Magnesium 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:
Magnesium Binding Sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium 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 Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 8a45
Go back to
Magnesium Binding Sites List in 8a45
Magnesium binding site 1 out
of 6 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 Magnesium with other atoms in the Mg 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:Mg702
b:21.6
occ:1.00
|
O
|
A:MET218
|
2.0
|
31.3
|
1.0
|
|
O21
|
A:HTL701
|
2.0
|
22.8
|
1.0
|
|
O13
|
A:HTL701
|
2.2
|
27.9
|
1.0
|
|
O
|
A:HOH901
|
2.2
|
24.4
|
1.0
|
|
OD1
|
A:ASN216
|
2.2
|
27.9
|
1.0
|
|
OD1
|
A:ASP187
|
2.3
|
25.1
|
1.0
|
|
H
|
A:MET218
|
2.9
|
40.8
|
1.0
|
|
HD22
|
A:ASN216
|
3.0
|
31.4
|
1.0
|
|
C
|
A:MET218
|
3.1
|
35.0
|
1.0
|
|
CG
|
A:ASN216
|
3.1
|
26.1
|
1.0
|
|
CG
|
A:ASP187
|
3.3
|
27.6
|
1.0
|
|
P2
|
A:HTL701
|
3.3
|
27.7
|
1.0
|
|
P1
|
A:HTL701
|
3.4
|
23.6
|
1.0
|
|
H
|
A:GLY188
|
3.4
|
26.8
|
1.0
|
|
ND2
|
A:ASN216
|
3.4
|
26.1
|
1.0
|
|
H
|
A:ASN216
|
3.5
|
29.3
|
1.0
|
|
H
|
A:ASP187
|
3.5
|
26.4
|
1.0
|
|
HB2
|
A:MET218
|
3.6
|
42.1
|
1.0
|
|
O11
|
A:HTL701
|
3.6
|
27.3
|
1.0
|
|
OD2
|
A:ASP187
|
3.6
|
31.6
|
1.0
|
|
N
|
A:MET218
|
3.7
|
34.0
|
1.0
|
|
HA
|
A:SER219
|
3.8
|
42.2
|
1.0
|
|
CA
|
A:MET218
|
3.8
|
35.7
|
1.0
|
|
O22
|
A:HTL701
|
4.0
|
27.0
|
1.0
|
|
O5G
|
A:HTL701
|
4.1
|
26.9
|
1.0
|
|
N
|
A:ASP187
|
4.1
|
21.9
|
1.0
|
|
N
|
A:SER219
|
4.1
|
38.7
|
1.0
|
|
CB
|
A:MET218
|
4.1
|
35.1
|
1.0
|
|
N
|
A:GLY188
|
4.2
|
22.3
|
1.0
|
|
HD21
|
A:ASN216
|
4.2
|
31.4
|
1.0
|
|
HA3
|
A:GLY186
|
4.2
|
28.5
|
1.0
|
|
N
|
A:ASN216
|
4.3
|
24.4
|
1.0
|
|
CA
|
A:SER219
|
4.4
|
35.1
|
1.0
|
|
O
|
A:ASN214
|
4.4
|
23.0
|
1.0
|
|
HB3
|
A:MET218
|
4.4
|
42.1
|
1.0
|
|
CB
|
A:ASN216
|
4.4
|
26.9
|
1.0
|
|
O23
|
A:HTL701
|
4.4
|
26.2
|
1.0
|
|
CB
|
