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

Enzymatic activity of 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;

Other elements in 7jz2:

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

Iron (Fe) 30 atoms

Sodium Binding Sites:

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 7jz2

Go back to Sodium Binding Sites List in 7jz2
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 7jz2

Go back to Sodium Binding Sites List in 7jz2
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 7jz2

Go back to Sodium Binding Sites List in 7jz2
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

Reference:

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
Page generated: Mon Jan 25 15:54:10 2021

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