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Fluorine in PDB 4ysy: Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[(2,4-Dichlorophenyl)Methyl]-2-(Trifluoromethyl) Benzamide

Enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[(2,4-Dichlorophenyl)Methyl]-2-(Trifluoromethyl) Benzamide

All present enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[(2,4-Dichlorophenyl)Methyl]-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-[(2,4-Dichlorophenyl)Methyl]-2-(Trifluoromethyl) Benzamide, PDB code: 4ysy 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 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.120, 127.660, 220.736, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.8

Other elements in 4ysy:

The structure of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[(2,4-Dichlorophenyl)Methyl]-2-(Trifluoromethyl) Benzamide also contains other interesting chemical elements:

Iron (Fe) 20 atoms
Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[(2,4-Dichlorophenyl)Methyl]-2-(Trifluoromethyl) Benzamide (pdb code 4ysy). 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-[(2,4-Dichlorophenyl)Methyl]-2-(Trifluoromethyl) Benzamide, PDB code: 4ysy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4ysy

Go back to Fluorine Binding Sites List in 4ysy
Fluorine binding site 1 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[(2,4-Dichlorophenyl)Methyl]-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-[(2,4-Dichlorophenyl)Methyl]-2-(Trifluoromethyl) Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:61.6
occ:1.00
FAC B:E24304 0.0 61.6 1.0
CAV B:E24304 1.3 65.3 1.0
FAD B:E24304 2.1 61.1 1.0
CAU B:E24304 2.3 69.1 1.0
FAB B:E24304 2.3 63.1 1.0
CAJ B:E24304 3.0 70.0 1.0
NH1 C:ARG76 3.2 54.5 1.0
CAT B:E24304 3.2 73.2 1.0
OAA B:E24304 3.2 79.4 1.0
CG D:ASP106 3.3 69.6 1.0
CE2 D:TYR107 3.3 62.4 1.0
OD2 D:ASP106 3.4 67.0 1.0
CB D:ASP106 3.4 67.9 1.0
CD1 B:TRP197 3.5 50.4 1.0
OH D:TYR107 3.5 66.6 1.0
CAP B:E24304 3.6 76.7 1.0
NE1 B:TRP197 3.7 50.7 1.0
CZ D:TYR107 3.7 63.4 1.0
OD1 D:ASP106 3.8 72.0 1.0
CZ C:ARG76 4.0 54.0 1.0
CD2 D:TYR107 4.2 62.4 1.0
CAH B:E24304 4.3 73.7 1.0
NH2 C:ARG76 4.4 53.8 1.0
CAI B:E24304 4.4 74.3 1.0
CA D:ASP106 4.8 65.8 1.0
CG B:TRP197 4.8 49.7 1.0
CAG B:E24304 4.8 76.3 1.0
CE1 D:TYR107 4.8 63.3 1.0
O B:PRO193 4.8 43.3 1.0
NAO B:E24304 4.9 77.8 1.0
CD2 B:HIS240 4.9 63.9 1.0
NE C:ARG76 5.0 53.5 1.0
CA B:SER194 5.0 48.6 1.0

Fluorine binding site 2 out of 6 in 4ysy

Go back to Fluorine Binding Sites List in 4ysy
Fluorine binding site 2 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[(2,4-Dichlorophenyl)Methyl]-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-[(2,4-Dichlorophenyl)Methyl]-2-(Trifluoromethyl) Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:61.1
occ:1.00
FAD B:E24304 0.0 61.1 1.0
CAV B:E24304 1.3 65.3 1.0
FAC B:E24304 2.1 61.6 1.0
FAB B:E24304 2.2 63.1 1.0
CAU B:E24304 2.2 69.1 1.0
CAJ B:E24304 2.6 70.0 1.0
CA B:SER194 3.5 48.6 1.0
CAT B:E24304 3.5 73.2 1.0
CB B:SER194 3.5 49.8 1.0
CD2 B:HIS240 3.6 63.9 1.0
N B:SER194 3.7 46.9 1.0
OG B:SER194 3.8 53.7 1.0
OD1 D:ASP106 3.9 72.0 1.0
CAH B:E24304 3.9 73.7 1.0
CG D:ASP106 3.9 69.6 1.0
OD2 D:ASP106 4.0 67.0 1.0
CD1 B:ILE242 4.2 61.1 1.0
CG B:HIS240 4.2 62.5 1.0
C B:PRO193 4.2 45.7 1.0
CAP B:E24304 4.2 76.7 1.0
O B:PRO193 4.3 43.3 1.0
CD1 B:TRP197 4.3 50.4 1.0
NE2 B:HIS240 4.3 63.2 1.0
OAA B:E24304 4.3 79.4 1.0
CB B:HIS240 4.5 60.2 1.0
NE1 B:TRP197 4.6 50.7 1.0
CAI B:E24304 4.6 74.3 1.0
NH1 C:ARG76 4.7 54.5 1.0
CB D:ASP106 4.7 67.9 1.0
CAG B:E24304 4.8 76.3 1.0
C B:SER194 4.9 50.0 1.0
CB B:PRO193 5.0 44.5 1.0
NH2 C:ARG76 5.0 53.8 1.0