A:ASP187
|
4.5
|
24.7
|
1.0
|
|
H
|
A:ASP217
|
4.6
|
38.6
|
1.0
|
|
O12
|
A:HTL701
|
4.6
|
24.5
|
1.0
|
|
HZ2
|
A:LYS286
|
4.6
|
41.3
|
1.0
|
|
HA3
|
A:GLY188
|
4.6
|
30.2
|
1.0
|
|
N
|
A:ASP217
|
4.7
|
32.2
|
1.0
|
|
CA
|
A:ASN216
|
4.7
|
27.2
|
1.0
|
|
HA
|
A:MET218
|
4.7
|
42.9
|
1.0
|
|
C
|
A:ASN216
|
4.7
|
33.1
|
1.0
|
|
CA
|
A:ASP187
|
4.7
|
24.6
|
1.0
|
|
HD2
|
A:LYS286
|
4.8
|
39.8
|
1.0
|
|
HA
|
A:ASP215
|
4.8
|
30.5
|
1.0
|
|
HA2
|
A:GLY186
|
4.8
|
28.5
|
1.0
|
|
CA
|
A:GLY186
|
4.8
|
23.7
|
1.0
|
|
C
|
A:GLY186
|
4.8
|
24.3
|
1.0
|
|
HB3
|
A:ASN216
|
4.9
|
32.3
|
1.0
|
|
O
|
A:SER219
|
4.9
|
42.1
|
1.0
|
|
HB3
|
A:ASP187
|
4.9
|
29.6
|
1.0
|
|
C
|
A:ASP217
|
4.9
|
37.0
|
1.0
|
|
H
|
A:SER219
|
4.9
|
46.5
|
1.0
|
|
C
|
A:ASP187
|
4.9
|
24.3
|
1.0
|
|
CA
|
A:GLY188
|
5.0
|
25.1
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 8a45
Go back to
Magnesium Binding Sites List in 8a45
Magnesium binding site 2 out
of 6 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 Magnesium with other atoms in the Mg 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:Mg702
b:19.3
occ:1.00
|
O
|
B:MET218
|
2.0
|
28.3
|
1.0
|
|
O22
|
B:HTL701
|
2.2
|
22.9
|
1.0
|
|
OD1
|
B:ASN216
|
2.2
|
22.4
|
1.0
|
|
OD1
|
B:ASP187
|
2.2
|
24.4
|
1.0
|
|
O13
|
B:HTL701
|
2.2
|
25.8
|
1.0
|
|
O
|
B:HOH876
|
2.4
|
22.1
|
1.0
|
|
H
|
B:MET218
|
3.0
|
36.0
|
1.0
|
|
HD21
|
B:ASN216
|
3.0
|
29.4
|
1.0
|
|
CG
|
B:ASN216
|
3.1
|
23.8
|
1.0
|
|
C
|
B:MET218
|
3.1
|
27.7
|
1.0
|
|
CG
|
B:ASP187
|
3.2
|
26.6
|
1.0
|
|
P2
|
B:HTL701
|
3.3
|
23.8
|
1.0
|
|
H
|
B:GLY188
|
3.3
|
25.8
|
1.0
|
|
P1
|
B:HTL701
|
3.4
|
22.2
|
1.0
|
|
ND2
|
B:ASN216
|
3.4
|
24.4
|
1.0
|
|
H
|
B:ASP187
|
3.4
|
27.5
|
1.0
|
|
H
|
B:ASN216
|
3.5
|
29.2
|
1.0
|
|
O11
|
B:HTL701
|
3.6
|
24.6
|
1.0
|
|
OD2
|
B:ASP187
|
3.6
|
28.2
|
1.0
|
|
HB2
|
B:MET218
|
3.6
|
37.0
|
1.0
|
|
N
|
B:MET218
|
3.7
|
29.9
|
1.0
|
