Fluorine in PDB 3vr9: Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil
Protein crystallography data
The structure of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil, PDB code: 3vr9
was solved by
H.Shimizu,
T.Shiba,
D.K.Inaoka,
A.Osanai,
K.Kita,
K.Sakamoto,
S.Harada,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.39 /
3.01
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
124.011,
135.333,
220.498,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.6 /
27.7
|
Other elements in 3vr9:
The structure of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil
(pdb code 3vr9). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil, PDB code: 3vr9:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 3vr9
Go back to
Fluorine Binding Sites List in 3vr9
Fluorine binding site 1 out
of 6 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F202
b:76.2
occ:1.00
|
F1
|
C:FTN202
|
0.0
|
76.2
|
1.0
|
C1
|
C:FTN202
|
1.3
|
74.0
|
1.0
|
F3
|
C:FTN202
|
2.1
|
73.9
|
1.0
|
F2
|
C:FTN202
|
2.2
|
73.8
|
1.0
|
C2
|
C:FTN202
|
2.3
|
74.3
|
1.0
|
O1
|
C:FTN202
|
2.6
|
74.8
|
1.0
|
C3
|
C:FTN202
|
2.9
|
76.0
|
1.0
|
NH1
|
C:ARG76
|
3.0
|
66.7
|
1.0
|
C8
|
C:FTN202
|
3.1
|
76.1
|
1.0
|
CD1
|
B:TRP197
|
3.3
|
65.2
|
1.0
|
C7
|
C:FTN202
|
3.3
|
75.8
|
1.0
|
CE2
|
D:TYR107
|
3.3
|
74.8
|
1.0
|
OH
|
D:TYR107
|
3.5
|
75.4
|
1.0
|
NE1
|
B:TRP197
|
3.5
|
64.6
|
1.0
|
OD1
|
D:ASP106
|
3.6
|
73.5
|
1.0
|
CZ
|
D:TYR107
|
3.8
|
75.3
|
1.0
|
CZ
|
C:ARG76
|
4.1
|
65.4
|
1.0
|
CG
|
D:ASP106
|
4.1
|
73.8
|
1.0
|
CB
|
D:ASP106
|
4.2
|
74.3
|
1.0
|
C4
|
C:FTN202
|
4.2
|
77.5
|
1.0
|
O
|
B:PRO193
|
4.3
|
64.3
|
1.0
|
CD2
|
D:TYR107
|
4.3
|
74.9
|
1.0
|
N
|
C:FTN202
|
4.4
|
75.8
|
1.0
|
C6
|
C:FTN202
|
4.5
|
77.6
|
1.0
|
CG
|
B:TRP197
|
4.6
|
64.8
|
1.0
|
NH2
|
C:ARG76
|
4.7
|
65.1
|
1.0
|
CE2
|
B:TRP197
|
4.8
|
65.3
|
1.0
|
C5
|
C:FTN202
|
4.9
|
78.8
|
1.0
|
C
|
B:PRO193
|
5.0
|
64.3
|
1.0
|
CE1
|
D:TYR107
|
5.0
|
75.0
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 3vr9
Go back to
Fluorine Binding Sites List in 3vr9
Fluorine binding site 2 out
of 6 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F202
b:73.8
occ:1.00
|
F2
|
C:FTN202
|
0.0
|
73.8
|
1.0
|
C1
|
C:FTN202
|
1.3
|
74.0
|
1.0
|
F3
|
