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Fluorine in PDB 3ae9: Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide

Enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide

All present enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide, PDB code: 3ae9 was solved by S.Harada, T.Sasaki, M.Shindo, Y.Kido, D.K.Inaoka, J.Omori, A.Osanai, K.Sakamoto, J.Mao, S.Matsuoka, M.Inoue, T.Honma, A.Tanaka, K.Kita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.76 / 3.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.609, 84.249, 295.646, 90.00, 90.00, 90.00
R / Rfree (%) 25.7 / 30.7

Other elements in 3ae9:

The structure of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-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-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide (pdb code 3ae9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide, PDB code: 3ae9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3ae9

Go back to Fluorine Binding Sites List in 3ae9
Fluorine binding site 1 out of 8 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-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-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1201

b:0.1
occ:1.00
 F1 C:FD81201 0.0 0.1 1.0
C1 C:FD81201 1.3 0.1 1.0
F3 C:FD81201 2.1 0.0 1.0
F2 C:FD81201 2.2 0.1 1.0
C2 C:FD81201 2.3 0.1 1.0
C3 C:FD81201 3.0 0.1 1.0
C8 C:FD81201 3.0 0.2 1.0
NE1 B:TRP173 3.2 0.7 1.0
N C:FD81201 3.3 0.2 1.0
CD1 B:TRP173 3.3 0.7 1.0
C7 C:FD81201 3.4 1.0 1.0
O1 C:FD81201 3.6 0.2 1.0
N B:SER170 3.6 1.0 1.0
CB B:PRO169 3.7 1.0 1.0
C B:PRO169 3.8 0.7 1.0
CA B:SER170 3.9 0.6 1.0
CD1 B:ILE218 4.0 96.4 1.0
C9 C:FD81201 4.1 0.3 1.0
CB B:SER170 4.1 0.2 1.0
O B:PRO169 4.2 0.9 1.0
C4 C:FD81201 4.3 1.0 1.0
CA B:PRO169 4.4 0.3 1.0
CE2 B:TRP173 4.5 0.0 1.0
C6 C:FD81201 4.6 0.9 1.0
OH D:TYR91 4.6 0.5 1.0
CG B:TRP173 4.6 0.0 1.0
CG B:PRO169 4.6 0.2 1.0
C14 C:FD81201 4.7 0.3 1.0
OG B:SER170 4.9 0.4 1.0
C10 C:FD81201 4.9 0.3 1.0
C5 C:FD81201 4.9 0.9 1.0
NH1 C:ARG46 4.9 95.2 1.0

Fluorine binding site 2 out of 8 in 3ae9

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Fluorine binding site 2 out of 8 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-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-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1201

b:0.1
occ:1.00
 F2 C:FD81201 0.0 0.1 1.0
C1 C:FD81201 1.3 0.1 1.0
F3 C:FD81201 2.1 0.0 1.0
F1 C:FD81201 2.2 0.1 1.0
C2 C:FD81201 2.3 0.1 1.0
OH D:TYR91 2.7 0.5 1.0
O1 C:FD81201 2.9 0.2 1.0
C3 C:FD81201 3.0 0.1 1.0
C8 C:FD81201 3.0 0.2 1.0
CZ D:TYR91 3.2 0.1 1.0
NH1 C:ARG46 3.2 95.2 1.0
CD1 B:TRP173 3.4 0.7 1.0
C7 C:FD81201 3.4 1.0 1.0
CE2 D:TYR91 3.5 0.6 1.0
NE1 B:TRP173 3.5 0.7 1.0
N C:FD81201 4.0 0.2 1.0
CE1 D:TYR91 4.2 0.7 1.0
C4 C:FD81201 4.3 1.0 1.0
CZ C:ARG46 4.3 93.9 1.0
NH2 C:ARG46 4.6 93.0 1.0
C6 C:FD81201 4.6 0.9 1.0
CD2 D:TYR91 4.6 0.7 1.0
CG B:TRP173 4.6 0.0 1.0
CE2 B:TRP173 4.7 0.0 1.0
CB D:ASP90 4.8 0.8 1.0
C9 C:FD81201 4.8 0.3 1.0
OD2 D:ASP90 4.8 0.4 1.0
C14 C:FD81201 4.9 0.3 1.0
C5 C:FD81201 4.9 0.9 1.0

Fluorine binding site 3 out of 8 in 3ae9

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Fluorine binding site 3 out of 8 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-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-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1201

b:0.0
occ:1.00
 F3 C:FD81201 0.0 0.0 1.0
C1 C:FD81201 1.3 0.1 1.0
F1 C:FD81201 2.1 0.1 1.0
F2 C:FD81201 2.1 0.1 1.0
C2 C:FD81201 2.3 0.1 1.0
C7 C:FD81201 2.6 1.0 1.0
C3 C:FD81201 3.6 0.1 1.0
CB B:SER170 3.7 0.2 1.0
OD2 D:ASP90 3.8 0.4 1.0
OG B:SER170 3.8 0.4 1.0
CD1 B:TRP173 4.0 0.7 1.0
CA B:SER170 4.0 0.6 1.0
NH1 C:ARG46 4.0 95.2 1.0
C6 C:FD81201 4.0 0.9 1.0
CG D:ASP90 4.1 0.8 1.0
CD2 B:HIS216 4.1 95.3 1.0
NH2 C:ARG46 4.3 93.0 1.0
C8 C:FD81201 4.3 0.2 1.0
CB D:ASP90 4.4 0.8 1.0
N B:SER170 4.5 1.0 1.0
NE1 B:TRP173 4.5 0.7 1.0
CZ C:ARG46 4.6 93.9 1.0
OD1 D:ASP90 4.6 0.7 1.0
OH D:TYR91 4.7 0.5 1.0
O1 C:FD81201 4.7 0.2 1.0
NE2 B:HIS216 4.7 96.7 1.0
C4 C:FD81201 4.7 1.0 1.0
CD1 B:ILE218 4.9 96.4 1.0
C5 C:FD81201 4.9 0.9 1.0

