Magnesium 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:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
13;
Binding sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 13 binding sites of Magnesium where determined in the
Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa, PDB code: 8a29:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 13 in 8a29
Go back to
Magnesium Binding Sites List in 8a29
Magnesium binding site 1 out
of 13 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg702
b:34.6
occ:1.00
|
O
|
A:HOH851
|
2.5
|
49.4
|
1.0
|
|
OD1
|
A:ASP187
|
2.6
|
35.5
|
1.0
|
|
O
|
A:HOH820
|
2.7
|
30.7
|
1.0
|
|
OD1
|
A:ASN216
|
2.7
|
39.5
|
1.0
|
|
HD22
|
A:ASN216
|
3.1
|
36.6
|
1.0
|
|
O
|
A:HOH1087
|
3.3
|
43.7
|
1.0
|
|
H
|
A:GLY188
|
3.3
|
31.5
|
1.0
|
|
CG
|
A:ASN216
|
3.4
|
34.5
|
1.0
|
|
H
|
A:ASP187
|
3.5
|
32.6
|
1.0
|
|
CG
|
A:ASP187
|
3.5
|
32.1
|
1.0
|
|
ND2
|
A:ASN216
|
3.6
|
30.5
|
1.0
|
|
O
|
A:HOH1081
|
3.7
|
28.7
|
1.0
|
|
H
|
A:ASN216
|
3.9
|
35.1
|
1.0
|
|
OD2
|
A:ASP187
|
4.0
|
36.2
|
1.0
|
|
HA3
|
A:GLY186
|
4.0
|
29.1
|
1.0
|
|
N
|
A:ASP187
|
4.0
|
27.2
|
1.0
|
|
N
|
A:GLY188
|
4.1
|
26.2
|
1.0
|
|
HD21
|
A:ASN216
|
4.4
|
36.6
|
1.0
|
|
OD1
|
A:ASP217
|
4.5
|
53.1
|
1.0
|
|
HA2
|
A:GLY186
|
4.6
|
29.1
|
1.0
|
|
O
|
A:ASN214
|
4.6
|
25.6
|
1.0
|
|
HE2
|
A:LYS286
|
4.6
|
63.4
|
1.0
|
|
CA
|
A:GLY186
|
4.6
|
24.2
|
1.0
|
|
HA3
|
A:GLY188
|
4.6
|
27.7
|
1.0
|
|
N
|
A:ASN216
|
4.7
|
29.3
|
1.0
|
|
C
|
A:GLY186
|
4.7
|
23.6
|
1.0
|
|
CB
|
A:ASP187
|
4.7
|
29.3
|
1.0
|
|
CB
|
A:ASN216
|
4.8
|
30.5
|
1.0
|
|
CA
|
A:ASP187
|
4.8
|
21.9
|
1.0
|
|
HE3
|
A:LYS286
|
4.9
|
63.4
|
1.0
|
|
C
|
A:ASP187
|
5.0
|
27.6
|
1.0
|
|
CA
|
A:GLY188
|
5.0
|
23.1
|
1.0
|
|
Magnesium binding site 2 out
of 13 in 8a29
Go back to
Magnesium Binding Sites List in 8a29
Magnesium binding site 2 out
of 13 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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
|
A:Mg703
b:26.4
occ:1.00
|
O
|
A:TYR465
|
2.1
|
27.5
|
1.0
|
|
O
|
A:PHE467
|
2.3
|
25.9
|
1.0
|
|
OD1
|
A:ASP413
|
2.3
|
33.1
|
1.0
|
|
O
|
A:HOH970
|
2.4
|
39.0
|
1.0
|
|
OD2
|
A:ASP413
