Magnesium in PDB 6b04: Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)
Protein crystallography data
The structure of Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B), PDB code: 6b04
was solved by
M.-E.Picard,
M.Cusson,
R.Shi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
101.18 /
1.83
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
187.440,
122.449,
68.761,
90.00,
106.60,
90.00
|
R / Rfree (%)
|
15.7 /
19.1
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)
(pdb code 6b04). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the
Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B), PDB code: 6b04:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 6b04
Go back to
Magnesium Binding Sites List in 6b04
Magnesium binding site 1 out
of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:23.5
occ:1.00
|
O
|
A:HOH549
|
2.0
|
23.1
|
1.0
|
OD2
|
A:ASP151
|
2.0
|
23.2
|
1.0
|
OD1
|
A:ASP147
|
2.1
|
23.5
|
1.0
|
OAN
|
A:C6J401
|
2.1
|
21.2
|
1.0
|
O
|
A:HOH533
|
2.1
|
23.4
|
1.0
|
O
|
A:HOH715
|
2.2
|
23.0
|
1.0
|
CG
|
A:ASP147
|
3.0
|
22.6
|
1.0
|
CG
|
A:ASP151
|
3.0
|
24.4
|
1.0
|
MG
|
A:MG403
|
3.2
|
25.5
|
1.0
|
OD1
|
A:ASP151
|
3.2
|
25.5
|
1.0
|
PAK
|
A:C6J401
|
3.3
|
23.4
|
1.0
|
OD2
|
A:ASP147
|
3.3
|
23.6
|
1.0
|
OAM
|
A:C6J401
|
3.5
|
22.6
|
1.0
|
OD1
|
A:ASP218
|
3.9
|
30.9
|
1.0
|
NE2
|
A:GLN215
|
4.1
|
27.4
|
1.0
|
OAL
|
A:C6J401
|
4.2
|
22.4
|
1.0
|
OE1
|
A:GLN215
|
4.2
|
31.5
|
1.0
|
O
|
A:HOH699
|
4.2
|
22.2
|
1.0
|
O
|
A:HOH548
|
4.2
|
21.9
|
1.0
|
OD2
|
A:ASP218
|
4.3
|
27.8
|
1.0
|
CG
|
A:ASP218
|
4.3
|
29.1
|
1.0
|
NZ
|
A:LYS310
|
4.3
|
33.1
|
1.0
|
CAD
|
A:C6J401
|
4.4
|
25.1
|
1.0
|
CB
|
A:ASP147
|
4.4
|
21.3
|
1.0
|
CB
|
A:ASP151
|
4.4
|
27.1
|
1.0
|
CD
|
A:GLN215
|
4.6
|
30.3
|
1.0
|
NZ
|
A:LYS244
|
4.6
|
21.4
|
1.0
|
CAH
|
A:C6J401
|
4.7
|
24.9
|
1.0
|
CE
|
A:LYS310
|
4.7
|
31.3
|
1.0
|
CAE
|
A:C6J401
|
4.7
|
25.4
|
1.0
|
CAG
|
A:C6J401
|
4.8
|
23.5
|
1.0
|
OAQ
|
A:C6J401
|
4.8
|
23.2
|
1.0
|
O
|
A:ASP147
|
4.8
|
24.7
|
1.0
|
CAC
|
A:C6J401
|
4.9
|
23.8
|
1.0
|
O
|
A:HOH546
|
4.9
|
23.0
|
1.0
|