|
CA
|
B:MET218
|
3.8
|
30.4
|
1.0
|
|
HA
|
B:SER219
|
3.9
|
35.1
|
1.0
|
|
O23
|
B:HTL701
|
3.9
|
22.5
|
1.0
|
|
O5G
|
B:HTL701
|
4.0
|
24.7
|
1.0
|
|
N
|
B:ASP187
|
4.0
|
22.9
|
1.0
|
|
N
|
B:GLY188
|
4.1
|
21.5
|
1.0
|
|
CB
|
B:MET218
|
4.2
|
30.8
|
1.0
|
|
N
|
B:SER219
|
4.2
|
29.5
|
1.0
|
|
HA3
|
B:GLY186
|
4.2
|
24.9
|
1.0
|
|
HD22
|
B:ASN216
|
4.2
|
29.4
|
1.0
|
|
N
|
B:ASN216
|
4.3
|
24.3
|
1.0
|
|
O
|
B:ASN214
|
4.3
|
22.1
|
1.0
|
|
CB
|
B:ASN216
|
4.4
|
25.3
|
1.0
|
|
HB3
|
B:MET218
|
4.4
|
37.0
|
1.0
|
|
CB
|
B:ASP187
|
4.5
|
22.3
|
1.0
|
|
CA
|
B:SER219
|
4.5
|
29.2
|
1.0
|
|
O21
|
B:HTL701
|
4.5
|
21.4
|
1.0
|
|
HD2
|
B:LYS286
|
4.5
|
37.2
|
1.0
|
|
HZ2
|
B:LYS286
|
4.6
|
36.7
|
1.0
|
|
H
|
B:ASP217
|
4.6
|
32.3
|
1.0
|
|
O12
|
B:HTL701
|
4.6
|
24.5
|
1.0
|
|
HA3
|
B:GLY188
|
4.7
|
26.8
|
1.0
|
|
CA
|
B:ASP187
|
4.7
|
22.9
|
1.0
|
|
N
|
B:ASP217
|
4.7
|
26.9
|
1.0
|
|
CA
|
B:ASN216
|
4.7
|
27.5
|
1.0
|
|
C
|
B:ASN216
|
4.7
|
28.1
|
1.0
|
|
HA
|
B:MET218
|
4.7
|
36.6
|
1.0
|
|
HA2
|
B:GLY186
|
4.8
|
24.9
|
1.0
|
|
CA
|
B:GLY186
|
4.8
|
20.7
|
1.0
|
|
C
|
B:GLY186
|
4.8
|
21.6
|
1.0
|
|
HA
|
B:ASP215
|
4.8
|
28.1
|
1.0
|
|
HB3
|
B:ASN216
|
4.8
|
30.4
|
1.0
|
|
C
|
B:ASP187
|
4.9
|
22.5
|
1.0
|
|
HB3
|
B:ASP187
|
4.9
|
26.8
|
1.0
|
|
C
|
B:ASP217
|
4.9
|
32.4
|
1.0
|
|
O
|
B:SER219
|
4.9
|
28.5
|
1.0
|
|
H
|
B:SER219
|
5.0
|
35.4
|
1.0
|
|
CA
|
B:GLY188
|
5.0
|
22.3
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 8a45
Go back to
Magnesium Binding Sites List in 8a45
Magnesium binding site 3 out
of 6 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 Magnesium with other atoms in the Mg 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:Mg702
b:17.6
occ:1.00
|
O
|
C:MET218
|
2.0
|
28.7
|
1.0
|
|
O21
|
C:HTL701
|
2.1
|
25.3
|
1.0
|
|
OD1
|
C:ASN216
|
2.2
|
25.5
|
1.0
|
|
OD1
|
C:ASP187
|
2.2
|
25.9
|
1.0
|
|
O13
|
C:HTL701
|
2.2
|
27.0
