Atomistry » Fluorine » PDB 4ymq-4zg9 » 4ysy
Atomistry »
  Fluorine »
    PDB 4ymq-4zg9 »
      4ysy »

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: Thu Aug 1 07:04:19 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy