Sodium in PDB 7jz2: Succinate: Quinone Oxidoreductase Sqr From E.Coli K12

All present enzymatic activity of Succinate: Quinone Oxidoreductase Sqr From E.Coli K12:
1.3.5.1;

The structure of Succinate: Quinone Oxidoreductase Sqr From E.Coli K12 also contains other interesting chemical elements:

Iron

(Fe)

30 atoms

The binding sites of Sodium atom in the Succinate: Quinone Oxidoreductase Sqr From E.Coli K12 (pdb code 7jz2). 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: Quinone Oxidoreductase Sqr From E.Coli K12, PDB code: 7jz2:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Succinate: Quinone Oxidoreductase Sqr From E.Coli K12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Succinate: Quinone Oxidoreductase Sqr From E.Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:28.7 occ:1.00 O A:GLY358 2.4 33.3 1.0 O A:MET356 2.5 31.5 1.0 O A:GLU388 2.7 28.7 1.0 N A:GLY358 2.9 33.3 1.0 C A:GLY358 3.1 33.3 1.0 C A:MET357 3.1 33.3 1.0 CA A:GLY358 3.2 33.3 1.0 O A:MET357 3.4 33.3 1.0 C A:MET356 3.5 31.5 1.0 C A:GLU388 3.8 28.7 1.0 CA A:MET357 3.8 33.3 1.0 N A:MET357 4.1 33.3 1.0 CG A:GLU388 4.1 28.7 1.0 O A:ALA390 4.1 30.3 1.0 CE2 A:TYR355 4.3 30.4 1.0 CA A:GLU388 4.3 28.7 1.0 N A:GLY359 4.3 32.5 1.0 OH A:TYR355 4.3 30.4 1.0 CE A:MET356 4.5 31.5 1.0 CG A:MET356 4.6 31.5 1.0 CZ A:TYR355 4.6 30.4 1.0 CA A:CYS391 4.6 34.2 1.0 C A:ALA390 4.7 30.3 1.0 CA A:MET356 4.7 31.5 1.0 CB A:MET356 4.7 31.5 1.0 CB A:GLU388 4.8 28.7 1.0 N A:ILE389 4.9 29.6 1.0 N A:CYS391 4.9 34.2 1.0 CA A:GLY359 5.0 32.5 1.0 C A:ILE389 5.0 29.6 1.0 O A:ILE389 5.0 29.6 1.0 CB A:CYS391 5.0 34.2 1.0

Sodium binding site 2 out of 3 in the Succinate: Quinone Oxidoreductase Sqr From E.Coli K12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Succinate: Quinone Oxidoreductase Sqr From E.Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na602 b:29.3 occ:1.00 O E:GLY358 2.4 33.3 1.0 O E:MET356 2.5 31.8 1.0 O E:GLU388 2.7 28.9 1.0 N E:GLY358 2.9 33.3 1.0 C E:GLY358 3.1 33.3 1.0 C E:MET357 3.1 34.1 1.0 CA E:GLY358 3.2 33.3 1.0 O E:MET357 3.4 34.1 1.0 C E:MET356 3.5 31.8 1.0 C E:GLU388 3.8 28.9 1.0 CA E:MET357 3.8 34.1 1.0 N E:MET357 4.1 34.1 1.0 CG E:GLU388 4.1 28.9 1.0 O E:ALA390 4.1 31.1 1.0 CE2 E:TYR355 4.3 31.1 1.0 CA E:GLU388 4.3 28.9 1.0 N E:GLY359 4.3 32.7 1.0 OH E:TYR355 4.3 31.1 1.0 CE E:MET356 4.5 31.8 1.0 CG E:MET356 4.6 31.8 1.0 CZ E:TYR355 4.6 31.1 1.0 CA E:CYS391 4.6 34.2 1.0 C E:ALA390 4.7 31.1 1.0 CA E:MET356 4.7 31.8 1.0 CB E:MET356 4.7 31.8 1.0 CB E:GLU388 4.8 28.9 1.0 N E:ILE389 4.9 29.7 1.0 N E:CYS391 4.9 34.2 1.0 CA E:GLY359 5.0 32.7 1.0 C E:ILE389 5.0 29.7 1.0 O E:ILE389 5.0 29.7 1.0 CB E:CYS391 5.0 34.2 1.0

Sodium binding site 3 out of 3 in the Succinate: Quinone Oxidoreductase Sqr From E.Coli K12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Succinate: Quinone Oxidoreductase Sqr From E.Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ I:Na602 b:29.2 occ:1.00 O I:GLY358 2.4 33.7 1.0 O I:MET356 2.5 32.2 1.0 O I:GLU388 2.7 28.9 1.0 N I:GLY358 2.9 33.7 1.0 C I:GLY358 3.1 33.7 1.0 C I:MET357 3.1 33.8 1.0 CA I:GLY358 3.2 33.7 1.0 O I:MET357 3.4 33.8 1.0 C I:MET356 3.5 32.2 1.0 C I:GLU388 3.8 28.9 1.0 CA I:MET357 3.8 33.8 1.0 N I:MET357 4.1 33.8 1.0 CG I:GLU388 4.1 28.9 1.0 O I:ALA390 4.1 31.4 1.0 CE2 I:TYR355 4.3 31.5 1.0 CA I:GLU388 4.3 28.9 1.0 N I:GLY359 4.3 33.5 1.0 OH I:TYR355 4.3 31.5 1.0 CE I:MET356 4.5 32.2 1.0 CG I:MET356 4.6 32.2 1.0 CZ I:TYR355 4.6 31.5 1.0 CA I:CYS391 4.6 34.4 1.0 C I:ALA390 4.7 31.4 1.0 CA I:MET356 4.7 32.2 1.0 CB I:MET356 4.7 32.2 1.0 CB I:GLU388 4.8 28.9 1.0 N I:ILE389 4.9 29.7 1.0 N I:CYS391 4.9 34.4 1.0 CA I:GLY359 5.0 33.5 1.0 C I:ILE389 5.0 29.7 1.0 O I:ILE389 5.0 29.7 1.0 CB I:CYS391 5.0 34.4 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