|
1.0
|
|
O
|
C:HOH916
|
2.4
|
22.4
|
1.0
|
|
H
|
C:MET218
|
2.9
|
38.6
|
1.0
|
|
CG
|
C:ASN216
|
3.1
|
27.4
|
1.0
|
|
HD21
|
C:ASN216
|
3.1
|
34.2
|
1.0
|
|
C
|
C:MET218
|
3.2
|
30.2
|
1.0
|
|
CG
|
C:ASP187
|
3.2
|
24.8
|
1.0
|
|
H
|
C:GLY188
|
3.3
|
24.9
|
1.0
|
|
P1
|
C:HTL701
|
3.4
|
23.9
|
1.0
|
|
P2
|
C:HTL701
|
3.4
|
23.5
|
1.0
|
|
H
|
C:ASN216
|
3.4
|
31.6
|
1.0
|
|
ND2
|
C:ASN216
|
3.5
|
28.4
|
1.0
|
|
H
|
C:ASP187
|
3.5
|
23.3
|
1.0
|
|
OD2
|
C:ASP187
|
3.5
|
32.1
|
1.0
|
|
HB2
|
C:MET218
|
3.6
|
40.6
|
1.0
|
|
O11
|
C:HTL701
|
3.6
|
26.0
|
1.0
|
|
N
|
C:MET218
|
3.7
|
32.1
|
1.0
|
|
CA
|
C:MET218
|
3.8
|
33.2
|
1.0
|
|
O5G
|
C:HTL701
|
4.0
|
26.7
|
1.0
|
|
HA
|
C:SER219
|
4.0
|
38.5
|
1.0
|
|
O22
|
C:HTL701
|
4.0
|
26.9
|
1.0
|
|
N
|
C:ASP187
|
4.1
|
19.4
|
1.0
|
|
N
|
C:GLY188
|
4.1
|
20.7
|
1.0
|
|
N
|
C:ASN216
|
4.2
|
26.3
|
1.0
|
|
CB
|
C:MET218
|
4.2
|
33.8
|
1.0
|
|
HA3
|
C:GLY186
|
4.2
|
26.3
|
1.0
|
|
N
|
C:SER219
|
4.2
|
29.6
|
1.0
|
|
HD22
|
C:ASN216
|
4.3
|
34.2
|
1.0
|
|
O
|
C:ASN214
|
4.3
|
21.9
|
1.0
|
|
CB
|
C:ASN216
|
4.4
|
25.0
|
1.0
|
|
CB
|
C:ASP187
|
4.5
|
25.2
|
1.0
|
|
H
|
C:ASP217
|
4.5
|
33.5
|
1.0
|
|
O23
|
C:HTL701
|
4.5
|
21.6
|
1.0
|
|
CA
|
C:SER219
|
4.6
|
32.1
|
1.0
|
|
HA3
|
C:GLY188
|
4.6
|
25.8
|
1.0
|
|
O12
|
C:HTL701
|
4.6
|
22.7
|
1.0
|
|
HA
|
C:ASP215
|
4.6
|
28.5
|
1.0
|
|
N
|
C:ASP217
|
4.6
|
27.9
|
1.0
|
|
CA
|
C:ASN216
|
4.6
|
27.8
|
1.0
|
|
C
|
C:ASN216
|
4.7
|
28.9
|
1.0
|
|
CA
|
C:ASP187
|
4.7
|
21.2
|
1.0
|
|
HD2
|
C:LYS286
|
4.7
|
34.3
|
1.0
|
|
HZ2
|
C:LYS286
|
4.7
|
41.9
|
1.0
|
|
HA
|
C:MET218
|
4.7
|
39.9
|
1.0
|
|
HB3
|
C:MET218
|
4.7
|
40.6
|
1.0
|
|
HA2
|
C:GLY186
|
4.8
|
26.3
|
1.0
|
|
CA
|
C:GLY186
|
4.8
|
21.8
|
1.0
|
|
C
|
C:GLY186
|
4.8
|
20.7
|
1.0
|
|
HB3
|
C:ASN216
|
4.8
|
30.1
|
1.0
|
|
HB3
|
C:ASP187
|
4.8
|
30.3
|
1.0
|
|
C
|
C:ASP187
|
4.9
|
20.9
|
1.0
|
|
C
|
C:ASP217
|
4.9
