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Fluorine in PDB 4ysx: Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23

Enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23

All present enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23, PDB code: 4ysx 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 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.200, 127.909, 220.546, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.1

Other elements in 4ysx:

The structure of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23 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 the Specific Inhibitor NN23 (pdb code 4ysx). 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 the Specific Inhibitor NN23, PDB code: 4ysx:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4ysx

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Fluorine binding site 1 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:38.0
occ:1.00
 FAG B:E23304 0.0 38.0 1.0
CAX B:E23304 1.3 38.4 1.0
FAF B:E23304 2.2 38.6 1.0
FAE B:E23304 2.2 36.3 1.0
CAV B:E23304 2.4 38.9 1.0
OAD B:E23304 3.1 37.5 1.0
CD1 B:TRP197 3.1 35.4 1.0
NH1 C:ARG76 3.2 38.2 1.0
CAM B:E23304 3.2 39.4 1.0
CAU B:E23304 3.2 38.8 1.0
OH D:TYR107 3.3 41.1 1.0
CE2 D:TYR107 3.3 44.9 1.0
NE1 B:TRP197 3.4 37.6 1.0
CZ D:TYR107 3.5 45.2 1.0
CB D:ASP106 3.5 43.9 1.0
CAR B:E23304 3.5 40.5 1.0
OD2 D:ASP106 3.5 43.5 1.0
CG D:ASP106 3.6 44.1 1.0
CZ C:ARG76 4.2 36.2 1.0
CD2 D:TYR107 4.3 45.9 1.0
OD1 D:ASP106 4.3 44.8 1.0
CG B:TRP197 4.4 34.7 1.0
O D:HOH309 4.4 41.9 1.0
CAJ B:E23304 4.5 38.3 1.0
CAI B:E23304 4.5 39.6 1.0
CE1 D:TYR107 4.5 44.6 1.0
NH2 C:ARG76 4.7 38.4 1.0
CE2 B:TRP197 4.7 37.5 1.0
CA D:ASP106 4.8 44.4 1.0
NAQ B:E23304 4.8 41.0 1.0
CA B:SER194 4.8 33.4 1.0
O B:PRO193 4.8 35.7 1.0
CAH B:E23304 5.0 39.0 1.0

Fluorine binding site 2 out of 6 in 4ysx

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Fluorine binding site 2 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:38.6
occ:1.00
 FAF B:E23304 0.0 38.6 1.0
CAX B:E23304 1.3 38.4 1.0
FAE B:E23304 2.1 36.3 1.0
FAG B:E23304 2.2 38.0 1.0
CAV B:E23304 2.3 38.9 1.0
OAD B:E23304 2.7 37.5 1.0
CAR B:E23304 2.7 40.5 1.0
CAU B:E23304 2.8 38.8 1.0
NE1 B:TRP197 3.0 37.6 1.0
CD1 B:TRP197 3.2 35.4 1.0
C B:PRO193 3.3 34.8 1.0
CB B:PRO193 3.3 33.1 1.0
N B:SER194 3.4 33.8 1.0
CAM B:E23304 3.4 39.4 1.0
O B:PRO193 3.5 35.7 1.0
NAQ B:E23304 3.7 41.0 1.0
CA B:SER194 3.7 33.4 1.0
CA B:PRO193 3.9 33.4 1.0
CD1 B:ILE242 4.1 39.1 1.0
CAJ B:E23304 4.1 38.3 1.0
CE2 B:TRP197 4.3 37.5 1.0
CB B:SER194 4.3 33.9 1.0
CG B:TRP197 4.5 34.7 1.0
OH D:TYR107 4.5 41.1 1.0
CAP B:E23304 4.6 41.2 1.0
CG B:PRO193 4.6 34.4 1.0
CAI B:E23304 4.6 39.6 1.0
CE2 D:TYR107 4.8 44.9 1.0
CAH B:E23304 4.9 39.0 1.0
N B:PRO193 4.9 32.9 1.0
NH1 C:ARG76 5.0 38.2 1.0

Fluorine binding site 3 out of 6 in 4ysx

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Fluorine binding site 3 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:36.3
occ:1.00
 FAE B:E23304 0.0 36.3 1.0
CAX B:E23304 1.3 38.4 1.0
FAF B:E23304 2.1 38.6 1.0
FAG B:E23304 2.2 38.0 1.0
CAV B:E23304 2.3 38.9 1.0
CAM B:E23304 2.6 39.4 1.0
CD2 B:HIS240 3.3 50.6 1.0
CB B:SER194 3.4 33.9 1.0
CA B:SER194 3.6 33.4 1.0
CAU B:E23304 3.6 38.8 1.0
OD2 D:ASP106 3.8 43.5 1.0
OG B:SER194 3.8 30.4 1.0
CG D:ASP106 3.9 44.1 1.0
O D:HOH309 3.9 41.9 1.0
N B:SER194 3.9 33.8 1.0
CAI B:E23304 3.9 39.6 1.0
OD1 D:ASP106 4.0 44.8 1.0
CG B:HIS240 4.1 46.0 1.0
NE2 B:HIS240 4.1 51.4 1.0
CD1 B:TRP197 4.3 35.4 1.0
CD1 B:ILE242 4.3 39.1 1.0
CAR B:E23304 4.3 40.5 1.0
NH1 C:ARG76 4.3 38.2 1.0
OAD B:E23304 4.3 37.5 1.0
C B:PRO193 4.5 34.8 1.0
CB B:HIS240 4.5 42.7 1.0
CB D:ASP106 4.5 43.9 1.0
CAJ B:E23304 4.6 38.3 1.0
NE1 B:TRP197 4.6 37.6 1.0
O B:PRO193 4.7 35.7 1.0
NH2 C:ARG76 4.8 38.4 1.0
CAH B:E23304 4.8 39.0 1.0
CZ C:ARG76 4.8 36.2 1.0
C B:SER194 5.0 34.7 1.0

