Magnesium in PDB 1rqi: Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate
Enzymatic activity of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate
All present enzymatic activity of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate:
2.5.1.10;
Protein crystallography data
The structure of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate, PDB code: 1rqi
was solved by
D.J.Hosfield,
Y.Zhang,
D.R.Dougan,
A.Brooun,
L.W.Tari,
R.V.Swanson,
J.Finn,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.03 /
2.42
|
Space group
|
P 41 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.839,
88.839,
174.769,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.3 /
25.9
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate
(pdb code 1rqi). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate, PDB code: 1rqi:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 1rqi
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Magnesium Binding Sites List in 1rqi
Magnesium binding site 1 out
of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg603
b:26.3
occ:1.00
|
O
|
A:HOH717
|
2.0
|
20.9
|
1.0
|
O
|
A:HOH718
|
2.0
|
25.5
|
1.0
|
O8
|
A:DST401
|
2.1
|
36.9
|
1.0
|
O5
|
A:DST401
|
2.1
|
26.2
|
1.0
|
O
|
A:HOH734
|
2.2
|
20.3
|
1.0
|
OD2
|
A:ASP244
|
2.2
|
24.5
|
1.0
|
CG
|
A:ASP244
|
3.3
|
23.3
|
1.0
|
P3
|
A:DST401
|
3.3
|
33.0
|
1.0
|
P1
|
A:DST401
|
3.4
|
27.4
|
1.0
|
O2
|
A:DST401
|
3.5
|
30.7
|
1.0
|
OD1
|
A:ASP244
|
3.6
|
22.8
|
1.0
|
O
|
A:HOH835
|
3.6
|
34.2
|
1.0
|
OD2
|
A:ASP248
|
3.8
|
28.8
|
1.0
|
OD2
|
A:ASP263
|
4.0
|
31.8
|
1.0
|
O
|
A:ASP244
|
4.1
|
22.4
|
1.0
|
O
|
A:HOH719
|
4.1
|
26.2
|
1.0
|
OD1
|
A:ASP263
|
4.1
|
31.0
|
1.0
|
NE2
|
A:GLN241
|
4.3
|
23.1
|
1.0
|
NZ
|
A:LYS258
|
4.3
|
24.6
|
1.0
|
O6
|
A:DST401
|
4.4
|
27.7
|
1.0
|
O7
|
A:DST401
|
4.4
|
32.4
|
1.0
|
O4
|
A:DST401
|
4.5
|
29.8
|
1.0
|
CG
|
A:ASP248
|
4.5
|
27.0
|
1.0
|
CG
|
A:ASP263
|
4.5
|
31.6
|
1.0
|
CB
|
A:ASP244
|
4.5
|
23.1
|
1.0
|
S9
|
A:DST401
|
4.6
|
41.7
|
1.0
|
C
|
A:ASP244
|
4.6
|
23.1
|
1.0
|
CB
|
A:ASP248
|
4.7
|
25.2
|
1.0
|
OD1
|
A:ASP245
|
4.7
|
26.2
|
1.0
|
O
|
A:HOH737
|
4.8
|
29.5
|
1.0
|
CE
|
A:LYS258
|
4.9
|
24.5
|
1.0
|
C3
|
A:IPR501
|
4.9
|
28.9
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 1rqi
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Magnesium Binding Sites List in 1rqi
