Vanadium in PDB 5n6y: Azotobacter Vinelandii Vanadium Nitrogenase

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

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

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

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

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 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 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

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