CA
|
A:ASP147
|
5.0
|
20.9
|
1.0
|
|
Magnesium binding site 2 out
of 9 in 6b04
Go back to
Magnesium Binding Sites List in 6b04
Magnesium binding site 2 out
of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:25.5
occ:1.00
|
OAN
|
A:C6J401
|
2.0
|
21.2
|
1.0
|
OAQ
|
A:C6J401
|
2.0
|
23.2
|
1.0
|
O
|
A:HOH699
|
2.0
|
22.2
|
1.0
|
OD2
|
A:ASP147
|
2.1
|
23.6
|
1.0
|
O
|
A:HOH546
|
2.1
|
23.0
|
1.0
|
OD2
|
A:ASP151
|
2.2
|
23.2
|
1.0
|
CG
|
A:ASP147
|
3.0
|
22.6
|
1.0
|
MG
|
A:MG402
|
3.2
|
23.5
|
1.0
|
CG
|
A:ASP151
|
3.3
|
24.4
|
1.0
|
PAI
|
A:C6J401
|
3.3
|
24.1
|
1.0
|
PAK
|
A:C6J401
|
3.3
|
23.4
|
1.0
|
OD1
|
A:ASP147
|
3.4
|
23.5
|
1.0
|
CB
|
A:ASP151
|
3.7
|
27.1
|
1.0
|
CAH
|
A:C6J401
|
3.7
|
24.9
|
1.0
|
OAL
|
A:C6J401
|
3.8
|
22.4
|
1.0
|
O
|
A:HOH596
|
3.8
|
30.9
|
1.0
|
CAG
|
A:C6J401
|
4.1
|
23.5
|
1.0
|
OAP
|
A:C6J401
|
4.1
|
24.4
|
1.0
|
NH2
|
A:ARG156
|
4.2
|
27.6
|
1.0
|
O
|
A:HOH715
|
4.3
|
23.0
|
1.0
|
O
|
A:HOH570
|
4.3
|
22.6
|
1.0
|
CB
|
A:ASP147
|
4.4
|
21.3
|
1.0
|
OD1
|
A:ASP151
|
4.4
|
25.5
|
1.0
|
O
|
A:HOH626
|
4.4
|
25.9
|
1.0
|
OG
|
A:SER153
|
4.5
|
29.0
|
1.0
|
O
|
A:ASP147
|
4.5
|
24.7
|
1.0
|
OAO
|
A:C6J401
|
4.5
|
24.9
|
1.0
|
OAM
|
A:C6J401
|
4.6
|
22.6
|
1.0
|
OD1
|
A:ASP148
|
4.6
|
30.1
|
1.0
|
O
|
A:HOH549
|
4.7
|
23.1
|
1.0
|
C
|
A:ASP147
|
4.7
|
23.7
|
1.0
|
O
|
A:HOH652
|
4.8
|
31.5
|
1.0
|
MG
|
A:MG404
|
4.8
|
25.6
|
1.0
|
O
|
A:HOH548
|
4.9
|
21.9
|
1.0
|
O
|
A:HOH533
|
4.9
|
23.4
|
1.0
|
CAE
|
A:C6J401
|
4.9
|
25.4
|
1.0
|
CAD
|
A:C6J401
|
5.0
|
25.1
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 6b04
Go back to
Magnesium Binding Sites List in 6b04
Magnesium binding site 3 out
of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:25.6
occ:1.00
|
OAL
|
A:C6J401
|
2.0
|
22.4
|
1.0
|
OD2
|
A:ASP287
|
2.1
|
23.8
|
1.0
|
OAP
|
A:C6J401
|
2.1
|
24.4
|
1.0
|
O
|
A:HOH570
|
2.1
|
22.6
|
1.0
|
O
|
A:HOH565
|
2.2
|
21.8
|
1.0
|
O
|
A:HOH642
|
2.2
|
24.3
|
1.0
|
CG
|
A:ASP287
|
3.1
|
25.4
|
1.0
|
PAI
|
A:C6J401
|
3.2
|
24.1
|
1.0
|
PAK
|
A:C6J401
|
3.3
|
23.4
|
1.0
|
CAH
|
A:C6J401
|
3.5
|
24.9
|
1.0
