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Cobalt in PDB 4ns3: Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis Bound with Nad and Cobalamin

Enzymatic activity of Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis Bound with Nad and Cobalamin

All present enzymatic activity of Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis Bound with Nad and Cobalamin:
1.5.1.12;

Protein crystallography data

The structure of Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis Bound with Nad and Cobalamin, PDB code: 4ns3 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) 20.05 / 2.38
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.855, 164.855, 260.242, 90.00, 90.00, 120.00
R / Rfree (%) 15.7 / 20.5

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis Bound with Nad and Cobalamin (pdb code 4ns3). 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 Bound with Nad and Cobalamin, PDB code: 4ns3:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 4ns3

Go back to Cobalt Binding Sites List in 4ns3
Cobalt binding site 1 out of 4 in the Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis Bound with Nad and Cobalamin


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 Bound with Nad and Cobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co601

b:21.8
occ:1.00
 CO A:B12601 0.0 21.8 1.0
N24 A:B12601 1.9 21.6 1.0
N21 A:B12601 1.9 19.1 1.0
N23 A:B12601 1.9 20.8 1.0
N22 A:B12601 1.9 19.3 1.0
N3B A:B12601 2.4 17.0 1.0
C19 A:B12601 2.7 16.9 1.0
C1 A:B12601 2.9 17.1 1.0
C4 A:B12601 2.9 18.4 1.0
C9 A:B12601 2.9 17.8 1.0
C11 A:B12601 2.9 17.2 1.0
C14 A:B12601 2.9 18.1 1.0
C6 A:B12601 2.9 17.7 1.0
C16 A:B12601 3.0 17.6 1.0
C2B A:B12601 3.2 17.6 1.0
C10 A:B12601 3.2 17.9 1.0
C5 A:B12601 3.3 16.8 1.0
C9B A:B12601 3.4 17.6 1.0
C15 A:B12601 3.4 18.9 1.0
C20 A:B12601 3.7 14.7 1.0
C4B A:B12601 3.9 17.2 1.0
C2 A:B12601 4.0 19.2 1.0
C18 A:B12601 4.1 16.8 1.0
C3 A:B12601 4.1 20.7 1.0
C13 A:B12601 4.2 17.3 1.0
O A:HOH823 4.2 21.5 1.0
C8 A:B12601 4.2 16.6 1.0
C7 A:B12601 4.2 17.7 1.0
C17 A:B12601 4.2 18.1 1.0
N29 A:B12601 4.2 14.7 1.0
O39 A:B12601 4.3 16.6 1.0
C12 A:B12601 4.3 19.9 1.0
C27 A:B12601 4.4 16.5 1.0
N1B A:B12601 4.4 18.6 1.0
C8B A:B12601 4.6 19.8 1.0
C26 A:B12601 4.6 19.0 1.0
C38 A:B12601 4.7 17.3 1.0
C35 A:B12601 4.8 18.7 1.0
O28 A:B12601 4.9 19.2 1.0
C53 A:B12601 4.9 15.7 1.0
C41 A:B12601 4.9 16.5 1.0
C54 A:B12601 5.0 14.3 1.0
C37 A:B12601 5.0 18.3 1.0

Cobalt binding site 2 out of 4 in 4ns3

Go back to Cobalt Binding Sites List in 4ns3
Cobalt binding site 2 out of 4 in the Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis Bound with Nad and Cobalamin


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 Bound with Nad and Cobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co601

b:20.6
occ:1.00
 CO B:B12601 0.0 20.6 1.0
N24 B:B12601 1.9 20.5 1.0
N21 B:B12601 1.9 23.2 1.0
N22 B:B12601 1.9 21.3 1.0
N23 B:B12601 1.9 25.1 1.0
N3B B:B12601 2.4 19.3 1.0
C19 B:B12601 2.7 20.2 1.0
O B:HOH794 2.8 22.3 1.0
C4 B:B12601 2.8 21.1 1.0
C1 B:B12601 2.8 21.4 1.0
C9 B:B12601 2.9 21.7 1.0
C11 B:B12601 2.9 23.4 1.0
C14 B:B12601 2.9 21.9 1.0
C6 B:B12601 2.9 20.7 1.0
C16 B:B12601 3.0 22.0 1.0
C10 B:B12601 3.3 21.1 1.0
C5 B:B12601 3.3 23.9 1.0
C2B B:B12601 3.3 19.8 1.0
C15 B:B12601 3.4 23.0 1.0
C9B B:B12601 3.5 21.0 1.0
C20 B:B12601 3.7 18.8 1.0
O39 B:B12601 3.9 26.5 1.0
C2 B:B12601 4.0 19.4 1.0
C4B B:B12601 4.0 21.1 1.0
C3 B:B12601 4.1 20.7 1.0
C18 B:B12601 4.1 20.7 1.0
C13 B:B12601 4.2 21.2 1.0
C7 B:B12601 4.2 19.4 1.0
C8 B:B12601 4.2 20.1 1.0
C17 B:B12601 4.2 21.8 1.0
O B:HOH1144 4.2 31.0 1.0
C12 B:B12601 4.3 24.6 1.0
C26 B:B12601 4.5 20.9 1.0
O B:HOH750 4.5 19.4 1.0
N1B B:B12601 4.5 20.3 1.0
C38 B:B12601 4.6 25.8 1.0
C8B B:B12601 4.7 22.4 1.0
C35 B:B12601 4.7 21.9 1.0
C37 B:B12601 4.8 22.0 1.0
C53 B:B12601 4.9 20.6 1.0
C54 B:B12601 4.9 19.6 1.0
C41 B:B12601 4.9 18.9 1.0
C48 B:B12601 5.0 20.5 1.0

