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:
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: Mon Oct 7 04:55:12 2024
|