|
2.8
|
33.3
|
1.0
|
|
CG
|
A:ASP413
|
2.9
|
31.4
|
1.0
|
|
C
|
A:TYR465
|
3.2
|
24.6
|
1.0
|
|
O
|
A:HOH863
|
3.3
|
30.1
|
1.0
|
|
C
|
A:PHE467
|
3.4
|
26.2
|
1.0
|
|
HA
|
A:TYR465
|
3.5
|
28.4
|
1.0
|
|
HA
|
A:ASP468
|
3.5
|
41.6
|
1.0
|
|
C
|
A:LEU466
|
3.9
|
33.6
|
1.0
|
|
HD2
|
A:LYS386
|
3.9
|
34.1
|
1.0
|
|
O
|
A:LEU466
|
3.9
|
34.3
|
1.0
|
|
CA
|
A:TYR465
|
3.9
|
23.7
|
1.0
|
|
O
|
A:GLY464
|
3.9
|
27.5
|
1.0
|
|
H
|
A:GLY469
|
4.0
|
37.8
|
1.0
|
|
N
|
A:PHE467
|
4.1
|
32.3
|
1.0
|
|
N
|
A:LEU466
|
4.1
|
28.7
|
1.0
|
|
HA
|
A:LEU466
|
4.1
|
32.7
|
1.0
|
|
N
|
A:ASP468
|
4.3
|
27.8
|
1.0
|
|
HZ2
|
A:LYS386
|
4.3
|
41.8
|
1.0
|
|
CA
|
A:LEU466
|
4.3
|
27.2
|
1.0
|
|
CA
|
A:ASP468
|
4.3
|
34.6
|
1.0
|
|
CA
|
A:PHE467
|
4.4
|
24.7
|
1.0
|
|
CB
|
A:ASP413
|
4.4
|
29.5
|
1.0
|
|
H
|
A:PHE467
|
4.5
|
38.8
|
1.0
|
|
O
|
A:HOH901
|
4.5
|
20.0
|
1.0
|
|
O
|
A:HOH1060
|
4.6
|
37.9
|
1.0
|
|
HB3
|
A:PHE467
|
4.6
|
36.5
|
1.0
|
|
N
|
A:GLY469
|
4.7
|
31.5
|
1.0
|
|
HB2
|
A:ASP413
|
4.8
|
35.4
|
1.0
|
|
C
|
A:GLY464
|
4.8
|
24.7
|
1.0
|
|
CD
|
A:LYS386
|
4.8
|
28.4
|
1.0
|
|
CG
|
A:TYR465
|
4.8
|
23.1
|
1.0
|
|
O
|
A:GLY469
|
4.9
|
24.0
|
1.0
|
|
HA
|
A:ASP413
|
4.9
|
33.0
|
1.0
|
|
HB3
|
A:ASP413
|
4.9
|
35.4
|
1.0
|
|
N
|
A:TYR465
|
4.9
|
23.9
|
1.0
|
|
CD1
|
A:TYR465
|
4.9
|
27.2
|
1.0
|
|
HE3
|
A:LYS386
|
4.9
|
41.3
|
1.0
|
|
H
|
A:LEU466
|
4.9
|
34.5
|
1.0
|
|
HD1
|
A:TYR465
|
5.0
|
32.7
|
1.0
|
|
Magnesium binding site 3 out
of 13 in 8a29
Go back to
Magnesium Binding Sites List in 8a29
Magnesium binding site 3 out
of 13 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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
|
B:Mg701
b:28.5
occ:1.00
|
O
|
B:ALA302
|
2.3
|
29.5
|
1.0
|
|
O
|
B:GLY299
|
2.3
|
27.8
|
1.0
|
|
O
|
B:HOH894
|
2.5
|
25.3
|
1.0
|
|
O
|
B:HOH1098
|
2.6
|
39.5
|
1.0
|
|
O
|
B:HOH1068
|
3.2
|
45.8
|
1.0
|
|
C
|
B:GLY299
|
3.4
|
27.0
|
1.0
|
|
H
|
B:ALA302
|
3.5
|
28.0
|
1.0
|
|
C
|
B:ALA302
|
3.5
|
28.1
|
1.0
|
|
HA
|
B:ILE303
|
3.5
|
36.0
|
1.0
|
|
HA2
|
B:GLY299
|
3.7
|
33.2
|
1.0
|
|
HG22
|
B:ILE303
|
3.8
|
30.7
|
1.0
|
|
HA
|
B:TYR300
|
4.1
|
36.8
|
1.0
|
|
CA
|
B:GLY299
|
4.1
