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

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

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

Protein crystallography data

The structure of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound, PDB code: 2wdr 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) 46.52 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 119.955, 186.128, 204.034, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 22.8

Other elements in 2wdr:

The structure of E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound also contains other interesting chemical elements:

Iron (Fe) 30 atoms
Chlorine (Cl) 15 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol Bound (pdb code 2wdr). 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 Pentachlorophenol Bound, PDB code: 2wdr:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2wdr

Go back to Sodium Binding Sites List in 2wdr
Sodium binding site 1 out of 3 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol 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 Pentachlorophenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1590

b:2.0
occ:1.00
O A:GLY358 2.4 48.4 1.0
O A:GLU388 2.5 48.9 1.0
O A:MET356 2.7 48.0 1.0
O A:ALA390 2.7 48.7 1.0
O A:MET357 3.0 48.0 1.0
C A:MET357 3.4 48.0 1.0
C A:GLU388 3.5 48.8 1.0
C A:GLY358 3.6 48.4 1.0
C A:ALA390 3.7 48.5 1.0
OH A:TYR355 3.7 48.8 1.0
C A:MET356 3.8 48.0 1.0
N A:GLY358 3.9 48.3 1.0
CA A:MET357 4.0 47.9 1.0
CA A:GLU388 4.0 48.8 1.0
CA A:GLY358 4.3 48.4 1.0
N A:ALA390 4.3 48.6 1.0
CZ A:TYR355 4.3 48.6 1.0
N A:MET357 4.4 48.0 1.0
CE2 A:TYR355 4.4 48.4 1.0
N A:CYS391 4.4 48.5 1.0
CA A:CYS391 4.5 48.5 1.0
CE A:MET356 4.5 49.3 1.0
CG A:GLU388 4.5 48.8 1.0
O A:GLY387 4.5 48.5 1.0
C A:ILE389 4.6 48.8 1.0
N A:GLY359 4.6 48.2 1.0
N A:ILE389 4.6 48.7 1.0
CA A:ALA390 4.6 48.6 1.0
CB A:CYS391 4.7 48.4 1.0
CG A:MET356 4.8 48.4 1.0
CA A:GLY359 4.8 48.3 1.0
CB A:GLU388 4.9 48.8 1.0
CA A:ILE389 5.0 48.6 1.0

Sodium binding site 2 out of 3 in 2wdr

Go back to Sodium Binding Sites List in 2wdr
Sodium binding site 2 out of 3 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol 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 Pentachlorophenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1590

b:12.1
occ:1.00
O E:GLY358 2.4 48.2 1.0
O E:ALA390 2.6 48.6 1.0
O E:GLU388 2.6 48.7 1.0
O E:MET356 2.8 47.7 1.0
O E:MET357 2.9 48.1 1.0
C E:MET357 3.3 48.1 1.0
C E:GLY358 3.5 48.3 1.0
C E:ALA390 3.6 48.4 1.0
C E:GLU388 3.6 48.6 1.0
OH E:TYR355 3.8 48.7 1.0
C E:MET356 3.9 47.9 1.0
N E:GLY358 3.9 48.3 1.0
CA E:MET357 4.0 47.9 1.0
CA E:GLU388 4.1 48.6 1.0
CA E:GLY358 4.2 48.3 1.0
N E:ALA390 4.2 48.5 1.0
CA E:CYS391 4.3 48.5 1.0
N E:CYS391 4.3 48.4 1.0
CZ E:TYR355 4.4 48.5 1.0
N E:MET357 4.4 47.9 1.0
O E:GLY387 4.4 48.4 1.0
CE2 E:TYR355 4.5 48.3 1.0
CE E:MET356 4.5 49.4 1.0
N E:GLY359 4.5 48.2 1.0
CA E:ALA390 4.6 48.4 1.0
CB E:CYS391 4.6 48.4 1.0
C E:ILE389 4.6 48.7 1.0
CG E:GLU388 4.6 48.8 1.0
N E:ILE389 4.7 48.7 1.0
CA E:GLY359 4.8 48.2 1.0
CG E:MET356 5.0 48.4 1.0
CB E:GLU388 5.0 48.6 1.0

Sodium binding site 3 out of 3 in 2wdr

Go back to Sodium Binding Sites List in 2wdr
Sodium binding site 3 out of 3 in the E. Coli Succinate:Quinone Oxidoreductase (Sqr) with Pentachlorophenol 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 Pentachlorophenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na1590

b:21.6
occ:1.00
O I:GLU388 2.5 48.6 1.0
O I:MET356 2.6 47.8 1.0
O I:GLY358 2.7 48.4 1.0
O I:ALA390 2.7 48.7 1.0
O I:MET357 3.2 48.1 1.0
OH I:TYR355 3.4 48.6 1.0
C I:GLU388 3.5 48.6 1.0
C I:MET357 3.5 48.0 1.0
C I:MET356 3.8 47.9 1.0
C I:ALA390 3.8 48.5 1.0
CA I:GLU388 3.8 48.6 1.0
C I:GLY358 3.8 48.3 1.0
CA I:MET357 4.0 47.9 1.0
CZ I:TYR355 4.0 48.6 1.0
N I:GLY358 4.1 48.2 1.0
CE2 I:TYR355 4.2 48.3 1.0
CG I:GLU388 4.3 48.8 1.0
N I:MET357 4.4 47.9 1.0
O I:GLY387 4.4 48.5 1.0
N I:ALA390 4.4 48.6 1.0
CA I:GLY358 4.5 48.3 1.0
CE I:MET356 4.6 49.3 1.0
N I:ILE389 4.6 48.6 1.0
N I:CYS391 4.6 48.5 1.0
CA I:CYS391 4.6 48.6 1.0
CB I:GLU388 4.7 48.6 1.0
C I:ILE389 4.7 48.7 1.0
CA I:ALA390 4.7 48.6 1.0
N I:GLY359 4.9 48.3 1.0
CG I:MET356 5.0 48.4 1.0
N I:GLU388 5.0 48.6 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: Tue Dec 15 05:57:22 2020

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