Sodium in PDB 8a45: Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate
Enzymatic activity of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate
All present enzymatic activity of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate:
2.2.1.7;
Protein crystallography data
The structure of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate, PDB code: 8a45
was solved by
R.Hamid,
A.Hirsch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.59 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
117.12,
138.013,
231.626,
90,
90,
90
|
R / Rfree (%)
|
18.3 /
21.7
|
Other elements in 8a45:
The structure of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate
(pdb code 8a45). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate, PDB code: 8a45:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 8a45
Go back to
Sodium Binding Sites List in 8a45
Sodium binding site 1 out
of 4 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na706
b:25.8
occ:1.00
|
O
|
A:HOH1119
|
2.2
|
37.5
|
1.0
|
O
|
A:GLY299
|
2.3
|
28.8
|
1.0
|
O
|
A:ALA302
|
2.3
|
26.8
|
1.0
|
O
|
A:HOH1048
|
2.4
|
29.7
|
1.0
|
O
|
A:HOH1112
|
2.6
|
40.7
|
1.0
|
C
|
A:GLY299
|
3.3
|
30.6
|
1.0
|
HA2
|
A:GLY299
|
3.4
|
37.4
|
1.0
|
H
|
A:ALA302
|
3.5
|
31.8
|
1.0
|
C
|
A:ALA302
|
3.6
|
28.0
|
1.0
|
HA
|
A:ILE303
|
3.7
|
31.9
|
1.0
|
CA
|
A:GLY299
|
3.9
|
31.1
|
1.0
|
HG22
|
A:ILE303
|
4.1
|
33.8
|
1.0
|
HA
|
A:TYR300
|
4.1
|
34.4
|
1.0
|
N
|
A:ALA302
|
4.3
|
26.5
|
1.0
|
HA3
|
A:GLY299
|
4.3
|
37.4
|
1.0
|
N
|
A:TYR300
|
4.4
|
27.8
|
1.0
|
N
|
A:ILE303
|
4.5
|
25.8
|
1.0
|
HB3
|
A:ALA302
|
4.5
|
33.0
|
1.0
|
CA
|
A:ILE303
|
4.5
|
26.5
|
1.0
|
CA
|
A:ALA302
|
4.5
|
27.3
|
1.0
|
O
|
A:ILE298
|
4.6
|
31.9
|
1.0
|
CA
|
A:TYR300
|
4.7
|
28.6
|
1.0
|
O
|
A:HOH1133
|
4.7
|
50.2
|
1.0
|
H
|
A:HIS301
|
4.7
|
34.0
|
1.0
|
HG23
|
A:ILE303
|
4.8
|
33.8
|
1.0
|
CG2
|
A:ILE303
|
4.8
|
28.1
|
1.0
|
N
|
A:HIS301
|
5.0
|
28.3
|
1.0
|
|
Sodium binding site 2 out
of 4 in 8a45
Go back to
Sodium Binding Sites List in 8a45
Sodium binding site 2 out
of 4 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na703
b:24.4
occ:1.00
|
O
|
B:HOH863
|
2.2
|
36.4
|
1.0
|
O
|
B:GLY299
|
2.3
|
27.5
|
1.0
|
O
|
B:ALA302
|
2.3
|
30.0
|
1.0
|
O
|
B:HOH1057
|
2.4
|
40.4
|
1.0
|
O
|
B:HOH1079
|
2.5
|
37.1
|
1.0
|
O
|
B:HOH1059
|
2.6
|
28.1
|
1.0
|
C
|
B:GLY299
|
3.4
|
26.3
|
1.0
|
C
|
B:ALA302
|
3.6
|
30.4
|
1.0
|
HA
|
B:ILE303
|
3.6
|
37.5
|
1.0
|
H
|
B:ALA302
|
3.6
|
31.9
|
1.0
|
HA2
|
B:GLY299
|
3.7
|
32.0
|
1.0
|
O
|
B:HOH1135
|
3.9
|
36.2
|
1.0
|
HG22
|
B:ILE303
|
4.0
|
37.1
|
1.0
|
CA
|
B:GLY299
|
4.1
|
26.6
|
1.0
|
HA
|
B:TYR300
|
4.2
|
33.8
|
1.0
|
N
|
B:ALA302
|
4.4
|
26.5
|
1.0
|
CA
|
B:ILE303
|
4.4
|
31.2
|
1.0
|
N
|
B:ILE303
|
4.4
|
25.6
|
1.0
|
O
|
B:HOH1120
|
4.4
|
46.9
|
1.0
|
HA3
|
B:GLY299
|