|
27.7
|
1.0
|
|
N
|
B:ALA302
|
4.2
|
23.3
|
1.0
|
|
CA
|
B:ILE303
|
4.3
|
30.0
|
1.0
|
|
N
|
B:ILE303
|
4.3
|
23.1
|
1.0
|
|
HB3
|
B:ALA302
|
4.4
|
31.3
|
1.0
|
|
CA
|
B:ALA302
|
4.4
|
26.6
|
1.0
|
|
N
|
B:TYR300
|
4.5
|
27.0
|
1.0
|
|
O
|
B:HOH1085
|
4.5
|
37.3
|
1.0
|
|
O
|
B:ILE298
|
4.6
|
25.6
|
1.0
|
|
HA3
|
B:GLY299
|
4.6
|
33.2
|
1.0
|
|
CG2
|
B:ILE303
|
4.6
|
25.6
|
1.0
|
|
CA
|
B:TYR300
|
4.7
|
30.7
|
1.0
|
|
H
|
B:HIS301
|
4.8
|
30.0
|
1.0
|
|
HG23
|
B:ILE303
|
4.8
|
30.7
|
1.0
|
|
CB
|
B:ALA302
|
5.0
|
26.1
|
1.0
|
|
N
|
B:HIS301
|
5.0
|
25.0
|
1.0
|
|
Magnesium binding site 4 out
of 13 in 8a29
Go back to
Magnesium Binding Sites List in 8a29
Magnesium binding site 4 out
of 13 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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
|
B:Mg702
b:26.3
occ:1.00
|
O
|
B:TYR465
|
2.1
|
24.5
|
1.0
|
|
OD1
|
B:ASP413
|
2.2
|
29.8
|
1.0
|
|
O
|
B:HOH1005
|
2.3
|
29.4
|
1.0
|
|
O
|
B:PHE467
|
2.3
|
26.1
|
1.0
|
|
O
|
B:HOH831
|
2.6
|
33.2
|
1.0
|
|
OD2
|
B:ASP413
|
2.7
|
32.1
|
1.0
|
|
CG
|
B:ASP413
|
2.8
|
25.6
|
1.0
|
|
C
|
B:TYR465
|
3.2
|
24.2
|
1.0
|
|
O
|
B:HOH888
|
3.4
|
25.3
|
1.0
|
|
HA
|
B:ASP468
|
3.4
|
33.5
|
1.0
|
|
C
|
B:PHE467
|
3.5
|
24.4
|
1.0
|
|
HA
|
B:TYR465
|
3.5
|
26.2
|
1.0
|
|
H
|
B:GLY469
|
3.9
|
30.1
|
1.0
|
|
CA
|
B:TYR465
|
3.9
|
21.9
|
1.0
|
|
O
|
B:GLY464
|
3.9
|
25.0
|
1.0
|
|
C
|
B:LEU466
|
4.0
|
24.7
|
1.0
|
|
HD2
|
B:LYS386
|
4.0
|
34.5
|
1.0
|
|
O
|
B:LEU466
|
4.1
|
25.4
|
1.0
|
|
HE3
|
B:LYS386
|
4.1
|
51.1
|
1.0
|
|
HA
|
B:LEU466
|
4.2
|
30.3
|
1.0
|
|
N
|
B:PHE467
|
4.2
|
28.1
|
1.0
|
|
CA
|
B:ASP468
|
4.2
|
27.9
|
1.0
|
|
N
|
B:LEU466
|
4.2
|
24.8
|
1.0
|
|
N
|
B:ASP468
|
4.3
|
25.6
|
1.0
|
|
CB
|
B:ASP413
|
4.3
|
24.5
|
1.0
|
|
CA
|
B:LEU466
|
4.4
|
25.2
|
1.0
|
|
CA
|
B:PHE467
|
4.5
|
27.9
|
1.0
|
|
O
|
B:HOH920
|
4.5
|
21.3
|
1.0
|
|
H
|
B:PHE467
|
4.5
|
33.7
|
1.0
|
|
N
|
B:GLY469
|
4.6
|
25.1
|
1.0
|
|
HB2
|
B:ASP413
|
4.7
|
29.4
|
1.0
|
|
HA
|
B:ASP413
|
4.7
|
25.7
|
1.0
|
|
HB3
|
B:ASP413
|
4.7
|
29.4
|
1.0
|
|
HB3
|
B:PHE467
|
4.8
|
26.8
|
1.0
|
|
HZ2
|
B:LYS386
|
4.8
|
43.4
|
1.0
|
|
C
|
B:GLY464
|
4.8
|
