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Fluorine in PDB 4ytm: Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide

Enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide

All present enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide, PDB code: 4ytm was solved by S.Harada, T.Shiba, D.Sato, A.Yamamoto, M.Nagahama, A.Yone, D.K.Inaoka, K.Sakamoto, M.Inoue, T.Honma, K.Kita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.654, 126.426, 220.873, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 24.5

Other elements in 4ytm:

The structure of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide also contains other interesting chemical elements:

Iron (Fe) 20 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide (pdb code 4ytm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide, PDB code: 4ytm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4ytm

Go back to Fluorine Binding Sites List in 4ytm
Fluorine binding site 1 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F202

b:97.2
occ:1.00
 F1 C:F6A202 0.0 97.2 1.0
C1 C:F6A202 1.3 97.5 1.0
F3 C:F6A202 2.1 95.4 1.0
F2 C:F6A202 2.1 0.5 1.0
C2 C:F6A202 2.3 95.3 1.0
O C:F6A202 2.4 92.6 1.0
C8 C:F6A202 2.8 96.5 1.0
C3 C:F6A202 2.9 95.8 1.0
NE1 B:TRP197 3.1 45.8 1.0
CD1 B:TRP197 3.1 47.5 1.0
CB B:PRO193 3.3 56.0 1.0
N B:SER194 3.5 50.3 1.0
C7 C:F6A202 3.5 92.3 1.0
C B:PRO193 3.6 50.6 1.0
N C:F6A202 3.9 97.2 1.0
CA B:SER194 3.9 53.0 1.0
O B:PRO193 4.0 48.1 1.0
CA B:PRO193 4.1 53.3 1.0
CD1 B:ILE242 4.2 61.7 1.0
C4 C:F6A202 4.3 95.8 1.0
CE2 B:TRP197 4.3 46.5 1.0
CG B:TRP197 4.4 47.9 1.0
CG B:PRO193 4.5 58.0 1.0
CB B:SER194 4.6 52.4 1.0
C9 C:F6A202 4.6 98.1 1.0
C6 C:F6A202 4.7 96.6 1.0
OH D:TYR107 4.7 67.4 1.0
NH1 C:ARG76 4.7 63.6 1.0
CE2 D:TYR107 4.9 71.9 1.0
OD1 D:ASP106 4.9 88.3 1.0
CD2 B:TRP197 5.0 46.6 1.0
C5 C:F6A202 5.0 97.0 1.0

Fluorine binding site 2 out of 6 in 4ytm

Go back to Fluorine Binding Sites List in 4ytm
Fluorine binding site 2 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F202

b:0.5
occ:1.00
 F2 C:F6A202 0.0 0.5 1.0
C1 C:F6A202 1.3 97.5 1.0
F1 C:F6A202 2.1 97.2 1.0
F3 C:F6A202 2.2 95.4 1.0
C2 C:F6A202 2.3 95.3 1.0
O C:F6A202 2.9 92.6 1.0
NH1 C:ARG76 2.9 63.6 1.0
C3 C:F6A202 3.2 95.8 1.0
C7 C:F6A202 3.2 92.3 1.0
CG D:ASP106 3.2 83.8 1.0
CD1 B:TRP197 3.4 47.5 1.0
CB D:ASP106 3.4 79.1 1.0
C8 C:F6A202 3.5 96.5 1.0
OD1 D:ASP106 3.5 88.3 1.0
OD2 D:ASP106 3.6 80.7 1.0
OH D:TYR107 3.7 67.4 1.0
CE2 D:TYR107 3.7 71.9 1.0
NE1 B:TRP197 3.7 45.8 1.0
CZ D:TYR107 3.9 69.4 1.0
CZ C:ARG76 3.9 63.2 1.0
NH2 C:ARG76 4.3 61.8 1.0
C4 C:F6A202 4.4 95.8 1.0
C6 C:F6A202 4.5 96.6 1.0
CD2 D:TYR107 4.6 72.0 1.0
CG B:TRP197 4.7 47.9 1.0
CA D:ASP106 4.8 74.1 1.0
N C:F6A202 4.8 97.2 1.0
CE1 D:TYR107 4.9 70.2 1.0
NE C:ARG76 4.9 63.5 1.0
C5 C:F6A202 4.9 97.0 1.0
CA B:SER194 5.0 53.0 1.0