|
35.7
|
1.0
|
|
CA
|
C:GLY188
|
4.9
|
21.5
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 8a45
Go back to
Magnesium Binding Sites List in 8a45
Magnesium binding site 4 out
of 6 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 Magnesium with other atoms in the Mg 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
|
D:Mg702
b:21.3
occ:1.00
|
O13
|
D:HTL701
|
2.0
|
27.9
|
1.0
|
|
OD1
|
D:ASP187
|
2.1
|
29.5
|
1.0
|
|
O
|
D:MET218
|
2.2
|
29.5
|
1.0
|
|
OD1
|
D:ASN216
|
2.2
|
31.8
|
1.0
|
|
O22
|
D:HTL701
|
2.2
|
28.5
|
1.0
|
|
O
|
D:HOH867
|
2.3
|
26.7
|
1.0
|
|
HD21
|
D:ASN216
|
3.1
|
37.0
|
1.0
|
|
CG
|
D:ASN216
|
3.1
|
31.9
|
1.0
|
|
CG
|
D:ASP187
|
3.1
|
30.4
|
1.0
|
|
H
|
D:MET218
|
3.1
|
43.0
|
1.0
|
|
H
|
D:GLY188
|
3.2
|
32.0
|
1.0
|
|
C
|
D:MET218
|
3.3
|
34.7
|
1.0
|
|
P1
|
D:HTL701
|
3.3
|
26.3
|
1.0
|
|
H
|
D:ASP187
|
3.3
|
29.8
|
1.0
|
|
P2
|
D:HTL701
|
3.4
|
28.9
|
1.0
|
|
ND2
|
D:ASN216
|
3.4
|
30.8
|
1.0
|
|
H
|
D:ASN216
|
3.4
|
38.5
|
1.0
|
|
OD2
|
D:ASP187
|
3.5
|
33.8
|
1.0
|
|
O11
|
D:HTL701
|
3.7
|
29.0
|
1.0
|
|
HA
|
D:SER219
|
3.8
|
40.6
|
1.0
|
|
N
|
D:MET218
|
3.9
|
35.8
|
1.0
|
|
HB2
|
D:MET218
|
3.9
|
42.7
|
1.0
|
|
N
|
D:ASP187
|
3.9
|
24.8
|
1.0
|
|
N
|
D:GLY188
|
3.9
|
26.7
|
1.0
|
|
HA3
|
D:GLY186
|
4.0
|
30.5
|
1.0
|
|
CA
|
D:MET218
|
4.0
|
34.3
|
1.0
|
|
O23
|
D:HTL701
|
4.1
|
28.9
|
1.0
|
|
O5G
|
D:HTL701
|
4.1
|
29.9
|
1.0
|
|
HD22
|
D:ASN216
|
4.3
|
37.0
|
1.0
|
|
N
|
D:ASN216
|
4.3
|
32.0
|
1.0
|
|
O
|
D:ASN214
|
4.3
|
26.0
|
1.0
|
|
N
|
D:SER219
|
4.3
|
33.3
|
1.0
|
|
CB
|
D:ASP187
|
4.3
|
30.1
|
1.0
|
|
O12
|
D:HTL701
|
4.4
|
26.2
|
1.0
|
|
CB
|
D:ASN216
|
4.4
|
32.9
|
1.0
|
|
CB
|
D:MET218
|
4.4
|
35.5
|
1.0
|
|
HA3
|
D:GLY188
|
4.5
|
31.6
|
1.0
|
|
CA
|
D:ASP187
|
4.5
|
29.2
|
1.0
|
|
CA
|
D:SER219
|
4.5
|
33.8
|
1.0
|
|
C
|
D:GLY186
|
4.6
|
26.5
|
1.0
|
|
O21
|
D:HTL701
|
4.6
|
31.1
|
1.0
|
|
CA
|