22.8
|
1.0
|
|
CD
|
B:LYS386
|
4.8
|
28.8
|
1.0
|
|
CE
|
B:LYS386
|
4.9
|
42.6
|
1.0
|
|
CG
|
B:TYR465
|
4.9
|
27.5
|
1.0
|
|
O
|
B:GLY469
|
4.9
|
22.8
|
1.0
|
|
HB3
|
B:LYS386
|
4.9
|
27.6
|
1.0
|
|
N
|
B:TYR465
|
4.9
|
24.1
|
1.0
|
|
CA
|
B:ASP413
|
4.9
|
21.4
|
1.0
|
|
Magnesium binding site 5 out
of 13 in 8a29
Go back to
Magnesium Binding Sites List in 8a29
Magnesium binding site 5 out
of 13 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg 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
|
B:Mg703
b:37.6
occ:1.00
|
OD1
|
B:ASP187
|
2.5
|
29.9
|
1.0
|
|
OD1
|
B:ASN216
|
2.6
|
30.8
|
1.0
|
|
O
|
B:HOH876
|
2.7
|
25.1
|
1.0
|
|
OD2
|
B:ASP217
|
3.0
|
52.2
|
1.0
|
|
CG
|
B:ASP187
|
3.2
|
30.2
|
1.0
|
|
OD2
|
B:ASP187
|
3.3
|
26.5
|
1.0
|
|
H
|
B:GLY188
|
3.3
|
30.7
|
1.0
|
|
HD22
|
B:ASN216
|
3.3
|
37.4
|
1.0
|
|
CG
|
B:ASN216
|
3.4
|
30.6
|
1.0
|
|
H
|
B:ASP187
|
3.6
|
20.7
|
1.0
|
|
H
|
B:ASN216
|
3.7
|
30.8
|
1.0
|
|
ND2
|
B:ASN216
|
3.7
|
31.2
|
1.0
|
|
O
|
B:HOH1087
|
4.1
|
43.9
|
1.0
|
|
N
|
B:GLY188
|
4.1
|
25.6
|
1.0
|
|
O
|
B:HOH1133
|
4.1
|
25.2
|
1.0
|
|
HE3
|
B:LYS286
|
4.2
|
58.6
|
1.0
|
|
N
|
B:ASP187
|
4.2
|
17.3
|
1.0
|
|
CG
|
B:ASP217
|
4.2
|
45.8
|
1.0
|
|
O
|
B:HOH1100
|
4.4
|
36.7
|
1.0
|
|
HA3
|
B:GLY186
|
4.4
|
32.1
|
1.0
|
|
N
|
B:ASN216
|
4.5
|
25.7
|
1.0
|
|
CB
|
B:ASP187
|
4.5
|
25.9
|
1.0
|
|
HD21
|
B:ASN216
|
4.5
|
37.4
|
1.0
|
|
HA3
|
B:GLY188
|
4.6
|
31.4
|
1.0
|
|
O
|
B:ASN214
|
4.6
|
24.9
|
1.0
|
|
H
|
B:ASP217
|
4.7
|
38.9
|
1.0
|
|
CB
|
B:ASN216
|
4.7
|
26.9
|
1.0
|
|
CA
|
B:ASP187
|
4.7
|
25.1
|
1.0
|
|
N
|
B:ASP217
|
4.9
|
32.5
|
1.0
|
|
HA
|
B:ASP215
|
4.9
|
29.0
|
1.0
|
|
C
|
B:ASP187
|
4.9
|
24.4
|
1.0
|
|
CA
|
B:ASN216
|
4.9
|
32.6
|
1.0
|
|
C
|
B:ASN216
|
4.9
|
34.4
|
1.0
|
|
HB3
|
B:ASP187
|
4.9
|
31.1
|
1.0
|
|
C
|
B:GLY186
|
4.9
|
27.6
|
1.0
|
|
CA
|
B:GLY188
|
5.0
|
26.2
|
1.0
|
|
OD1
|
B:ASP217
|
5.0
|
49.4
|
1.0
|
|
HA2
|
B:GLY186
|
5.0
|
32.1
|
1.0
|
|
Magnesium binding site 6 out
of 13 in 8a29
Go back to
Magnesium Binding Sites List in 8a29
Magnesium binding site 6 out
of 13 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg704
b:51.0
occ:1.00