|
OD1
|
A:ASP287
|
3.6
|
25.6
|
1.0
|
O
|
A:HOH548
|
3.8
|
21.9
|
1.0
|
OAQ
|
A:C6J401
|
4.1
|
23.2
|
1.0
|
O
|
A:ASP287
|
4.1
|
21.1
|
1.0
|
O
|
A:HOH699
|
4.2
|
22.2
|
1.0
|
OAN
|
A:C6J401
|
4.2
|
21.2
|
1.0
|
NE2
|
A:GLN284
|
4.2
|
21.1
|
1.0
|
OD1
|
A:ASP291
|
4.2
|
37.9
|
1.0
|
OD2
|
A:ASP305
|
4.3
|
27.2
|
1.0
|
OAM
|
A:C6J401
|
4.3
|
22.6
|
1.0
|
CB
|
A:ASP287
|
4.3
|
22.8
|
1.0
|
OD1
|
A:ASP305
|
4.4
|
26.3
|
1.0
|
OAO
|
A:C6J401
|
4.5
|
24.9
|
1.0
|
NZ
|
A:LYS301
|
4.5
|
48.5
|
1.0
|
C
|
A:ASP287
|
4.5
|
20.7
|
1.0
|
OD1
|
A:ASP288
|
4.6
|
22.1
|
1.0
|
CB
|
A:ASP291
|
4.7
|
29.2
|
1.0
|
CG
|
A:ASP291
|
4.8
|
30.6
|
1.0
|
CG
|
A:ASP305
|
4.8
|
27.6
|
1.0
|
CE
|
A:LYS301
|
4.8
|
51.1
|
1.0
|
MG
|
A:MG403
|
4.8
|
25.5
|
1.0
|
O
|
A:HOH621
|
4.9
|
55.4
|
1.0
|
N
|
A:ASP288
|
5.0
|
21.7
|
1.0
|
CA
|
A:ASP287
|
5.0
|
23.3
|
1.0
|
|
Magnesium binding site 4 out
of 9 in 6b04
Go back to
Magnesium Binding Sites List in 6b04
Magnesium binding site 4 out
of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:23.1
occ:1.00
|
OAL
|
B:C6J401
|
2.0
|
21.0
|
1.0
|
O
|
B:HOH525
|
2.0
|
22.1
|
1.0
|
OD1
|
B:ASP147
|
2.0
|
21.1
|
1.0
|
O
|
B:HOH680
|
2.1
|
21.6
|
1.0
|
O
|
B:HOH546
|
2.1
|
22.4
|
1.0
|
OD2
|
B:ASP151
|
2.1
|
20.7
|
1.0
|
CG
|
B:ASP151
|
3.0
|
20.9
|
1.0
|
CG
|
B:ASP147
|
3.0
|
21.0
|
1.0
|
MG
|
B:MG403
|
3.1
|
21.7
|
1.0
|
OD1
|
B:ASP151
|
3.2
|
24.1
|
1.0
|
PAK
|
B:C6J401
|
3.3
|
20.8
|
1.0
|
OD2
|
B:ASP147
|
3.3
|
21.8
|
1.0
|
OAM
|
B:C6J401
|
3.4
|
21.5
|
1.0
|
OD1
|
B:ASP218
|
3.9
|
31.0
|
1.0
|
O
|
B:HOH647
|
4.1
|
21.0
|
1.0
|
OE1
|
B:GLN215
|
4.2
|
27.6
|
1.0
|
NE2
|
B:GLN215
|
4.2
|
27.0
|
1.0
|
OAN
|
B:C6J401
|
4.2
|
20.6
|
1.0
|
O
|
B:HOH542
|
4.2
|
21.1
|
1.0
|
OD2
|
B:ASP218
|
4.3
|
28.0
|
1.0
|
NZ
|
B:LYS310
|
4.3
|
28.4
|
1.0
|
CG
|
B:ASP218
|
4.3
|
27.3
|
1.0
|
CAD
|
B:C6J401
|
4.4
|
22.9
|
1.0
|
CB
|
B:ASP147
|
4.4
|
21.7
|
1.0
|
CB
|
B:ASP151
|
4.4
|
22.5
|
1.0
|
CAH
|
B:C6J401
|
4.6
|
21.2
|
1.0
|
NZ
|
B:LYS244
|
4.6
|
21.2
|
1.0
|
CD
|
B:GLN215
|
4.6
|
29.0
|
1.0
|
OAP
|
B:C6J401
|
4.7
|
22.1
|
1.0
|
CAE
|
B:C6J401
