Sodium in PDB 8a4d: 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor
Enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor
All present enzymatic activity of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor:
2.2.1.7;
Protein crystallography data
The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor, PDB code: 8a4d
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)
|
48.54 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
116.618,
137.618,
231.681,
90,
90,
90
|
R / Rfree (%)
|
17.6 /
24.1
|
Other elements in 8a4d:
The structure of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor
(pdb code 8a4d). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor, PDB code: 8a4d:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 8a4d
Go back to
Sodium Binding Sites List in 8a4d
Sodium binding site 1 out
of 5 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na704
b:40.4
occ:1.00
|
O
|
A:HOH1096
|
2.2
|
38.9
|
1.0
|
O
|
A:HOH1042
|
2.3
|
37.5
|
1.0
|
HH12
|
A:ARG145
|
2.6
|
34.8
|
1.0
|
O
|
D:HOH921
|
2.8
|
25.4
|
1.0
|
HG22
|
A:THR152
|
3.4
|
25.9
|
1.0
|
NH1
|
A:ARG145
|
3.4
|
29.1
|
1.0
|
HA
|
A:THR152
|
3.5
|
27.6
|
1.0
|
HH22
|
A:ARG145
|
3.7
|
30.7
|
1.0
|
CZ
|
A:ARG108
|
3.7
|
31.7
|
1.0
|
HD2
|
A:ARG108
|
3.8
|
29.7
|
1.0
|
HB
|
A:THR152
|
3.8
|
28.5
|
1.0
|
NE
|
A:ARG108
|
3.8
|
30.0
|
1.0
|
HH11
|
A:ARG145
|
3.9
|
34.8
|
1.0
|
NH2
|
A:ARG108
|
3.9
|
22.5
|
1.0
|
HB3
|
D:CYS382
|
4.0
|
26.9
|
1.0
|
HE
|
A:ARG108
|
4.0
|
36.0
|
1.0
|
NH1
|
A:ARG108
|
4.0
|
31.6
|
1.0
|
HH21
|
A:ARG108
|
4.1
|
27.0
|
1.0
|
CG2
|
A:THR152
|
4.2
|
21.6
|
1.0
|
O
|
D:CYS382
|
4.2
|
21.9
|
1.0
|
HH22
|
A:ARG108
|
4.2
|
27.0
|
1.0
|
HH11
|
A:ARG108
|
4.2
|
37.8
|
1.0
|
CB
|
A:THR152
|
4.3
|
23.8
|
1.0
|
HH12
|
A:ARG108
|
4.3
|
37.8
|
1.0
|
NH2
|
A:ARG145
|
4.3
|
25.6
|
1.0
|
CA
|
A:THR152
|
4.3
|
23.0
|
1.0
|
CD
|
A:ARG108
|
4.3
|
24.8
|
1.0
|
CZ
|
A:ARG145
|
4.4
|
22.6
|
1.0
|
OE2
|
D:GLU383
|
4.5
|
28.5
|
1.0
|
HG21
|
A:THR152
|
4.6
|
25.9
|
1.0
|
O
|
A:HOH911
|
