Sodium in PDB 6hl2: Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form

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

The structure of Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form, PDB code: 6hl2 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)	73.48 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.190, 116.438, 189.449, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 19.5

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

Iron	(Fe)	12 atoms
Chlorine	(Cl)	8 atoms

The binding sites of Sodium atom in the Wild-Type Nuoef From Aquifex Aeolicus - Oxidized Form (pdb code 6hl2). 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, PDB code: 6hl2:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:34.8 occ:1.00 OD1 B:ASP94 2.5 24.7 1.0 O B:HOH740 2.6 22.4 1.0 O B:HOH726 2.7 22.1 1.0 O B:ALA179 2.7 22.9 1.0 O B:HOH644 2.8 31.3 1.0 CG B:ASP94 3.3 24.5 1.0 OD2 B:ASP94 3.4 29.1 1.0 C B:ALA179 3.6 23.8 1.0 N B:ALA179 3.7 24.8 1.0 CB B:CYS182 3.9 22.8 1.0 CA B:ALA179 4.1 23.4 1.0 CA B:GLY176 4.2 19.5 1.0 CB B:ARG135 4.2 16.8 1.0 CA B:ARG135 4.3 17.3 1.0 CE1 B:TYR133 4.3 24.2 1.0 N B:GLY178 4.3 21.1 1.0 N B:ALA177 4.3 22.1 1.0 C B:GLY178 4.4 29.3 1.0 OH B:TYR133 4.5 26.4 1.0 N B:TYR180 4.6 19.7 1.0 C B:GLY176 4.6 23.6 1.0 O B:HOH702 4.7 39.9 1.0 CB B:ASP94 4.7 18.6 1.0 CB B:ALA179 4.8 24.6 1.0 CA B:GLY178 4.8 21.6 1.0 SG B:CYS182 4.8 28.0 1.0 CA B:CYS182 4.9 21.8 1.0 N B:GLY136 4.9 18.2 1.0 CZ B:TYR133 4.9 26.2 1.0 OG B:SER96 5.0 26.4 1.0 CA B:TYR180 5.0 18.1 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na503 b:36.1 occ:1.00 OD1 D:ASP94 2.4 24.6 1.0 O D:HOH718 2.6 21.6 1.0 O D:ALA179 2.7 22.9 1.0 O D:HOH730 2.8 20.8 1.0 O D:HOH619 2.9 29.3 1.0 CG D:ASP94 3.2 24.9 1.0 OD2 D:ASP94 3.3 27.6 1.0 C D:ALA179 3.6 25.7 1.0 N D:ALA179 3.7 27.4 1.0 CB D:CYS182 3.9 23.2 1.0 CA D:ALA179 4.2 25.6 1.0 CA D:GLY176 4.2 18.7 1.0 CB D:ARG135 4.2 17.3 1.0 CE1 D:TYR133 4.3 23.2 1.0 CA D:ARG135 4.3 18.0 1.0 N D:GLY178 4.4 24.3 1.0 N D:ALA177 4.4 23.7 1.0 C D:GLY178 4.5 32.5 1.0 OH D:TYR133 4.5 27.3 1.0 N D:TYR180 4.6 21.5 1.0 CB D:ASP94 4.6 17.2 1.0 C D:GLY176 4.7 24.2 1.0 CB D:ALA179 4.8 25.9 1.0 SG D:CYS182 4.8 28.5 1.0 CA D:CYS182 4.8 21.6 1.0 CA D:GLY178 4.9 25.0 1.0 O D:HOH651 4.9 35.3 1.0 CZ D:TYR133 4.9 26.3 1.0 CA D:TYR180 4.9 20.9 1.0 OG D:SER96 4.9 24.4 1.0 N D:GLY136 5.0 19.6 1.0 N D:CYS182 5.0 19.9 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