Atomistry » Cobalt » PDB 4j2m-4ngl » 4lem
Atomistry »
  Cobalt »
    PDB 4j2m-4ngl »
      4lem »

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

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: Sun Dec 13 10:45:10 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy