Sodium in PDB 6wu6: Succinate-Coenzyme Q Reductase

All present enzymatic activity of Succinate-Coenzyme Q Reductase:
1.3.5.1;

The structure of Succinate-Coenzyme Q Reductase also contains other interesting chemical elements:

Iron

(Fe)

30 atoms

The binding sites of Sodium atom in the Succinate-Coenzyme Q Reductase (pdb code 6wu6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Succinate-Coenzyme Q Reductase, PDB code: 6wu6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Succinate-Coenzyme Q Reductase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Succinate-Coenzyme Q Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:29.9 occ:1.00 O A:GLY358 2.3 37.5 1.0 C A:GLY358 2.7 37.5 1.0 CG A:MET356 2.8 34.9 1.0 CE A:MET356 2.8 34.9 1.0 CA A:GLY359 2.8 43.6 1.0 N A:GLY359 2.9 43.6 1.0 SD A:MET356 3.1 34.9 1.0 O A:ILE389 3.7 41.8 1.0 O A:MET356 3.7 34.9 1.0 CB A:MET356 3.8 34.9 1.0 CE A:MET236 3.8 30.8 1.0 CA A:GLY358 3.9 37.5 1.0 CA A:ILE389 4.2 41.8 1.0 N A:GLY358 4.2 37.5 1.0 O A:GLU388 4.2 44.2 1.0 C A:MET356 4.3 34.9 1.0 C A:GLY359 4.3 43.6 1.0 SD A:MET236 4.4 30.8 1.0 C A:ILE389 4.4 41.8 1.0 CA A:MET356 4.6 34.9 1.0 C A:MET357 4.7 39.4 1.0 CG2 A:VAL223 4.8 43.1 1.0 N A:ILE360 4.9 44.6 1.0 CG1 A:ILE389 4.9 41.8 1.0 O A:MET357 4.9 39.4 1.0 CB A:ILE389 5.0 41.8 1.0

Sodium binding site 2 out of 3 in the Succinate-Coenzyme Q Reductase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Succinate-Coenzyme Q Reductase within 5.0Å range: probe atom residue distance (Å) B Occ E:Na602 b:29.9 occ:1.00 O E:GLY358 2.3 37.5 1.0 C E:GLY358 2.7 37.5 1.0 CG E:MET356 2.8 34.9 1.0 CE E:MET356 2.8 34.9 1.0 CA E:GLY359 2.8 43.6 1.0 N E:GLY359 2.9 43.6 1.0 SD E:MET356 3.1 34.9 1.0 O E:ILE389 3.7 41.8 1.0 O E:MET356 3.7 34.9 1.0 CB E:MET356 3.8 34.9 1.0 CE E:MET236 3.8 30.8 1.0 CA E:GLY358 3.9 37.5 1.0 CA E:ILE389 4.2 41.8 1.0 N E:GLY358 4.2 37.5 1.0 O E:GLU388 4.2 44.2 1.0 C E:MET356 4.3 34.9 1.0 C E:GLY359 4.3 43.6 1.0 SD E:MET236 4.4 30.8 1.0 C E:ILE389 4.4 41.8 1.0 CA E:MET356 4.6 34.9 1.0 C E:MET357 4.7 39.4 1.0 CG2 E:VAL223 4.8 43.1 1.0 N E:ILE360 4.9 44.6 1.0 CG1 E:ILE389 4.9 41.8 1.0 O E:MET357 4.9 39.4 1.0 CB E:ILE389 5.0 41.8 1.0

Sodium binding site 3 out of 3 in the Succinate-Coenzyme Q Reductase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Succinate-Coenzyme Q Reductase within 5.0Å range: probe atom residue distance (Å) B Occ I:Na602 b:29.9 occ:1.00 O I:GLY358 2.3 37.5 1.0 C I:GLY358 2.7 37.5 1.0 CG I:MET356 2.8 34.9 1.0 CE I:MET356 2.8 34.9 1.0 CA I:GLY359 2.8 43.6 1.0 N I:GLY359 2.9 43.6 1.0 SD I:MET356 3.1 34.9 1.0 O I:ILE389 3.7 41.8 1.0 O I:MET356 3.7 34.9 1.0 CB I:MET356 3.8 34.9 1.0 CE I:MET236 3.8 30.8 1.0 CA I:GLY358 3.9 37.5 1.0 CA I:ILE389 4.2 41.8 1.0 N I:GLY358 4.2 37.5 1.0 O I:GLU388 4.2 44.2 1.0 C I:MET356 4.3 34.9 1.0 C I:GLY359 4.3 43.6 1.0 SD I:MET236 4.4 30.8 1.0 C I:ILE389 4.4 41.8 1.0 CA I:MET356 4.6 34.9 1.0 C I:MET357 4.7 39.4 1.0 CG2 I:VAL223 4.8 43.1 1.0 N I:ILE360 4.9 44.6 1.0 CG1 I:ILE389 4.9 41.8 1.0 O I:MET357 4.9 39.4 1.0 CB I:ILE389 5.0 41.8 1.0

C.C.Su, M.Lyu, C.E.Morgan, J.R.Bolla, C.V.Robinson, E.W.Yu. A 'Build and Retrieve' Methodology to Simultaneously Solve Cryo-Em Structures of Membrane Proteins. Nat.Methods V. 18 69 2021.
ISSN: ESSN 1548-7105
PubMed: 33408407
DOI: 10.1038/S41592-020-01021-2