Sodium in PDB 6c12: Sdha-Sdhe Complex

All present enzymatic activity of Sdha-Sdhe Complex:
1.3.5.1;

The structure of Sdha-Sdhe Complex, PDB code: 6c12 was solved by M.J.Maher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.89 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.980, 100.030, 232.130, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 25.8

The binding sites of Sodium atom in the Sdha-Sdhe Complex (pdb code 6c12). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Sdha-Sdhe Complex, PDB code: 6c12:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Sdha-Sdhe Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sdha-Sdhe Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:14.8 occ:1.00 O B:GLU388 2.3 14.3 1.0 O B:MET356 2.4 14.1 1.0 O B:GLY358 2.4 14.1 1.0 O B:HOH715 2.5 14.4 1.0 O B:ALA390 2.5 15.1 1.0 O B:MET357 3.1 14.4 1.0 C B:GLU388 3.3 14.1 1.0 C B:MET357 3.4 14.4 1.0 C B:GLY358 3.5 14.2 1.0 C B:MET356 3.5 13.9 1.0 C B:ALA390 3.6 15.2 1.0 CA B:MET357 3.9 14.4 1.0 N B:GLY358 3.9 14.4 1.0 CA B:GLU388 3.9 14.0 1.0 N B:ALA390 4.1 14.7 1.0 N B:MET357 4.2 14.2 1.0 C B:ILE389 4.2 14.4 1.0 CA B:GLY358 4.2 14.4 1.0 CE B:MET356 4.3 13.8 1.0 N B:ILE389 4.3 14.2 1.0 N B:GLY359 4.4 14.2 1.0 CG B:GLU388 4.4 13.4 1.0 OH B:TYR355 4.4 13.5 1.0 CA B:ALA390 4.4 15.0 1.0 O B:GLY387 4.4 14.2 1.0 O B:ILE389 4.5 14.3 1.0 N B:CYS391 4.5 15.5 1.0 O B:HOH718 4.5 15.0 1.0 CA B:GLY359 4.5 14.0 1.0 CB B:MET356 4.5 13.6 1.0 CE1 B:TYR355 4.6 13.7 1.0 CG B:MET356 4.6 13.7 1.0 CA B:ILE389 4.6 14.3 1.0 O B:HOH750 4.6 26.5 1.0 CA B:MET356 4.7 13.6 1.0 CA B:CYS391 4.7 15.7 1.0 CZ B:TYR355 4.8 13.7 1.0 CB B:GLU388 4.8 13.7 1.0

Sodium binding site 2 out of 2 in the Sdha-Sdhe Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sdha-Sdhe Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:17.0 occ:1.00 O A:GLU388 2.3 16.3 1.0 O A:HOH711 2.4 18.0 1.0 O A:ALA390 2.4 19.6 1.0 O A:GLY358 2.6 15.9 1.0 O A:MET356 2.6 14.9 1.0 O A:MET357 3.1 16.6 1.0 C A:GLU388 3.3 16.5 1.0 C A:MET357 3.4 16.3 1.0 C A:ALA390 3.5 19.9 1.0 C A:GLY358 3.6 16.1 1.0 C A:MET356 3.7 15.1 1.0 CA A:MET357 3.9 16.2 1.0 N A:GLY358 3.9 16.2 1.0 CA A:GLU388 4.0 16.3 1.0 N A:ALA390 4.0 18.9 1.0 C A:ILE389 4.2 18.0 1.0 CA A:GLY358 4.3 16.2 1.0 N A:MET357 4.3 15.7 1.0 O A:HOH743 4.3 16.8 1.0 N A:ILE389 4.3 16.9 1.0 O A:GLY387 4.4 17.2 1.0 N A:CYS391 4.4 20.7 1.0 CA A:ALA390 4.4 19.6 1.0 OH A:TYR355 4.4 16.3 1.0 N A:GLY359 4.5 16.0 1.0 CG A:GLU388 4.5 15.2 1.0 CA A:CYS391 4.5 21.3 1.0 O A:ILE389 4.6 18.0 1.0 CE2 A:TYR355 4.6 16.1 1.0 O A:HOH807 4.6 25.1 1.0 CA A:ILE389 4.7 17.1 1.0 CE A:MET356 4.7 14.6 1.0 CA A:GLY359 4.7 15.9 1.0 CZ A:TYR355 4.8 16.1 1.0 CB A:MET356 4.8 14.5 1.0 CB A:GLU388 4.8 15.8 1.0 CA A:MET356 4.9 14.7 1.0 CB A:CYS391 5.0 20.7 1.0 CG A:MET356 5.0 14.5 1.0

M.J.Maher, A.S.Herath, S.R.Udagedara, D.A.Dougan, K.N.Truscott. Crystal Structure of Bacterial Succinate:Quinone Oxidoreductase Flavoprotein Sdha in Complex with Its Assembly Factor Sdhe. Proc. Natl. Acad. Sci. V. 115 2982 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29514959
DOI: 10.1073/PNAS.1800195115