Magnesium binding site 2 out
of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg604
b:34.2
occ:1.00
|
O7
|
A:DST401
|
2.0
|
32.4
|
1.0
|
O
|
A:HOH721
|
2.0
|
26.6
|
1.0
|
O
|
A:HOH722
|
2.0
|
32.2
|
1.0
|
OD1
|
A:ASP111
|
2.0
|
26.4
|
1.0
|
O
|
A:HOH738
|
2.1
|
32.5
|
1.0
|
OD2
|
A:ASP105
|
2.3
|
21.9
|
1.0
|
CG
|
A:ASP111
|
2.9
|
26.1
|
1.0
|
MG
|
A:MG605
|
3.1
|
24.8
|
1.0
|
CG
|
A:ASP105
|
3.1
|
21.8
|
1.0
|
OD2
|
A:ASP111
|
3.1
|
25.7
|
1.0
|
OD1
|
A:ASP105
|
3.2
|
18.9
|
1.0
|
P3
|
A:DST401
|
3.3
|
33.0
|
1.0
|
NZ
|
A:LYS268
|
3.8
|
33.9
|
1.0
|
S9
|
A:DST401
|
3.9
|
41.7
|
1.0
|
O
|
A:HOH719
|
3.9
|
26.2
|
1.0
|
O
|
A:HOH885
|
4.0
|
50.1
|
1.0
|
OE1
|
A:GLN179
|
4.0
|
26.7
|
1.0
|
OD2
|
A:ASP182
|
4.0
|
29.1
|
1.0
|
O8
|
A:DST401
|
4.2
|
36.9
|
1.0
|
CB
|
A:ASP111
|
4.3
|
25.7
|
1.0
|
O
|
A:HOH720
|
4.5
|
26.0
|
1.0
|
O2
|
A:DST401
|
4.5
|
30.7
|
1.0
|
NE2
|
A:GLN179
|
4.5
|
27.1
|
1.0
|
CE
|
A:LYS268
|
4.5
|
32.6
|
1.0
|
CB
|
A:ASP105
|
4.6
|
21.0
|
1.0
|
O6
|
A:DST401
|
4.6
|
27.7
|
1.0
|
CG
|
A:ASP182
|
4.6
|
25.8
|
1.0
|
NZ
|
A:LYS202
|
4.6
|
22.7
|
1.0
|
O
|
A:HOH835
|
4.7
|
34.2
|
1.0
|
CD
|
A:GLN179
|
4.7
|
25.8
|
1.0
|
OD1
|
A:ASP182
|
4.7
|
27.9
|
1.0
|
O
|
A:HOH735
|
4.8
|
24.3
|
1.0
|
O
|
A:ASP105
|
5.0
|
20.7
|
1.0
|
C10
|
A:DST401
|
5.0
|
41.8
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 1rqi
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Magnesium Binding Sites List in 1rqi
Magnesium binding site 3 out
of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg605
b:24.8
occ:1.00
|
O
|
A:HOH720
|
1.8
|
26.0
|
1.0
|
O
|
A:HOH719
|
2.0
|
26.2
|
1.0
|
O6
|
A:DST401
|
2.0
|
27.7
|
1.0
|
OD1
|
A:ASP105
|
2.2
|
18.9
|
1.0
|
OD1
|
A:ASP111
|
2.2
|
26.4
|
1.0
|
O7
|
A:DST401
|
2.2
|
32.4
|
1.0
|
MG
|
A:MG604
|
3.1
|
34.2
|
1.0
|
CG
|
A:ASP111
|
3.2
|
26.1
|
1.0
|
P1
|
A:DST401
|
3.2
|
27.4
|
1.0
|
CG
|
A:ASP105
|
3.3
|
21.8
|
1.0
|
P3
|
A:DST401
|
3.3
|
33.0
|
1.0
|
O2
|
A:DST401
|
3.5
|
30.7
|
1.0
|
CB
|
A:ASP111
|
3.6
|
25.7
|
1.0
|
OD2
|
A:ASP105
|
3.6
|
21.9
|
1.0
|
OD2
|
A:ASP113
|
3.7
|
31.3
|
1.0
|
O5
|
A:DST401
|
3.9
|
26.2
|
1.0
|
O8
|
A:DST401
|
4.0
|
36.9
|
1.0
|
O
|
A:HOH735
|
4.1
|
24.3
|
1.0
|
O
|
A:HOH738
|
4.3
|
32.5
|
1.0
|
NH1
|
A:ARG116
|
4.3
|
21.6
|
1.0
|
O
|
A:HOH718
|
4.3
|
25.5
|
1.0
|
OD2
|
A:ASP111
|
4.3
|
25.7
|
1.0
|
O4
|
A:DST401
|
4.4
|
29.8
|
1.0
|
OD2
|
A:ASP106
|
4.5
