Sodium in PDB 2wu2: Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhc HIS84MET Mutant
Enzymatic activity of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhc HIS84MET Mutant
All present enzymatic activity of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhc HIS84MET 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) Sdhc HIS84MET Mutant, PDB code: 2wu2
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)
|
48.00 /
2.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
120.033,
183.363,
202.720,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.689 /
21.431
|
Other elements in 2wu2:
The structure of Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhc HIS84MET Mutant also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhc HIS84MET Mutant
(pdb code 2wu2). 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) Sdhc HIS84MET Mutant, PDB code: 2wu2:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 2wu2
Go back to
Sodium Binding Sites List in 2wu2
Sodium binding site 1 out
of 3 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhc HIS84MET 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) Sdhc HIS84MET Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1590
b:22.2
occ:1.00
|
O
|
A:GLY358
|
2.4
|
34.7
|
1.0
|
O
|
A:ALA390
|
2.4
|
33.1
|
1.0
|
O
|
A:GLU388
|
2.5
|
31.9
|
1.0
|
O
|
A:MET356
|
2.6
|
31.5
|
1.0
|
O
|
A:MET357
|
3.1
|
34.0
|
1.0
|
C
|
A:MET357
|
3.4
|
34.5
|
1.0
|
C
|
A:GLU388
|
3.5
|
30.4
|
1.0
|
C
|
A:GLY358
|
3.5
|
35.2
|
1.0
|
C
|
A:ALA390
|
3.6
|
33.8
|
1.0
|
C
|
A:MET356
|
3.8
|
32.9
|
1.0
|
OH
|
A:TYR355
|
3.9
|
33.2
|
1.0
|
N
|
A:GLY358
|
3.9
|
35.2
|
1.0
|
CA
|
A:MET357
|
4.0
|
33.8
|
1.0
|
CA
|
A:GLU388
|
4.0
|
30.6
|
1.0
|
O
|
A:HOH2176
|
4.2
|
23.9
|
1.0
|
N
|
A:ALA390
|
4.3
|
31.8
|
1.0
|
CA
|
A:GLY358
|
4.3
|
35.5
|
1.0
|
O
|
A:GLY387
|
4.3
|
31.4
|
1.0
|
N
|
A:MET357
|
4.4
|
33.3
|
1.0
|
C
|
A:ILE389
|
4.4
|
31.5
|
1.0
|
O
|
A:HOH2157
|
4.4
|
29.0
|
1.0
|
N
|
A:CYS391
|
4.5
|
34.4
|
1.0
|
CZ
|
A:TYR355
|
4.5
|
32.2
|
1.0
|
CG
|
A:GLU388
|
4.5
|
30.1
|
1.0
|
N
|
A:GLY359
|
4.5
|
35.0
|
1.0
|
N
|
A:ILE389
|
4.5
|
29.8
|
1.0
|
CA
|
A:CYS391
|
4.5
|
34.9
|
1.0
|
CE2
|
A:TYR355
|
4.6
|
32.0
|
1.0
|
CE
|
A:MET356
|
4.6
|
31.0
|
1.0
|
CA
|
A:ALA390
|
4.6
|
32.6
|
1.0
|
CA
|
A:GLY359
|
4.6
|
33.7
|
1.0
|
O
|
A:ILE389
|
4.7
|
31.9
|
1.0
|
CA
|
A:ILE389
|
4.8
|
30.2
|
1.0
|
CG
|
A:MET356
|
4.8
|
33.7
|
1.0
|
CB
|
A:CYS391
|
4.9
|
35.5
|
1.0
|
O
|
A:HOH2171
|
4.9
|
33.6
|
1.0
|
CB
|
A:GLU388
|
4.9
|
30.2
|
1.0
|
CB
|
A:MET356
|
4.9
|
31.9
|
1.0
|
CA
|
A:MET356
|
5.0
|
32.5
|
1.0
|
|
Sodium binding site 2 out
of 3 in 2wu2
Go back to
Sodium Binding Sites List in 2wu2
Sodium binding site 2 out
of 3 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhc HIS84MET 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) Sdhc HIS84MET Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na1590
b:30.6
occ:1.00
|
O
|
E:GLY358
|
2.3
|
42.3
|
1.0
|
O
|
E:GLU388
|
2.4
|
39.1
|
1.0
|
O
|
E:ALA390
|
2.4
|
39.6
|
1.0
|
O
|
E:MET356
|
2.6
|
39.2
|
1.0
|
O
