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Sodium in PDB 2wp9: Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant

Enzymatic activity of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR Mutant

All present enzymatic activity of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR 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) Sdhb HIS207THR Mutant, PDB code: 2wp9 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) 48.85 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 119.853, 183.803, 202.777, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.2

Other elements in 2wp9:

The structure of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR 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) Sdhb HIS207THR Mutant (pdb code 2wp9). 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) Sdhb HIS207THR Mutant, PDB code: 2wp9:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2wp9

Go back to Sodium Binding Sites List in 2wp9
Sodium binding site 1 out of 3 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR 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) Sdhb HIS207THR Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1590

b:31.6
occ:1.00
O A:ALA390 2.3 41.4 1.0
O A:GLY358 2.5 42.1 1.0
O A:GLU388 2.5 38.8 1.0
O A:MET356 2.7 41.0 1.0
O A:MET357 3.1 42.9 1.0
C A:GLU388 3.5 38.4 1.0
C A:MET357 3.5 42.9 1.0
C A:GLY358 3.5 43.3 1.0
C A:ALA390 3.5 41.6 1.0
C A:MET356 3.8 41.7 1.0
CA A:GLU388 4.0 38.4 1.0
OH A:TYR355 4.0 47.6 1.0
N A:GLY358 4.0 43.2 1.0
CA A:MET357 4.1 42.6 1.0
N A:ALA390 4.1 40.4 1.0
O A:GLY387 4.2 38.4 1.0
CA A:GLY358 4.3 43.6 1.0
C A:ILE389 4.4 40.0 1.0
N A:CYS391 4.4 42.2 1.0
N A:MET357 4.4 42.4 1.0
CA A:CYS391 4.4 43.4 1.0
N A:GLY359 4.5 43.1 1.0
CA A:ALA390 4.5 41.0 1.0
N A:ILE389 4.5 38.0 1.0
CG A:GLU388 4.5 39.5 1.0
CA A:GLY359 4.6 42.9 1.0
CZ A:TYR355 4.6 43.5 1.0
CB A:CYS391 4.7 43.9 1.0
CE2 A:TYR355 4.7 42.3 1.0
O A:ILE389 4.8 40.5 1.0
CG A:MET356 4.8 42.1 1.0
CE A:MET356 4.8 40.9 1.0
CA A:ILE389 4.8 38.9 1.0
CB A:GLU388 4.9 37.8 1.0

Sodium binding site 2 out of 3 in 2wp9

Go back to Sodium Binding Sites List in 2wp9
Sodium binding site 2 out of 3 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR 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) Sdhb HIS207THR Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1590

b:37.8
occ:1.00
O E:GLY358 2.3 51.4 1.0
O E:MET356 2.5 49.7 1.0
O E:ALA390 2.5 49.2 1.0
O E:GLU388 2.6 47.6 1.0
O E:MET357 2.7 51.5 1.0
C E:MET357 3.2 51.7 1.0
C E:GLY358 3.3 52.9 1.0
C E:GLU388 3.6 47.2 1.0
C E:MET356 3.6 50.9 1.0
C E:ALA390 3.7 49.3 1.0
N E:GLY358 3.8 52.6 1.0
CA E:MET357 3.8 51.2 1.0
CA E:GLY358 4.1 53.2 1.0
OH E:TYR355 4.1 54.3 1.0
CA E:GLU388 4.2 46.6 1.0
N E:MET357 4.2 51.5 1.0
N E:GLY359 4.3 53.2 1.0
N E:ALA390 4.4 48.5 1.0
CA E:CYS391 4.5 50.8 1.0
N E:CYS391 4.5 49.9 1.0
O E:GLY387 4.5 45.8 1.0
C E:ILE389 4.5 49.0 1.0
CA E:GLY359 4.6 52.9 1.0
CZ E:TYR355 4.6 50.8 1.0
N E:ILE389 4.6 47.4 1.0
CG E:MET356 4.6 53.2 1.0
CG E:GLU388 4.6 48.8 1.0
CB E:CYS391 4.7 51.9 1.0
CA E:ALA390 4.7 49.0 1.0
CE2 E:TYR355 4.7 49.9 1.0
CE E:MET356 4.8 52.5 1.0
O E:ILE389 4.8 50.2 1.0
CA E:MET356 4.9 51.4 1.0
CB E:MET356 4.9 51.6 1.0
CA E:ILE389 5.0 48.4 1.0

Sodium binding site 3 out of 3 in 2wp9

Go back to Sodium Binding Sites List in 2wp9
Sodium binding site 3 out of 3 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhb HIS207THR 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) Sdhb HIS207THR Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na1590

b:49.9
occ:1.00
O I:ALA390 2.5 58.3 1.0
O I:GLU388 2.5 57.0 1.0
O I:MET356 2.6 60.6 1.0
O I:GLY358 2.7 61.4 1.0
O I:MET357 3.0 62.1 1.0
C I:MET357 3.4 62.6 1.0
C I:GLU388 3.5 55.9 1.0
OH I:TYR355 3.7 64.7 1.0
C I:ALA390 3.7 58.4 1.0
C I:GLY358 3.7 62.9 1.0
C I:MET356 3.8 61.9 1.0
CA I:GLU388 3.9 55.1 1.0
CA I:MET357 4.0 62.6 1.0
N I:GLY358 4.1 63.7 1.0
O I:GLY387 4.2 54.5 1.0
CZ I:TYR355 4.3 61.5 1.0
N I:ALA390 4.3 57.0 1.0
N I:MET357 4.3 62.7 1.0
CG I:GLU388 4.4 57.9 1.0
CA I:GLY358 4.5 63.9 1.0
CE2 I:TYR355 4.5 61.1 1.0
CA I:CYS391 4.5 60.5 1.0
N I:CYS391 4.5 59.2 1.0
N I:ILE389 4.6 55.3 1.0
C I:ILE389 4.6 57.4 1.0
CA I:ALA390 4.7 57.6 1.0
N I:GLY359 4.7 63.1 1.0
CB I:GLU388 4.8 55.2 1.0
CB I:CYS391 4.8 61.9 1.0
CG I:MET356 4.8 63.0 1.0
CA I:GLY359 4.9 62.2 1.0
CA I:ILE389 5.0 56.4 1.0
N I:GLU388 5.0 54.1 1.0
CA I:MET356 5.0 62.0 1.0
O I:ILE389 5.0 58.4 1.0

Reference:

J.Ruprecht, S.Iwata, R.A.Rothery, J.H.Weiner, E.Maklashina, G.Cecchini. Perturbation of the Quinone-Binding Site of Complex II Alters the Electronic Properties of the Proximal [3FE-4S] Iron-Sulfur Cluster. J. Biol. Chem. V. 286 12756 2011.
ISSN: ESSN 1083-351X
PubMed: 21310949
DOI: 10.1074/JBC.M110.209874
Page generated: Tue Dec 15 05:58:11 2020

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