Sodium in PDB 8a29: Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
Enzymatic activity of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
All present enzymatic activity of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa:
2.2.1.7;
Protein crystallography data
The structure of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa, PDB code: 8a29
was solved by
R.Hamid,
S.Adam,
A.Lacour,
L.Monjas,
A.Hirsch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.59 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
116.444,
137.631,
232.082,
90,
90,
90
|
R / Rfree (%)
|
17.1 /
22.4
|
Other elements in 8a29:
The structure of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
(pdb code 8a29). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa, PDB code: 8a29:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 8a29
Go back to
Sodium Binding Sites List in 8a29
Sodium binding site 1 out
of 5 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na705
b:29.4
occ:1.00
|
O
|
A:ALA302
|
2.4
|
32.2
|
1.0
|
O
|
A:GLY299
|
2.5
|
30.3
|
1.0
|
O
|
A:HOH935
|
2.7
|
31.2
|
1.0
|
O
|
A:HOH1088
|
2.7
|
47.3
|
1.0
|
HA
|
A:ILE303
|
3.6
|
36.3
|
1.0
|
C
|
A:ALA302
|
3.6
|
27.7
|
1.0
|
C
|
A:GLY299
|
3.6
|
30.3
|
1.0
|
H
|
A:ALA302
|
3.7
|
32.0
|
1.0
|
O
|
A:HOH1068
|
3.8
|
39.0
|
1.0
|
HA2
|
A:GLY299
|
3.8
|
34.3
|
1.0
|
O
|
A:HOH1091
|
4.0
|
43.1
|
1.0
|
HG22
|
A:ILE303
|
4.2
|
29.6
|
1.0
|
HA
|
A:TYR300
|
4.3
|
36.1
|
1.0
|
CA
|
A:GLY299
|
4.3
|
28.6
|
1.0
|
O
|
A:HOH1113
|
4.3
|
33.9
|
1.0
|
CA
|
A:ILE303
|
4.4
|
30.2
|
1.0
|
N
|
A:ALA302
|
4.4
|
26.7
|
1.0
|
N
|
A:ILE303
|
4.5
|
24.2
|
1.0
|
CA
|
A:ALA302
|
4.6
|
28.4
|
1.0
|
O
|
A:HOH968
|
4.6
|
39.9
|
1.0
|
HB3
|
A:ALA302
|
4.6
|
26.6
|
1.0
|
N
|
A:TYR300
|
4.6
|
27.1
|
1.0
|
HA3
|
A:GLY299
|
4.8
|
34.3
|
1.0
|
HG23
|
A:ILE303
|
4.8
|
29.6
|
1.0
|
O
|
A:ILE298
|
4.8
|
29.0
|
1.0
|
CA
|
A:TYR300
|
4.9
|
30.1
|
1.0
|
CG2
|
A:ILE303
|
4.9
|
24.7
|
1.0
|
|
Sodium binding site 2 out
of 5 in 8a29
Go back to
Sodium Binding Sites List in 8a29
Sodium binding site 2 out
of 5 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na703
b:26.2
occ:1.00
|
O
|
C:HOH1057
|
2.2
|
36.5
|
1.0
|
O
|
C:ALA302
|
2.2
|
26.1
|
1.0
|
O
|
C:GLY299
|
2.4
|
26.4
|
1.0
|
O
|
C:HOH1013
|
2.6
|
27.8
|
1.0
|
O
|
C:HOH1054
|
2.8
|
48.8
|
1.0
|
