Sodium in PDB 6hla: Wild-Type Nuoef From Aquifex Aeolicus - Reduced Form Bound to Nadh

All present enzymatic activity of Wild-Type Nuoef From Aquifex Aeolicus - Reduced Form Bound to Nadh:
1.6.5.11;

The structure of Wild-Type Nuoef From Aquifex Aeolicus - Reduced Form Bound to Nadh, PDB code: 6hla 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)	99.20 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.642, 116.431, 189.452, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 24.1

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

Iron

(Fe)

12 atoms

The binding sites of Sodium atom in the Wild-Type Nuoef From Aquifex Aeolicus - Reduced Form Bound to Nadh (pdb code 6hla). 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 - Reduced Form Bound to Nadh, PDB code: 6hla:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Wild-Type Nuoef From Aquifex Aeolicus - Reduced Form Bound to Nadh


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 - Reduced Form Bound to Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:30.3 occ:1.00 OD1 B:ASP94 2.5 15.6 1.0 O B:HOH743 2.6 22.6 1.0 O B:ALA179 2.6 25.0 1.0 O B:HOH696 2.8 12.8 1.0 CG B:ASP94 3.3 19.9 1.0 OD2 B:ASP94 3.3 22.1 1.0 C B:ALA179 3.6 22.8 1.0 N B:ALA179 3.7 25.0 1.0 CB B:CYS182 3.8 18.7 1.0 O B:HOH812 3.9 29.8 1.0 CA B:GLY176 4.1 16.3 1.0 CA B:ALA179 4.1 24.2 1.0 CB B:ARG135 4.3 7.8 1.0 N B:ALA177 4.3 18.9 1.0 CA B:ARG135 4.3 9.0 1.0 N B:GLY178 4.4 20.5 1.0 CE1 B:TYR133 4.5 19.0 1.0 C B:GLY178 4.5 27.9 1.0 N B:TYR180 4.6 15.3 1.0 C B:GLY176 4.6 21.8 1.0 OH B:TYR133 4.6 20.1 1.0 OG B:SER96 4.7 27.2 1.0 CB B:ASP94 4.7 13.9 1.0 CB B:ALA179 4.7 26.1 1.0 CA B:CYS182 4.8 17.7 1.0 SG B:CYS182 4.8 23.4 1.0 CA B:GLY178 4.9 21.7 1.0 N B:GLY136 4.9 12.6 1.0 OE1 B:GLU137 4.9 18.7 1.0 O B:ASP94 5.0 15.7 1.0 CA B:TYR180 5.0 13.6 1.0 N B:CYS182 5.0 18.0 1.0 C B:CYS182 5.0 21.2 1.0

Sodium binding site 2 out of 2 in the Wild-Type Nuoef From Aquifex Aeolicus - Reduced Form Bound to Nadh


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 - Reduced Form Bound to Nadh within 5.0Å range: probe atom residue distance (Å) B Occ D:Na504 b:31.0 occ:1.00 OD1 D:ASP94 2.4 17.5 1.0 O D:ALA179 2.6 24.5 1.0 O D:HOH704 2.6 19.8 1.0 O D:HOH681 3.0 13.8 1.0 CG D:ASP94 3.1 18.4 1.0 OD2 D:ASP94 3.1 26.4 1.0 O D:HOH737 3.5 30.5 1.0 C D:ALA179 3.6 25.5 1.0 CB D:CYS182 3.8 18.4 1.0 N D:ALA179 3.9 27.0 1.0 CA D:GLY176 4.2 20.7 1.0 CA D:ALA179 4.2 24.9 1.0 CB D:ARG135 4.3 15.1 1.0 CA D:ARG135 4.3 16.5 1.0 CE1 D:TYR133 4.4 19.1 1.0 N D:ALA177 4.4 23.4 1.0 N D:TYR180 4.5 19.8 1.0 N D:GLY178 4.5 24.9 1.0 CB D:ASP94 4.6 16.2 1.0 OG D:SER96 4.6 21.8 1.0 OH D:TYR133 4.6 20.0 1.0 C D:GLY178 4.6 32.3 1.0 CA D:CYS182 4.7 17.7 1.0 C D:GLY176 4.7 25.1 1.0 CB D:ALA179 4.8 25.9 1.0 SG D:CYS182 4.8 23.0 1.0 CA D:TYR180 4.9 16.9 1.0 C D:CYS182 4.9 21.8 1.0 O D:ASP94 4.9 22.6 1.0 N D:CYS182 4.9 17.1 1.0 N D:GLY136 5.0 15.9 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