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Sodium in PDB 2wdq: E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Carboxin Bound

Enzymatic activity of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Carboxin Bound

All present enzymatic activity of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Carboxin Bound:
1.3.5.1; 1.3.99.1;

Protein crystallography data

The structure of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Carboxin Bound, PDB code: 2wdq 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) 133.63 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 119.400, 178.460, 200.940, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20

Other elements in 2wdq:

The structure of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Carboxin Bound 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 Carboxin Bound (pdb code 2wdq). 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 Carboxin Bound, PDB code: 2wdq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2wdq

Go back to Sodium Binding Sites List in 2wdq
Sodium binding site 1 out of 3 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Carboxin Bound


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 Carboxin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1590

b:22.6
occ:1.00
 O A:HOH2137 2.2 46.5 1.0
O A:GLU388 2.5 34.4 1.0
O A:MET356 2.6 38.3 1.0
O A:GLY358 2.6 38.2 1.0
O A:ALA390 2.6 37.5 1.0
O A:MET357 3.1 38.5 1.0
C A:MET357 3.4 38.5 1.0
C A:GLU388 3.4 34.7 1.0
C A:GLY358 3.6 38.6 1.0
C A:MET356 3.7 38.0 1.0
C A:ALA390 3.8 37.4 1.0
OH A:TYR355 3.9 36.1 1.0
CA A:GLU388 4.0 34.3 1.0
N A:GLY358 4.0 38.1 1.0
CA A:MET357 4.0 38.1 1.0
O A:HOH2163 4.0 30.7 1.0
CA A:GLY358 4.3 38.4 1.0
N A:MET357 4.4 38.2 1.0
CG A:GLU388 4.4 37.3 1.0
O A:GLY387 4.4 35.0 1.0
CZ A:TYR355 4.4 35.3 1.0
N A:ALA390 4.4 35.8 1.0
C A:ILE389 4.4 35.5 1.0
CE2 A:TYR355 4.5 34.6 1.0
O A:HOH2158 4.5 35.1 1.0
CE A:MET356 4.5 39.9 1.0
N A:ILE389 4.5 34.7 1.0
N A:GLY359 4.6 38.1 1.0
N A:CYS391 4.6 37.7 1.0
CA A:CYS391 4.7 38.5 1.0
O A:ILE389 4.7 35.3 1.0
CA A:ALA390 4.7 36.1 1.0
CB A:MET356 4.8 37.4 1.0
O A:HOH2157 4.8 37.8 1.0
CB A:GLU388 4.8 33.9 1.0
CA A:GLY359 4.8 37.8 1.0
CA A:ILE389 4.8 35.2 1.0
CA A:MET356 4.9 37.0 1.0
CG A:MET356 5.0 37.7 1.0

Sodium binding site 2 out of 3 in 2wdq

Go back to Sodium Binding Sites List in 2wdq
Sodium binding site 2 out of 3 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Carboxin Bound


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 Carboxin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1590

b:24.3
occ:1.00
 O E:HOH2119 1.8 36.1 1.0
O E:GLY358 2.4 38.5 1.0
O E:GLU388 2.5 34.6 1.0
O E:MET356 2.6 38.1 1.0
O E:ALA390 2.7 37.2 1.0
O E:MET357 2.9 38.4 1.0
C E:MET357 3.3 38.5 1.0
C E:GLY358 3.4 38.4 1.0
C E:GLU388 3.5 34.8 1.0
C E:ALA390 3.8 37.1 1.0
C E:MET356 3.8 37.6 1.0
N E:GLY358 3.8 38.2 1.0
CA E:MET357 4.0 38.2 1.0
OH E:TYR355 4.0 37.1 1.0
CA E:GLU388 4.1 34.5 1.0
CA E:GLY358 4.2 37.7 1.0
O E:HOH2143 4.3 38.3 1.0
O E:HOH2120 4.4 31.7 1.0
N E:MET357 4.4 38.2 1.0
C E:ILE389 4.4 35.8 1.0
N E:GLY359 4.4 38.0 1.0
N E:ALA390 4.4 36.0 1.0
CG E:GLU388 4.5 37.7 1.0
O E:GLY387 4.5 34.8 1.0
CE E:MET356 4.5 39.7 1.0
N E:ILE389 4.5 34.6 1.0
CZ E:TYR355 4.6 35.4 1.0
N E:CYS391 4.6 37.8 1.0
O E:ILE389 4.6 36.1 1.0
CA E:GLY359 4.6 38.1 1.0
CA E:CYS391 4.6 38.2 1.0
CE2 E:TYR355 4.7 34.7 1.0
CA E:ALA390 4.7 36.1 1.0
CB E:MET356 4.8 37.5 1.0
CA E:ILE389 4.8 35.2 1.0
CG E:MET356 4.9 37.6 1.0
CB E:CYS391 4.9 38.5 1.0
CB E:GLU388 4.9 34.0 1.0
CA E:MET356 4.9 37.1 1.0

Sodium binding site 3 out of 3 in 2wdq

Go back to Sodium Binding Sites List in 2wdq
Sodium binding site 3 out of 3 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Carboxin Bound


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 Carboxin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na1590

b:29.3
occ:1.00
 O I:HOH2102 2.1 55.5 1.0
O I:GLU388 2.6 34.3 1.0
O I:MET356 2.6 38.1 1.0
O I:GLY358 2.6 38.6 1.0
O I:ALA390 2.6 37.3 1.0
O I:MET357 3.0 38.2 1.0
C I:MET357 3.3 38.3 1.0
C I:GLU388 3.5 34.6 1.0
C I:GLY358 3.6 38.7 1.0
C I:MET356 3.7 37.8 1.0
C I:ALA390 3.8 37.1 1.0
OH I:TYR355 3.9 37.1 1.0
CA I:MET357 3.9 38.0 1.0
N I:GLY358 3.9 37.9 1.0
O I:HOH2112 4.0 43.2 1.0
CA I:GLU388 4.0 34.6 1.0
CA I:GLY358 4.3 38.2 1.0
O I:HOH2104 4.3 37.0 1.0
N I:MET357 4.3 38.2 1.0
N I:ALA390 4.4 36.2 1.0
O I:GLY387 4.4 34.9 1.0
CG I:GLU388 4.4 37.2 1.0
CZ I:TYR355 4.5 34.9 1.0
C I:ILE389 4.5 35.7 1.0
CE2 I:TYR355 4.5 34.2 1.0
N I:GLY359 4.6 38.3 1.0
N I:ILE389 4.6 34.6 1.0
N I:CYS391 4.6 37.5 1.0
CA I:CYS391 4.7 38.3 1.0
CE I:MET356 4.7 39.7 1.0
CA I:ALA390 4.7 36.3 1.0
O I:ILE389 4.8 35.7 1.0
CA I:GLY359 4.8 38.1 1.0
CB I:GLU388 4.8 34.3 1.0
CA I:ILE389 4.9 35.5 1.0
CB I:MET356 4.9 37.3 1.0
O I:HOH2116 4.9 39.0 1.0
CA I:MET356 4.9 37.1 1.0
CB I:CYS391 5.0 38.5 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: ESSN 1083-351X
PubMed: 19710024
DOI: 10.1074/JBC.M109.010058
Page generated: Sun Aug 17 11:53:45 2025

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