|
H
|
B:ASP455
|
2.0
|
29.4
|
1.0
|
|
HB2
|
B:HIS483
|
2.1
|
36.4
|
1.0
|
|
HB2
|
B:GLU454
|
2.8
|
33.0
|
1.0
|
|
N
|
B:ASP455
|
2.8
|
24.5
|
1.0
|
|
HB2
|
B:ASP455
|
2.8
|
29.0
|
1.0
|
|
OE1
|
B:GLU454
|
3.0
|
29.7
|
1.0
|
|
O
|
B:HIS483
|
3.0
|
32.7
|
1.0
|
|
CB
|
B:HIS483
|
3.0
|
30.3
|
1.0
|
|
HB3
|
B:ASP455
|
3.1
|
29.0
|
1.0
|
|
O
|
B:PRO484
|
3.1
|
29.4
|
1.0
|
|
H
|
B:GLU454
|
3.1
|
28.0
|
1.0
|
|
C
|
B:HIS483
|
3.3
|
31.7
|
1.0
|
|
CB
|
B:ASP455
|
3.3
|
24.1
|
1.0
|
|
HB3
|
B:HIS483
|
3.3
|
36.4
|
1.0
|
|
OD1
|
B:ASP453
|
3.3
|
24.9
|
1.0
|
|
H
|
B:HIS483
|
3.3
|
38.4
|
1.0
|
|
CG
|
B:ASP453
|
3.3
|
22.4
|
1.0
|
|
CA
|
B:HIS483
|
3.5
|
31.7
|
1.0
|
|
N
|
B:GLU454
|
3.5
|
23.3
|
1.0
|
|
HB2
|
B:ASP453
|
3.5
|
30.7
|
1.0
|
|
OD2
|
B:ASP453
|
3.6
|
28.6
|
1.0
|
|
HG12
|
B:ILE485
|
3.6
|
36.6
|
1.0
|
|
CA
|
B:ASP455
|
3.6
|
22.6
|
1.0
|
|
CB
|
B:GLU454
|
3.7
|
27.5
|
1.0
|
|
O
|
B:HOH840
|
3.7
|
31.5
|
1.0
|
|
C
|
B:GLU454
|
3.7
|
23.4
|
1.0
|
|
N
|
B:HIS483
|
3.8
|
32.0
|
1.0
|
|
CA
|
B:GLU454
|
3.8
|
23.1
|
1.0
|
|
C
|
B:PRO484
|
3.9
|
28.9
|
1.0
|
|
HG13
|
B:ILE485
|
4.0
|
36.6
|
1.0
|
|
O
|
B:HOH810
|
4.0
|
27.9
|
1.0
|
|
CB
|
B:ASP453
|
4.0
|
25.6
|
1.0
|
|
HD1
|
B:HIS483
|
4.0
|
37.3
|
1.0
|
|
CD
|
B:GLU454
|
4.0
|
31.2
|
1.0
|
|
N
|
B:PRO484
|
4.1
|
33.3
|
1.0
|
|
CG
|
B:HIS483
|
4.1
|
32.1
|
1.0
|
|
HA
|
B:ASP455
|
4.2
|
27.1
|
1.0
|
|
HA
|
B:ILE485
|
4.2
|
33.7
|
1.0
|
|
CG1
|
B:ILE485
|
4.2
|
30.5
|
1.0
|
|
HB3
|
B:GLU454
|
4.3
|
33.0
|
1.0
|
|
H
|
B:GLU456
|
4.3
|
30.3
|
1.0
|
|
C
|
B:ASP453
|
4.3
|
23.9
|
1.0
|
|
ND1
|
B:HIS483
|
4.4
|
31.1
|
1.0
|
|
HA
|
B:HIS483
|
4.4
|
38.0
|
1.0
|
|
CG
|
B:GLU454
|
4.4
|
23.7
|
1.0
|
|
CA
|
B:PRO484
|
4.6
|
33.9
|
1.0
|
|
N
|
B:ILE485
|
4.7
|
29.3
|
1.0
|
|
CG
|
B:ASP455
|
4.7
|
27.1
|
1.0
|
|
HD2
|
B:PRO484
|
4.7
|
40.5
|
1.0
|
|
HB3
|
B:ASP453
|
4.8
|
30.7
|
1.0
|
|
O
|
B:HOH976
|
4.8
|
35.6
|
1.0
|
|
HA
|
B:GLU454
|
4.8
|
27.7
|
1.0
|
|
CA
|
B:ASP453
|
4.8
|
25.0
|
1.0
|
|
CA
|
B:ILE485
|
4.8
|
28.1
|
1.0
|
|
C
|
B:ASP455
|
4.8
|
24.8
|
1.0
|
|
N
|
B:GLU456
|
4.9
|
25.2
|
1.0
|
|
O
|
B:GLU454
|
4.9
|
21.0
|
1.0
|
|
HG2
|
B:GLU454
|
4.9
|
28.4
|