D:GLY186
|
4.6
|
25.4
|
1.0
|
|
HA2
|
D:GLY186
|
4.6
|
30.5
|
1.0
|
|
H
|
D:ASP217
|
4.6
|
40.2
|
1.0
|
|
HA
|
D:ASP215
|
4.7
|
35.2
|
1.0
|
|
C
|
D:ASP187
|
4.7
|
25.4
|
1.0
|
|
CA
|
D:ASN216
|
4.7
|
32.7
|
1.0
|
|
HB3
|
D:ASP187
|
4.7
|
36.2
|
1.0
|
|
N
|
D:ASP217
|
4.7
|
33.5
|
1.0
|
|
HZ1
|
D:LYS286
|
4.7
|
38.9
|
1.0
|
|
C
|
D:ASN216
|
4.8
|
34.3
|
1.0
|
|
HB3
|
D:MET218
|
4.8
|
42.7
|
1.0
|
|
CA
|
D:GLY188
|
4.8
|
26.3
|
1.0
|
|
HB3
|
D:ASN216
|
4.8
|
39.5
|
1.0
|
|
HD2
|
D:LYS286
|
4.9
|
40.1
|
1.0
|
|
HA
|
D:MET218
|
4.9
|
41.2
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 8a45
Go back to
Magnesium Binding Sites List in 8a45
Magnesium binding site 5 out
of 6 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 Magnesium with other atoms in the Mg binding
site number 5 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:Mg702
b:17.4
occ:1.00
|
O
|
E:MET218
|
2.0
|
29.9
|
1.0
|
|
O13
|
E:HTL701
|
2.1
|
26.8
|
1.0
|
|
O21
|
E:HTL701
|
2.1
|
24.7
|
1.0
|
|
OD1
|
E:ASN216
|
2.2
|
27.6
|
1.0
|
|
O
|
E:HOH896
|
2.2
|
25.2
|
1.0
|
|
OD1
|
E:ASP187
|
2.2
|
29.0
|
1.0
|
|
HD21
|
E:ASN216
|
3.0
|
33.6
|
1.0
|
|
H
|
E:MET218
|
3.1
|
42.0
|
1.0
|
|
CG
|
E:ASN216
|
3.1
|
28.7
|
1.0
|
|
C
|
E:MET218
|
3.2
|
31.0
|
1.0
|
|
CG
|
E:ASP187
|
3.2
|
28.2
|
1.0
|
|
H
|
E:GLY188
|
3.2
|
27.3
|
1.0
|
|
P1
|
E:HTL701
|
3.3
|
24.1
|
1.0
|
|
P2
|
E:HTL701
|
3.3
|
25.1
|
1.0
|
|
ND2
|
E:ASN216
|
3.4
|
27.9
|
1.0
|
|
H
|
E:ASP187
|
3.5
|
28.3
|
1.0
|
|
H
|
E:ASN216
|
3.5
|
32.7
|
1.0
|
|
OD2
|
E:ASP187
|
3.5
|
29.1
|
1.0
|
|
O11
|
E:HTL701
|
3.6
|
22.8
|
1.0
|
|
N
|
E:MET218
|
3.8
|
35.0
|
1.0
|
|
HA
|
E:SER219
|
3.8
|
38.0
|
1.0
|
|
HB2
|
E:MET218
|
3.8
|
39.1
|
1.0
|
|
CA
|
E:MET218
|
3.9
|
32.9
|
1.0
|
|
O22
|
E:HTL701
|
4.0
|
26.4
|
1.0
|
|
N
|
E:ASP187
|
4.0
|
23.6
|
1.0
|
|
N
|
E:GLY188
|
4.0
|
22.7
|
1.0
|
|
O5G
|
E:HTL701
|
4.1
|
28.0
|
1.0
|
|
HA3
|
