Sodium in PDB 6r7p: Crystal Structure of Oxidized Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M

The structure of Crystal Structure of Oxidized Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M, PDB code: 6r7p was solved by D.Wohlwend, E.Gnandt, T.Friedrich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.73 / 3.22
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.410, 114.640, 187.870, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.7

The structure of Crystal Structure of Oxidized Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M also contains other interesting chemical elements:

Iron	(Fe)	12 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Oxidized Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M (pdb code 6r7p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Oxidized Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M, PDB code: 6r7p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Oxidized Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Oxidized Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M within 5.0Å range: probe atom residue distance (Å) B Occ B:Na506 b:76.9 occ:1.00 OD1 B:ASP94 2.7 59.4 1.0 O B:HOH622 2.7 54.9 1.0 O B:ALA179 2.8 65.2 1.0 CA B:GLY176 3.6 48.4 1.0 CG B:ASP94 3.6 58.6 1.0 CB B:CYS182 3.6 73.1 1.0 N B:ALA179 3.7 64.3 1.0 C B:ALA179 3.8 66.5 1.0 OD2 B:ASP94 3.9 59.8 1.0 N B:ALA177 4.0 53.3 1.0 N B:GLY178 4.0 58.3 1.0 CE1 B:TYR133 4.1 45.2 1.0 OH B:TYR133 4.1 48.5 1.0 SG B:CYS182 4.3 76.0 1.0 C B:GLY176 4.3 50.7 1.0 CA B:ALA179 4.3 67.3 1.0 SD B:MET96 4.4 74.3 1.0 CA B:ARG135 4.5 43.0 1.0 CB B:ARG135 4.5 43.1 1.0 CA B:GLY178 4.6 60.5 1.0 C B:GLY178 4.6 63.1 1.0 CZ B:TYR133 4.6 46.7 1.0 N B:GLY176 4.7 46.4 1.0 CB B:ALA179 4.8 69.2 1.0 CG B:MET96 4.8 71.8 1.0 N B:TYR180 4.9 68.5 1.0 CA B:CYS182 4.9 73.2 1.0 CB B:ASP94 4.9 57.0 1.0 C B:ALA177 4.9 58.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Oxidized Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Oxidized Aquifex Aeolicus Nadh-Quinone Oxidoreductase Subunits Nuoe and Nuof S96M within 5.0Å range: probe atom residue distance (Å) B Occ D:Na504 b:69.7 occ:1.00 OD1 D:ASP94 2.6 51.9 1.0 O D:ALA179 2.7 61.9 1.0 O D:HOH608 2.9 30.6 1.0 CG D:ASP94 3.5 51.3 1.0 N D:ALA179 3.6 62.0 1.0 C D:ALA179 3.7 63.8 1.0 OD2 D:ASP94 3.7 53.2 1.0 CA D:GLY176 3.8 48.9 1.0 N D:GLY178 3.9 57.2 1.0 CB D:CYS182 3.9 71.1 1.0 N D:ALA177 4.0 53.8 1.0 SD D:MET96 4.1 66.3 1.0 OH D:TYR133 4.2 48.5 1.0 CA D:ALA179 4.2 64.7 1.0 CE1 D:TYR133 4.2 44.4 1.0 CA D:GLY178 4.3 58.8 1.0 C D:GLY178 4.3 61.1 1.0 CG D:MET96 4.3 63.2 1.0 SG D:CYS182 4.4 74.9 1.0 C D:GLY176 4.4 51.5 1.0 CA D:ARG135 4.5 41.5 1.0 CB D:ARG135 4.5 42.0 1.0 CB D:ALA179 4.6 66.3 1.0 CZ D:TYR133 4.7 46.1 1.0 C D:ALA177 4.8 58.4 1.0 N D:TYR180 4.8 66.6 1.0 CB D:ASP94 4.9 49.3 1.0 N D:GLY176 4.9 46.4 1.0

M.Schulte, K.Frick, E.Gnandt, S.Jurkovic, S.Burschel, R.Labatzke, K.Aierstock, D.Fiegen, D.Wohlwend, S.Gerhardt, O.Einsle, T.Friedrich. A Mechanism to Prevent Production of Reactive Oxygen Species By Escherichia Coli Respiratory Complex I. Nat Commun V. 10 2551 2019.
ISSN: ESSN 2041-1723
PubMed: 31186428
DOI: 10.1038/S41467-019-10429-0