1.0
|
|
C
|
B:ASN482
|
5.0
|
36.7
|
1.0
|
|
CD
|
B:PRO484
|
5.0
|
33.8
|
1.0
|
|
Magnesium binding site 7 out
of 13 in 8a29
Go back to
Magnesium Binding Sites List in 8a29
Magnesium binding site 7 out
of 13 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg701
b:41.0
occ:1.00
|
O
|
C:HOH816
|
2.5
|
37.4
|
1.0
|
|
OD1
|
C:ASN216
|
2.6
|
44.1
|
1.0
|
|
OD1
|
C:ASP187
|
2.6
|
38.8
|
1.0
|
|
H
|
C:GLY188
|
3.1
|
29.3
|
1.0
|
|
OD2
|
C:ASP217
|
3.3
|
70.4
|
1.0
|
|
H
|
C:ASP187
|
3.4
|
37.3
|
1.0
|
|
HD21
|
C:ASN216
|
3.4
|
47.7
|
1.0
|
|
CG
|
C:ASP187
|
3.5
|
36.0
|
1.0
|
|
O
|
C:HOH1078
|
3.5
|
30.6
|
1.0
|
|
CG
|
C:ASN216
|
3.6
|
41.9
|
1.0
|
|
O
|
C:HOH1044
|
3.7
|
39.2
|
1.0
|
|
H
|
C:ASN216
|
3.8
|
43.5
|
1.0
|
|
ND2
|
C:ASN216
|
3.9
|
39.7
|
1.0
|
|
OD2
|
C:ASP187
|
3.9
|
48.0
|
1.0
|
|
N
|
C:ASP187
|
3.9
|
31.1
|
1.0
|
|
N
|
C:GLY188
|
4.0
|
24.4
|
1.0
|
|
HA3
|
C:GLY186
|
4.0
|
28.7
|
1.0
|
|
CG
|
C:ASP217
|
4.4
|
65.4
|
1.0
|
|
HE3
|
C:LYS286
|
4.4
|
64.7
|
1.0
|
|
O
|
C:ASN214
|
4.5
|
28.0
|
1.0
|
|
N
|
C:ASN216
|
4.6
|
36.2
|
1.0
|
|
HA3
|
C:GLY188
|
4.6
|
29.2
|
1.0
|
|
C
|
C:GLY186
|
4.6
|
32.1
|
1.0
|
|
CB
|
C:ASP187
|
4.6
|
38.0
|
1.0
|
|
CA
|
C:ASP187
|
4.6
|
27.5
|
1.0
|
|
CA
|
C:GLY186
|
4.7
|
23.9
|
1.0
|
|
HB2
|
C:ASP217
|
4.7
|
69.0
|
1.0
|
|
HD22
|
C:ASN216
|
4.7
|
47.7
|
1.0
|
|
HA2
|
C:GLY186
|
4.8
|
28.7
|
1.0
|
|
HA
|
C:ASP215
|
4.8
|
34.3
|
1.0
|
|
C
|
C:ASP187
|
4.8
|
27.4
|
1.0
|
|
CA
|
C:GLY188
|
4.9
|
24.4
|
1.0
|
|
CB
|
C:ASN216
|
4.9
|
34.3
|
1.0
|
|
Magnesium binding site 8 out
of 13 in 8a29
Go back to
Magnesium Binding Sites List in 8a29
Magnesium binding site 8 out
of 13 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg702
b:22.7
occ:1.00
|
O
|
C:TYR465
|
2.1
|
26.0
|
1.0
|
|
O
|
C:PHE467
|
2.2
|
27.0
|
1.0
|
|
OD1
|
C:ASP413
|
2.4
|
26.5
|
1.0
|
|
O
|
C:HOH954
|
2.4
|
34.3
|
1.0
|
|
O
|
C:HOH1005
|
2.4
|
31.6
|
1.0
|
|
O
|
C:HOH960
|
2.5
|
33.8
|
1.0
|
|
OD2
|
C:ASP413
|
2.7
|
29.1
|
1.0
|
|
CG
|
C:ASP413
|
2.9
|
29.6
|
1.0
|
|
O
|
C:HOH865
|
3.2
|
28.2
|
1.0
|
|
C
|
C:TYR465
|
3.2
|
22.5
|
1.0
|
|
HA
|
C:ASP468
|
3.4
|
32.1
|
1.0
|
|
C
|
C:PHE467
|
3.4
|
24.3
|
1.0