C:FTN202
|
2.1
|
73.9
|
1.0
|
F1
|
C:FTN202
|
2.2
|
76.2
|
1.0
|
C2
|
C:FTN202
|
2.2
|
74.3
|
1.0
|
C3
|
C:FTN202
|
3.0
|
76.0
|
1.0
|
C8
|
C:FTN202
|
3.2
|
76.1
|
1.0
|
C7
|
C:FTN202
|
3.3
|
75.8
|
1.0
|
O1
|
C:FTN202
|
3.3
|
74.8
|
1.0
|
O
|
B:PRO193
|
3.5
|
64.3
|
1.0
|
C
|
B:PRO193
|
3.5
|
64.3
|
1.0
|
CD1
|
B:ILE242
|
3.6
|
68.7
|
1.0
|
N
|
B:SER194
|
3.7
|
64.5
|
1.0
|
CA
|
B:SER194
|
3.7
|
65.1
|
1.0
|
CB
|
B:PRO193
|
3.8
|
64.3
|
1.0
|
CB
|
B:SER194
|
3.9
|
65.5
|
1.0
|
N
|
C:FTN202
|
4.1
|
75.8
|
1.0
|
C4
|
C:FTN202
|
4.2
|
77.5
|
1.0
|
CD1
|
B:TRP197
|
4.2
|
65.2
|
1.0
|
CA
|
B:PRO193
|
4.3
|
64.0
|
1.0
|
NE1
|
B:TRP197
|
4.3
|
64.6
|
1.0
|
OG
|
B:SER194
|
4.4
|
66.6
|
1.0
|
C6
|
C:FTN202
|
4.4
|
77.6
|
1.0
|
NH1
|
C:ARG76
|
4.7
|
66.7
|
1.0
|
CG
|
B:PRO193
|
4.7
|
63.4
|
1.0
|
OD1
|
D:ASP106
|
4.8
|
73.5
|
1.0
|
C5
|
C:FTN202
|
4.8
|
78.8
|
1.0
|
CD
|
B:PRO193
|
4.8
|
63.1
|
1.0
|
C9
|
C:FTN202
|
4.9
|
74.5
|
1.0
|
N
|
B:PRO193
|
5.0
|
63.0
|
1.0
|
CG1
|
B:ILE242
|
5.0
|
66.7
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 3vr9
Go back to
Fluorine Binding Sites List in 3vr9
Fluorine binding site 3 out
of 6 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F202
b:73.9
occ:1.00
|
F3
|
C:FTN202
|
0.0
|
73.9
|
1.0
|
C1
|
C:FTN202
|
1.3
|
74.0
|
1.0
|
F2
|
C:FTN202
|
2.1
|
73.8
|
1.0
|
F1
|
C:FTN202
|
2.1
|
76.2
|
1.0
|
C2
|
C:FTN202
|
2.3
|
74.3
|
1.0
|
C7
|
C:FTN202
|
2.6
|
75.8
|
1.0
|
OD1
|
D:ASP106
|
2.8
|
73.5
|
1.0
|
CG
|
D:ASP106
|
3.5
|
73.8
|
1.0
|
NH1
|
C:ARG76
|
3.6
|
66.7
|
1.0
|
CD2
|
B:HIS240
|
3.7
|
70.9
|
1.0
|
C3
|
C:FTN202
|
3.7
|
76.0
|
1.0
|
OG
|
B:SER194
|
3.9
|
66.6
|
1.0
|
CG
|
B:HIS240
|
3.9
|
69.8
|
1.0
|
C6
|
C:FTN202
|
4.0
|
77.6
|
1.0
|
OD2
|
D:ASP106
|
4.1
|
71.7
|
1.0
|
CB
|
B:SER194
|
4.1
|
65.5
|
1.0
|
NH2
|
C:ARG76
|
4.2
|
65.1
|
1.0
|
CZ
|
C:ARG76
|
4.2
|
65.4
|
1.0
|
CB
|
B:HIS240
|
4.2
|
70.0
|
1.0
|
CB
|
D:ASP106
|
4.3
|
74.3
|
1.0
|
NE2
|
B:HIS240
|
4.3
|
72.4
|
1.0
|
CA
|
B:SER194
|
4.4
|
65.1
|
1.0
|
O1
|
C:FTN202
|
4.4
|
74.8
|
1.0
|
C8
|
C:FTN202
|
4.5
|
76.1
|
1.0
|
ND1
|
B:HIS240
|
4.7
|
70.0
|
1.0
|
CD1
|
B:ILE242
|
4.7
|
68.7
|
1.0
|
C4
|
C:FTN202
|
4.8
|
77.5
|
1.0
|
CD1
|
B:TRP197
|
4.8
|
65.2
|
1.0
|
C5
|
C:FTN202
|
4.9
|
78.8