Fluorine binding site 3 out of 6 in 4ysy

Go back to Fluorine Binding Sites List in 4ysy
Fluorine binding site 3 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[(2,4-Dichlorophenyl)Methyl]-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-[(2,4-Dichlorophenyl)Methyl]-2-(Trifluoromethyl) Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:63.1
occ:1.00
FAB B:E24304 0.0 63.1 1.0
CAV B:E24304 1.4 65.3 1.0
FAD B:E24304 2.2 61.1 1.0
FAC B:E24304 2.3 61.6 1.0
CAU B:E24304 2.3 69.1 1.0
OAA B:E24304 2.6 79.4 1.0
CAP B:E24304 2.7 76.7 1.0
NE1 B:TRP197 2.7 50.7 1.0
CAT B:E24304 2.8 73.2 1.0
CD1 B:TRP197 3.1 50.4 1.0
O B:PRO193 3.2 43.3 1.0
C B:PRO193 3.3 45.7 1.0
CB B:PRO193 3.4 44.5 1.0
NAO B:E24304 3.5 77.8 1.0
CAJ B:E24304 3.6 70.0 1.0
N B:SER194 3.6 46.9 1.0
CE2 B:TRP197 4.0 50.7 1.0
CA B:PRO193 4.0 45.4 1.0
CA B:SER194 4.0 48.6 1.0
CAI B:E24304 4.2 74.3 1.0
CAN B:E24304 4.3 79.0 1.0
CG B:TRP197 4.4 49.7 1.0
OH D:TYR107 4.5 66.6 1.0
CE2 D:TYR107 4.5 62.4 1.0
CD1 B:ILE242 4.5 61.1 1.0
CG B:PRO193 4.7 44.3 1.0
CAH B:E24304 4.7 73.7 1.0
CZ2 B:TRP197 4.7 50.0 1.0
CB B:SER194 4.8 49.8 1.0
CD2 B:TRP197 4.8 50.7 1.0
CAG B:E24304 4.9 76.3 1.0
CZ D:TYR107 5.0 63.4 1.0

Fluorine binding site 4 out of 6 in 4ysy

Go back to Fluorine Binding Sites List in 4ysy
Fluorine binding site 4 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[(2,4-Dichlorophenyl)Methyl]-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-[(2,4-Dichlorophenyl)Methyl]-2-(Trifluoromethyl) Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F304

b:62.4
occ:1.00
FAC F:E24304 0.0 62.4 1.0
CAV F:E24304 1.4 62.8 1.0
FAB F:E24304 2.2 62.8 1.0
FAD F:E24304 2.2 57.1 1.0
CAU F:E24304 2.3 65.6 1.0
OAA F:E24304 3.0 75.0 1.0
NH1 G:ARG76 3.1 60.3 1.0
CAT F:E24304 3.2 68.9 1.0
CAJ F:E24304 3.2 66.2 1.0
CD1 F:TRP197 3.3 58.0 1.0
CG H:ASP106 3.3 59.6 1.0
CE2 H:TYR107 3.4 61.2 1.0
OD2 H:ASP106 3.4 57.3 1.0
CAP F:E24304 3.4 73.2 1.0
CB H:ASP106 3.5 60.6 1.0
NE1 F:TRP197 3.6 57.2 1.0
OH H:TYR107 3.6 57.9 1.0
CZ H:TYR107 3.8 60.5 1.0
OD1 H:ASP106 3.8 61.9 1.0
CZ G:ARG76 3.9 61.4 1.0
CD2 H:TYR107 4.3 60.3 1.0
NH2 G:ARG76 4.3 60.7 1.0
CAI F:E24304 4.4 65.1 1.0
CAH F:E24304 4.4 64.5 1.0
CG F:TRP197 4.5 58.5 1.0
NAO F:E24304 4.7 76.8 1.0
CA H:ASP106 4.8 61.3 1.0
CE1 H:TYR107 4.8 60.3 1.0
NE G:ARG76 4.9 61.1 1.0
CA F:SER194 4.9 62.1 1.0
CAG F:E24304 4.9 63.4 1.0
CE2 F:TRP197 5.0 58.3 1.0