E:GLY186
|
4.2
|
29.0
|
1.0
|
|
HB3
|
E:MET218
|
4.2
|
39.1
|
1.0
|
|
CB
|
E:MET218
|
4.2
|
32.6
|
1.0
|
|
HD22
|
E:ASN216
|
4.2
|
33.6
|
1.0
|
|
N
|
E:SER219
|
4.2
|
31.9
|
1.0
|
|
N
|
E:ASN216
|
4.3
|
27.2
|
1.0
|
|
O
|
E:ASN214
|
4.4
|
25.4
|
1.0
|
|
CB
|
E:ASN216
|
4.4
|
28.6
|
1.0
|
|
CB
|
E:ASP187
|
4.5
|
25.8
|
1.0
|
|
O12
|
E:HTL701
|
4.5
|
26.1
|
1.0
|
|
CA
|
E:SER219
|
4.5
|
31.6
|
1.0
|
|
O23
|
E:HTL701
|
4.5
|
21.7
|
1.0
|
|
HA3
|
E:GLY188
|
4.6
|
29.4
|
1.0
|
|
CA
|
E:ASP187
|
4.7
|
26.1
|
1.0
|
|
H
|
E:ASP217
|
4.7
|
36.0
|
1.0
|
|
CA
|
E:ASN216
|
4.7
|
29.9
|
1.0
|
|
N
|
E:ASP217
|
4.7
|
29.9
|
1.0
|
|
HA2
|
E:GLY186
|
4.7
|
29.0
|
1.0
|
|
C
|
E:ASN216
|
4.7
|
29.3
|
1.0
|
|
CA
|
E:GLY186
|
4.8
|
24.1
|
1.0
|
|
C
|
E:GLY186
|
4.8
|
24.1
|
1.0
|
|
HB3
|
E:ASN216
|
4.8
|
34.3
|
1.0
|
|
HA
|
E:MET218
|
4.8
|
39.5
|
1.0
|
|
C
|
E:ASP187
|
4.8
|
20.8
|
1.0
|
|
HZ1
|
E:LYS286
|
4.9
|
39.0
|
1.0
|
|
HA
|
E:ASP215
|
4.9
|
34.5
|
1.0
|
|
HB3
|
E:ASP187
|
4.9
|
31.0
|
1.0
|
|
CA
|
E:GLY188
|
4.9
|
24.5
|
1.0
|
|
O
|
E:SER219
|
4.9
|
34.4
|
1.0
|
|
HD2
|
E:LYS286
|
4.9
|
31.6
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 8a45
Go back to
Magnesium Binding Sites List in 8a45
Magnesium binding site 6 out
of 6 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 Magnesium with other atoms in the Mg binding
site number 6 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
|
F:Mg702
b:17.7
occ:1.00
|
OD1
|
F:ASP187
|
2.0
|
24.7
|
1.0
|
|
O
|
F:MET218
|
2.0
|
24.6
|
1.0
|
|
O13
|
F:HTL701
|
2.1
|
22.4
|
1.0
|
|
O23
|
F:HTL701
|
2.2
|
24.9
|
1.0
|
|
O
|
F:HOH846
|
2.2
|
23.2
|
1.0
|
|
OD1
|
F:ASN216
|
2.3
|
25.3
|
1.0
|
|
H
|
F:MET218
|
3.0
|
40.0
|
1.0
|
|
CG
|
F:ASP187
|
3.1
|
24.1
|
1.0
|
|
HD21
|
F:ASN216
|
3.1
|
27.7
|
1.0
|
|
CG
|
F:ASN216
|
3.1
|
25.5
|
1.0
|
|
H
|
F:GLY188
|
3.2
|
27.5
|
1.0
|
|
C
|
F:MET218
|
3.2
|
26.9
|
1.0
|
|
P1
|
F:HTL701