Fluorine binding site 3 out of 6 in 4ytm

Go back to Fluorine Binding Sites List in 4ytm
Fluorine binding site 3 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F202

b:95.4
occ:1.00
 F3 C:F6A202 0.0 95.4 1.0
C1 C:F6A202 1.3 97.5 1.0
F1 C:F6A202 2.1 97.2 1.0
F2 C:F6A202 2.2 0.5 1.0
C2 C:F6A202 2.3 95.3 1.0
C7 C:F6A202 2.7 92.3 1.0
OD1 D:ASP106 3.5 88.3 1.0
CA B:SER194 3.6 53.0 1.0
CB B:SER194 3.6 52.4 1.0
CD2 B:HIS240 3.7 68.3 1.0
C3 C:F6A202 3.7 95.8 1.0
N B:SER194 3.8 50.3 1.0
CG D:ASP106 3.8 83.8 1.0
OG B:SER194 4.0 54.6 1.0
OD2 D:ASP106 4.0 80.7 1.0
C6 C:F6A202 4.1 96.6 1.0
CG B:HIS240 4.1 64.1 1.0
O C:F6A202 4.2 92.6 1.0
CD1 B:ILE242 4.3 61.7 1.0
CD1 B:TRP197 4.3 47.5 1.0
CB B:HIS240 4.4 61.0 1.0
C8 C:F6A202 4.4 96.5 1.0
NH1 C:ARG76 4.4 63.6 1.0
NE2 B:HIS240 4.4 70.1 1.0
C B:PRO193 4.5 50.6 1.0
CB D:ASP106 4.7 79.1 1.0
C4 C:F6A202 4.8 95.8 1.0
NH2 C:ARG76 4.8 61.8 1.0
NE1 B:TRP197 4.8 45.8 1.0
CB B:PRO193 4.8 56.0 1.0
CZ C:ARG76 4.9 63.2 1.0
C5 C:F6A202 4.9 97.0 1.0
O B:LYS238 4.9 66.9 1.0
O B:PRO193 5.0 48.1 1.0
C B:SER194 5.0 52.2 1.0
ND1 B:HIS240 5.0 64.8 1.0

Fluorine binding site 4 out of 6 in 4ytm

Go back to Fluorine Binding Sites List in 4ytm
Fluorine binding site 4 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F202

b:72.4
occ:1.00
 F1 G:F6A202 0.0 72.4 1.0
C1 G:F6A202 1.3 71.2 1.0
F3 G:F6A202 2.2 67.7 1.0
F2 G:F6A202 2.2 75.5 1.0
C2 G:F6A202 2.3 72.1 1.0
O G:F6A202 2.3 72.8 1.0
C3 G:F6A202 2.9 74.8 1.0
C8 G:F6A202 3.0 78.0 1.0
CD1 F:TRP197 3.1 50.3 1.0
NH1 G:ARG76 3.3 72.1 1.0
NE1 F:TRP197 3.4 51.1 1.0
C7 G:F6A202 3.4 75.0 1.0
CE2 H:TYR107 3.5 59.1 1.0
OH H:TYR107 3.7 55.7 1.0
CG H:ASP106 3.7 73.9 1.0
CB H:ASP106 3.8 70.9 1.0
CZ H:TYR107 4.0 57.9 1.0
OD2 H:ASP106 4.0 72.7 1.0
OD1 H:ASP106 4.1 75.2 1.0
C4 G:F6A202 4.3 73.7 1.0
N G:F6A202 4.3 81.0 1.0
CZ G:ARG76 4.3 72.0 1.0
CG F:TRP197 4.4 49.8 1.0
CD2 H:TYR107 4.5 57.0 1.0
C6 G:F6A202 4.6 80.3 1.0
CE2 F:TRP197 4.7 50.2 1.0
NH2 G:ARG76 4.8 73.2 1.0
CA F:SER194 4.8 56.9 1.0
C5 G:F6A202 4.9 77.2 1.0

