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Fluorine in PDB 4ytp: Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide

Enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide

All present enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide, PDB code: 4ytp 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 (°) 71.429, 84.008, 294.817, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 26.9

Other elements in 4ytp:

The structure of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide also contains other interesting chemical elements:

Iron (Fe) 10 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide (pdb code 4ytp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide, PDB code: 4ytp:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4ytp

Go back to Fluorine Binding Sites List in 4ytp
Fluorine binding site 1 out of 3 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)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 Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F302

b:61.7
occ:1.00
 FAG C:E23302 0.0 61.7 1.0
CAX C:E23302 1.3 60.6 1.0
FAE C:E23302 2.2 61.2 1.0
FAF C:E23302 2.2 58.7 1.0
CAV C:E23302 2.3 60.3 1.0
OH D:TYR91 2.9 45.6 1.0
CE2 D:TYR91 3.0 46.5 1.0
NH1 C:ARG46 3.1 58.8 1.0
CAM C:E23302 3.1 59.8 1.0
OAD C:E23302 3.2 55.8 1.0
CAU C:E23302 3.2 59.6 1.0
CZ D:TYR91 3.2 45.8 1.0
OD2 D:ASP90 3.2 53.4 1.0
CAR C:E23302 3.5 56.9 1.0
CD1 B:TRP173 3.9 63.6 1.0
CB D:ASP90 3.9 56.0 1.0
NH2 C:ARG46 3.9 62.1 1.0
CG D:ASP90 3.9 58.0 1.0
CZ C:ARG46 4.0 58.6 1.0
CD2 D:TYR91 4.0 46.3 1.0
NE1 B:TRP173 4.3 62.2 1.0
CAI C:E23302 4.4 60.0 1.0
CE1 D:TYR91 4.4 45.0 1.0
CAJ C:E23302 4.4 60.0 1.0
NAQ C:E23302 4.8 58.2 1.0
CAH C:E23302 4.9 60.0 1.0
CD2 B:HIS216 4.9 49.1 1.0

Fluorine binding site 2 out of 3 in 4ytp

Go back to Fluorine Binding Sites List in 4ytp
Fluorine binding site 2 out of 3 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)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 Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F302

b:58.7
occ:1.00
 FAF C:E23302 0.0 58.7 1.0
CAX C:E23302 1.3 60.6 1.0
FAE C:E23302 2.1 61.2 1.0
FAG C:E23302 2.2 61.7 1.0
CAV C:E23302 2.3 60.3 1.0
OAD C:E23302 2.7 55.8 1.0
CAR C:E23302 2.7 56.9 1.0
CAU C:E23302 2.8 59.6 1.0
CD1 B:TRP173 3.2 63.6 1.0
NE1 B:TRP173 3.3 62.2 1.0
CB B:PRO169 3.4 48.4 1.0
NAQ C:E23302 3.5 58.2 1.0
CAM C:E23302 3.5 59.8 1.0
C B:PRO169 3.8 50.9 1.0
N B:SER170 3.9 53.7 1.0
O B:PRO169 4.0 49.7 1.0
OH D:TYR91 4.2 45.6 1.0
CAJ C:E23302 4.2 60.0 1.0
CA B:PRO169 4.2 49.2 1.0
CA B:SER170 4.3 53.2 1.0
CE2 D:TYR91 4.3 46.5 1.0
CAP C:E23302 4.3 61.2 1.0
OG B:SER170 4.4 50.8 1.0
CD1 B:ILE218 4.5 49.4 1.0
CG B:TRP173 4.5 62.1 1.0
CG B:PRO169 4.6 49.2 1.0
CE2 B:TRP173 4.6 63.0 1.0
CAI C:E23302 4.7 60.0 1.0
CZ D:TYR91 4.7 45.8 1.0
OD2 D:ASP90 4.8 53.4 1.0
NH1 C:ARG46 4.9 58.8 1.0
CAH C:E23302 5.0 60.0 1.0
CB B:SER170 5.0 53.2 1.0

Fluorine binding site 3 out of 3 in 4ytp

Go back to Fluorine Binding Sites List in 4ytp
Fluorine binding site 3 out of 3 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)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 Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F302

b:61.2
occ:1.00
 FAE C:E23302 0.0 61.2 1.0
CAX C:E23302 1.3 60.6 1.0
FAF C:E23302 2.1 58.7 1.0
FAG C:E23302 2.2 61.7 1.0
CAV C:E23302 2.3 60.3 1.0
CAM C:E23302 2.7 59.8 1.0
OG B:SER170 3.1 50.8 1.0
OD2 D:ASP90 3.2 53.4 1.0
CAU C:E23302 3.6 59.6 1.0
CD2 B:HIS216 3.6 49.1 1.0
CD1 B:ILE218 3.9 49.4 1.0
CA B:SER170 4.1 53.2 1.0
CAI C:E23302 4.1 60.0 1.0
CB B:SER170 4.1 53.2 1.0
N B:SER170 4.2 53.7 1.0
CG D:ASP90 4.2 58.0 1.0
CAR C:E23302 4.3 56.9 1.0
NH1 C:ARG46 4.3 58.8 1.0
NH2 C:ARG46 4.4 62.1 1.0
OAD C:E23302 4.4 55.8 1.0
NE2 B:HIS216 4.5 48.6 1.0
CG B:HIS216 4.6 48.5 1.0
C B:PRO169 4.7 50.9 1.0
CD1 B:TRP173 4.7 63.6 1.0
CAJ C:E23302 4.7 60.0 1.0
CZ C:ARG46 4.8 58.6 1.0
CB B:PRO169 4.8 48.4 1.0
O B:ARG214 4.8 38.5 1.0
OH D:TYR91 4.9 45.6 1.0
CB D:ASP90 4.9 56.0 1.0
CAH C:E23302 4.9 60.0 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: Tue Jul 15 01:47:35 2025

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