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Sodium in PDB 2ws3: Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant

Enzymatic activity of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant

All present enzymatic activity of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant:
1.3.5.1; 1.3.99.1;

Protein crystallography data

The structure of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant, PDB code: 2ws3 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) 49.03 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 119.850, 184.710, 203.310, 90.00, 90.00, 90.00
R / Rfree (%) 21.87 / 25.271

Other elements in 2ws3:

The structure of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant also contains other interesting chemical elements:

Iron (Fe) 30 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant (pdb code 2ws3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant, PDB code: 2ws3:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2ws3

Go back to Sodium Binding Sites List in 2ws3
Sodium binding site 1 out of 3 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1589

b:27.2
occ:1.00
O A:GLU388 2.3 49.8 1.0
O A:GLY358 2.5 53.2 1.0
O A:ALA390 2.6 51.6 1.0
O A:MET356 2.6 51.9 1.0
O A:MET357 2.9 54.0 1.0
C A:GLU388 3.4 48.8 1.0
C A:MET357 3.4 54.2 1.0
C A:GLY358 3.6 54.5 1.0
C A:ALA390 3.7 52.0 1.0
C A:MET356 3.8 52.4 1.0
OH A:TYR355 3.8 50.8 1.0
CA A:GLU388 3.9 48.3 1.0
CA A:MET357 4.0 53.9 1.0
N A:GLY358 4.1 54.8 1.0
N A:ALA390 4.2 50.4 1.0
CZ A:TYR355 4.3 50.4 1.0
CE2 A:TYR355 4.3 50.9 1.0
N A:MET357 4.4 53.6 1.0
CG A:GLU388 4.4 48.6 1.0
CA A:GLY358 4.4 55.4 1.0
O A:GLY387 4.4 48.5 1.0
CE A:MET356 4.5 51.7 1.0
N A:ILE389 4.5 48.6 1.0
N A:CYS391 4.5 53.4 1.0
C A:ILE389 4.6 50.4 1.0
N A:GLY359 4.6 54.9 1.0
CA A:ALA390 4.6 51.2 1.0
CA A:CYS391 4.6 54.3 1.0
CB A:GLU388 4.7 47.7 1.0
CA A:GLY359 4.7 53.9 1.0
CA A:ILE389 4.8 49.4 1.0
CG A:MET356 4.9 52.6 1.0
CA A:MET356 5.0 52.0 1.0
N A:GLU388 5.0 48.0 1.0

Sodium binding site 2 out of 3 in 2ws3

Go back to Sodium Binding Sites List in 2ws3
Sodium binding site 2 out of 3 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1589

b:45.2
occ:1.00
O E:GLU388 2.4 58.6 1.0
O E:GLY358 2.4 61.5 1.0
O E:ALA390 2.6 59.5 1.0
O E:MET356 2.7 61.2 1.0
O E:MET357 3.0 62.1 1.0
C E:MET357 3.4 62.4 1.0
C E:GLU388 3.4 57.7 1.0
C E:GLY358 3.5 62.7 1.0
C E:ALA390 3.7 59.5 1.0
C E:MET356 3.8 62.0 1.0
CA E:GLU388 3.9 57.1 1.0
OH E:TYR355 3.9 59.0 1.0
N E:GLY358 4.0 63.2 1.0
CA E:MET357 4.0 62.3 1.0
N E:ALA390 4.2 58.2 1.0
CA E:GLY358 4.3 63.6 1.0
CE2 E:TYR355 4.3 60.0 1.0
N E:MET357 4.4 62.7 1.0
CZ E:TYR355 4.4 59.2 1.0
O E:GLY387 4.4 56.3 1.0
CE E:MET356 4.4 61.4 1.0
CG E:GLU388 4.4 58.3 1.0
N E:CYS391 4.4 60.4 1.0
N E:ILE389 4.5 57.5 1.0
N E:GLY359 4.5 63.2 1.0
C E:ILE389 4.5 58.7 1.0
CA E:CYS391 4.5 61.1 1.0
CA E:ALA390 4.6 58.6 1.0
CA E:GLY359 4.7 62.5 1.0
CG E:MET356 4.8 62.6 1.0
CB E:GLU388 4.8 57.0 1.0
CA E:ILE389 4.8 58.1 1.0
CB E:CYS391 4.9 62.3 1.0

Sodium binding site 3 out of 3 in 2ws3

Go back to Sodium Binding Sites List in 2ws3
Sodium binding site 3 out of 3 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd TYR83PHE Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na1589

b:53.3
occ:1.00
O I:GLU388 2.3 0.2 1.0
O I:ALA390 2.5 1.0 1.0
O I:MET356 2.8 0.2 1.0
O I:GLY358 2.8 0.3 1.0
O I:MET357 3.2 0.1 1.0
C I:GLU388 3.2 0.4 1.0
OH I:TYR355 3.6 0.2 1.0
C I:ALA390 3.6 0.7 1.0
CA I:GLU388 3.7 0.2 1.0
C I:MET357 3.7 0.6 1.0
C I:GLY358 3.9 0.1 1.0
C I:MET356 4.0 0.2 1.0
CZ I:TYR355 4.1 0.3 1.0
O I:GLY387 4.1 0.0 1.0
CE2 I:TYR355 4.1 0.0 1.0
N I:ALA390 4.1 0.8 1.0
CA I:MET357 4.2 0.9 1.0
CG I:GLU388 4.2 0.1 1.0
N I:GLY358 4.4 0.1 1.0
N I:ILE389 4.4 0.5 1.0
CA I:ALA390 4.5 0.1 1.0
N I:CYS391 4.5 0.9 1.0
CB I:GLU388 4.6 0.7 1.0
N I:MET357 4.6 0.7 1.0
C I:ILE389 4.6 0.7 1.0
CA I:CYS391 4.7 0.3 1.0
CA I:GLY358 4.7 0.2 1.0
CE I:MET356 4.7 0.9 1.0
N I:GLU388 4.7 0.2 1.0
C I:GLY387 4.8 0.4 1.0
CA I:ILE389 4.8 0.4 1.0
N I:GLY359 4.9 0.3 1.0

Reference:

J.Ruprecht, V.Yankovskaya, E.Maklashina, S.Iwata, G.Cecchini. Succinate Dehydrogenase Activity To Be Published.
Page generated: Tue Dec 15 05:58:18 2020

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