Fluorine binding site 5 out of 6 in 4ytm

Go back to Fluorine Binding Sites List in 4ytm
Fluorine binding site 5 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F202

b:75.5
occ:1.00
 F2 G:F6A202 0.0 75.5 1.0
C1 G:F6A202 1.3 71.2 1.0
F3 G:F6A202 2.1 67.7 1.0
F1 G:F6A202 2.2 72.4 1.0
C2 G:F6A202 2.3 72.1 1.0
C7 G:F6A202 2.7 75.0 1.0
OD1 H:ASP106 3.1 75.2 1.0
CD2 F:HIS240 3.2 66.4 1.0
CG H:ASP106 3.2 73.9 1.0
OD2 H:ASP106 3.3 72.7 1.0
NE2 F:HIS240 3.6 67.0 1.0
OG F:SER194 3.6 57.6 1.0
C3 G:F6A202 3.7 74.8 1.0
CB F:SER194 3.7 56.7 1.0
NH1 G:ARG76 3.9 72.1 1.0
CA F:SER194 3.9 56.9 1.0
CG F:HIS240 4.0 65.5 1.0
C6 G:F6A202 4.1 80.3 1.0
CB H:ASP106 4.1 70.9 1.0
O G:F6A202 4.2 72.8 1.0
NH2 G:ARG76 4.3 73.2 1.0
C8 G:F6A202 4.4 78.0 1.0
CZ G:ARG76 4.4 72.0 1.0
N F:SER194 4.4 54.8 1.0
CE1 F:HIS240 4.5 67.0 1.0
CD1 F:TRP197 4.6 50.3 1.0
CB F:HIS240 4.6 64.5 1.0
ND1 F:HIS240 4.7 64.7 1.0
C4 G:F6A202 4.8 73.7 1.0
CD1 F:ILE242 4.8 72.8 1.0
C5 G:F6A202 4.9 77.2 1.0

Fluorine binding site 6 out of 6 in 4ytm

Go back to Fluorine Binding Sites List in 4ytm
Fluorine binding site 6 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-Biphenyl-3-Yl-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F202

b:67.7
occ:1.00
 F3 G:F6A202 0.0 67.7 1.0
C1 G:F6A202 1.3 71.2 1.0
F2 G:F6A202 2.1 75.5 1.0
F1 G:F6A202 2.2 72.4 1.0
C2 G:F6A202 2.3 72.1 1.0
O G:F6A202 3.0 72.8 1.0
C3 G:F6A202 3.0 74.8 1.0
N F:SER194 3.1 54.8 1.0
C8 G:F6A202 3.1 78.0 1.0
CA F:SER194 3.3 56.9 1.0
C7 G:F6A202 3.4 75.0 1.0
C F:PRO193 3.5 56.2 1.0
CB F:PRO193 3.7 58.9 1.0
CD1 F:TRP197 3.7 50.3 1.0
CB F:SER194 3.7 56.7 1.0
CD1 F:ILE242 3.8 72.8 1.0
O F:PRO193 3.8 55.9 1.0
NE1 F:TRP197 3.9 51.1 1.0
N G:F6A202 4.1 81.0 1.0
CA F:PRO193 4.2 56.3 1.0
C4 G:F6A202 4.3 73.7 1.0
OG F:SER194 4.3 57.6 1.0
C6 G:F6A202 4.5 80.3 1.0
C F:SER194 4.7 55.4 1.0
CG F:TRP197 4.8 49.8 1.0
CG F:PRO193 4.8 59.0 1.0
OD1 H:ASP106 4.9 75.2 1.0
CD2 F:HIS240 4.9 66.4 1.0
C5 G:F6A202 4.9 77.2 1.0
C9 G:F6A202 5.0 83.1 1.0
CE2 F:TRP197 5.0 50.2 1.0

Reference:

D.K.Inaoka, T.Shiba, D.Sato, E.O.Balogun, T.Sasaki, M.Nagahama, M.Oda, S.Matsuoka, J.Ohmori, T.Honma, M.Inoue, K.Kita, S.Harada. Structural Insights Into the Molecular Design of Flutolanil Derivatives Targeted For Fumarate Respiration of Parasite Mitochondria Int J Mol Sci V. 16 15287 2015.
ISSN: ESSN 1422-0067
PubMed: 26198225
DOI: 10.3390/IJMS160715287
Page generated: Sun Dec 13 12:16:19 2020

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