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Sodium in PDB 2wu5: Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd HIS71MET Mutant

Enzymatic activity of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd HIS71MET Mutant

All present enzymatic activity of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd HIS71MET 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 HIS71MET Mutant, PDB code: 2wu5 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) 46.83 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 120.060, 183.820, 203.420, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 25.2

Other elements in 2wu5:

The structure of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd HIS71MET 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 HIS71MET Mutant (pdb code 2wu5). 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 HIS71MET Mutant, PDB code: 2wu5:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2wu5

Go back to Sodium Binding Sites List in 2wu5
Sodium binding site 1 out of 3 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd HIS71MET 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 HIS71MET Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1590

b:35.4
occ:1.00
O A:ALA390 2.3 58.9 1.0
O A:GLY358 2.9 63.4 1.0
O A:MET356 3.0 54.7 1.0
O A:GLU388 3.1 71.3 1.0
O A:MET357 3.3 46.9 1.0
C A:ALA390 3.5 60.9 1.0
C A:MET357 3.6 71.0 1.0
C A:GLU388 3.7 52.5 1.0
C A:GLY358 3.7 74.2 1.0
OH A:TYR355 3.8 78.6 1.0
CA A:GLU388 4.0 63.4 1.0
C A:MET356 4.1 56.5 1.0
O A:HOH2044 4.1 31.5 1.0
N A:GLY358 4.1 52.4 1.0
CA A:MET357 4.1 51.5 1.0
N A:ALA390 4.2 60.2 1.0
O A:GLY387 4.3 54.4 1.0
N A:CYS391 4.3 70.1 1.0
CA A:CYS391 4.4 43.9 1.0
CZ A:TYR355 4.4 62.0 1.0
CA A:GLY358 4.4 41.0 1.0
CE2 A:TYR355 4.5 54.4 1.0
CA A:ALA390 4.5 57.5 1.0
C A:ILE389 4.5 82.2 1.0
N A:GLY359 4.6 41.6 1.0
N A:ILE389 4.6 63.8 1.0
N A:MET357 4.6 52.2 1.0
CG A:GLU388 4.6 33.6 1.0
O A:HOH2043 4.7 49.6 1.0
CA A:GLY359 4.8 48.3 1.0
CB A:CYS391 4.8 48.3 1.0
CB A:GLU388 4.9 52.1 1.0
CE A:MET356 4.9 33.5 1.0
CA A:ILE389 5.0 52.2 1.0

Sodium binding site 2 out of 3 in 2wu5

Go back to Sodium Binding Sites List in 2wu5
Sodium binding site 2 out of 3 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd HIS71MET 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 HIS71MET Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1590

b:39.9
occ:1.00
O E:ALA390 2.4 66.1 1.0
O E:MET356 3.0 65.2 1.0
O E:GLY358 3.1 72.2 1.0
O E:GLU388 3.2 81.4 1.0
O E:MET357 3.3 61.7 1.0
C E:MET357 3.6 71.7 1.0
C E:ALA390 3.6 55.9 1.0
OH E:TYR355 3.6 73.6 1.0
C E:GLU388 3.7 50.4 1.0
C E:GLY358 3.9 85.1 1.0
CA E:GLU388 4.0 62.4 1.0
C E:MET356 4.1 60.3 1.0
CA E:MET357 4.1 44.4 1.0
N E:GLY358 4.2 62.4 1.0
CZ E:TYR355 4.2 80.7 1.0
O E:GLY387 4.2 50.8 1.0
CE2 E:TYR355 4.3 61.6 1.0
N E:ALA390 4.3 54.7 1.0
N E:CYS391 4.5 67.0 1.0
CA E:CYS391 4.5 61.9 1.0
CA E:GLY358 4.6 57.6 1.0
N E:MET357 4.6 56.4 1.0
CG E:GLU388 4.6 78.1 1.0
CA E:ALA390 4.6 50.3 1.0
N E:ILE389 4.6 81.1 1.0
C E:ILE389 4.7 80.2 1.0
N E:GLY359 4.8 65.6 1.0
CB E:GLU388 4.9 64.8 1.0
CD2 E:HIS395 5.0 56.5 1.0
CA E:GLY359 5.0 56.5 1.0
CB E:CYS391 5.0 54.0 1.0

Sodium binding site 3 out of 3 in 2wu5

Go back to Sodium Binding Sites List in 2wu5
Sodium binding site 3 out of 3 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd HIS71MET 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 HIS71MET Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na1590

b:64.3
occ:1.00
O I:ALA390 2.5 82.0 1.0
O I:MET356 2.9 70.8 1.0
O I:GLU388 3.2 80.0 1.0
O I:GLY358 3.2 88.5 1.0
O I:MET357 3.4 72.4 1.0
OH I:TYR355 3.5 92.9 1.0
C I:MET357 3.6 83.7 1.0
C I:GLU388 3.7 66.4 1.0
C I:ALA390 3.7 65.6 1.0
CA I:GLU388 3.9 53.4 1.0
C I:MET356 4.0 76.3 1.0
CZ I:TYR355 4.0 82.6 1.0
CA I:MET357 4.0 46.0 1.0
C I:GLY358 4.1 82.1 1.0
CE2 I:TYR355 4.1 70.6 1.0
O I:GLY387 4.2 58.8 1.0
N I:GLY358 4.3 76.9 1.0
N I:ALA390 4.4 85.9 1.0
CG I:GLU388 4.5 76.2 1.0
N I:MET357 4.5 73.9 1.0
N I:CYS391 4.6 77.5 1.0
CA I:CYS391 4.6 54.6 1.0
CA I:GLY358 4.7 51.3 1.0
CA I:ALA390 4.7 70.1 1.0
N I:ILE389 4.7 88.4 1.0
CB I:GLU388 4.8 73.2 1.0
C I:ILE389 4.8 96.3 1.0
CD2 I:HIS395 4.8 79.4 1.0
N I:GLY359 5.0 63.5 1.0
N I:GLU388 5.0 78.2 1.0

Reference:

J.Ruprecht, V.Yankovskaya, E.Maklashina, S.Iwata, G.Cecchini. Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhd HIS71MET Mutant To Be Published.
Page generated: Mon Oct 7 04:56:51 2024

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