4.8
|
21.0
|
1.0
|
O
|
A:THR152
|
4.8
|
20.7
|
1.0
|
HE2
|
A:MET168
|
4.9
|
25.7
|
1.0
|
HD3
|
A:ARG108
|
4.9
|
29.7
|
1.0
|
HG23
|
A:THR152
|
4.9
|
25.9
|
1.0
|
CB
|
D:CYS382
|
5.0
|
22.4
|
1.0
|
O
|
A:HOH1029
|
5.0
|
24.8
|
1.0
|
C
|
D:CYS382
|
5.0
|
19.9
|
1.0
|
|
Sodium binding site 2 out
of 5 in 8a4d
Go back to
Sodium Binding Sites List in 8a4d
Sodium binding site 2 out
of 5 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na704
b:32.3
occ:1.00
|
O
|
C:ALA302
|
2.0
|
32.5
|
1.0
|
O
|
C:HOH1011
|
2.5
|
32.5
|
1.0
|
O
|
C:GLY299
|
2.6
|
31.4
|
1.0
|
O
|
C:HOH1059
|
2.7
|
50.3
|
1.0
|
C
|
C:ALA302
|
3.2
|
32.7
|
1.0
|
H
|
C:ALA302
|
3.3
|
33.1
|
1.0
|
HA
|
C:ILE303
|
3.5
|
43.9
|
1.0
|
C
|
C:GLY299
|
3.7
|
26.5
|
1.0
|
HA2
|
C:GLY299
|
3.9
|
32.9
|
1.0
|
HG22
|
C:ILE303
|
3.9
|
39.4
|
1.0
|
N
|
C:ALA302
|
4.0
|
27.7
|
1.0
|
HB3
|
C:ALA302
|
4.1
|
42.4
|
1.0
|
N
|
C:ILE303
|
4.1
|
31.4
|
1.0
|
CA
|
C:ALA302
|
4.1
|
30.9
|
1.0
|
HA
|
C:TYR300
|
4.2
|
40.1
|
1.0
|
O
|
C:HOH1058
|
4.2
|
44.4
|
1.0
|
CA
|
C:ILE303
|
4.3
|
36.6
|
1.0
|
CA
|
C:GLY299
|
4.4
|
27.5
|
1.0
|
O
|
C:HOH1013
|
4.4
|
32.6
|
1.0
|
N
|
C:TYR300
|
4.7
|
30.3
|
1.0
|
CB
|
C:ALA302
|
4.7
|
35.4
|
1.0
|
CG2
|
C:ILE303
|
4.8
|
32.9
|
1.0
|
CA
|
C:TYR300
|
4.8
|
33.5
|
1.0
|
O
|
C:ILE298
|
4.8
|
30.9
|
1.0
|
HG23
|
C:ILE303
|
4.9
|
39.4
|
1.0
|
HA3
|
C:GLY299
|
4.9
|
32.9
|
1.0
|
H
|
C:HIS301
|
4.9
|
38.5
|
1.0
|
H
|
C:ILE303
|
4.9
|
37.6
|
1.0
|
HA
|
C:ALA302
|
5.0
|
37.1
|
1.0
|
|
Sodium binding site 3 out
of 5 in 8a4d
Go back to
Sodium Binding Sites List in 8a4d
Sodium binding site 3 out
of 5 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na705
b:26.3
occ:1.00
|
H
|
C:VAL592
|
2.1
|
22.8
|
1.0
|
O
|
C:HOH880
|
2.6
|
20.3
|
1.0
|
O
|
C:HOH904
|
2.8
|
15.3
|
1.0
|
O
|
C:HOH978
|
2.8
|
15.5
|
1.0
|
N
|
C:VAL592
|
2.9
|
19.1
|
1.0
|
HA
|
C:TYR591
|
3.0
|
20.7
|
1.0
|
HB
|
C:VAL592
|
3.0
|
20.0
|
1.0
|
HG
|
C:SER434
|
3.1
|
18.4
|
1.0
|
HG23
|
C:VAL592
|
3.1
|
24.3
|
1.0
|
HB3
|
C:PRO429
|
3.3
|
29.1
|
1.0