|
|
HA
|
C:TYR465
|
3.6
|
26.9
|
1.0
|
|
H
|
C:GLY469
|
3.8
|
33.4
|
1.0
|
|
O
|
C:GLY464
|
3.9
|
20.0
|
1.0
|
|
C
|
C:LEU466
|
3.9
|
28.4
|
1.0
|
|
CA
|
C:TYR465
|
4.0
|
22.4
|
1.0
|
|
HD2
|
C:LYS386
|
4.0
|
41.5
|
1.0
|
|
O
|
C:LEU466
|
4.0
|
24.5
|
1.0
|
|
HA
|
C:LEU466
|
4.1
|
29.1
|
1.0
|
|
N
|
C:LEU466
|
4.1
|
24.5
|
1.0
|
|
CA
|
C:ASP468
|
4.2
|
26.7
|
1.0
|
|
N
|
C:PHE467
|
4.2
|
31.4
|
1.0
|
|
N
|
C:ASP468
|
4.2
|
28.0
|
1.0
|
|
CA
|
C:LEU466
|
4.3
|
24.2
|
1.0
|
|
HZ2
|
C:LYS386
|
4.3
|
37.6
|
1.0
|
|
CB
|
C:ASP413
|
4.4
|
28.2
|
1.0
|
|
CA
|
C:PHE467
|
4.4
|
28.2
|
1.0
|
|
O
|
C:HOH814
|
4.5
|
19.7
|
1.0
|
|
N
|
C:GLY469
|
4.5
|
27.9
|
1.0
|
|
HE3
|
C:LYS386
|
4.6
|
40.2
|
1.0
|
|
H
|
C:PHE467
|
4.6
|
37.7
|
1.0
|
|
HB3
|
C:PHE467
|
4.6
|
31.4
|
1.0
|
|
HA
|
C:ASP413
|
4.8
|
29.3
|
1.0
|
|
C
|
C:GLY464
|
4.8
|
21.6
|
1.0
|
|
HB2
|
C:ASP413
|
4.8
|
33.8
|
1.0
|
|
O
|
C:GLY469
|
4.8
|
20.3
|
1.0
|
|
HB3
|
C:ASP413
|
4.8
|
33.8
|
1.0
|
|
CD
|
C:LYS386
|
4.9
|
34.6
|
1.0
|
|
N
|
C:TYR465
|
4.9
|
21.2
|
1.0
|
|
CG
|
C:TYR465
|
4.9
|
27.8
|
1.0
|
|
H
|
C:LEU466
|
4.9
|
29.4
|
1.0
|
|
C
|
C:ASP468
|
4.9
|
27.8
|
1.0
|
|
Magnesium binding site 9 out
of 13 in 8a29
Go back to
Magnesium Binding Sites List in 8a29
Magnesium binding site 9 out
of 13 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg702
b:43.5
occ:1.00
|
OD1
|
D:ASP187
|
2.1
|
43.4
|
1.0
|
|
OD1
|
D:ASN216
|
2.5
|
52.0
|
1.0
|
|
O
|
D:HOH972
|
2.6
|
43.0
|
1.0
|
|
H
|
D:GLY188
|
3.1
|
36.6
|
1.0
|
|
O
|
D:HOH1091
|
3.2
|
36.5
|
1.0
|
|
CG
|
D:ASP187
|
3.2
|
42.9
|
1.0
|
|
H
|
D:ASP187
|
3.2
|
42.0
|
1.0
|
|
O
|
D:HOH1083
|
3.2
|
45.4
|
1.0
|
|
CG
|
D:ASN216
|
3.6
|
59.4
|
1.0
|
|
HD22
|
D:ASN216
|
3.6
|
70.3
|
1.0
|
|
HZ3
|
D:LYS286
|
3.7
|
77.7
|
1.0
|
|
OD2
|
D:ASP187
|
3.7
|
49.4
|
1.0
|
|
N
|
D:ASP187
|
3.8
|
35.0
|
1.0
|
|
N
|
D:GLY188
|
3.9
|
30.5
|
1.0
|
|
HA3
|
D:GLY186
|
3.9
|
35.6
|
1.0
|
|
H
|
D:ASN216
|
4.0
|
71.5
|
1.0
|
|
ND2
|
D:ASN216
|
4.0
|
58.6
|
1.0
|
|
CB
|
D:ASP187
|
4.4
|
38.1
|
1.0
|
|
CA
|
D:ASP187
|
4.5
|
38.5
|
1.0
|
|
HA3
|
D:GLY188
|
4.5
|
36.5
|
1.0
|
|
NZ
|
D:LYS286
|
4.5
|
64.7
|
1.0
|
|
O
|
D:ASN216
|
