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Fluorine in PDB 3abv: Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-Biphenyl-3-Yl-2-Trifluoromethyl-Benzamide

Enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-Biphenyl-3-Yl-2-Trifluoromethyl-Benzamide

All present enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-Biphenyl-3-Yl-2-Trifluoromethyl-Benzamide:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-Biphenyl-3-Yl-2-Trifluoromethyl-Benzamide, PDB code: 3abv 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) 37.63 / 3.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.702, 84.170, 294.432, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 25.3

Other elements in 3abv:

The structure of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-Biphenyl-3-Yl-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-Biphenyl-3-Yl-2-Trifluoromethyl-Benzamide (pdb code 3abv). 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-Biphenyl-3-Yl-2-Trifluoromethyl-Benzamide, PDB code: 3abv:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3abv

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

b:60.2
occ:1.00
 F1 B:F6A1201 0.0 60.2 1.0
C1 B:F6A1201 1.3 60.2 1.0
F3 B:F6A1201 2.1 60.0 1.0
F2 B:F6A1201 2.2 60.2 1.0
C2 B:F6A1201 2.3 60.2 1.0
O B:F6A1201 2.7 60.8 1.0
C8 B:F6A1201 2.7 60.8 1.0
C3 B:F6A1201 2.9 60.6 1.0
NE1 B:TRP173 3.1 61.2 1.0
CD1 B:TRP173 3.2 60.6 1.0
CB B:PRO169 3.5 59.7 1.0
N B:F6A1201 3.5 61.1 1.0
C7 B:F6A1201 3.5 60.2 1.0
C B:PRO169 3.7 57.9 1.0
N B:SER170 3.8 56.9 1.0
O B:PRO169 3.9 58.7 1.0
OG B:SER170 4.1 58.0 1.0
CD1 B:ILE218 4.1 49.8 1.0
CA B:SER170 4.2 56.9 1.0
C4 B:F6A1201 4.2 60.5 1.0
CA B:PRO169 4.2 58.1 1.0
CE2 B:TRP173 4.4 61.3 1.0
CG B:TRP173 4.5 60.2 1.0
OH D:TYR91 4.5 63.7 1.0
C9 B:F6A1201 4.6 61.3 1.0
C6 B:F6A1201 4.7 60.6 1.0
CB B:SER170 4.7 56.6 1.0
CG B:PRO169 4.7 59.4 1.0
CE2 D:TYR91 4.8 64.4 1.0
NH1 C:ARG46 4.8 53.9 1.0
C5 B:F6A1201 5.0 60.5 1.0

Fluorine binding site 2 out of 3 in 3abv

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

b:60.2
occ:1.00
 F2 B:F6A1201 0.0 60.2 1.0
C1 B:F6A1201 1.3 60.2 1.0
F1 B:F6A1201 2.2 60.2 1.0
F3 B:F6A1201 2.2 60.0 1.0
C2 B:F6A1201 2.3 60.2 1.0
NH1 C:ARG46 3.0 53.9 1.0
C7 B:F6A1201 3.1 60.2 1.0
O B:F6A1201 3.1 60.8 1.0
C3 B:F6A1201 3.2 60.6 1.0
OD2 D:ASP90 3.2 52.0 1.0
OH D:TYR91 3.4 63.7 1.0
C8 B:F6A1201 3.5 60.8 1.0
CE2 D:TYR91 3.5 64.4 1.0
CD1 B:TRP173 3.7 60.6 1.0
CZ D:TYR91 3.7 63.5 1.0
CG D:ASP90 3.7 53.6 1.0
CB D:ASP90 3.9 55.7 1.0
NE1 B:TRP173 4.0 61.2 1.0
CZ C:ARG46 4.1 53.2 1.0
NH2 C:ARG46 4.2 52.9 1.0
C6 B:F6A1201 4.3 60.6 1.0
C4 B:F6A1201 4.4 60.5 1.0
CD2 D:TYR91 4.5 65.1 1.0
OD1 D:ASP90 4.5 53.7 1.0
OG B:SER170 4.5 58.0 1.0
CD2 B:HIS216 4.6 53.2 1.0
CE1 D:TYR91 4.7 63.0 1.0
N B:F6A1201 4.7 61.1 1.0
NE2 B:HIS216 4.8 54.1 1.0
C5 B:F6A1201 4.9 60.5 1.0
CG B:TRP173 4.9 60.2 1.0

Fluorine binding site 3 out of 3 in 3abv

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

b:60.0
occ:1.00
 F3 B:F6A1201 0.0 60.0 1.0
C1 B:F6A1201 1.3 60.2 1.0
F1 B:F6A1201 2.1 60.2 1.0
F2 B:F6A1201 2.2 60.2 1.0
C2 B:F6A1201 2.3 60.2 1.0
C7 B:F6A1201 2.7 60.2 1.0
OG B:SER170 2.9 58.0 1.0
CD2 B:HIS216 3.1 53.2 1.0
OD2 D:ASP90 3.7 52.0 1.0
C3 B:F6A1201 3.7 60.6 1.0
NE2 B:HIS216 3.8 54.1 1.0
CD1 B:ILE218 4.0 49.8 1.0
CB B:SER170 4.0 56.6 1.0
C6 B:F6A1201 4.1 60.6 1.0
CG B:HIS216 4.2 52.8 1.0
CA B:SER170 4.2 56.9 1.0
CG D:ASP90 4.3 53.6 1.0
N B:SER170 4.3 56.9 1.0
C8 B:F6A1201 4.3 60.8 1.0
NH1 C:ARG46 4.3 53.9 1.0
O B:F6A1201 4.4 60.8 1.0
O B:ARG214 4.6 50.9 1.0
OD1 D:ASP90 4.6 53.7 1.0
CD1 B:TRP173 4.7 60.6 1.0
CB B:HIS216 4.7 52.0 1.0
C4 B:F6A1201 4.8 60.5 1.0
NH2 C:ARG46 4.8 52.9 1.0
C B:PRO169 4.8 57.9 1.0
C5 B:F6A1201 4.9 60.5 1.0
CZ C:ARG46 5.0 53.2 1.0
CG1 B:ILE218 5.0 50.5 1.0
CE1 B:HIS216 5.0 54.3 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 17:05:42 2024

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