|
1.0
|
CE1
|
B:HIS240
|
4.9
|
72.5
|
1.0
|
O
|
B:PRO193
|
4.9
|
64.3
|
1.0
|
N
|
B:SER194
|
5.0
|
64.5
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 3vr9
Go back to
Fluorine Binding Sites List in 3vr9
Fluorine binding site 4 out
of 6 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F304
b:68.4
occ:1.00
|
F1
|
F:FTN304
|
0.0
|
68.4
|
1.0
|
C1
|
F:FTN304
|
1.3
|
67.8
|
1.0
|
F2
|
F:FTN304
|
2.2
|
66.9
|
1.0
|
F3
|
F:FTN304
|
2.2
|
67.0
|
1.0
|
C2
|
F:FTN304
|
2.3
|
67.4
|
1.0
|
O1
|
F:FTN304
|
2.6
|
65.3
|
1.0
|
CE2
|
H:TYR107
|
3.0
|
74.8
|
1.0
|
C3
|
F:FTN304
|
3.0
|
66.8
|
1.0
|
NH1
|
G:ARG76
|
3.1
|
68.8
|
1.0
|
OH
|
H:TYR107
|
3.1
|
75.3
|
1.0
|
C8
|
F:FTN304
|
3.2
|
67.1
|
1.0
|
NE1
|
F:TRP197
|
3.2
|
60.1
|
1.0
|
C7
|
F:FTN304
|
3.3
|
67.4
|
1.0
|
CD1
|
F:TRP197
|
3.3
|
59.3
|
1.0
|
CZ
|
H:TYR107
|
3.4
|
74.6
|
1.0
|
OD1
|
H:ASP106
|
3.4
|
75.5
|
1.0
|
CD2
|
H:TYR107
|
4.0
|
74.3
|
1.0
|
CG
|
H:ASP106
|
4.0
|
75.8
|
1.0
|
CB
|
H:ASP106
|
4.2
|
76.2
|
1.0
|
CZ
|
G:ARG76
|
4.3
|
68.7
|
1.0
|
C4
|
F:FTN304
|
4.3
|
66.7
|
1.0
|
C6
|
F:FTN304
|
4.5
|
69.1
|
1.0
|
N
|
F:FTN304
|
4.5
|
69.7
|
1.0
|
CE2
|
F:TRP197
|
4.5
|
59.5
|
1.0
|
CE1
|
H:TYR107
|
4.6
|
74.2
|
1.0
|
CG
|
F:TRP197
|
4.7
|
60.9
|
1.0
|
CA
|
F:SER194
|
4.8
|
65.0
|
1.0
|
NH2
|
G:ARG76
|
4.8
|
68.7
|
1.0
|
C5
|
F:FTN304
|
4.9
|
68.4
|
1.0
|
N
|
F:SER194
|
4.9
|
65.7
|
1.0
|
OD2
|
H:ASP106
|
5.0
|
73.9
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 3vr9
Go back to
Fluorine Binding Sites List in 3vr9
Fluorine binding site 5 out
of 6 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F304
b:66.9
occ:1.00
|
F2
|
F:FTN304
|
0.0
|
66.9
|
1.0
|
C1
|
F:FTN304
|
1.3
|
67.8
|
1.0
|
F3
|
F:FTN304
|
2.1
|
67.0
|
1.0
|
F1
|
F:FTN304
|
2.2
|
68.4
|
1.0
|
C2
|
F:FTN304
|
2.3
|
67.4
|
1.0
|
O1
|
F:FTN304
|
2.8
|
65.3
|
1.0
|
C3
|
F:FTN304
|
3.0
|
66.8
|
1.0
|
C8
|
F:FTN304
|
3.0
|
67.1
|
1.0
|
N
|
F:SER194
|
3.1
|
65.7
|
1.0
|
NE1
|
F:TRP197
|
3.3
|
60.1
|
1.0
|
CA
|
F:SER194
|
3.4
|
65.0
|
1.0
|
CB
|
F:PRO193
|
3.4
|
65.7
|
1.0
|
C7
|
F:FTN304
|
3.4
|
67.4
|
1.0
|
C
|
F:PRO193
|
3.5
|
66.0
|
1.0
|
CD1
|
F:TRP197
|
3.6
|
59.3
|
1.0
|
CD1
|
F:ILE242
|
3.7
|
70.6
|
1.0
|
CB
|
F:SER194
|
3.8
|
65.1
|
1.0
|
N
|
F:FTN304