|
4.7
|
22.8
|
1.0
|
CE
|
B:LYS310
|
4.7
|
29.4
|
1.0
|
CAG
|
B:C6J401
|
4.8
|
21.0
|
1.0
|
O
|
B:ASP147
|
4.8
|
24.8
|
1.0
|
O
|
B:HOH522
|
5.0
|
20.6
|
1.0
|
CAC
|
B:C6J401
|
5.0
|
23.1
|
1.0
|
O
|
B:HOH589
|
5.0
|
24.8
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 6b04
Go back to
Magnesium Binding Sites List in 6b04
Magnesium binding site 5 out
of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg403
b:21.7
occ:1.00
|
OAP
|
B:C6J401
|
2.0
|
22.1
|
1.0
|
OD2
|
B:ASP147
|
2.1
|
21.8
|
1.0
|
O
|
B:HOH647
|
2.1
|
21.0
|
1.0
|
OAL
|
B:C6J401
|
2.1
|
21.0
|
1.0
|
OD2
|
B:ASP151
|
2.2
|
20.7
|
1.0
|
O
|
B:HOH522
|
2.2
|
20.6
|
1.0
|
CG
|
B:ASP147
|
3.0
|
21.0
|
1.0
|
MG
|
B:MG402
|
3.1
|
23.1
|
1.0
|
PAK
|
B:C6J401
|
3.3
|
20.8
|
1.0
|
PAI
|
B:C6J401
|
3.3
|
22.5
|
1.0
|
CG
|
B:ASP151
|
3.3
|
20.9
|
1.0
|
OD1
|
B:ASP147
|
3.3
|
21.1
|
1.0
|
CAH
|
B:C6J401
|
3.6
|
21.2
|
1.0
|
CB
|
B:ASP151
|
3.8
|
22.5
|
1.0
|
O
|
B:HOH612
|
3.8
|
24.7
|
1.0
|
OAN
|
B:C6J401
|
3.8
|
20.6
|
1.0
|
CAG
|
B:C6J401
|
4.0
|
21.0
|
1.0
|
OAQ
|
B:C6J401
|
4.0
|
22.6
|
1.0
|
NH2
|
B:ARG156
|
4.1
|
24.2
|
1.0
|
O
|
B:HOH680
|
4.2
|
21.6
|
1.0
|
O
|
B:HOH545
|
4.4
|
23.3
|
1.0
|
OD1
|
B:ASP151
|
4.4
|
24.1
|
1.0
|
OAO
|
B:C6J401
|
4.4
|
21.6
|
1.0
|
CB
|
B:ASP147
|
4.4
|
21.7
|
1.0
|
OD1
|
B:ASP148
|
4.5
|
25.3
|
1.0
|
O
|
B:HOH589
|
4.5
|
24.8
|
1.0
|
OG
|
B:SER153
|
4.5
|
27.6
|
1.0
|
OAM
|
B:C6J401
|
4.5
|
21.5
|
1.0
|
O
|
B:ASP147
|
4.5
|
24.8
|
1.0
|
O
|
B:HOH525
|
4.7
|
22.1
|
1.0
|
C
|
B:ASP147
|
4.7
|
20.9
|
1.0
|
CAE
|
B:C6J401
|
4.9
|
22.8
|
1.0
|
O
|
B:HOH546
|
4.9
|
22.4
|
1.0
|
MG
|
B:MG404
|
4.9
|
21.7
|
1.0
|
CAD
|
B:C6J401
|
4.9
|
22.9
|
1.0
|
O
|
B:HOH582
|
4.9
|
27.9
|
1.0
|
O
|
B:HOH542
|
4.9
|
21.1
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 6b04
Go back to
Magnesium Binding Sites List in 6b04
Magnesium binding site 6 out
of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg404
b:21.7
occ:1.00
|
OAQ
|
B:C6J401
|
2.0
|
22.6
|
1.0
|
OAN
|
B:C6J401
|
2.0
|
20.6
|
1.0
|
OD2
|
B:ASP287
|
2.1
|
21.8
|
1.0
|
O
|
B:HOH594
|
2.1
|
21.8
|
