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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:

Iron (Fe) 20 atoms

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

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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

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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

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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: Sun Dec 13 11:57:12 2020

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