|
E:MET357
|
2.9
|
41.5
|
1.0
|
C
|
E:MET357
|
3.3
|
41.4
|
1.0
|
C
|
E:GLY358
|
3.5
|
42.8
|
1.0
|
C
|
E:GLU388
|
3.5
|
37.4
|
1.0
|
C
|
E:ALA390
|
3.6
|
39.6
|
1.0
|
C
|
E:MET356
|
3.7
|
40.3
|
1.0
|
N
|
E:GLY358
|
3.9
|
42.5
|
1.0
|
OH
|
E:TYR355
|
3.9
|
38.9
|
1.0
|
CA
|
E:MET357
|
3.9
|
40.7
|
1.0
|
CA
|
E:GLU388
|
4.1
|
36.7
|
1.0
|
N
|
E:ALA390
|
4.2
|
38.0
|
1.0
|
CA
|
E:GLY358
|
4.2
|
43.0
|
1.0
|
N
|
E:MET357
|
4.3
|
40.7
|
1.0
|
C
|
E:ILE389
|
4.4
|
38.8
|
1.0
|
N
|
E:GLY359
|
4.4
|
43.1
|
1.0
|
O
|
E:GLY387
|
4.4
|
37.2
|
1.0
|
N
|
E:CYS391
|
4.5
|
40.3
|
1.0
|
CA
|
E:CYS391
|
4.5
|
40.7
|
1.0
|
CZ
|
E:TYR355
|
4.5
|
37.8
|
1.0
|
CG
|
E:GLU388
|
4.5
|
37.7
|
1.0
|
N
|
E:ILE389
|
4.5
|
37.0
|
1.0
|
CA
|
E:ALA390
|
4.6
|
38.5
|
1.0
|
CE2
|
E:TYR355
|
4.6
|
38.0
|
1.0
|
CA
|
E:GLY359
|
4.6
|
42.0
|
1.0
|
CE
|
E:MET356
|
4.7
|
40.2
|
1.0
|
O
|
E:ILE389
|
4.7
|
39.7
|
1.0
|
CG
|
E:MET356
|
4.8
|
42.5
|
1.0
|
CB
|
E:CYS391
|
4.8
|
42.2
|
1.0
|
CA
|
E:ILE389
|
4.8
|
37.9
|
1.0
|
CB
|
E:MET356
|
4.9
|
40.7
|
1.0
|
CA
|
E:MET356
|
4.9
|
40.9
|
1.0
|
O
|
E:HOH2125
|
5.0
|
32.2
|
1.0
|
CB
|
E:GLU388
|
5.0
|
36.9
|
1.0
|
|
Sodium binding site 3 out
of 3 in 2wu2
Go back to
Sodium Binding Sites List in 2wu2
Sodium binding site 3 out
of 3 in the Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhc HIS84MET 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) Sdhc HIS84MET Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Na1590
b:32.2
occ:1.00
|
O
|
I:GLU388
|
2.4
|
40.2
|
1.0
|
O
|
I:ALA390
|
2.5
|
41.3
|
1.0
|
O
|
I:MET356
|
2.5
|
40.7
|
1.0
|
O
|
I:GLY358
|
2.5
|
43.7
|
1.0
|
O
|
I:MET357
|
3.0
|
43.2
|
1.0
|
C
|
I:MET357
|
3.4
|
43.5
|
1.0
|
C
|
I:GLU388
|
3.4
|
38.9
|
1.0
|
C
|
I:GLY358
|
3.6
|
44.2
|
1.0
|
C
|
I:MET356
|
3.7
|
42.3
|
1.0
|
C
|
I:ALA390
|
3.7
|
41.4
|
1.0
|
OH
|
I:TYR355
|
3.8
|
41.1
|
1.0
|
O
|
I:HOH2123
|
3.9
|
27.0
|
1.0
|
N
|
I:GLY358
|
3.9
|
44.2
|
1.0
|
CA
|
I:MET357
|
3.9
|
42.9
|
1.0
|
CA
|
I:GLU388
|
4.0
|
38.3
|
1.0
|
N
|
I:ALA390
|
4.3
|
39.8
|
1.0
|
O
|
I:GLY387
|
4.3
|
38.9
|
1.0
|
CA
|
I:GLY358
|
4.3
|
44.8
|
1.0
|
N
|
I:MET357
|
4.3
|
42.9
|
1.0
|
CZ
|
I:TYR355
|
4.4
|
40.0
|
1.0
|
CG
|
I:GLU388
|
4.4
|
39.0
|
1.0
|
O
|
I:HOH2102
|
4.4
|
22.3
|
1.0
|
C
|
I:ILE389
|
4.5
|
40.1
|
1.0
|
CE2
|
I:TYR355
|
4.5
|
40.3
|
1.0
|
N
|
I:ILE389
|
4.5
|
38.4
|
1.0
|
N
|
I:GLY359
|
4.5
|
44.5
|
1.0
|
N
|
I:CYS391
|
4.6
|
42.3
|
1.0
|
CA
|
I:CYS391
|
4.6
|
43.0
|
1.0
|
CA
|
I:ALA390
|
4.6
|
40.3
|
1.0
|
CE
|
I:MET356
|
4.6
|
41.1
|
1.0
|
CA
|
I:GLY359
|
4.7
|
43.3
|
1.0
|
CG
|
I:MET356
|
4.8
|
43.9
|
1.0
|
O
|
I:ILE389
|
4.8
|
41.2
|
1.0
|
CB
|
I:MET356
|
4.8
|
42.2
|
1.0
|
CB
|
I:GLU388
|
4.8
|
38.3
|
1.0
|
CA
|
I:MET356
|
4.9
|
42.6
|
1.0
|
CA
|
I:ILE389
|
4.9
|
39.0
|
1.0
|
CB
|
I:CYS391
|
4.9
|
44.0
|
1.0
|
O
|
I:HOH2116
|
4.9
|
23.4
|
1.0
|
|
Reference:
J.Ruprecht,
V.Yankovskaya,
E.Maklashina,
S.Iwata,
G.Cecchini.
Crystal Structure of the E. Coli Succinate:Quinone Oxidoreductase (Sqr) Sdhc HIS84MET Mutant To Be Published.
Page generated: Mon Oct 7 04:56:11 2024
|