1.0
|
O
|
B:HOH644
|
2.2
|
21.6
|
1.0
|
O
|
B:HOH545
|
2.2
|
23.3
|
1.0
|
CG
|
B:ASP287
|
3.1
|
25.3
|
1.0
|
PAI
|
B:C6J401
|
3.3
|
22.5
|
1.0
|
PAK
|
B:C6J401
|
3.3
|
20.8
|
1.0
|
OD1
|
B:ASP287
|
3.6
|
21.8
|
1.0
|
CAH
|
B:C6J401
|
3.6
|
21.2
|
1.0
|
O
|
B:HOH542
|
3.8
|
21.1
|
1.0
|
O
|
B:HOH560
|
4.0
|
47.1
|
1.0
|
O
|
B:ASP287
|
4.1
|
21.9
|
1.0
|
OAP
|
B:C6J401
|
4.2
|
22.1
|
1.0
|
NE2
|
B:GLN284
|
4.2
|
19.7
|
1.0
|
O
|
B:HOH647
|
4.2
|
21.0
|
1.0
|
OD2
|
B:ASP305
|
4.3
|
23.5
|
1.0
|
OAL
|
B:C6J401
|
4.3
|
21.0
|
1.0
|
OD1
|
B:ASP291
|
4.3
|
32.7
|
1.0
|
CB
|
B:ASP287
|
4.3
|
22.5
|
1.0
|
OAO
|
B:C6J401
|
4.3
|
21.6
|
1.0
|
OD1
|
B:ASP305
|
4.4
|
26.6
|
1.0
|
OAM
|
B:C6J401
|
4.4
|
21.5
|
1.0
|
C
|
B:ASP287
|
4.5
|
20.1
|
1.0
|
NZ
|
B:LYS301
|
4.5
|
46.4
|
1.0
|
CB
|
B:ASP291
|
4.6
|
25.3
|
1.0
|
OD1
|
B:ASP288
|
4.6
|
20.8
|
1.0
|
CG
|
B:ASP305
|
4.8
|
25.1
|
1.0
|
CG
|
B:ASP291
|
4.8
|
30.0
|
1.0
|
CE
|
B:LYS301
|
4.8
|
45.4
|
1.0
|
O
|
B:HOH584
|
4.9
|
40.2
|
1.0
|
MG
|
B:MG403
|
4.9
|
21.7
|
1.0
|
N
|
B:ASP288
|
4.9
|
21.7
|
1.0
|
O
|
B:HOH612
|
4.9
|
24.7
|
1.0
|
CA
|
B:ASP287
|
5.0
|
21.3
|
1.0
|
|
Magnesium binding site 7 out
of 9 in 6b04
Go back to
Magnesium Binding Sites List in 6b04
Magnesium binding site 7 out
of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg402
b:23.7
occ:1.00
|
OAM
|
C:C6J401
|
2.0
|
21.6
|
1.0
|
O
|
C:HOH547
|
2.0
|
20.9
|
1.0
|
O
|
C:HOH528
|
2.1
|
21.1
|
1.0
|
OD1
|
C:ASP147
|
2.1
|
22.5
|
1.0
|
O
|
C:HOH696
|
2.1
|
21.1
|
1.0
|
OD2
|
C:ASP151
|
2.2
|
23.5
|
1.0
|
CG
|
C:ASP151
|
3.0
|
18.6
|
1.0
|
CG
|
C:ASP147
|
3.0
|
24.4
|
1.0
|
MG
|
C:MG403
|
3.1
|
21.2
|
1.0
|
OD1
|
C:ASP151
|
3.2
|
24.6
|
1.0
|
OD2
|
C:ASP147
|
3.3
|
22.9
|
1.0
|
PAK
|
C:C6J401
|
3.3
|
23.1
|
1.0
|
OAN
|
C:C6J401
|
3.5
|
23.0
|
1.0
|
OD1
|
C:ASP218
|
3.8
|
26.9
|
1.0
|
OE1
|
C:GLN215
|
4.1
|
25.4
|
1.0
|
NE2
|
C:GLN215
|
4.1
|
26.3
|
1.0
|
O
|
C:HOH649
|
4.2
|
21.4
|
1.0
|
O
|
C:HOH548
|
4.2
|
24.5
|
1.0
|
OD2
|
C:ASP218
|
4.2
|
25.7
|
1.0
|
OAL
|
C:C6J401
|
4.3
|
24.7
|
1.0
|
CG
|
C:ASP218
|
4.3
|
27.9
|
1.0
|
CAD
|