Fluorine binding site 5 out of 6 in 4ysy

Go back to Fluorine Binding Sites List in 4ysy
Fluorine binding site 5 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[(2,4-Dichlorophenyl)Methyl]-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-[(2,4-Dichlorophenyl)Methyl]-2-(Trifluoromethyl) Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F304

b:57.1
occ:1.00
FAD F:E24304 0.0 57.1 1.0
CAV F:E24304 1.3 62.8 1.0
FAB F:E24304 2.1 62.8 1.0
FAC F:E24304 2.2 62.4 1.0
CAU F:E24304 2.3 65.6 1.0
CAJ F:E24304 2.6 66.2 1.0
CD2 F:HIS240 3.4 72.9 1.0
OD2 H:ASP106 3.4 57.3 1.0
CB F:SER194 3.5 62.9 1.0
CG H:ASP106 3.6 59.6 1.0
CAT F:E24304 3.6 68.9 1.0
OD1 H:ASP106 3.6 61.9 1.0
OG F:SER194 3.6 65.8 1.0
CA F:SER194 3.7 62.1 1.0
CAH F:E24304 3.9 64.5 1.0
CG F:HIS240 4.0 70.3 1.0
N F:SER194 4.1 58.7 1.0
NE2 F:HIS240 4.1 71.7 1.0
CD1 F:ILE242 4.3 66.0 1.0
NH1 G:ARG76 4.3 60.3 1.0
CAP F:E24304 4.3 73.2 1.0
NH2 G:ARG76 4.4 60.7 1.0
CB F:HIS240 4.4 66.6 1.0
OAA F:E24304 4.4 75.0 1.0
CD1 F:TRP197 4.5 58.0 1.0
CB H:ASP106 4.5 60.6 1.0
CZ G:ARG76 4.6 61.4 1.0
CAI F:E24304 4.7 65.1 1.0
C F:PRO193 4.7 58.0 1.0
CAG F:E24304 4.8 63.4 1.0
NE1 F:TRP197 4.9 57.2 1.0
ND1 F:HIS240 4.9 70.2 1.0
CE1 F:HIS240 5.0 71.2 1.0

Fluorine binding site 6 out of 6 in 4ysy

Go back to Fluorine Binding Sites List in 4ysy
Fluorine binding site 6 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with N-[(2,4-Dichlorophenyl)Methyl]-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-[(2,4-Dichlorophenyl)Methyl]-2-(Trifluoromethyl) Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F304

b:62.8
occ:1.00
FAB F:E24304 0.0 62.8 1.0
CAV F:E24304 1.3 62.8 1.0
FAD F:E24304 2.1 57.1 1.0
FAC F:E24304 2.2 62.4 1.0
CAU F:E24304 2.3 65.6 1.0
CAP F:E24304 2.8 73.2 1.0
CAT F:E24304 2.9 68.9 1.0
OAA F:E24304 2.9 75.0 1.0
NE1 F:TRP197 3.2 57.2 1.0
CD1 F:TRP197 3.2 58.0 1.0
N F:SER194 3.3 58.7 1.0
CB F:PRO193 3.4 56.9 1.0
C F:PRO193 3.4 58.0 1.0
CAJ F:E24304 3.4 66.2 1.0
CA F:SER194 3.6 62.1 1.0
NAO F:E24304 3.7 76.8 1.0
O F:PRO193 3.7 56.6 1.0
CA F:PRO193 4.0 57.4 1.0
CD1 F:ILE242 4.1 66.0 1.0
CB F:SER194 4.2 62.9 1.0
CAI F:E24304 4.2 65.1 1.0
CE2 F:TRP197 4.4 58.3 1.0
CG F:TRP197 4.4 58.5 1.0
CAN F:E24304 4.5 79.5 1.0
CAH F:E24304 4.6 64.5 1.0
CG F:PRO193 4.7 56.5 1.0
OG F:SER194 4.7 65.8 1.0
OH H:TYR107 4.9 57.9 1.0
CE2 H:TYR107 4.9 61.2 1.0
CAG F:E24304 4.9 63.4 1.0
C F:SER194 5.0 62.5 1.0
CG H:ASP106 5.0 59.6 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 12:16:16 2020

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