|
CB
|
C:VAL592
|
3.6
|
16.7
|
1.0
|
HD1
|
C:TYR591
|
3.7
|
25.7
|
1.0
|
HB2
|
C:ALA432
|
3.7
|
27.2
|
1.0
|
O
|
C:HOH962
|
3.7
|
18.2
|
1.0
|
CG2
|
C:VAL592
|
3.7
|
20.3
|
1.0
|
OG
|
C:SER434
|
3.8
|
15.4
|
1.0
|
HA
|
C:PRO429
|
3.8
|
27.4
|
1.0
|
CA
|
C:VAL592
|
3.8
|
20.8
|
1.0
|
CA
|
C:TYR591
|
3.8
|
17.3
|
1.0
|
HB3
|
C:ALA432
|
3.8
|
27.2
|
1.0
|
C
|
C:TYR591
|
3.8
|
21.5
|
1.0
|
HB1
|
C:ALA432
|
3.8
|
27.2
|
1.0
|
HD23
|
C:LEU423
|
3.9
|
27.9
|
1.0
|
CB
|
C:ALA432
|
4.0
|
22.7
|
1.0
|
HG21
|
C:VAL592
|
4.0
|
24.3
|
1.0
|
O
|
C:TYR590
|
4.0
|
18.7
|
1.0
|
O
|
C:VAL592
|
4.1
|
24.9
|
1.0
|
CB
|
C:PRO429
|
4.2
|
24.3
|
1.0
|
HD21
|
C:LEU423
|
4.3
|
27.9
|
1.0
|
CD2
|
C:LEU423
|
4.4
|
23.3
|
1.0
|
HB3
|
C:TYR591
|
4.4
|
26.1
|
1.0
|
HD22
|
C:LEU423
|
4.4
|
27.9
|
1.0
|
C
|
C:VAL592
|
4.5
|
19.9
|
1.0
|
CA
|
C:PRO429
|
4.5
|
22.9
|
1.0
|
CD1
|
C:TYR591
|
4.5
|
21.4
|
1.0
|
HG22
|
C:VAL592
|
4.6
|
24.3
|
1.0
|
HA
|
C:VAL592
|
4.6
|
24.9
|
1.0
|
HB2
|
C:PRO429
|
4.6
|
29.1
|
1.0
|
CB
|
C:TYR591
|
4.6
|
21.8
|
1.0
|
N
|
C:TYR591
|
4.8
|
18.9
|
1.0
|
C
|
C:TYR590
|
4.8
|
19.3
|
1.0
|
CB
|
C:SER434
|
5.0
|
17.4
|
1.0
|
CG1
|
C:VAL592
|
5.0
|
17.2
|
1.0
|
O
|
C:TYR591
|
5.0
|
23.3
|
1.0
|
|
Sodium binding site 4 out
of 5 in 8a4d
Go back to
Sodium Binding Sites List in 8a4d
Sodium binding site 4 out
of 5 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na703
b:26.7
occ:1.00
|
OD2
|
D:ASP455
|
2.6
|
23.1
|
1.0
|
O
|
D:HOH979
|
2.7
|
27.1
|
1.0
|
OE2
|
D:GLU456
|
2.8
|
17.8
|
1.0
|
O
|
D:HOH806
|
2.8
|
23.7
|
1.0
|
HB3
|
D:ASP455
|
3.1
|
25.7
|
1.0
|
HG2
|
D:GLU456
|
3.1
|
22.9
|
1.0
|
HH22
|
D:ARG500
|
3.3
|
33.4
|
1.0
|
CG
|
D:ASP455
|
3.6
|
23.5
|
1.0
|
CD
|
D:GLU456
|
3.7
|
20.2
|
1.0
|
HZ2
|
D:LYS459
|
3.8
|
32.3
|
1.0
|
HZ1
|
D:LYS459
|
3.8
|
32.3
|
1.0
|
CB
|
D:ASP455
|
3.8
|
21.5
|
1.0
|
HH12
|
D:ARG500
|
3.8
|
26.2
|
1.0
|
CG
|
D:GLU456
|
3.8
|
19.1
|
1.0
|
NH2
|
D:ARG500
|
4.0
|
27.9
|
1.0
|
HD2
|
D:LYS459
|
4.1
|
30.6
|
1.0
|
NZ
|
D:LYS459
|
4.2
|
27.0
|
1.0
|
HH21
|
