Molybdenum in PDB 5vq4: Nitrogenase AV1 at pH 5

All present enzymatic activity of Nitrogenase AV1 at pH 5:
1.18.6.1;

The structure of Nitrogenase AV1 at pH 5, PDB code: 5vq4 was solved by C.N.Morrison, T.Spatzal, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.54 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.315, 128.859, 108.359, 90.00, 110.89, 90.00
R / Rfree (%)	16.8 / 22.2

The structure of Nitrogenase AV1 at pH 5 also contains other interesting chemical elements:

Iron

(Fe)

32 atoms

The binding sites of Molybdenum atom in the Nitrogenase AV1 at pH 5 (pdb code 5vq4). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 2 binding sites of Molybdenum where determined in the Nitrogenase AV1 at pH 5, PDB code: 5vq4:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in the Nitrogenase AV1 at pH 5


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Nitrogenase AV1 at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mo502 b:16.1 occ:1.00 MO1 A:ICS502 0.0 16.1 1.0 O7 A:HCA501 2.1 18.3 1.0 O6 A:HCA501 2.2 18.8 1.0 S4B A:ICS502 2.3 15.5 1.0 S3B A:ICS502 2.3 15.4 1.0 S1B A:ICS502 2.4 14.4 1.0 ND1 A:HIS442 2.4 16.8 1.0 FE7 A:ICS502 2.7 16.2 1.0 FE6 A:ICS502 2.7 17.3 1.0 FE5 A:ICS502 2.7 17.7 1.0 C7 A:HCA501 3.0 19.6 1.0 C3 A:HCA501 3.1 20.5 1.0 CE1 A:HIS442 3.2 19.2 1.0 CG A:HIS442 3.5 18.2 1.0 CX A:ICS502 3.5 16.5 1.0 CB A:HIS442 3.9 16.2 1.0 C2 A:HCA501 4.0 21.1 1.0 O A:HOH629 4.0 18.6 1.0 O2 A:HCA501 4.1 21.9 1.0 C4 A:HCA501 4.2 18.9 1.0 O5 A:HCA501 4.2 15.4 1.0 C5 A:HCA501 4.3 19.4 1.0 NE2 A:HIS442 4.4 16.7 1.0 CD2 A:HIS442 4.6 19.6 1.0 C1 A:HCA501 4.6 23.0 1.0 CA A:HIS442 4.7 15.3 1.0 S2B A:ICS502 4.7 20.2 1.0 S5A A:ICS502 4.8 16.4 1.0 S3A A:ICS502 4.9 17.3 1.0

Molybdenum binding site 2 out of 2 in the Nitrogenase AV1 at pH 5


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Nitrogenase AV1 at pH 5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mo502 b:15.8 occ:1.00 MO1 C:ICS502 0.0 15.8 1.0 O5 C:HCA501 2.2 13.6 1.0 O7 C:HCA501 2.2 13.9 1.0 S4B C:ICS502 2.3 15.6 1.0 S3B C:ICS502 2.3 14.5 1.0 S1B C:ICS502 2.4 14.7 1.0 ND1 C:HIS442 2.5 15.3 1.0 FE6 C:ICS502 2.6 14.6 1.0 FE7 C:ICS502 2.7 14.9 1.0 FE5 C:ICS502 2.7 15.9 1.0 C7 C:HCA501 3.0 14.9 1.0 C3 C:HCA501 3.1 16.6 1.0 CE1 C:HIS442 3.3 15.7 1.0 CG C:HIS442 3.5 15.2 1.0 CX C:ICS502 3.6 14.9 1.0 CB C:HIS442 3.8 15.2 1.0 C2 C:HCA501 4.1 19.5 1.0 O6 C:HCA501 4.2 14.3 1.0 O C:HOH657 4.2 17.2 1.0 C4 C:HCA501 4.2 14.0 1.0 O1 C:HCA501 4.3 20.8 1.0 C5 C:HCA501 4.3 14.5 1.0 NE2 C:HIS442 4.5 15.2 1.0 CD2 C:HIS442 4.6 15.9 1.0 CA C:HIS442 4.7 13.5 1.0 C1 C:HCA501 4.7 21.3 1.0 S2B C:ICS502 4.7 14.7 1.0 S5A C:ICS502 4.8 15.2 1.0 S3A C:ICS502 5.0 15.4 1.0

C.N.Morrison, T.Spatzal, D.C.Rees. Reversible Protonated Resting State of the Nitrogenase Active Site. J. Am. Chem. Soc. V. 139 10856 2017.
ISSN: ESSN 1520-5126
PubMed: 28692802
DOI: 10.1021/JACS.7B05695