|
22.8
|
1.0
|
CB
|
A:ASP105
|
4.6
|
21.0
|
1.0
|
O
|
A:ASP105
|
4.6
|
20.7
|
1.0
|
O
|
A:HOH721
|
4.6
|
26.6
|
1.0
|
O
|
A:HOH722
|
4.7
|
32.2
|
1.0
|
CG
|
A:ASP113
|
4.9
|
28.7
|
1.0
|
S9
|
A:DST401
|
4.9
|
41.7
|
1.0
|
C
|
A:ASP105
|
4.9
|
20.8
|
1.0
|
O
|
A:HOH731
|
4.9
|
23.2
|
1.0
|
O
|
A:HOH733
|
5.0
|
37.6
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 1rqi
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Magnesium Binding Sites List in 1rqi
Magnesium binding site 4 out
of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg600
b:20.4
occ:1.00
|
O5
|
B:DST400
|
2.0
|
26.4
|
1.0
|
OD2
|
B:ASP244
|
2.1
|
23.4
|
1.0
|
O8
|
B:DST400
|
2.1
|
34.0
|
1.0
|
O
|
B:HOH701
|
2.2
|
17.0
|
1.0
|
O
|
B:HOH741
|
2.2
|
18.7
|
1.0
|
O
|
B:HOH700
|
2.2
|
24.0
|
1.0
|
CG
|
B:ASP244
|
3.3
|
20.7
|
1.0
|
P1
|
B:DST400
|
3.3
|
26.9
|
1.0
|
P3
|
B:DST400
|
3.4
|
31.6
|
1.0
|
O2
|
B:DST400
|
3.6
|
31.2
|
1.0
|
OD2
|
B:ASP248
|
3.7
|
29.4
|
1.0
|
OD1
|
B:ASP244
|
3.8
|
21.4
|
1.0
|
OD2
|
B:ASP263
|
4.1
|
30.0
|
1.0
|
OD1
|
B:ASP263
|
4.1
|
30.6
|
1.0
|
O
|
B:HOH702
|
4.1
|
20.1
|
1.0
|
NZ
|
B:LYS258
|
4.2
|
19.9
|
1.0
|
O
|
B:ASP244
|
4.2
|
20.6
|
1.0
|
O6
|
B:DST400
|
4.2
|
27.4
|
1.0
|
O4
|
B:DST400
|
4.3
|
27.2
|
1.0
|
CE
|
B:LYS258
|
4.3
|
20.7
|
1.0
|
O7
|
B:DST400
|
4.4
|
34.0
|
1.0
|
CG
|
B:ASP248
|
4.4
|
25.9
|
1.0
|
NE2
|
B:GLN241
|
4.4
|
15.0
|
1.0
|
CB
|
B:ASP244
|
4.5
|
20.6
|
1.0
|
CG
|
B:ASP263
|
4.6
|
29.4
|
1.0
|
OD1
|
B:ASP245
|
4.6
|
21.8
|
1.0
|
C
|
B:ASP244
|
4.6
|
20.9
|
1.0
|
S9
|
B:DST400
|
4.6
|
41.4
|
1.0
|
CB
|
B:ASP248
|
4.8
|
24.1
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 1rqi
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Magnesium Binding Sites List in 1rqi
Magnesium binding site 5 out
of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:23.3
occ:1.00
|
O
|
B:HOH704
|
2.0
|
31.5
|
1.0
|
O
|
B:HOH705
|
2.1
|
21.9
|
1.0
|
O7
|
B:DST400
|
2.1
|
34.0
|
1.0
|
OD2
|
B:ASP105
|
2.1
|
20.5
|
1.0
|
OD1
|
B:ASP111
|
2.1
|
21.3
|
1.0
|
O
|
B:HOH862
|
2.6
|
27.0
|
1.0
|
CG
|
B:ASP111
|
2.9
|
21.0
|
1.0
|
OD2
|
B:ASP111
|
2.9
|
19.6
|
1.0
|
CG
|
B:ASP105
|
3.1
|
20.1
|
1.0
|
MG
|
B:MG602
|
3.3
|
30.2
|
1.0
|
OD1
|
B:ASP105
|
3.3
|
20.0
|
1.0
|
P3
|
B:DST400
|
3.4
|
31.6
|
1.0
|
O
|
B:HOH702
|
3.9
|
20.1
|
1.0
|
S9
|
B:DST400
|
4.1
|
41.4
|
1.0
|
OD2
|
B:ASP182
|
4.1
|
28.1
|
1.0
|
NZ
|
