Atomistry » Sodium » PDB 2wd0-2wof » 2wdq
Atomistry »
  Sodium »
    PDB 2wd0-2wof »
      2wdq »

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: Tue Dec 15 05:57:19 2020

Last articles

Zn in 7RRP
Zn in 7OKY
Zn in 7OL0
Zn in 7OKX
Zn in 7ONB
Zn in 7RSF
Zn in 7OUF
Zn in 7OUG
Zn in 7OUH
Zn in 7RGN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy