Sodium in PDB 6hl3: Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+

All present enzymatic activity of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+:
1.6.5.11;

The structure of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+, PDB code: 6hl3 was solved by S.Gerhardt, T.Friedrich, O.Einsle, E.Gnandt, M.Schulte, D.Fiegen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.35 / 2.04
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.514, 115.759, 189.635, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.3

The structure of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ also contains other interesting chemical elements:

Iron	(Fe)	12 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ (pdb code 6hl3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+, PDB code: 6hl3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:35.6 occ:1.00 OD1 B:ASP94 2.5 25.1 1.0 O B:ALA179 2.6 28.1 1.0 O B:HOH698 2.8 20.7 1.0 O B:HOH681 2.8 17.8 1.0 O B:HOH603 2.9 29.8 1.0 OD2 B:ASP94 3.2 31.3 1.0 CG B:ASP94 3.2 25.3 1.0 C B:ALA179 3.5 27.8 1.0 N B:ALA179 3.7 27.3 1.0 CB B:CYS182 3.9 23.0 1.0 CA B:ALA179 4.1 26.3 1.0 CA B:GLY176 4.2 19.6 1.0 CB B:ARG135 4.2 15.8 1.0 CA B:ARG135 4.3 19.0 1.0 N B:GLY178 4.3 26.3 1.0 CE1 B:TYR133 4.4 22.0 1.0 N B:ALA177 4.4 23.7 1.0 C B:GLY178 4.4 31.7 1.0 N B:TYR180 4.5 22.9 1.0 OH B:TYR133 4.6 28.0 1.0 CB B:ASP94 4.6 20.7 1.0 C B:GLY176 4.7 25.5 1.0 CB B:ALA179 4.7 27.3 1.0 O B:HOH723 4.8 34.9 1.0 CA B:GLY178 4.8 26.9 1.0 CA B:TYR180 4.8 21.5 1.0 CA B:CYS182 4.8 22.1 1.0 OG B:SER96 4.9 30.9 1.0 N B:GLY136 4.9 21.1 1.0 CZ B:TYR133 5.0 27.1 1.0 SG B:CYS182 5.0 27.8 1.0 N B:CYS182 5.0 21.8 1.0

Sodium binding site 2 out of 2 in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form Bound to Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Na504 b:37.6 occ:1.00 OD1 D:ASP94 2.4 25.3 1.0 O D:HOH700 2.6 27.9 1.0 O D:ALA179 2.6 30.0 1.0 O D:HOH698 2.8 22.2 1.0 O D:HOH616 3.0 36.5 1.0 CG D:ASP94 3.2 26.8 1.0 OD2 D:ASP94 3.2 31.8 1.0 C D:ALA179 3.5 29.9 1.0 N D:ALA179 3.7 27.8 1.0 CB D:CYS182 3.9 23.5 1.0 CA D:ALA179 4.1 27.4 1.0 CA D:GLY176 4.1 21.2 1.0 CB D:ARG135 4.3 18.8 1.0 CA D:ARG135 4.3 20.4 1.0 CE1 D:TYR133 4.3 25.4 1.0 N D:ALA177 4.3 26.0 1.0 N D:GLY178 4.4 27.2 1.0 OH D:TYR133 4.5 29.2 1.0 C D:GLY178 4.5 31.8 1.0 N D:TYR180 4.5 24.9 1.0 C D:GLY176 4.6 27.2 1.0 CB D:ASP94 4.6 19.9 1.0 CB D:ALA179 4.7 28.5 1.0 CA D:CYS182 4.8 22.9 1.0 CA D:GLY178 4.9 27.0 1.0 CA D:TYR180 4.9 23.5 1.0 CZ D:TYR133 4.9 31.0 1.0 SG D:CYS182 4.9 28.2 1.0 N D:GLY136 4.9 22.9 1.0 N D:CYS182 4.9 22.2 1.0 OG D:SER96 5.0 34.2 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