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Vanadium in PDB 5n6y: Azotobacter Vinelandii Vanadium Nitrogenase

Enzymatic activity of Azotobacter Vinelandii Vanadium Nitrogenase

All present enzymatic activity of Azotobacter Vinelandii Vanadium Nitrogenase:
1.18.6.1;

Protein crystallography data

The structure of Azotobacter Vinelandii Vanadium Nitrogenase, PDB code: 5n6y was solved by D.Sippel, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 102.04 / 1.35
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.250, 79.790, 106.970, 84.06, 72.62, 75.15
R / Rfree (%) 10.9 / 14.6

Other elements in 5n6y:

The structure of Azotobacter Vinelandii Vanadium Nitrogenase also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Iron (Fe) 30 atoms

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Azotobacter Vinelandii Vanadium Nitrogenase (pdb code 5n6y). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Azotobacter Vinelandii Vanadium Nitrogenase, PDB code: 5n6y:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 5n6y

Go back to Vanadium Binding Sites List in 5n6y
Vanadium binding site 1 out of 2 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V502

b:10.2
occ:1.00
V1 A:8P8502 0.0 10.2 1.0
O5 A:HCA501 2.1 8.9 1.0
O7 A:HCA501 2.2 10.4 1.0
ND1 A:HIS423 2.3 10.3 1.0
S4B A:8P8502 2.3 10.4 1.0
S3B A:8P8502 2.3 11.2 1.0
S1B A:8P8502 2.3 10.2 1.0
FE5 A:8P8502 2.7 10.4 1.0
FE7 A:8P8502 2.7 10.5 1.0
FE6 A:8P8502 2.8 10.6 1.0
C7 A:HCA501 3.0 8.7 1.0
C3 A:HCA501 3.1 10.0 1.0
CE1 A:HIS423 3.2 9.8 1.0
CG A:HIS423 3.4 9.4 1.0
C1 A:8P8502 3.6 10.8 1.0
CB A:HIS423 3.8 9.2 1.0
C2 A:HCA501 4.0 11.1 1.0
O A:HOH760 4.2 12.5 1.0
O6 A:HCA501 4.2 12.5 1.0
C4 A:HCA501 4.2 11.5 1.0
O2 A:CO3503 4.3 11.0 1.0
O1 A:HCA501 4.4 13.1 1.0
C5 A:HCA501 4.4 12.4 1.0
NE2 A:HIS423 4.4 11.3 1.0
CD2 A:HIS423 4.5 11.9 1.0
CA A:HIS423 4.5 9.6 1.0
NZ A:LYS83 4.7 14.5 1.0
C1 A:HCA501 4.7 11.4 1.0
S2B A:8P8502 4.9 14.3 1.0
S5A A:8P8502 4.9 10.9 1.0

Vanadium binding site 2 out of 2 in 5n6y

Go back to Vanadium Binding Sites List in 5n6y
Vanadium binding site 2 out of 2 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:V502

b:9.0
occ:1.00
V1 D:8P8502 0.0 9.0 1.0
O6 D:HCA501 2.1 8.6 1.0
O7 D:HCA501 2.2 8.7 1.0
ND1 D:HIS423 2.3 9.2 1.0
S4B D:8P8502 2.3 9.4 1.0
S1B D:8P8502 2.3 9.5 1.0
S3B D:8P8502 2.4 10.1 1.0
FE5 D:8P8502 2.7 9.2 1.0
FE7 D:8P8502 2.7 9.3 1.0
FE6 D:8P8502 2.8 9.5 1.0
C7 D:HCA501 2.9 9.5 1.0
C3 D:HCA501 3.1 7.9 1.0
CE1 D:HIS423 3.2 9.5 1.0
CG D:HIS423 3.4 8.8 1.0
C1 D:8P8502 3.6 9.2 1.0
CB D:HIS423 3.8 8.3 1.0
C2 D:HCA501 4.0 9.7 1.0
O5 D:HCA501 4.2 10.6 1.0
O D:HOH820 4.2 11.8 1.0
C4 D:HCA501 4.3 8.4 1.0
O1 D:CO3503 4.3 10.2 1.0
O2 D:HCA501 4.3 10.9 1.0
C5 D:HCA501 4.3 10.5 1.0
NE2 D:HIS423 4.4 9.9 1.0
CD2 D:HIS423 4.5 9.6 1.0
CA D:HIS423 4.6 9.5 1.0
NZ D:LYS83 4.7 13.6 1.0
C1 D:HCA501 4.8 9.4 1.0
S2B D:8P8502 4.9 12.5 1.0
S5A D:8P8502 4.9 10.1 1.0

Reference:

D.Sippel, O.Einsle. The Structure of Vanadium Nitrogenase Reveals An Unusual Bridging Ligand. Nat. Chem. Biol. V. 13 956 2017.
ISSN: ESSN 1552-4469
PubMed: 28692069
DOI: 10.1038/NCHEMBIO.2428
Page generated: Thu Oct 29 07:05:59 2020

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