|
3.4
|
23.9
|
1.0
|
|
H
|
F:ASP187
|
3.4
|
26.3
|
1.0
|
|
P2
|
F:HTL701
|
3.4
|
24.9
|
1.0
|
|
ND2
|
F:ASN216
|
3.5
|
23.1
|
1.0
|
|
OD2
|
F:ASP187
|
3.5
|
27.0
|
1.0
|
|
H
|
F:ASN216
|
3.5
|
29.9
|
1.0
|
|
HB2
|
F:MET218
|
3.7
|
37.1
|
1.0
|
|
O11
|
F:HTL701
|
3.7
|
21.5
|
1.0
|
|
N
|
F:MET218
|
3.7
|
33.3
|
1.0
|
|
HA
|
F:SER219
|
3.8
|
32.6
|
1.0
|
|
CA
|
F:MET218
|
3.9
|
31.7
|
1.0
|
|
N
|
F:GLY188
|
3.9
|
22.9
|
1.0
|
|
N
|
F:ASP187
|
4.0
|
21.9
|
1.0
|
|
O5G
|
F:HTL701
|
4.1
|
27.1
|
1.0
|
|
O21
|
F:HTL701
|
4.1
|
26.6
|
1.0
|
|
CB
|
F:MET218
|
4.2
|
30.9
|
1.0
|
|
N
|
F:SER219
|
4.2
|
30.3
|
1.0
|
|
HA3
|
F:GLY186
|
4.2
|
28.1
|
1.0
|
|
HB3
|
F:MET218
|
4.3
|
37.1
|
1.0
|
|
N
|
F:ASN216
|
4.3
|
24.9
|
1.0
|
|
HD22
|
F:ASN216
|
4.3
|
27.7
|
1.0
|
|
CB
|
F:ASP187
|
4.3
|
23.4
|
1.0
|
|
O
|
F:ASN214
|
4.3
|
21.2
|
1.0
|
|
HA3
|
F:GLY188
|
4.4
|
26.6
|
1.0
|
|
CB
|
F:ASN216
|
4.5
|
26.2
|
1.0
|
|
CA
|
F:SER219
|
4.5
|
27.1
|
1.0
|
|
CA
|
F:ASP187
|
4.5
|
25.1
|
1.0
|
|
O12
|
F:HTL701
|
4.6
|
23.5
|
1.0
|
|
H
|
F:ASP217
|
4.6
|
37.3
|
1.0
|
|
O22
|
F:HTL701
|
4.6
|
25.6
|
1.0
|
|
C
|
F:ASP187
|
4.7
|
25.4
|
1.0
|
|
N
|
F:ASP217
|
4.7
|
31.1
|
1.0
|
|
HB3
|
F:ASP187
|
4.7
|
28.1
|
1.0
|
|
CA
|
F:ASN216
|
4.7
|
27.7
|
1.0
|
|
C
|
F:GLY186
|
4.7
|
22.5
|
1.0
|
|
C
|
F:ASN216
|
4.7
|
31.6
|
1.0
|
|
HA2
|
F:GLY186
|
4.8
|
28.1
|
1.0
|
|
CA
|
F:GLY188
|
4.8
|
22.1
|
1.0
|
|
CA
|
F:GLY186
|
4.8
|
23.4
|
1.0
|
|
HA
|
F:ASP215
|
4.8
|
28.2
|
1.0
|
|
HA
|
F:MET218
|
4.8
|
38.1
|
1.0
|
|
HD22
|
F:ASN223
|
4.8
|
38.9
|
1.0
|
|
HZ1
|
F:LYS286
|
4.9
|
36.4
|
1.0
|
|
HD2
|
F:LYS286
|
4.9
|
36.1
|
1.0
|
|
HB3
|
F:ASN216
|
4.9
|
31.5
|
1.0
|
|
C
|
F:ASP217
|
5.0
|
34.0
|
1.0
|
|
HB2
|
F:ASN223
|
5.0
|
43.0
|
1.0
|
|
HB2
|
F:ASP187
|
5.0
|
28.1
|
1.0
|
|
H
|
F:SER219
|
5.0
|
36.5
|
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: Thu Aug 14 21:54:31 2025
|