|
4.0
|
69.7
|
1.0
|
O
|
F:PRO193
|
4.1
|
66.1
|
1.0
|
CA
|
F:PRO193
|
4.1
|
65.8
|
1.0
|
CG
|
F:PRO193
|
4.2
|
65.8
|
1.0
|
C4
|
F:FTN304
|
4.3
|
66.7
|
1.0
|
CE2
|
F:TRP197
|
4.4
|
59.5
|
1.0
|
C6
|
F:FTN304
|
4.6
|
69.1
|
1.0
|
OG
|
F:SER194
|
4.7
|
63.9
|
1.0
|
OH
|
H:TYR107
|
4.7
|
75.3
|
1.0
|
C9
|
F:FTN304
|
4.7
|
71.5
|
1.0
|
CD
|
F:PRO193
|
4.8
|
65.5
|
1.0
|
N
|
F:PRO193
|
4.8
|
65.6
|
1.0
|
C
|
F:SER194
|
4.8
|
64.8
|
1.0
|
CE2
|
H:TYR107
|
4.9
|
74.8
|
1.0
|
CG
|
F:TRP197
|
4.9
|
60.9
|
1.0
|
OD1
|
H:ASP106
|
4.9
|
75.5
|
1.0
|
NH1
|
G:ARG76
|
4.9
|
68.8
|
1.0
|
C5
|
F:FTN304
|
4.9
|
68.4
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 3vr9
Go back to
Fluorine Binding Sites List in 3vr9
Fluorine binding site 6 out
of 6 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F304
b:67.0
occ:1.00
|
F3
|
F:FTN304
|
0.0
|
67.0
|
1.0
|
C1
|
F:FTN304
|
1.3
|
67.8
|
1.0
|
F2
|
F:FTN304
|
2.1
|
66.9
|
1.0
|
F1
|
F:FTN304
|
2.2
|
68.4
|
1.0
|
C2
|
F:FTN304
|
2.4
|
67.4
|
1.0
|
C7
|
F:FTN304
|
2.7
|
67.4
|
1.0
|
OD1
|
H:ASP106
|
3.1
|
75.5
|
1.0
|
CB
|
F:SER194
|
3.5
|
65.1
|
1.0
|
CD2
|
F:HIS240
|
3.7
|
70.6
|
1.0
|
OG
|
F:SER194
|
3.7
|
63.9
|
1.0
|
CA
|
F:SER194
|
3.7
|
65.0
|
1.0
|
C3
|
F:FTN304
|
3.7
|
66.8
|
1.0
|
CG
|
H:ASP106
|
3.8
|
75.8
|
1.0
|
CG
|
F:HIS240
|
3.9
|
70.5
|
1.0
|
C6
|
F:FTN304
|
4.1
|
69.1
|
1.0
|
NH1
|
G:ARG76
|
4.1
|
68.8
|
1.0
|
NE2
|
F:HIS240
|
4.1
|
72.9
|
1.0
|
N
|
F:SER194
|
4.2
|
65.7
|
1.0
|
OD2
|
H:ASP106
|
4.2
|
73.9
|
1.0
|
O1
|
F:FTN304
|
4.3
|
65.3
|
1.0
|
CB
|
F:HIS240
|
4.4
|
71.5
|
1.0
|
CD1
|
F:TRP197
|
4.4
|
59.3
|
1.0
|
C8
|
F:FTN304
|
4.4
|
67.1
|
1.0
|
ND1
|
F:HIS240
|
4.5
|
70.7
|
1.0
|
CD1
|
F:ILE242
|
4.5
|
70.6
|
1.0
|
NE1
|
F:TRP197
|
4.6
|
60.1
|
1.0
|
CE1
|
F:HIS240
|
4.6
|
72.4
|
1.0
|
CB
|
H:ASP106
|
4.7
|
76.2
|
1.0
|
CZ
|
G:ARG76
|
4.8
|
68.7
|
1.0
|
NH2
|
G:ARG76
|
4.8
|
68.7
|
1.0
|
C4
|
F:FTN304
|
4.9
|
66.7
|
1.0
|
O
|
F:LYS238
|
5.0
|
72.3
|
1.0
|
C5
|
F:FTN304
|
5.0
|
68.4
|
1.0
|
|
Reference:
H.Shimizu,
T.Shiba,
D.K.Inaoka,
A.Osanai,
K.Kita,
K.Sakamoto,
S.Harada.
Crystal Structure of Mitochondrial Quinol-Fumarate Reductase From Parasitic Nematode Ascaris Suum To Be Published.
Page generated: Wed Jul 31 23:20:54 2024
|