Fluorine binding site 4 out of 6 in 4ysx

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Fluorine binding site 4 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F202

b:36.9
occ:1.00
 FAG G:E23202 0.0 36.9 1.0
CAX G:E23202 1.3 39.6 1.0
FAF G:E23202 2.1 42.5 1.0
FAE G:E23202 2.2 42.8 1.0
CAV G:E23202 2.3 37.8 1.0
OAD G:E23202 2.6 41.7 1.0
CAR G:E23202 2.7 41.1 1.0
CAU G:E23202 2.8 38.2 1.0
NE1 F:TRP197 3.2 39.9 1.0
CD1 F:TRP197 3.2 40.6 1.0
CB F:PRO193 3.3 35.7 1.0
N F:SER194 3.4 35.8 1.0
C F:PRO193 3.4 37.3 1.0
CAM G:E23202 3.5 37.7 1.0
NAQ G:E23202 3.6 41.8 1.0
O F:PRO193 3.7 39.1 1.0
CA F:SER194 3.8 36.8 1.0
CD1 F:ILE242 4.0 36.6 1.0
CA F:PRO193 4.0 36.9 1.0
CAJ G:E23202 4.1 36.8 1.0
CB F:SER194 4.3 36.2 1.0
CE2 F:TRP197 4.4 39.3 1.0
CAP G:E23202 4.4 44.8 1.0
CG F:TRP197 4.5 39.0 1.0
CG F:PRO193 4.6 35.7 1.0
CAI G:E23202 4.6 36.4 1.0
OH H:TYR107 4.7 41.6 1.0
CAH G:E23202 4.9 36.9 1.0
NH1 G:ARG76 4.9 42.5 1.0
N F:PRO193 4.9 34.5 1.0
O F:HOH448 5.0 43.9 1.0

Fluorine binding site 5 out of 6 in 4ysx

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Fluorine binding site 5 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F202

b:42.5
occ:1.00
 FAF G:E23202 0.0 42.5 1.0
CAX G:E23202 1.3 39.6 1.0
FAG G:E23202 2.1 36.9 1.0
FAE G:E23202 2.1 42.8 1.0
CAV G:E23202 2.3 37.8 1.0
CAM G:E23202 2.6 37.7 1.0
CD2 F:HIS240 3.4 48.9 1.0
OD2 H:ASP106 3.5 37.2 1.0
CB F:SER194 3.5 36.2 1.0
CAU G:E23202 3.6 38.2 1.0
CA F:SER194 3.7 36.8 1.0
CG H:ASP106 3.8 40.5 1.0
OG F:SER194 3.9 36.0 1.0
O F:HOH448 3.9 43.9 1.0
N F:SER194 4.0 35.8 1.0
CAI G:E23202 4.0 36.4 1.0
OD1 H:ASP106 4.0 42.2 1.0
CG F:HIS240 4.2 46.4 1.0
NE2 F:HIS240 4.2 50.5 1.0
CD1 F:ILE242 4.3 36.6 1.0
CAR G:E23202 4.3 41.1 1.0
NH1 G:ARG76 4.3 42.5 1.0
OAD G:E23202 4.3 41.7 1.0
CD1 F:TRP197 4.4 40.6 1.0
CB H:ASP106 4.5 39.8 1.0
CB F:HIS240 4.5 41.6 1.0
C F:PRO193 4.6 37.3 1.0
CAJ G:E23202 4.7 36.8 1.0
NH2 G:ARG76 4.8 38.0 1.0
CZ G:ARG76 4.8 38.8 1.0
NE1 F:TRP197 4.8 39.9 1.0
CAH G:E23202 4.8 36.9 1.0
O F:PRO193 4.9 39.1 1.0

Fluorine binding site 6 out of 6 in 4ysx

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Fluorine binding site 6 out of 6 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F202

b:42.8
occ:1.00
 FAE G:E23202 0.0 42.8 1.0
CAX G:E23202 1.3 39.6 1.0
FAF G:E23202 2.1 42.5 1.0
FAG G:E23202 2.2 36.9 1.0
CAV G:E23202 2.3 37.8 1.0
OAD G:E23202 3.0 41.7 1.0
NH1 G:ARG76 3.1 42.5 1.0
CAU G:E23202 3.2 38.2 1.0
CAM G:E23202 3.2 37.7 1.0
CD1 F:TRP197 3.2 40.6 1.0
OD2 H:ASP106 3.2 37.2 1.0
CG H:ASP106 3.4 40.5 1.0
CB H:ASP106 3.4 39.8 1.0
CAR G:E23202 3.5 41.1 1.0
OH H:TYR107 3.5 41.6 1.0
NE1 F:TRP197 3.6 39.9 1.0
CE2 H:TYR107 3.7 44.3 1.0
CZ H:TYR107 3.7 44.9 1.0
CZ G:ARG76 4.1 38.8 1.0
OD1 H:ASP106 4.2 42.2 1.0
O F:HOH448 4.3 43.9 1.0
CAJ G:E23202 4.4 36.8 1.0
CAI G:E23202 4.5 36.4 1.0
CG F:TRP197 4.5 39.0 1.0
CE1 H:TYR107 4.5 46.9 1.0
CD2 H:TYR107 4.5 44.0 1.0
NH2 G:ARG76 4.6 38.0 1.0
NAQ G:E23202 4.7 41.8 1.0
CA H:ASP106 4.8 42.0 1.0
CA F:SER194 4.9 36.8 1.0
CE2 F:TRP197 4.9 39.3 1.0
CAH G:E23202 4.9 36.9 1.0
CD2 F:HIS240 5.0 48.9 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

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