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Sodium in PDB 2wdv: E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket

Enzymatic activity of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket

All present enzymatic activity of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket:
1.3.5.1; 1.3.99.1;

Protein crystallography data

The structure of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket, PDB code: 2wdv was solved by J.Ruprecht, V.Yankovskaya, E.Maklashina, S.Iwata, G.Cecchini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.85 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 120.340, 184.847, 204.720, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 23.3

Other elements in 2wdv:

The structure of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket also contains other interesting chemical elements:

Iron (Fe) 30 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket (pdb code 2wdv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket, PDB code: 2wdv:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2wdv

Go back to Sodium Binding Sites List in 2wdv
Sodium binding site 1 out of 3 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1590

b:2.0
occ:1.00
 O A:GLU388 2.4 55.2 1.0
O A:ALA390 2.4 55.4 1.0
O A:GLY358 2.5 55.2 1.0
O A:MET356 2.5 55.1 1.0
O A:MET357 3.1 54.9 1.0
C A:MET357 3.3 55.0 1.0
C A:GLU388 3.5 55.0 1.0
C A:GLY358 3.5 55.3 1.0
C A:ALA390 3.6 55.4 1.0
C A:MET356 3.6 55.1 1.0
OH A:TYR355 3.8 56.5 1.0
CA A:MET357 3.9 54.8 1.0
N A:GLY358 3.9 55.2 1.0
CA A:GLU388 4.0 55.0 1.0
N A:MET357 4.2 55.0 1.0
N A:ALA390 4.3 55.1 1.0
CA A:GLY358 4.3 55.2 1.0
CE2 A:TYR355 4.3 55.1 1.0
CZ A:TYR355 4.3 55.5 1.0
CE A:MET356 4.3 55.3 1.0
CG A:GLU388 4.4 55.2 1.0
N A:CYS391 4.5 55.5 1.0
N A:GLY359 4.5 55.2 1.0
O A:GLY387 4.5 55.1 1.0
CA A:ALA390 4.6 55.3 1.0
C A:ILE389 4.6 55.1 1.0
CA A:CYS391 4.6 55.2 1.0
N A:ILE389 4.6 54.9 1.0
CA A:GLY359 4.7 55.1 1.0
CB A:GLU388 4.8 54.8 1.0
CA A:MET356 4.8 55.0 1.0
CB A:MET356 4.9 55.0 1.0
CA A:ILE389 4.9 54.9 1.0
CG A:MET356 5.0 55.6 1.0
CB A:CYS391 5.0 55.1 1.0

Sodium binding site 2 out of 3 in 2wdv

Go back to Sodium Binding Sites List in 2wdv
Sodium binding site 2 out of 3 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1590

b:9.5
occ:1.00
 O E:MET356 2.4 54.9 1.0
O E:GLY358 2.4 55.2 1.0
O E:GLU388 2.5 55.1 1.0
O E:ALA390 2.6 55.5 1.0
O E:MET357 3.0 54.9 1.0
C E:MET357 3.2 55.0 1.0
C E:MET356 3.5 55.0 1.0
C E:GLY358 3.5 55.3 1.0
C E:GLU388 3.6 54.9 1.0
CA E:MET357 3.7 55.0 1.0
OH E:TYR355 3.8 56.2 1.0
C E:ALA390 3.8 55.3 1.0
N E:GLY358 3.8 55.2 1.0
N E:MET357 4.1 55.1 1.0
CE2 E:TYR355 4.1 55.1 1.0
CA E:GLU388 4.2 54.8 1.0
CZ E:TYR355 4.2 55.4 1.0
CA E:GLY358 4.2 55.2 1.0
CE E:MET356 4.3 55.2 1.0
N E:ALA390 4.4 55.2 1.0
CG E:GLU388 4.4 55.1 1.0
N E:GLY359 4.5 55.2 1.0
O E:GLY387 4.6 55.1 1.0
N E:CYS391 4.6 55.3 1.0
CA E:CYS391 4.6 55.2 1.0
N E:ILE389 4.7 55.1 1.0
C E:ILE389 4.7 55.0 1.0
CA E:ALA390 4.7 55.2 1.0
CA E:MET356 4.7 55.0 1.0
CA E:GLY359 4.8 55.2 1.0
CB E:MET356 4.8 55.1 1.0
CG E:MET356 4.9 55.6 1.0
CB E:GLU388 4.9 54.6 1.0
CB E:CYS391 5.0 55.1 1.0

Sodium binding site 3 out of 3 in 2wdv

Go back to Sodium Binding Sites List in 2wdv
Sodium binding site 3 out of 3 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with An Empty Quinone-Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na1590

b:41.7
occ:1.00
 O I:MET356 2.7 55.0 1.0
O I:ALA390 2.7 55.5 1.0
O I:GLU388 2.8 55.1 1.0
OH I:TYR355 2.9 56.4 1.0
O I:GLY358 3.3 55.2 1.0
O I:MET357 3.4 54.9 1.0
CZ I:TYR355 3.6 55.6 1.0
C I:MET357 3.6 55.0 1.0
C I:GLU388 3.7 54.9 1.0
CE2 I:TYR355 3.7 55.1 1.0
C I:MET356 3.8 55.0 1.0
CA I:MET357 3.9 55.0 1.0
CA I:GLU388 3.9 54.9 1.0
C I:ALA390 4.0 55.4 1.0
O I:GLY387 4.3 55.2 1.0
N I:MET357 4.3 55.0 1.0
C I:GLY358 4.4 55.3 1.0
CG I:GLU388 4.4 55.2 1.0
CD2 I:HIS395 4.4 55.6 1.0
N I:GLY358 4.4 55.1 1.0
N I:ALA390 4.6 55.1 1.0
CE1 I:TYR355 4.7 55.2 1.0
CB I:GLU388 4.7 54.8 1.0
CA I:CYS391 4.8 55.2 1.0
CD2 I:TYR355 4.8 55.1 1.0
N I:CYS391 4.8 55.4 1.0
N I:ILE389 4.9 55.0 1.0
CA I:ALA390 4.9 55.2 1.0
CA I:GLY358 5.0 55.2 1.0
N I:GLU388 5.0 55.2 1.0

Reference:

J.Ruprecht, V.Yankovskaya, E.Maklashina, S.Iwata, G.Cecchini. Structure of Escherichia Coli Succinate:Quinone Oxidoreductase with An Occupied and Empty Quinone- Binding Site. J.Biol.Chem. V. 284 29836 2009.
ISSN: ISSN 0021-9258
PubMed: 19710024
DOI: 10.1074/JBC.M109.010058
Page generated: Mon Oct 7 04:37:32 2024

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