Sodium in PDB 8qg1: Crystal Structure of Oxidized Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Adp-Ribose

The structure of Crystal Structure of Oxidized Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Adp-Ribose, PDB code: 8qg1 was solved by D.Wohlwend, T.Friedrich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.56 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.129, 116.146, 189.485, 90, 90, 90
R / Rfree (%)	17.8 / 20.7

The structure of Crystal Structure of Oxidized Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Adp-Ribose also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Iron	(Fe)	12 atoms

The binding sites of Sodium atom in the Crystal Structure of Oxidized Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Adp-Ribose (pdb code 8qg1). 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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Adp-Ribose, PDB code: 8qg1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Oxidized Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Adp-Ribose


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na506 b:68.4 occ:1.00 OE2 B:GLU53 3.3 56.9 1.0 NE1 B:TRP57 3.4 44.1 1.0 CG B:GLU53 3.6 51.0 1.0 CD B:GLU53 3.7 54.6 1.0 CE2 B:TRP57 4.3 43.5 1.0 CD1 B:TRP57 4.4 43.0 1.0 CZ2 B:TRP57 4.5 44.1 1.0 OE1 B:GLU53 4.8 54.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Oxidized Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Adp-Ribose


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 Respiratory Complex I Subunits Nuoef From Aquifex Aeolicus Bound to Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ D:Na508 b:61.8 occ:1.00 O D:HOH747 2.3 47.4 1.0 OE1 D:GLU53 2.7 50.9 1.0 N D:SER50 3.1 42.2 1.0 OG D:SER50 3.5 43.7 1.0 CD D:GLU53 3.5 51.1 1.0 CB D:GLU53 3.5 45.8 1.0 CA D:MET49 3.8 42.4 1.0 CB D:SER50 3.8 43.5 1.0 C D:MET49 3.9 41.7 1.0 CG D:GLU53 4.0 48.4 1.0 CA D:SER50 4.0 42.0 1.0 CB D:MET49 4.1 42.0 1.0 CG D:MET49 4.4 42.5 1.0 O D:HOH694 4.5 56.1 1.0 OE2 D:GLU53 4.5 51.8 1.0 O D:SER50 4.7 38.8 1.0 C D:SER50 4.9 40.3 1.0 O D:ASN48 4.9 44.6 1.0 CA D:GLU53 4.9 43.0 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