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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:

Magnesium (Mg) 3 atoms

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

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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: Sun Dec 13 10:45:10 2020

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