C:C6J401
|
4.4
|
26.6
|
1.0
|
CB
|
C:ASP147
|
4.5
|
22.2
|
1.0
|
CB
|
C:ASP151
|
4.5
|
24.7
|
1.0
|
NZ
|
C:LYS310
|
4.5
|
37.3
|
1.0
|
NZ
|
C:LYS244
|
4.6
|
21.4
|
1.0
|
CD
|
C:GLN215
|
4.6
|
27.7
|
1.0
|
CAH
|
C:C6J401
|
4.7
|
22.3
|
1.0
|
CE
|
C:LYS310
|
4.7
|
28.9
|
1.0
|
OAP
|
C:C6J401
|
4.7
|
23.1
|
1.0
|
CAE
|
C:C6J401
|
4.8
|
23.3
|
1.0
|
O
|
C:ASP147
|
4.8
|
24.5
|
1.0
|
CAG
|
C:C6J401
|
4.9
|
23.2
|
1.0
|
CAC
|
C:C6J401
|
4.9
|
24.6
|
1.0
|
O
|
C:HOH527
|
4.9
|
22.5
|
1.0
|
O
|
C:HOH563
|
5.0
|
26.8
|
1.0
|
CA
|
C:ASP147
|
5.0
|
24.3
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 6b04
Go back to
Magnesium Binding Sites List in 6b04
Magnesium binding site 8 out
of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg403
b:21.2
occ:1.00
|
OAP
|
C:C6J401
|
2.0
|
23.1
|
1.0
|
O
|
C:HOH649
|
2.0
|
21.4
|
1.0
|
OD2
|
C:ASP151
|
2.1
|
23.5
|
1.0
|
OAM
|
C:C6J401
|
2.1
|
21.6
|
1.0
|
OD2
|
C:ASP147
|
2.1
|
22.9
|
1.0
|
O
|
C:HOH527
|
2.2
|
22.5
|
1.0
|
CG
|
C:ASP147
|
3.0
|
24.4
|
1.0
|
MG
|
C:MG402
|
3.1
|
23.7
|
1.0
|
CG
|
C:ASP151
|
3.2
|
18.6
|
1.0
|
PAK
|
C:C6J401
|
3.2
|
23.1
|
1.0
|
PAI
|
C:C6J401
|
3.3
|
24.2
|
1.0
|
OD1
|
C:ASP147
|
3.4
|
22.5
|
1.0
|
CAH
|
C:C6J401
|
3.7
|
22.3
|
1.0
|
CB
|
C:ASP151
|
3.7
|
24.7
|
1.0
|
OAL
|
C:C6J401
|
3.9
|
24.7
|
1.0
|
O
|
C:HOH658
|
3.9
|
28.1
|
1.0
|
OAQ
|
C:C6J401
|
4.1
|
25.3
|
1.0
|
CAG
|
C:C6J401
|
4.1
|
23.2
|
1.0
|
O
|
C:HOH696
|
4.2
|
21.1
|
1.0
|
NH2
|
C:ARG156
|
4.2
|
26.5
|
1.0
|
OD1
|
C:ASP151
|
4.3
|
24.6
|
1.0
|
O
|
C:HOH540
|
4.4
|
24.6
|
1.0
|
CB
|
C:ASP147
|
4.4
|
22.2
|
1.0
|
O
|
C:HOH563
|
4.4
|
26.8
|
1.0
|
OG
|
C:SER153
|
4.5
|
31.6
|
1.0
|
OAN
|
C:C6J401
|
4.5
|
23.0
|
1.0
|
OAO
|
C:C6J401
|
4.5
|
22.2
|
1.0
|
O
|
C:ASP147
|
4.5
|
24.5
|
1.0
|
OD1
|
C:ASP148
|
4.5
|
26.5
|
1.0
|
C
|
C:ASP147
|
4.7
|
22.3
|
1.0
|
O
|
C:HOH528
|
4.7
|
21.1
|
1.0
|
O
|
C:HOH599
|
4.8
|
33.8
|
1.0
|
MG
|
C:MG404
|
4.8
|
26.5
|
1.0
|
O
|
C:HOH547
|
4.8
|
20.9
|
1.0
|
CAE
|
C:C6J401
|
4.9
|
23.3
|
1.0
|
O
|
C:HOH548
|
5.0
|
24.5
|
1.0
|
CAD
|
C:C6J401
|
5.0
|
26.6