4.5
|
66.6
|
1.0
|
|
HA2
|
D:GLY186
|
4.5
|
35.6
|
1.0
|
|
CA
|
D:GLY186
|
4.5
|
29.7
|
1.0
|
|
C
|
D:GLY186
|
4.6
|
38.2
|
1.0
|
|
HZ1
|
D:LYS286
|
4.6
|
77.7
|
1.0
|
|
C
|
D:ASP187
|
4.6
|
35.1
|
1.0
|
|
O
|
D:ASN214
|
4.7
|
37.4
|
1.0
|
|
N
|
D:ASN216
|
4.7
|
59.6
|
1.0
|
|
HB3
|
D:ASP187
|
4.8
|
45.7
|
1.0
|
|
CA
|
D:GLY188
|
4.8
|
30.4
|
1.0
|
|
HD21
|
D:ASN216
|
4.9
|
70.3
|
1.0
|
|
CB
|
D:ASN216
|
4.9
|
58.4
|
1.0
|
|
HA
|
D:ASP215
|
5.0
|
62.6
|
1.0
|
|
HZ2
|
D:LYS286
|
5.0
|
77.7
|
1.0
|
|
Magnesium binding site 10 out
of 13 in 8a29
Go back to
Magnesium Binding Sites List in 8a29
Magnesium binding site 10 out
of 13 in the Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Apo 1-Deoxy-D-Xylulose 5-Phosphate Synthase From Pseudomonas Aeruginosa within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg703
b:37.6
occ:1.00
|
OD1
|
E:ASP187
|
2.3
|
37.0
|
1.0
|
|
O
|
E:HOH833
|
2.6
|
31.8
|
1.0
|
|
OD1
|
E:ASN216
|
2.7
|
43.6
|
1.0
|
|
OD2
|
E:ASP217
|
2.8
|
54.7
|
1.0
|
|
H
|
E:GLY188
|
3.0
|
39.4
|
1.0
|
|
H
|
E:ASP187
|
3.2
|
30.7
|
1.0
|
|
CG
|
E:ASP187
|
3.3
|
35.7
|
1.0
|
|
O
|
E:HOH1111
|
3.4
|
28.7
|
1.0
|
|
HD22
|
E:ASN216
|
3.4
|
42.0
|
1.0
|
|
O
|
E:HOH1102
|
3.4
|
42.2
|
1.0
|
|
CG
|
E:ASN216
|
3.5
|
38.9
|
1.0
|
|
N
|
E:ASP187
|
3.7
|
25.6
|
1.0
|
|
N
|
E:GLY188
|
3.8
|
32.8
|
1.0
|
|
H
|
E:ASN216
|
3.8
|
38.2
|
1.0
|
|
ND2
|
E:ASN216
|
3.8
|
35.0
|
1.0
|
|
OD2
|
E:ASP187
|
3.8
|
33.4
|
1.0
|
|
HA3
|
E:GLY186
|
3.9
|
35.2
|
1.0
|
|
CG
|
E:ASP217
|
4.0
|
62.2
|
1.0
|
|
HA3
|
E:GLY188
|
4.3
|
32.9
|
1.0
|
|
CA
|
E:ASP187
|
4.4
|
31.4
|
1.0
|
|
CB
|
E:ASP187
|
4.4
|
29.7
|
1.0
|
|
C
|
E:GLY186
|
4.5
|
27.4
|
1.0
|
|
HA2
|
E:GLY186
|
4.5
|
35.2
|
1.0
|
|
CA
|
E:GLY186
|
4.5
|
29.4
|
1.0
|
|
O
|
E:ASN214
|
4.5
|
24.9
|
1.0
|
|
OD1
|
E:ASP217
|
4.5
|
67.5
|
1.0
|
|
C
|
E:ASP187
|
4.6
|
31.7
|
1.0
|
|
N
|
E:ASN216
|
4.6
|
31.8
|
1.0
|
|
HD21
|
E:ASN216
|
4.6
|
42.0
|
1.0
|
|
CA
|
E:GLY188
|
4.6
|
27.4
|
1.0
|
|
HA
|
E:ASP215
|
4.8
|
36.2
|
1.0
|
|
CB
|
E:ASN216
|
4.8
|
37.8
|
1.0
|
|
HB3
|
E:ASP187
|
4.9
|
35.6
|
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: Thu Aug 14 21:52:57 2025
|