D:ARG533
|
4.2
|
18.8
|
1.0
|
O
|
D:HOH902
|
4.3
|
29.5
|
1.0
|
H
|
D:GLU456
|
4.4
|
25.3
|
1.0
|
N
|
D:GLU456
|
4.4
|
21.1
|
1.0
|
HB2
|
D:ASP455
|
4.4
|
25.7
|
1.0
|
HA
|
D:GLU456
|
4.4
|
26.9
|
1.0
|
HG3
|
D:GLU456
|
4.4
|
22.9
|
1.0
|
OD1
|
D:ASP453
|
4.4
|
16.0
|
1.0
|
NH1
|
D:ARG500
|
4.5
|
21.9
|
1.0
|
HH21
|
D:ARG500
|
4.5
|
33.4
|
1.0
|
C
|
D:ASP455
|
4.5
|
20.4
|
1.0
|
O
|
D:HOH1089
|
4.6
|
31.8
|
1.0
|
OD2
|
D:ASP453
|
4.6
|
21.0
|
1.0
|
CZ
|
D:ARG500
|
4.7
|
27.2
|
1.0
|
OD1
|
D:ASP455
|
4.7
|
25.6
|
1.0
|
CA
|
D:GLU456
|
4.8
|
22.4
|
1.0
|
CA
|
D:ASP455
|
4.8
|
18.4
|
1.0
|
CD
|
D:LYS459
|
4.8
|
25.6
|
1.0
|
HZ3
|
D:LYS459
|
4.8
|
32.3
|
1.0
|
OE1
|
D:GLU456
|
4.9
|
17.3
|
1.0
|
CB
|
D:GLU456
|
4.9
|
20.4
|
1.0
|
HD3
|
D:LYS459
|
4.9
|
30.6
|
1.0
|
O
|
D:ASP455
|
5.0
|
19.6
|
1.0
|
NH2
|
D:ARG533
|
5.0
|
15.8
|
1.0
|
CG
|
D:ASP453
|
5.0
|
20.1
|
1.0
|
|
Sodium binding site 5 out
of 5 in 8a4d
Go back to
Sodium Binding Sites List in 8a4d
Sodium binding site 5 out
of 5 in the 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa with Thiamine Analog Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na707
b:42.9
occ:1.00
|
O
|
F:ALA302
|
2.2
|
32.3
|
1.0
|
O
|
F:HOH1107
|
2.6
|
48.5
|
1.0
|
O
|
F:GLY299
|
2.7
|
34.1
|
1.0
|
O
|
F:HOH1013
|
2.7
|
34.2
|
1.0
|
HA
|
F:ILE303
|
3.3
|
43.7
|
1.0
|
C
|
F:ALA302
|
3.4
|
34.4
|
1.0
|
H
|
F:ALA302
|
3.7
|
37.3
|
1.0
|
C
|
F:GLY299
|
3.8
|
30.7
|
1.0
|
HA2
|
F:GLY299
|
3.9
|
37.9
|
1.0
|
HG22
|
F:ILE303
|
3.9
|
37.7
|
1.0
|
O
|
F:HOH998
|
3.9
|
40.3
|
1.0
|
CA
|
F:ILE303
|
4.1
|
36.4
|
1.0
|
N
|
F:ILE303
|
4.2
|
41.0
|
1.0
|
CA
|
F:GLY299
|
4.4
|
31.6
|
1.0
|
N
|
F:ALA302
|
4.4
|
31.1
|
1.0
|
CA
|
F:ALA302
|
4.5
|
37.0
|
1.0
|
HA
|
F:TYR300
|
4.5
|
37.6
|
1.0
|
HB3
|
F:ALA302
|
4.6
|
41.3
|
1.0
|
CG2
|
F:ILE303
|
4.7
|
31.4
|
1.0
|
HA3
|
F:GLY299
|
4.7
|
37.9
|
1.0
|
N
|
F:TYR300
|
4.8
|
34.8
|
1.0
|
HG23
|
F:ILE303
|
4.9
|
37.7
|
1.0
|
|
Reference:
R.Hamid,
R.Hamid,
A.Hirsch.
N/A N/A.
Page generated: Wed Oct 9 10:26:57 2024
|