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 6b04
Go back to
Magnesium Binding Sites List in 6b04
Magnesium binding site 9 out
of 9 in the Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B)
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of CFFPPS2, A Lepidopteran Type-II Farnesyl Diphosphate Synthase, Complexed with [2-(1-Methylpyridin-2-Yl)-1- Phosphono-Ethyl]Phosphonic Acid (Inhibitor 1B) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg404
b:26.5
occ:1.00
|
OAL
|
C:C6J401
|
1.9
|
24.7
|
1.0
|
OAQ
|
C:C6J401
|
2.0
|
25.3
|
1.0
|
OD2
|
C:ASP287
|
2.1
|
25.0
|
1.0
|
O
|
C:HOH540
|
2.2
|
24.6
|
1.0
|
O
|
C:HOH574
|
2.2
|
23.8
|
1.0
|
O
|
C:HOH635
|
2.2
|
25.8
|
1.0
|
CG
|
C:ASP287
|
3.1
|
25.5
|
1.0
|
PAI
|
C:C6J401
|
3.2
|
24.2
|
1.0
|
PAK
|
C:C6J401
|
3.2
|
23.1
|
1.0
|
CAH
|
C:C6J401
|
3.5
|
22.3
|
1.0
|
OD1
|
C:ASP287
|
3.6
|
26.2
|
1.0
|
O
|
C:HOH548
|
3.9
|
24.5
|
1.0
|
OAP
|
C:C6J401
|
4.0
|
23.1
|
1.0
|
O
|
C:HOH649
|
4.1
|
21.4
|
1.0
|
O
|
C:HOH704
|
4.2
|
46.8
|
1.0
|
OD1
|
C:ASP291
|
4.2
|
35.4
|
1.0
|
OAM
|
C:C6J401
|
4.3
|
21.6
|
1.0
|
NE2
|
C:GLN284
|
4.3
|
23.0
|
1.0
|
OAN
|
C:C6J401
|
4.3
|
23.0
|
1.0
|
OAO
|
C:C6J401
|
4.3
|
22.2
|
1.0
|
O
|
C:ASP287
|
4.3
|
27.1
|
1.0
|
NZ
|
C:LYS301
|
4.3
|
50.7
|
1.0
|
OD2
|
C:ASP305
|
4.4
|
29.3
|
1.0
|
OD1
|
C:ASP305
|
4.4
|
31.3
|
1.0
|
CB
|
C:ASP287
|
4.4
|
25.3
|
1.0
|
OD1
|
C:ASP288
|
4.5
|
24.1
|
1.0
|
C
|
C:ASP287
|
4.6
|
22.8
|
1.0
|
CB
|
C:ASP291
|
4.7
|
31.3
|
1.0
|
CG
|
C:ASP305
|
4.8
|
28.8
|
1.0
|
CG
|
C:ASP291
|
4.8
|
35.0
|
1.0
|
MG
|
C:MG403
|
4.8
|
21.2
|
1.0
|
O
|
C:HOH559
|
4.8
|
40.8
|
1.0
|
O
|
C:HOH658
|
4.9
|
28.1
|
1.0
|
|
Reference:
M.E.Picard,
A.Nisole,
C.Beliveau,
S.Sen,
A.Barbar,
R.Shi,
M.Cusson.
Structural Characterization of A Lepidopteran Type-II Farnesyl Diphosphate Synthase From the Spruce Budworm, Choristoneura Fumiferana: Implications For Inhibitor Design. Insect Biochem. Mol. Biol. V. 92 84 2017.
ISSN: ISSN 1879-0240
PubMed: 29183817
DOI: 10.1016/J.IBMB.2017.11.011
Page generated: Mon Sep 30 19:26:10 2024
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