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: Tue Jul 30 17:19:02 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy