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

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

All present enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-(3-Dimethylaminomethyl-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-Dimethylaminomethyl-Phenyl)-2-Trifluoromethyl-Benzamide, PDB code: 3aea 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) 43.77 / 3.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.505, 83.751, 294.959, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 28.6

Other elements in 3aea:

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

Fluorine binding site 1 out of 3 in 3aea

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

b:0.6
occ:1.00
 F1 D:F9A1201 0.0 0.6 1.0
C1 D:F9A1201 1.3 0.6 1.0
F3 D:F9A1201 2.1 0.5 1.0
F2 D:F9A1201 2.2 0.6 1.0
C2 D:F9A1201 2.3 0.6 1.0
O D:F9A1201 2.7 0.7 1.0
C8 D:F9A1201 2.8 0.7 1.0
C3 D:F9A1201 2.9 0.6 1.0
NE1 B:TRP173 3.1 90.6 1.0
CD1 B:TRP173 3.1 89.8 1.0
C7 D:F9A1201 3.5 0.6 1.0
CB B:PRO169 3.6 86.8 1.0
C B:PRO169 3.6 85.1 1.0
N B:SER170 3.6 84.1 1.0
N1 D:F9A1201 3.7 0.9 1.0
O B:PRO169 3.8 86.1 1.0
CA B:SER170 3.9 84.0 1.0
CD1 B:ILE218 4.1 87.4 1.0
C4 D:F9A1201 4.2 0.5 1.0
CA B:PRO169 4.3 85.6 1.0
CE2 B:TRP173 4.3 91.5 1.0
CB B:SER170 4.4 83.4 1.0
OH D:TYR91 4.4 0.2 1.0
CG B:TRP173 4.4 90.2 1.0
C9 D:F9A1201 4.5 0.2 1.0
CE2 D:TYR91 4.7 0.9 1.0
C14 D:F9A1201 4.7 0.2 1.0
C6 D:F9A1201 4.7 0.6 1.0
CG B:PRO169 4.8 86.8 1.0
NH1 C:ARG46 4.8 88.8 1.0
CZ D:TYR91 4.9 0.3 1.0
C5 D:F9A1201 5.0 0.5 1.0

Fluorine binding site 2 out of 3 in 3aea

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

b:0.6
occ:1.00
 F2 D:F9A1201 0.0 0.6 1.0
C1 D:F9A1201 1.3 0.6 1.0
F1 D:F9A1201 2.2 0.6 1.0
F3 D:F9A1201 2.2 0.5 1.0
C2 D:F9A1201 2.3 0.6 1.0
NH1 C:ARG46 3.1 88.8 1.0
O D:F9A1201 3.2 0.7 1.0
C7 D:F9A1201 3.2 0.6 1.0
OH D:TYR91 3.2 0.2 1.0
C3 D:F9A1201 3.2 0.6 1.0
CZ D:TYR91 3.4 0.3 1.0
CE2 D:TYR91 3.5 0.9 1.0
CD1 B:TRP173 3.5 89.8 1.0
C8 D:F9A1201 3.6 0.7 1.0
CG D:ASP90 3.9 0.5 1.0
NE1 B:TRP173 3.9 90.6 1.0
CB D:ASP90 3.9 0.3 1.0
CZ C:ARG46 4.1 88.5 1.0
OD1 D:ASP90 4.2 0.3 1.0
OD2 D:ASP90 4.2 99.4 1.0
CE1 D:TYR91 4.2 0.4 1.0
NH2 C:ARG46 4.2 88.0 1.0
C6 D:F9A1201 4.4 0.6 1.0
CD2 D:TYR91 4.4 0.5 1.0
C4 D:F9A1201 4.4 0.5 1.0
CG B:TRP173 4.8 90.2 1.0
N1 D:F9A1201 4.8 0.9 1.0
C5 D:F9A1201 4.9 0.5 1.0
CD1 D:TYR91 4.9 1.0 1.0

Fluorine binding site 3 out of 3 in 3aea

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

b:0.5
occ:1.00
 F3 D:F9A1201 0.0 0.5 1.0
C1 D:F9A1201 1.3 0.6 1.0
F1 D:F9A1201 2.1 0.6 1.0
F2 D:F9A1201 2.2 0.6 1.0
C2 D:F9A1201 2.3 0.6 1.0
C7 D:F9A1201 2.7 0.6 1.0
CB B:SER170 3.4 83.4 1.0
CD2 B:HIS216 3.6 88.4 1.0
C3 D:F9A1201 3.7 0.6 1.0
CA B:SER170 3.7 84.0 1.0
OG B:SER170 3.7 83.9 1.0
OD1 D:ASP90 3.9 0.3 1.0
CD1 B:ILE218 4.0 87.4 1.0
N B:SER170 4.0 84.1 1.0
C6 D:F9A1201 4.1 0.6 1.0
CG D:ASP90 4.2 0.5 1.0
NE2 B:HIS216 4.3 89.2 1.0
NH1 C:ARG46 4.4 88.8 1.0
C8 D:F9A1201 4.4 0.7 1.0
OD2 D:ASP90 4.4 99.4 1.0
CD1 B:TRP173 4.4 89.8 1.0
O D:F9A1201 4.5 0.7 1.0
CG B:HIS216 4.6 88.6 1.0
C B:PRO169 4.6 85.1 1.0
O B:ARG214 4.7 85.8 1.0
NH2 C:ARG46 4.7 88.0 1.0
C4 D:F9A1201 4.8 0.5 1.0
NE1 B:TRP173 4.9 90.6 1.0
CB D:ASP90 4.9 0.3 1.0
C5 D:F9A1201 4.9 0.5 1.0
O B:PRO169 4.9 86.1 1.0
CZ C:ARG46 5.0 88.5 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 17:06:13 2024

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