Molybdenum in PDB 5vq3: Nitrogenase CP1 at pH 6.5

All present enzymatic activity of Nitrogenase CP1 at pH 6.5:
1.18.6.1;

The structure of Nitrogenase CP1 at pH 6.5, PDB code: 5vq3 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)	40.00 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.477, 147.963, 116.694, 90.00, 103.51, 90.00
R / Rfree (%)	15.9 / 18.5

The structure of Nitrogenase CP1 at pH 6.5 also contains other interesting chemical elements:

Iron

(Fe)

32 atoms

The binding sites of Molybdenum atom in the Nitrogenase CP1 at pH 6.5 (pdb code 5vq3). 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 CP1 at pH 6.5, PDB code: 5vq3:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Nitrogenase CP1 at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mo602 b:18.5 occ:1.00 MO1 A:ICS602 0.0 18.5 1.0 O7 A:HCA601 2.1 18.1 1.0 O6 A:HCA601 2.2 17.8 1.0 S4B A:ICS602 2.4 18.8 1.0 S1B A:ICS602 2.4 19.6 1.0 ND1 A:HIS482 2.4 22.2 1.0 S3B A:ICS602 2.4 19.5 1.0 FE7 A:ICS602 2.7 19.4 1.0 FE5 A:ICS602 2.7 18.5 1.0 FE6 A:ICS602 2.7 18.9 1.0 C7 A:HCA601 3.0 18.7 1.0 C3 A:HCA601 3.1 19.2 1.0 CE1 A:HIS482 3.2 22.0 1.0 CG A:HIS482 3.4 17.0 1.0 CX A:ICS602 3.5 19.6 1.0 CB A:HIS482 3.8 17.7 1.0 C2 A:HCA601 4.0 21.1 1.0 O2 A:HCA601 4.1 21.1 1.0 O A:HOH797 4.2 20.8 1.0 O5 A:HCA601 4.2 20.0 1.0 C4 A:HCA601 4.2 20.5 1.0 C5 A:HCA601 4.2 21.3 1.0 NE2 A:HIS482 4.4 22.8 1.0 CD2 A:HIS482 4.5 20.3 1.0 C1 A:HCA601 4.6 22.9 1.0 CA A:HIS482 4.7 16.9 1.0 S5A A:ICS602 4.8 21.7 1.0 S2B A:ICS602 4.8 19.7 1.0 S3A A:ICS602 4.8 19.7 1.0

Molybdenum binding site 2 out of 2 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Nitrogenase CP1 at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mo602 b:16.9 occ:1.00 MO1 C:ICS602 0.0 16.9 1.0 O7 C:HCA601 2.2 16.2 1.0 O5 C:HCA601 2.2 14.5 1.0 S4B C:ICS602 2.3 17.0 1.0 S1B C:ICS602 2.3 18.5 1.0 ND1 C:HIS482 2.3 18.0 1.0 S3B C:ICS602 2.4 17.0 1.0 FE5 C:ICS602 2.7 17.6 1.0 FE7 C:ICS602 2.7 18.1 1.0 FE6 C:ICS602 2.7 17.6 1.0 C7 C:HCA601 3.0 15.7 1.0 C3 C:HCA601 3.1 17.2 1.0 CE1 C:HIS482 3.2 18.0 1.0 CG C:HIS482 3.4 15.8 1.0 CX C:ICS602 3.5 18.9 1.0 CB C:HIS482 3.8 16.4 1.0 C2 C:HCA601 4.0 18.8 1.0 O C:HOH825 4.2 19.8 1.0 O1 C:HCA601 4.2 22.3 1.0 C5 C:HCA601 4.2 18.8 1.0 C4 C:HCA601 4.2 17.6 1.0 O6 C:HCA601 4.2 17.2 1.0 NE2 C:HIS482 4.4 18.7 1.0 CD2 C:HIS482 4.5 17.6 1.0 C1 C:HCA601 4.6 22.3 1.0 CA C:HIS482 4.7 15.3 1.0 S5A C:ICS602 4.8 18.9 1.0 S2B C:ICS602 4.8 18.9 1.0 S3A C:ICS602 4.8 19.2 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