4.5
|
32.0
|
1.0
|
O
|
B:HOH1029
|
4.5
|
36.0
|
1.0
|
N
|
B:TYR300
|
4.5
|
24.9
|
1.0
|
HB3
|
B:ALA302
|
4.5
|
32.8
|
1.0
|
CA
|
B:ALA302
|
4.5
|
27.5
|
1.0
|
CA
|
B:TYR300
|
4.8
|
28.1
|
1.0
|
CG2
|
B:ILE303
|
4.9
|
30.9
|
1.0
|
O
|
B:ILE298
|
4.9
|
26.6
|
1.0
|
H
|
B:HIS301
|
4.9
|
35.1
|
1.0
|
HG23
|
B:ILE303
|
4.9
|
37.1
|
1.0
|
|
Sodium binding site 3 out
of 4 in 8a45
Go back to
Sodium Binding Sites List in 8a45
Sodium binding site 3 out
of 4 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na703
b:23.6
occ:1.00
|
O
|
C:HOH1087
|
2.2
|
33.4
|
1.0
|
O
|
C:ALA302
|
2.3
|
27.5
|
1.0
|
O
|
C:GLY299
|
2.4
|
28.8
|
1.0
|
O
|
C:HOH1101
|
2.4
|
36.0
|
1.0
|
O
|
C:HOH1059
|
2.5
|
28.5
|
1.0
|
C
|
C:ALA302
|
3.5
|
31.2
|
1.0
|
C
|
C:GLY299
|
3.5
|
26.6
|
1.0
|
HA
|
C:ILE303
|
3.5
|
39.5
|
1.0
|
H
|
C:ALA302
|
3.6
|
31.1
|
1.0
|
HA2
|
C:GLY299
|
3.9
|
30.1
|
1.0
|
HG22
|
C:ILE303
|
3.9
|
36.3
|
1.0
|
HA
|
C:TYR300
|
4.0
|
33.0
|
1.0
|
O
|
C:HOH1161
|
4.2
|
40.0
|
1.0
|
CA
|
C:GLY299
|
4.3
|
25.0
|
1.0
|
N
|
C:ALA302
|
4.3
|
25.9
|
1.0
|
CA
|
C:ILE303
|
4.4
|
32.9
|
1.0
|
N
|
C:ILE303
|
4.4
|
31.1
|
1.0
|
N
|
C:TYR300
|
4.5
|
25.6
|
1.0
|
CA
|
C:ALA302
|
4.5
|
25.6
|
1.0
|
HB3
|
C:ALA302
|
4.5
|
34.2
|
1.0
|
CA
|
C:TYR300
|
4.6
|
27.5
|
1.0
|
HA3
|
C:GLY299
|
4.6
|
30.1
|
1.0
|
O
|
C:HOH1030
|
4.7
|
32.1
|
1.0
|
CG2
|
C:ILE303
|
4.8
|
30.2
|
1.0
|
H
|
C:HIS301
|
4.8
|
31.1
|
1.0
|
HG23
|
C:ILE303
|
5.0
|
36.3
|
1.0
|
|
Sodium binding site 4 out
of 4 in 8a45
Go back to
Sodium Binding Sites List in 8a45
Sodium binding site 4 out
of 4 in the Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na704
b:31.8
occ:1.00
|
O
|
E:ALA302
|
2.2
|
30.2
|
1.0
|
O
|
E:HOH1068
|
2.2
|
39.8
|
1.0
|
O
|
E:HOH1052
|
2.4
|
33.3
|
1.0
|
O
|
E:GLY299
|
2.4
|
27.7
|
1.0
|
O
|
E:HOH1038
|
2.5
|
38.7
|
1.0
|
H
|
E:ALA302
|
3.4
|
35.4
|
1.0
|
C
|
E:ALA302
|
3.4
|
31.9
|
1.0
|
C
|
E:GLY299
|
3.5
|
32.0
|
1.0
|
HA
|
E:ILE303
|
3.6
|
40.0
|
1.0
|
HA2
|
E:GLY299
|
3.7
|
39.3
|
1.0
|
N
|
E:ALA302
|
4.1
|
29.4
|
1.0
|
HA
|
E:TYR300
|
4.1
|
37.4
|
1.0
|
HG22
|
E:ILE303
|
4.2
|
40.0
|
1.0
|
HB3
|
E:ALA302
|
4.2
|
33.9
|
1.0
|
CA
|
E:GLY299
|
4.2
|
32.7
|
1.0
|
CA
|
E:ALA302
|
4.3
|
31.4
|
1.0
|
N
|
E:ILE303
|
4.3
|
31.4
|
1.0
|
CA
|
E:ILE303
|
4.4
|
33.2
|
1.0
|
O
|
E:HOH1041
|
4.5
|
37.1
|
1.0
|
N
|
E:TYR300
|
4.5
|
32.0
|
1.0
|
HA3
|
E:GLY299
|
4.6
|
39.3
|
1.0
|
CA
|
E:TYR300
|
4.7
|
31.1
|
1.0
|
CB
|
E:ALA302
|
4.7
|
28.2
|
1.0
|
H
|
E:HIS301
|
4.8
|
32.8
|
1.0
|
O
|
E:ILE298
|
4.9
|
32.6
|
1.0
|
CG2
|
E:ILE303
|
4.9
|
33.3
|
1.0
|
HG23
|
E:ILE303
|
5.0
|
40.0
|
1.0
|
N
|
E:HIS301
|
5.0
|
27.3
|
1.0
|
|
Reference:
R.Hamid,
A.Hirsch.
Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with 2-Acetyl Thiamine Diphosphate To Be Published.
Page generated: Wed Oct 9 10:26:31 2024
|