Fluorine binding site 4 out of 8 in 3ae9

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Fluorine binding site 4 out of 8 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-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 Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1201

b:0.1
occ:1.00
 F4 C:FD81201 0.0 0.1 1.0
C16 C:FD81201 1.4 0.0 1.0
C15 C:FD81201 2.5 0.9 1.0
C17 C:FD81201 2.5 0.1 1.0
F5 C:FD81201 2.9 0.1 1.0
O2 C:FD81201 2.9 0.7 1.0
CD1 C:ILE30 3.3 1.0 1.0
C20 C:FD81201 3.9 0.1 1.0
C18 C:FD81201 3.9 0.1 1.0
CG2 C:ILE30 3.9 0.4 1.0
C13 C:FD81201 4.0 0.5 1.0
CG1 C:ILE30 4.2 0.3 1.0
C12 C:FD81201 4.3 0.5 1.0
CB C:ILE30 4.3 0.9 1.0
C19 C:FD81201 4.4 0.1 1.0
CH2 B:TRP173 4.7 0.6 1.0
CZ2 B:TRP173 4.9 0.9 1.0

Fluorine binding site 5 out of 8 in 3ae9

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Fluorine binding site 5 out of 8 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-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 Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1201

b:0.1
occ:1.00
 F5 C:FD81201 0.0 0.1 1.0
C17 C:FD81201 1.4 0.1 1.0
C18 C:FD81201 2.5 0.1 1.0
C16 C:FD81201 2.5 0.0 1.0
F6 C:FD81201 2.9 0.1 1.0
F4 C:FD81201 2.9 0.1 1.0
C19 C:FD81201 3.9 0.1 1.0
C15 C:FD81201 3.9 0.9 1.0
CD1 C:ILE30 4.2 1.0 1.0
C20 C:FD81201 4.4 0.1 1.0

Fluorine binding site 6 out of 8 in 3ae9

Go back to Fluorine Binding Sites List in 3ae9
Fluorine binding site 6 out of 8 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-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 Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1201

b:0.1
occ:1.00
 F6 C:FD81201 0.0 0.1 1.0
C18 C:FD81201 1.4 0.1 1.0
C17 C:FD81201 2.5 0.1 1.0
C19 C:FD81201 2.5 0.1 1.0
F5 C:FD81201 2.9 0.1 1.0
F7 C:FD81201 2.9 0.2 1.0
C20 C:FD81201 3.9 0.1 1.0
C16 C:FD81201 3.9 0.0 1.0
C15 C:FD81201 4.4 0.9 1.0

Fluorine binding site 7 out of 8 in 3ae9

Go back to Fluorine Binding Sites List in 3ae9
Fluorine binding site 7 out of 8 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1201

b:0.2
occ:1.00
 F7 C:FD81201 0.0 0.2 1.0
C19 C:FD81201 1.4 0.1 1.0
C20 C:FD81201 2.5 0.1 1.0
C18 C:FD81201 2.5 0.1 1.0
F8 C:FD81201 2.9 0.2 1.0
F6 C:FD81201 2.9 0.1 1.0
C17 C:FD81201 3.9 0.1 1.0
C15 C:FD81201 3.9 0.9 1.0
CG2 C:ILE43 4.2 0.8 1.0
C16 C:FD81201 4.4 0.0 1.0
CD1 C:ILE43 4.8 0.5 1.0

Fluorine binding site 8 out of 8 in 3ae9

Go back to Fluorine Binding Sites List in 3ae9
Fluorine binding site 8 out of 8 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Pentafluorophenyloxy-Phenyl)-2-Trifluoromethyl-Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1201

b:0.2
occ:1.00
 F8 C:FD81201 0.0 0.2 1.0
C20 C:FD81201 1.4 0.1 1.0
C19 C:FD81201 2.5 0.1 1.0
C15 C:FD81201 2.5 0.9 1.0
F7 C:FD81201 2.9 0.2 1.0
O2 C:FD81201 3.0 0.7 1.0
C13 C:FD81201 3.1 0.5 1.0
C14 C:FD81201 3.3 0.3 1.0
CG2 C:ILE43 3.3 0.8 1.0
CD1 C:ILE43 3.4 0.5 1.0
CG1 C:ILE43 3.6 0.9 1.0
C12 C:FD81201 3.8 0.5 1.0
C18 C:FD81201 3.9 0.1 1.0
C16 C:FD81201 3.9 0.0 1.0
CB C:ILE43 4.1 0.6 1.0
C9 C:FD81201 4.2 0.3 1.0
C17 C:FD81201 4.4 0.1 1.0
C11 C:FD81201 4.5 0.4 1.0
C10 C:FD81201 4.7 0.3 1.0
O1 C:FD81201 4.7 0.2 1.0
N C:FD81201 5.0 0.2 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: Wed Jul 31 17:06:11 2024

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