Sodium in PDB 8e3t: Gallium-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation

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

The structure of Gallium-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation, PDB code: 8e3t 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)	54.13 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.607, 127.968, 107.269, 90, 108.85, 90
R / Rfree (%)	22.3 / 24.3

The structure of Gallium-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 Gallium-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation (pdb code 8e3t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Gallium-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation, PDB code: 8e3t:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Gallium-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 Gallium-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:28.8 occ:0.99 S3A B:UFF601 2.2 28.0 1.0 S2A B:UFF601 2.4 27.6 1.0 SG B:CYS95 2.4 24.0 1.0 S1 B:UFF601 2.6 29.8 1.0 FE4 B:UFF601 2.6 27.7 0.9 FE2 B:UFF601 2.7 28.0 0.9 FE3 B:UFF601 2.8 27.0 1.0 FE8 B:UFF601 2.9 30.0 1.0 H B:CYS95 2.9 31.5 1.0 N B:CYS95 3.1 26.2 1.0 HA B:CYS95 3.1 29.3 1.0 CB B:CYS95 3.4 26.2 1.0 CA B:CYS95 3.4 24.4 1.0 HG B:SER92 3.4 39.3 1.0 S4B B:UFF601 3.7 27.4 1.0 HB3 B:CYS95 3.7 31.5 1.0 FE5 B:UFF601 3.8 30.7 0.5 C B:GLY94 3.8 26.5 1.0 S4A B:UFF601 3.9 29.2 1.0 HA3 B:GLY94 4.0 33.5 1.0 O B:HOH957 4.1 30.0 1.0 OG B:SER92 4.1 32.7 1.0 HB2 B:CYS95 4.2 31.5 1.0 HD2 B:TYR98 4.3 30.0 1.0 CA B:GLY94 4.4 27.9 1.0 O B:GLY94 4.5 25.0 1.0 SG A:CYS88 4.7 27.8 1.0 HB B:THR152 4.7 33.7 1.0 HB2 B:SER92 4.7 36.2 1.0 H B:GLY94 4.7 34.0 1.0 HB3 A:CYS62 4.7 35.7 1.0 HA3 A:GLY185 4.8 38.4 1.0 N B:GLY94 4.8 28.3 1.0 SG A:CYS154 4.9 28.1 1.0 C B:CYS95 4.9 24.1 1.0 SG A:CYS62 4.9 30.9 1.0 S3B B:UFF601 4.9 25.6 1.0 HG B:CYS153 5.0 32.0 1.0

Sodium binding site 2 out of 2 in the Gallium-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 Gallium-Reconstituted Nitrogenase Mofep Mutant S188A From Azotobacter Vinelandii After Ids Oxidation within 5.0Å range: probe atom residue distance (Å) B Occ D:Na603 b:29.0 occ:1.00 S3A D:UFF601 2.4 28.3 1.0 SG D:CYS95 2.4 23.9 1.0 S2A D:UFF601 2.5 28.1 1.0 S1 D:UFF601 2.5 28.7 1.0 FE4 D:UFF601 2.7 25.4 0.8 FE2 D:UFF601 2.8 26.1 0.8 FE8 D:UFF601 2.8 27.6 0.9 H D:CYS95 3.0 29.0 1.0 FE3 D:UFF601 3.0 27.6 0.9 HA D:CYS95 3.1 28.5 1.0 N D:CYS95 3.2 24.1 1.0 CB D:CYS95 3.4 24.4 1.0 CA D:CYS95 3.4 23.8 1.0 HG D:SER92 3.6 40.9 1.0 HB3 D:CYS95 3.7 29.3 1.0 FE5 D:UFF601 3.8 27.0 0.6 S4B D:UFF601 3.8 24.6 1.0 C D:GLY94 3.9 24.6 1.0 O D:HOH920 4.0 30.5 1.0 S4A D:UFF601 4.0 30.2 1.0 HA3 D:GLY94 4.1 31.5 1.0 OG D:SER92 4.1 34.0 1.0 HB2 D:CYS95 4.2 29.3 1.0 HD2 D:TYR98 4.3 27.9 1.0 CA D:GLY94 4.5 26.2 1.0 FE6 D:UFF601 4.5 27.9 1.0 O D:GLY94 4.5 22.4 1.0 HB2 D:SER92 4.7 35.0 1.0 HB D:THR152 4.7 32.8 1.0 O D:HOH735 4.7 31.9 1.0 SG C:CYS88 4.8 28.0 1.0 H D:GLY94 4.8 31.4 1.0 HB3 C:CYS62 4.9 35.4 1.0 HA3 C:GLY185 4.9 39.5 1.0 N D:GLY94 4.9 26.2 1.0 SG C:CYS154 4.9 30.4 1.0 O D:SER92 4.9 26.1 1.0 C D:CYS95 4.9 22.8 1.0 SG C:CYS62 4.9 27.6 1.0 HG D:CYS153 4.9 36.4 1.0 S3B D:UFF601 5.0 22.1 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