B:LYS268
|
4.2
|
28.9
|
1.0
|
OE1
|
B:GLN179
|
4.3
|
28.0
|
1.0
|
O
|
B:HOH742
|
4.3
|
51.9
|
1.0
|
O8
|
B:DST400
|
4.3
|
34.0
|
1.0
|
NE2
|
B:GLN179
|
4.3
|
26.9
|
1.0
|
NZ
|
B:LYS202
|
4.3
|
14.7
|
1.0
|
CB
|
B:ASP111
|
4.3
|
21.4
|
1.0
|
CE
|
B:LYS268
|
4.4
|
29.0
|
1.0
|
CB
|
B:ASP105
|
4.5
|
19.0
|
1.0
|
O2
|
B:DST400
|
4.6
|
31.2
|
1.0
|
CG
|
B:ASP182
|
4.6
|
25.2
|
1.0
|
OD1
|
B:ASP182
|
4.6
|
26.6
|
1.0
|
O
|
B:ASP105
|
4.7
|
19.1
|
1.0
|
CD
|
B:GLN179
|
4.7
|
25.4
|
1.0
|
O6
|
B:DST400
|
4.8
|
27.4
|
1.0
|
O
|
B:HOH703
|
4.8
|
21.3
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 1rqi
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Magnesium Binding Sites List in 1rqi
Magnesium binding site 6 out
of 6 in the Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate
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Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:30.2
occ:1.00
|
O
|
B:HOH702
|
1.9
|
20.1
|
1.0
|
O6
|
B:DST400
|
2.0
|
27.4
|
1.0
|
OD1
|
B:ASP105
|
2.0
|
20.0
|
1.0
|
O
|
B:HOH703
|
2.1
|
21.3
|
1.0
|
OD1
|
B:ASP111
|
2.2
|
21.3
|
1.0
|
O7
|
B:DST400
|
2.4
|
34.0
|
1.0
|
CG
|
B:ASP105
|
3.1
|
20.1
|
1.0
|
CG
|
B:ASP111
|
3.3
|
21.0
|
1.0
|
MG
|
B:MG601
|
3.3
|
23.3
|
1.0
|
P1
|
B:DST400
|
3.3
|
26.9
|
1.0
|
P3
|
B:DST400
|
3.3
|
31.6
|
1.0
|
O2
|
B:DST400
|
3.4
|
31.2
|
1.0
|
OD2
|
B:ASP105
|
3.4
|
20.5
|
1.0
|
CB
|
B:ASP111
|
3.7
|
21.4
|
1.0
|
NH1
|
B:ARG116
|
3.8
|
20.3
|
1.0
|
OD2
|
B:ASP113
|
4.0
|
26.0
|
1.0
|
O5
|
B:DST400
|
4.0
|
26.4
|
1.0
|
O8
|
B:DST400
|
4.1
|
34.0
|
1.0
|
O
|
B:ASP105
|
4.2
|
19.1
|
1.0
|
OD2
|
B:ASP106
|
4.2
|
19.1
|
1.0
|
OD2
|
B:ASP111
|
4.3
|
19.6
|
1.0
|
O
|
B:HOH701
|
4.4
|
17.0
|
1.0
|
CB
|
B:ASP105
|
4.4
|
19.0
|
1.0
|
O4
|
B:DST400
|
4.5
|
27.2
|
1.0
|
C
|
B:ASP105
|
4.6
|
18.9
|
1.0
|
O
|
B:HOH714
|
4.8
|
25.6
|
1.0
|
O
|
B:HOH862
|
4.8
|
27.0
|
1.0
|
O
|
B:HOH704
|
4.8
|
31.5
|
1.0
|
S9
|
B:DST400
|
4.9
|
41.4
|
1.0
|
O
|
B:HOH705
|
5.0
|
21.9
|
1.0
|
CZ
|
B:ARG116
|
5.0
|
19.4
|
1.0
|
|
Reference:
D.J.Hosfield,
Y.Zhang,
D.R.Dougan,
A.Brooun,
L.W.Tari,
R.V.Swanson,
J.Finn.
Structural Basis For Bisphosphonate-Mediated Inhibition of Isoprenoid Biosynthesis J.Biol.Chem. V. 279 8526 2004.
ISSN: ISSN 0021-9258
PubMed: 14672944
DOI: 10.1074/JBC.C300511200
Page generated: Tue Aug 13 13:04:37 2024
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