Cobalt binding site 3 out of 4 in 4ns3

Go back to Cobalt Binding Sites List in 4ns3
Cobalt binding site 3 out of 4 in the Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis Bound with Nad and Cobalamin


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 Bound with Nad and Cobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co601

b:44.5
occ:1.00
 CO C:B12601 0.0 44.5 1.0
N24 C:B12601 1.9 49.1 1.0
N21 C:B12601 1.9 57.4 1.0
N23 C:B12601 1.9 56.3 1.0
N22 C:B12601 1.9 58.2 1.0
N3B C:B12601 2.4 46.4 1.0
C19 C:B12601 2.7 49.0 1.0
C4 C:B12601 2.8 54.9 1.0
C1 C:B12601 2.9 51.5 1.0
C14 C:B12601 2.9 53.5 1.0
C9 C:B12601 2.9 57.6 1.0
C11 C:B12601 2.9 54.4 1.0
C6 C:B12601 2.9 59.7 1.0
C16 C:B12601 3.0 48.0 1.0
C10 C:B12601 3.3 56.2 1.0
C5 C:B12601 3.3 56.2 1.0
C2B C:B12601 3.3 45.2 1.0
C15 C:B12601 3.3 52.3 1.0
C9B C:B12601 3.4 49.2 1.0
C20 C:B12601 3.8 41.0 1.0
C4B C:B12601 3.8 48.2 1.0
C2 C:B12601 3.9 52.6 1.0
C3 C:B12601 4.0 51.4 1.0
C13 C:B12601 4.1 53.6 1.0
C18 C:B12601 4.1 46.3 1.0
C26 C:B12601 4.1 55.7 1.0
C17 C:B12601 4.2 46.8 1.0
C8 C:B12601 4.2 59.8 1.0
C7 C:B12601 4.2 59.9 1.0
C12 C:B12601 4.3 53.2 1.0
N1B C:B12601 4.5 43.8 1.0
C38 C:B12601 4.5 64.5 1.0
O39 C:B12601 4.6 62.7 1.0
C8B C:B12601 4.6 48.9 1.0
N40 C:B12601 4.6 67.9 1.0
C35 C:B12601 4.7 57.8 1.0
C48 C:B12601 4.7 50.0 1.0
C53 C:B12601 4.8 50.5 1.0
C42 C:B12601 4.9 58.3 1.0
C54 C:B12601 4.9 46.6 1.0
C37 C:B12601 5.0 60.0 1.0

Cobalt binding site 4 out of 4 in 4ns3

Go back to Cobalt Binding Sites List in 4ns3
Cobalt binding site 4 out of 4 in the Crystal Structure of the Delta-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis Bound with Nad and Cobalamin


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 Bound with Nad and Cobalamin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co601

b:18.7
occ:1.00
 CO D:B12601 0.0 18.7 1.0
N24 D:B12601 1.9 26.7 1.0
N21 D:B12601 1.9 30.5 1.0
N22 D:B12601 1.9 33.5 1.0
N23 D:B12601 1.9 31.4 1.0
N3B D:B12601 2.4 24.9 1.0
C19 D:B12601 2.7 20.7 1.0
C1 D:B12601 2.8 21.5 1.0
C4 D:B12601 2.9 20.9 1.0
C9 D:B12601 2.9 24.7 1.0
C14 D:B12601 2.9 22.3 1.0
C11 D:B12601 2.9 26.2 1.0
C6 D:B12601 2.9 21.5 1.0
C16 D:B12601 3.0 23.4 1.0
C10 D:B12601 3.2 25.7 1.0
C2B D:B12601 3.3 24.2 1.0
C5 D:B12601 3.3 20.3 1.0
C15 D:B12601 3.4 21.9 1.0
C9B D:B12601 3.4 23.2 1.0
C20 D:B12601 3.7 19.7 1.0
C4B D:B12601 4.0 21.1 1.0
C2 D:B12601 4.0 23.0 1.0
C18 D:B12601 4.1 21.7 1.0
C3 D:B12601 4.1 21.8 1.0
C13 D:B12601 4.1 25.1 1.0
C8 D:B12601 4.2 23.0 1.0
C17 D:B12601 4.2 22.7 1.0
C7 D:B12601 4.2 23.9 1.0
C12 D:B12601 4.3 28.8 1.0
N29 D:B12601 4.4 17.4 1.0
C27 D:B12601 4.5 19.6 1.0
N1B D:B12601 4.5 24.1 1.0
O39 D:B12601 4.5 26.1 1.0
C8B D:B12601 4.6 24.1 1.0
C26 D:B12601 4.6 22.4 1.0
O D:HOH845 4.8 29.3 1.0
C35 D:B12601 4.8 22.1 1.0
C41 D:B12601 4.9 25.8 1.0
C53 D:B12601 4.9 23.5 1.0
C38 D:B12601 4.9 26.7 1.0
O28 D:B12601 4.9 21.1 1.0
C48 D:B12601 4.9 26.5 1.0

Reference:

T.Lagautriere, G.Bashiri, E.N.Baker. Use of A "Silver Bullet" to Resolve Crystal Lattice Dislocation Disorder: A Cobalamin Complex of Delta (1)-Pyrroline-5-Carboxylate Dehydrogenase From Mycobacterium Tuberculosis. J.Struct.Biol. 2014.
ISSN: ESSN 1095-8657
PubMed: 25557497
DOI: 10.1016/J.JSB.2014.12.007
Page generated: Tue Jul 30 17:23:23 2024

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