Sodium in PDB 8qhk: Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide

The structure of Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide, PDB code: 8qhk was solved by D.Wohlwend, T.Friedrich, S.Bucka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.54 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.413, 116.013, 189.741, 90, 90, 90
R / Rfree (%)	16.7 / 20

The structure of Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide also contains other interesting chemical elements:

Iron

(Fe)

12 atoms

The binding sites of Sodium atom in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide (pdb code 8qhk). 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 Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide, PDB code: 8qhk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide


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 Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na507 b:47.8 occ:1.00 OE1 B:GLU108 2.4 27.2 1.0 O B:HOH810 2.4 33.2 1.0 O B:HOH692 2.5 30.7 1.0 CD B:GLU108 3.5 27.1 1.0 NE B:ARG109 3.5 22.5 1.0 CB B:GLU108 3.6 24.5 1.0 CG2 B:ILE7 3.8 29.9 1.0 CG2 B:ILE105 3.9 27.6 1.0 NH2 B:ARG109 3.9 25.4 1.0 CA B:ILE105 3.9 25.2 1.0 O B:ARG104 4.0 22.6 1.0 CG B:GLU108 4.1 25.6 1.0 CZ B:ARG109 4.1 24.3 1.0 O B:HOH862 4.3 28.4 1.0 CB B:ILE105 4.3 28.3 1.0 CG B:ARG109 4.3 22.1 1.0 CD B:ARG109 4.3 22.2 1.0 NE B:ARG104 4.4 23.0 1.0 C B:ARG104 4.4 22.8 1.0 N B:ILE105 4.4 23.6 1.0 CG B:ARG104 4.5 21.4 1.0 OE2 B:GLU108 4.5 31.1 1.0 O B:PRO8 4.6 24.6 1.0 O B:HOH779 4.7 24.1 1.0 CD1 B:ILE7 4.8 30.7 1.0 CD B:ARG104 4.9 22.1 1.0 CA B:GLU108 4.9 23.3 1.0 CB B:ILE7 4.9 29.5 1.0 O B:ILE105 5.0 23.6 1.0 C B:ILE105 5.0 23.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide


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 Reduced Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Reduced 3-Acetylpyridine Adenine Dinucleotide within 5.0Å range: probe atom residue distance (Å) B Occ C:Na204 b:61.6 occ:1.00 O D:HOH904 2.4 56.1 1.0 O C:HOH392 2.7 49.3 1.0 O C:HOH353 3.6 49.9 1.0 CG2 C:VAL87 3.8 33.7 1.0 CB C:PRO124 3.9 38.7 1.0 CG C:PRO124 4.2 41.1 1.0 CG1 C:VAL87 4.4 34.1 1.0 CB C:VAL87 4.5 33.5 1.0

D.Wohlwend, L.Merono, S.Bucka, K.Ritter, H.J.Jessen, T.Friedrich. Structures of 3-Acetylpyridine Adenine Dinucleotide and Adp-Ribose Bound to the Electron Input Module of Respiratory Complex I. Structure 2024.
ISSN: ISSN 0969-2126
PubMed: 38503292
DOI: 10.1016/J.STR.2024.02.013