Sodium in PDB 6o7s: Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State

All present enzymatic activity of Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State:
1.18.6.1;

The structure of Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State, PDB code: 6o7s was solved by H.L.Rutledge, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.45 / 2.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.775, 128.050, 107.539, 90.00, 108.97, 90.00
R / Rfree (%)	17 / 20.8

The structure of Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State also contains other interesting chemical elements:

Molybdenum	(Mo)	2 atoms
Iron	(Fe)	28 atoms

The binding sites of Sodium atom in the Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State (pdb code 6o7s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State, PDB code: 6o7s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:28.6 occ:1.00 SG A:CYS88 2.4 23.3 1.0 S4B B:LPJ601 2.5 21.8 1.0 S2B B:LPJ601 2.5 21.6 1.0 S1 B:LPJ601 2.5 26.0 1.0 FE4 B:LPJ601 2.7 25.2 1.0 FE8 B:LPJ601 2.7 26.6 0.9 H A:CYS88 2.7 24.6 1.0 FE7 B:LPJ601 2.9 17.5 1.0 FE6 B:LPJ601 3.0 20.4 1.0 N A:CYS88 3.1 20.4 1.0 HA A:CYS88 3.4 27.1 1.0 CB A:CYS88 3.5 24.4 1.0 HA3 A:GLY87 3.5 24.8 1.0 CA A:CYS88 3.6 22.5 1.0 S3A B:LPJ601 3.6 24.8 1.0 HB3 A:CYS88 3.9 29.4 1.0 C A:GLY87 3.9 22.0 1.0 S3B B:LPJ601 4.0 22.9 1.0 CA A:GLY87 4.1 20.6 1.0 HB2 A:CYS88 4.3 29.4 1.0 HE2 A:TYR91 4.3 23.3 1.0 H A:GLY87 4.4 27.6 1.0 FE2 B:LPJ601 4.5 27.2 1.0 HD2 A:TYR91 4.5 25.1 1.0 SG B:CYS95 4.6 22.2 1.0 N A:GLY87 4.6 23.0 1.0 HD2 B:TYR98 4.7 26.5 1.0 HB3 B:CYS95 4.8 27.2 1.0 HB3 A:GLU153 4.8 30.9 1.0 S4A B:LPJ601 4.9 24.8 1.0 HA B:CYS95 4.9 25.2 1.0 O A:GLY87 4.9 22.4 1.0 HB2 A:PRO85 5.0 27.6 1.0 HA2 A:GLY87 5.0 24.8 1.0 SG B:CYS70 5.0 19.8 1.0

Sodium binding site 2 out of 2 in the Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii in the Indigo Carmine Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:24.7 occ:1.00 S2B D:LPJ601 2.4 21.2 1.0 S4B D:LPJ601 2.4 20.4 1.0 SG C:CYS88 2.5 20.2 1.0 FE8 D:LPJ601 2.5 26.0 0.9 S1 D:LPJ601 2.5 23.1 1.0 FE7 D:LPJ601 2.6 17.8 1.0 FE6 D:LPJ601 2.7 19.6 1.0 FE4 D:LPJ601 2.8 22.7 1.0 H C:CYS88 2.9 24.7 1.0 N C:CYS88 3.3 20.5 1.0 HA3 C:GLY87 3.5 22.4 1.0 CB C:CYS88 3.7 21.8 1.0 HA C:CYS88 3.7 22.2 1.0 S3B D:LPJ601 3.7 19.2 1.0 CA C:CYS88 3.8 18.5 1.0 S3A D:LPJ601 3.8 25.0 1.0 C C:GLY87 4.1 19.5 1.0 HB3 C:CYS88 4.1 26.3 1.0 CA C:GLY87 4.2 18.6 1.0 H C:GLY87 4.4 23.6 1.0 HE2 C:TYR91 4.4 20.7 1.0 HB2 C:CYS88 4.5 26.3 1.0 SG D:CYS95 4.5 23.8 1.0 FE2 D:LPJ601 4.6 23.4 1.0 N C:GLY87 4.6 19.6 1.0 HB3 D:CYS95 4.7 24.4 1.0 HD2 C:TYR91 4.8 21.9 1.0 SG D:CYS70 4.8 18.3 1.0 HB2 C:PRO85 4.8 24.7 1.0 HB3 C:GLU153 4.8 25.5 1.0 SG D:CYS153 4.8 23.1 1.0 HD2 C:PRO85 4.9 26.5 1.0 S4A D:LPJ601 4.9 21.0 1.0 HA D:CYS95 5.0 25.8 1.0 HA2 C:GLY87 5.0 22.4 1.0

H.L.Rutledge, J.Rittle, L.M.Williamson, W.A.Xu, D.M.Gagnon, F.A.Tezcan. Redox-Dependent Metastability of the Nitrogenase P-Cluster. J.Am.Chem.Soc. V. 141 10091 2019.
ISSN: ESSN 1520-5126
PubMed: 31146522
DOI: 10.1021/JACS.9B04555