29.5
|
1.0
|
N21
|
D:B12601
|
1.8
|
27.9
|
1.0
|
N23
|
D:B12601
|
1.9
|
30.4
|
1.0
|
N24
|
D:B12601
|
1.9
|
29.5
|
1.0
|
N22
|
D:B12601
|
1.9
|
33.2
|
1.0
|
N3B
|
D:B12601
|
2.3
|
32.6
|
1.0
|
C19
|
D:B12601
|
2.7
|
29.0
|
1.0
|
C1
|
D:B12601
|
2.8
|
27.5
|
1.0
|
C4
|
D:B12601
|
2.8
|
27.9
|
1.0
|
C6
|
D:B12601
|
2.8
|
30.7
|
1.0
|
C14
|
D:B12601
|
2.9
|
27.7
|
1.0
|
C11
|
D:B12601
|
2.9
|
33.2
|
1.0
|
C16
|
D:B12601
|
2.9
|
27.2
|
1.0
|
C9
|
D:B12601
|
2.9
|
34.6
|
1.0
|
C5
|
D:B12601
|
3.2
|
28.3
|
1.0
|
C2B
|
D:B12601
|
3.2
|
34.1
|
1.0
|
C9B
|
D:B12601
|
3.3
|
29.9
|
1.0
|
C10
|
D:B12601
|
3.3
|
35.2
|
1.0
|
C15
|
D:B12601
|
3.3
|
27.2
|
1.0
|
C20
|
D:B12601
|
3.5
|
24.9
|
1.0
|
C4B
|
D:B12601
|
3.8
|
28.9
|
1.0
|
C18
|
D:B12601
|
4.0
|
29.2
|
1.0
|
C2
|
D:B12601
|
4.0
|
29.4
|
1.0
|
C3
|
D:B12601
|
4.1
|
26.6
|
1.0
|
C17
|
D:B12601
|
4.1
|
32.0
|
1.0
|
N29
|
D:B12601
|
4.1
|
25.3
|
1.0
|
C7
|
D:B12601
|
4.1
|
35.6
|
1.0
|
C13
|
D:B12601
|
4.2
|
29.2
|
1.0
|
C12
|
D:B12601
|
4.2
|
33.8
|
1.0
|
C8
|
D:B12601
|
4.2
|
35.0
|
1.0
|
N40
|
D:B12601
|
4.3
|
48.0
|
1.0
|
O
|
D:HOH869
|
4.3
|
32.9
|
1.0
|
N1B
|
D:B12601
|
4.4
|
32.1
|
1.0
|
C27
|
D:B12601
|
4.5
|
30.9
|
1.0
|
C38
|
D:B12601
|
4.5
|
50.2
|
1.0
|
C8B
|
D:B12601
|
4.5
|
31.7
|
1.0
|
C35
|
D:B12601
|
4.7
|
28.9
|
1.0
|
C26
|
D:B12601
|
4.7
|
30.9
|
1.0
|
C46
|
D:B12601
|
4.8
|
35.4
|
1.0
|
C37
|
D:B12601
|
4.8
|
39.6
|
1.0
|
C53
|
D:B12601
|
4.9
|
25.0
|
1.0
|
C55
|
D:B12601
|
4.9
|
34.2
|
1.0
|
C41
|
D:B12601
|
5.0
|
38.5
|
1.0
|
O39
|
D:B12601
|
5.0
|
41.0
|
1.0
|
C54
|
D:B12601
|
5.0
|
33.2
|
1.0
|
|
Reference:
T.Lagautriere,
G.Bashiri,
E.N.Baker.
Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis To Be Published.
Page generated: Tue Jul 30 17:19:02 2024
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