Sodium in PDB 8e3u: Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation

All present enzymatic activity of Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation:
1.18.6.1;

The structure of Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation, PDB code: 8e3u 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)	79.89 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.259, 129.009, 107.76, 90, 109.22, 90
R / Rfree (%)	20.2 / 25.3

The structure of Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation also contains other interesting chemical elements:

Iron	(Fe)	30 atoms
Molybdenum	(Mo)	2 atoms

The binding sites of Sodium atom in the Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation (pdb code 8e3u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation, PDB code: 8e3u:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:25.5 occ:0.70 S3A A:UFF601 2.1 40.5 1.0 SG B:CYS95 2.2 29.0 1.0 FE8 A:UFF601 2.4 34.5 0.8 S1 A:UFF601 2.4 32.6 1.0 FE4 A:UFF601 2.5 31.6 0.7 S2A A:UFF601 2.8 34.8 1.0 HA B:CYS95 3.0 39.3 1.0 FE2 A:UFF601 3.0 33.4 0.7 FE3 A:UFF601 3.1 32.2 0.8 FE5 A:UFF601 3.1 32.5 0.5 H B:CYS95 3.2 31.3 1.0 N B:CYS95 3.3 26.1 1.0 CB B:CYS95 3.4 36.4 1.0 CA B:CYS95 3.4 32.8 1.0 S4B A:UFF601 3.5 29.4 1.0 HB3 B:CYS95 3.8 43.7 1.0 HD2 B:TYR98 4.1 29.6 1.0 C B:GLY94 4.1 32.3 1.0 SG A:CYS88 4.2 29.2 1.0 S4A A:UFF601 4.2 27.8 1.0 HB2 B:CYS95 4.2 43.7 1.0 HA3 B:GLY94 4.3 41.3 1.0 HG B:SER92 4.3 61.4 1.0 FE6 A:UFF601 4.5 30.9 1.0 S3B A:UFF601 4.5 31.3 1.0 OG B:SER92 4.7 51.2 1.0 SG A:CYS62 4.7 36.2 1.0 HB B:THR152 4.7 35.7 1.0 S2B A:UFF601 4.7 24.5 1.0 CA B:GLY94 4.8 34.4 1.0 HE2 B:TYR98 4.8 40.6 1.0 O B:GLY94 4.8 30.4 1.0 HB3 A:CYS88 4.9 38.5 1.0 C B:CYS95 4.9 33.6 1.0 HG A:CYS62 4.9 43.5 1.0 CD2 B:TYR98 4.9 24.7 1.0 FE7 A:UFF601 5.0 29.1 1.0 HA A:CYS88 5.0 44.9 1.0

Sodium binding site 2 out of 2 in the Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Nickel-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:27.6 occ:0.75 S3A C:UFF601 2.2 34.9 1.0 S1 C:UFF601 2.2 35.8 1.0 SG D:CYS95 2.3 28.6 1.0 FE8 C:UFF601 2.5 34.8 0.8 FE4 C:UFF601 2.5 34.2 0.8 S2A C:UFF601 2.6 32.7 1.0 FE2 C:UFF601 2.6 36.2 0.7 FE3 C:UFF601 2.8 32.5 0.8 HA D:CYS95 3.1 33.9 1.0 H D:CYS95 3.1 39.0 1.0 N D:CYS95 3.3 32.5 1.0 CB D:CYS95 3.4 34.7 1.0 CA D:CYS95 3.4 28.2 1.0 S4B C:UFF601 3.7 32.7 1.0 HB3 D:CYS95 3.8 41.6 1.0 S4A C:UFF601 3.8 28.8 1.0 FE5 C:UFF601 3.9 40.4 0.7 HG D:SER92 4.0 47.7 1.0 C D:GLY94 4.0 32.2 1.0 HA3 D:GLY94 4.1 38.1 1.0 HD2 D:TYR98 4.2 38.0 1.0 HB2 D:CYS95 4.3 41.6 1.0 O D:HOH708 4.3 29.4 1.0 OG D:SER92 4.4 39.8 1.0 FE6 C:UFF601 4.4 31.8 1.0 SG C:CYS88 4.4 35.7 1.0 SG C:CYS154 4.6 40.5 1.0 CA D:GLY94 4.6 31.8 1.0 HB D:THR152 4.6 39.5 1.0 SG C:CYS62 4.7 40.1 1.0 S3B C:UFF601 4.7 36.7 1.0 HB2 D:SER92 4.7 45.0 1.0 O D:GLY94 4.7 27.2 1.0 HA3 C:GLY185 4.9 52.9 1.0 C D:CYS95 4.9 34.0 1.0 HB3 C:CYS88 5.0 46.8 1.0

H.L.Rutledge, M.J.Field, J.Rittle, M.T.Green, F.A.Tezcan. Role of Serine Coordination in the Structural and Functional Protection of the Nitrogenase P-Cluster. J.Am.Chem.Soc. V. 144 22101 2022.
ISSN: ESSN 1520-5126
PubMed: 36445204
DOI: 10.1021/JACS.2C09480