C
|
C:ALA302
|
3.4
|
33.6
|
1.0
|
H
|
C:ALA302
|
3.5
|
30.1
|
1.0
|
C
|
C:GLY299
|
3.5
|
23.6
|
1.0
|
HA
|
C:ILE303
|
3.5
|
36.7
|
1.0
|
HG22
|
C:ILE303
|
3.8
|
37.0
|
1.0
|
HA2
|
C:GLY299
|
3.9
|
33.7
|
1.0
|
HA
|
C:TYR300
|
4.0
|
36.2
|
1.0
|
N
|
C:ALA302
|
4.3
|
25.1
|
1.0
|
CA
|
C:GLY299
|
4.3
|
28.1
|
1.0
|
N
|
C:ILE303
|
4.3
|
31.1
|
1.0
|
CA
|
C:ILE303
|
4.3
|
30.6
|
1.0
|
O
|
C:HOH1074
|
4.4
|
44.9
|
1.0
|
CA
|
C:ALA302
|
4.4
|
33.1
|
1.0
|
O
|
C:HOH1031
|
4.5
|
35.8
|
1.0
|
N
|
C:TYR300
|
4.5
|
23.8
|
1.0
|
HB3
|
C:ALA302
|
4.6
|
41.2
|
1.0
|
CG2
|
C:ILE303
|
4.6
|
30.8
|
1.0
|
CA
|
C:TYR300
|
4.7
|
30.2
|
1.0
|
HA3
|
C:GLY299
|
4.7
|
33.7
|
1.0
|
HG23
|
C:ILE303
|
4.8
|
37.0
|
1.0
|
O
|
C:ILE298
|
4.9
|
32.6
|
1.0
|
H
|
C:HIS301
|
4.9
|
28.5
|
1.0
|
O
|
C:HOH1096
|
4.9
|
39.2
|
1.0
|
CB
|
C:ALA302
|
5.0
|
34.3
|
1.0
|
|
Sodium binding site 3 out
of 5 in 8a29
Go back to
Sodium Binding Sites List in 8a29
Sodium binding site 3 out
of 5 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na703
b:54.4
occ:1.00
|
O
|
D:HOH987
|
2.2
|
52.0
|
1.0
|
O
|
D:ALA302
|
2.3
|
46.6
|
1.0
|
O
|
D:GLY299
|
2.5
|
55.4
|
1.0
|
O
|
D:HOH1070
|
2.5
|
47.9
|
1.0
|
O
|
D:HOH1077
|
2.6
|
54.7
|
1.0
|
O
|
D:HOH993
|
2.7
|
44.9
|
1.0
|
C
|
D:ALA302
|
3.5
|
41.0
|
1.0
|
H
|
D:ALA302
|
3.6
|
49.8
|
1.0
|
C
|
D:GLY299
|
3.6
|
52.3
|
1.0
|
HA
|
D:ILE303
|
3.7
|
56.7
|
1.0
|
HA2
|
D:GLY299
|
3.8
|
65.8
|
1.0
|
CA
|
D:GLY299
|
4.3
|
54.8
|
1.0
|
N
|
D:ALA302
|
4.3
|
41.5
|
1.0
|
HA
|
D:TYR300
|
4.4
|
65.1
|
1.0
|
N
|
D:ILE303
|
4.4
|
43.3
|
1.0
|
HG22
|
D:ILE303
|
4.4
|
53.5
|
1.0
|
CA
|
D:ALA302
|
4.5
|
46.0
|
1.0
|
HB3
|
D:ALA302
|
4.5
|
46.7
|
1.0
|
CA
|
D:ILE303
|
4.5
|
47.2
|
1.0
|
HA3
|
D:GLY299
|
4.7
|
65.8
|
1.0
|
N
|
D:TYR300
|
4.7
|
54.5
|
1.0
|
O
|
D:HOH1122
|
4.8
|
58.2
|
1.0
|
CA
|
D:TYR300
|
5.0
|
54.3
|
1.0
|
CB
|
D:ALA302
|
5.0
|
38.9
|
1.0
|
O
|
D:ILE298
|
5.0
|
52.9
|
1.0
|
|
Sodium binding site 4 out
of 5 in 8a29
Go back to
Sodium Binding Sites List in 8a29
Sodium binding site 4 out
of 5 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na705
b:24.6
occ:1.00
|
O
|
E:HOH1051
|
2.2
|
39.9
|
1.0
|
OD2
|
E:ASP488
|
2.3
|
23.5
|
1.0
|
O
|
E:HOH1045
|
2.4
|
42.8
|
1.0
|
O
|
E:HOH1086
|
2.6
|
34.0
|
1.0
|
OD2
|
E:ASP486
|
2.6
|
31.6
|
1.0
|
OD1
|
E:ASP486
|
2.6
|
27.0
|
1.0
|
CG
|
E:ASP486
|
3.0
|
29.6
|
1.0
|
HB2
|
E:ASP488
|
3.2
|
27.3
|
1.0
|
CG
|
E:ASP488
|
3.4
|
26.4
|
1.0
|
CB
|
E:ASP488
|
3.8
|
22.8
|
1.0
|
H
|
E:ASP488
|
4.1
|
27.7
|
1.0
|
HB3
|
E:ASP488
|
4.4
|
27.3
|
1.0
|
OD1
|
E:ASP488
|
4.5
|
22.2
|
1.0
|
O
|
E:HOH809
|
4.5
|
25.2
|
1.0
|
CB
|
E:ASP486
|
4.5
|
25.6
|
1.0
|
HD2
|
E:PRO487
|
4.8
|
33.0
|
1.0
|
N
|
E:ASP488
|
4.8
|
23.1
|
1.0
|
HB2
|
E:ASP486
|
4.9
|
30.7
|
1.0
|
HB3
|
E:ASP486
|
4.9
|
30.7
|
1.0
|
CA
|
E:ASP488
|
5.0
|
26.7
|
1.0
|
|
Sodium binding site 5 out
of 5 in 8a29
Go back to
Sodium Binding Sites List in 8a29
Sodium binding site 5 out
of 5 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na707
b:37.3
occ:1.00
|
O
|
F:HOH1127
|
2.4
|
34.6
|
1.0
|
O
|
F:HOH1159
|
2.4
|
37.8
|
1.0
|
HB2
|
F:GLN490
|
2.8
|
34.1
|
1.0
|
HE2
|
F:LYS459
|
2.9
|
29.5
|
1.0
|
HG2
|
F:LYS459
|
2.9
|
22.3
|
1.0
|
O
|
F:GLN490
|
3.2
|
20.4
|
1.0
|
O
|
F:PRO491
|
3.4
|
19.7
|
1.0
|
HG12
|
F:VAL492
|
3.4
|
24.2
|
1.0
|
CB
|
F:GLN490
|
3.6
|
28.4
|
1.0
|
HB3
|
F:GLN490
|
3.6
|
34.1
|
1.0
|
C
|
F:GLN490
|
3.7
|
25.4
|
1.0
|
HG13
|
F:VAL492
|
3.7
|
24.2
|
1.0
|
CE
|
F:LYS459
|
3.8
|
24.6
|
1.0
|
CG
|
F:LYS459
|
3.8
|
18.6
|
1.0
|
CG1
|
F:VAL492
|
4.0
|
20.1
|
1.0
|
C
|
F:PRO491
|
4.0
|
22.8
|
1.0
|
HD3
|
F:LYS459
|
4.0
|
27.9
|
1.0
|
CD
|
F:LYS459
|
4.1
|
23.2
|
1.0
|
H
|
F:GLN490
|
4.2
|
29.8
|
1.0
|
CA
|
F:GLN490
|
4.2
|
22.6
|
1.0
|
HE3
|
F:LYS459
|
4.2
|
29.5
|
1.0
|
N
|
F:PRO491
|
4.3
|
24.5
|
1.0
|
HG3
|
F:LYS459
|
4.4
|
22.3
|
1.0
|
HG11
|
F:VAL492
|
4.5
|
24.2
|
1.0
|
HB3
|
F:LYS459
|
4.5
|
23.1
|
1.0
|
HZ3
|
F:LYS459
|
4.6
|
29.2
|
1.0
|
CA
|
F:PRO491
|
4.6
|
22.8
|
1.0
|
HA
|
F:VAL492
|
4.6
|
21.3
|
1.0
|
N
|
F:GLN490
|
4.7
|
24.8
|
1.0
|
N
|
F:VAL492
|
4.7
|
17.6
|
1.0
|
HA
|
F:PRO491
|
4.7
|
27.4
|
1.0
|
NZ
|
F:LYS459
|
4.7
|
24.4
|
1.0
|
O
|
F:HOH844
|
4.7
|
24.8
|
1.0
|
CB
|
F:LYS459
|
4.8
|
19.2
|
1.0
|
O
|
F:HOH851
|
4.8
|
26.5
|
1.0
|
CG
|
F:GLN490
|
4.8
|
30.0
|
1.0
|
HG3
|
F:GLN490
|
4.8
|
36.0
|
1.0
|
HZ1
|
F:LYS459
|
5.0
|
29.2
|
1.0
|
|
Reference:
R.Hamid,
S.Adam,
A.Lacour,
L.Monjas,
A.Hirsch.
Structural Analysis of 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa and Klebsiella Pneumoniae Reveals Conformational Changes Upon Cofactor Binding To Be Published.
Page generated: Wed Oct 9 10:25:45 2024
|