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Fluorine in PDB 3mdt: Voriconazole Complex of Cytochrome P450 46A1

Enzymatic activity of Voriconazole Complex of Cytochrome P450 46A1

All present enzymatic activity of Voriconazole Complex of Cytochrome P450 46A1:
1.14.13.98;

Protein crystallography data

The structure of Voriconazole Complex of Cytochrome P450 46A1, PDB code: 3mdt was solved by N.Mast, C.Charvet, I.Pikuleva, C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.86 / 2.30
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 121.600, 121.600, 143.830, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 28.7

Other elements in 3mdt:

The structure of Voriconazole Complex of Cytochrome P450 46A1 also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Voriconazole Complex of Cytochrome P450 46A1 (pdb code 3mdt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Voriconazole Complex of Cytochrome P450 46A1, PDB code: 3mdt:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3mdt

Go back to Fluorine Binding Sites List in 3mdt
Fluorine binding site 1 out of 6 in the Voriconazole Complex of Cytochrome P450 46A1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Voriconazole Complex of Cytochrome P450 46A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:44.6
occ:1.00
 F1 A:VOR506 0.0 44.6 1.0
C16 A:VOR506 1.3 44.6 1.0
C19 A:VOR506 2.3 45.1 1.0
C13 A:VOR506 2.5 44.6 1.0
C12 A:VOR506 3.0 43.0 1.0
N6 A:VOR506 3.1 45.2 1.0
C10 A:VOR506 3.2 44.2 1.0
CZ A:PHE121 3.2 24.2 1.0
CE1 A:PHE121 3.3 24.5 1.0
C15 A:VOR506 3.3 45.1 1.0
C24 A:VOR506 3.4 45.7 1.0
C22 A:VOR506 3.6 45.5 1.0
C18 A:VOR506 3.7 45.5 1.0
C17 A:VOR506 3.7 45.1 1.0
N9 A:VOR506 3.7 46.0 1.0
C23 A:VOR506 3.9 45.6 1.0
C11 A:VOR506 3.9 44.6 1.0
CE2 A:PHE121 4.0 24.1 1.0
CD1 A:PHE121 4.0 24.4 1.0
C20 A:VOR506 4.2 45.3 1.0
CG2 A:ILE301 4.2 11.8 1.0
N5 A:VOR506 4.3 41.9 1.0
O4 A:VOR506 4.4 43.5 1.0
F2 A:VOR506 4.5 45.6 1.0
CD2 A:PHE121 4.6 24.1 1.0
CG A:PHE121 4.7 24.3 1.0
F3 A:VOR506 4.7 46.4 1.0
CB A:ILE301 4.7 12.3 1.0
CB A:ALA302 4.8 12.0 1.0
N A:ALA302 4.9 12.0 1.0
O A:THR298 5.0 14.5 1.0

Fluorine binding site 2 out of 6 in 3mdt

Go back to Fluorine Binding Sites List in 3mdt
Fluorine binding site 2 out of 6 in the Voriconazole Complex of Cytochrome P450 46A1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Voriconazole Complex of Cytochrome P450 46A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:45.6
occ:1.00
 F2 A:VOR506 0.0 45.6 1.0
C18 A:VOR506 1.3 45.5 1.0
C23 A:VOR506 2.4 45.6 1.0
C15 A:VOR506 2.4 45.1 1.0
C11 A:VOR506 2.8 44.6 1.0
C17 A:VOR506 3.1 45.1 1.0
C13 A:VOR506 3.1 44.6 1.0
O A:HOH977 3.5 16.7 1.0
C10 A:VOR506 3.5 44.2 1.0
C20 A:VOR506 3.6 45.3 1.0
N9 A:VOR506 3.7 46.0 1.0
N6 A:VOR506 3.7 45.2 1.0
C16 A:VOR506 3.7 44.6 1.0
C14 A:VOR506 4.0 45.3 1.0
C22 A:VOR506 4.1 45.5 1.0
O4 A:VOR506 4.1 43.5 1.0
C19 A:VOR506 4.1 45.1 1.0
C24 A:VOR506 4.2 45.7 1.0
CD2 A:LEU112 4.2 26.0 1.0
CD1 A:LEU112 4.3 25.9 1.0
O A:HOH618 4.3 19.4 1.0
O A:ALA474 4.4 19.0 1.0
F1 A:VOR506 4.5 44.6 1.0
NH2 A:ARG226 4.8 30.6 1.0
C12 A:VOR506 4.8 43.0 1.0
O A:HOH611 4.8 27.6 1.0
CG A:LEU112 4.9 25.6 1.0

Fluorine binding site 3 out of 6 in 3mdt

Go back to Fluorine Binding Sites List in 3mdt
Fluorine binding site 3 out of 6 in the Voriconazole Complex of Cytochrome P450 46A1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Voriconazole Complex of Cytochrome P450 46A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:46.4
occ:1.00
 F3 A:VOR506 0.0 46.4 1.0
C22 A:VOR506 1.3 45.5 1.0
C20 A:VOR506 2.3 45.3 1.0
C19 A:VOR506 2.4 45.1 1.0
CB A:SER127 3.6 21.2 1.0
CB A:LEU112 3.6 25.4 1.0
C17 A:VOR506 3.7 45.1 1.0
C16 A:VOR506 3.7 44.6 1.0
CD1 A:LEU112 3.9 25.9 1.0
CA A:SER127 4.1 21.2 1.0
N A:SER127 4.2 21.0 1.0
CG A:PHE121 4.2 24.3 1.0
CB A:PHE121 4.2 24.0 1.0
C13 A:VOR506 4.2 44.6 1.0
CG A:LEU112 4.3 25.6 1.0
CD2 A:PHE121 4.3 24.1 1.0
OG A:SER127 4.4 21.6 1.0
CB A:VAL126 4.5 20.9 1.0
CG1 A:VAL126 4.5 20.9 1.0
CD2 A:TYR109 4.5 23.5 1.0
F1 A:VOR506 4.7 44.6 1.0
CD1 A:PHE121 4.7 24.4 1.0
CD2 A:LEU112 4.8 26.0 1.0
C A:VAL126 4.8 21.0 1.0
O A:TYR109 4.8 23.4 1.0
CA A:LEU112 4.9 25.4 1.0
C A:LEU112 4.9 25.4 1.0
CE2 A:PHE121 4.9 24.1 1.0

Fluorine binding site 4 out of 6 in 3mdt

Go back to Fluorine Binding Sites List in 3mdt
Fluorine binding site 4 out of 6 in the Voriconazole Complex of Cytochrome P450 46A1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Voriconazole Complex of Cytochrome P450 46A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F506

b:44.6
occ:1.00
 F1 B:VOR506 0.0 44.6 1.0
C16 B:VOR506 1.3 44.6 1.0
C19 B:VOR506 2.3 45.1 1.0
C13 B:VOR506 2.4 44.6 1.0
C12 B:VOR506 2.7 43.0 1.0
C10 B:VOR506 3.0 44.2 1.0
N6 B:VOR506 3.1 45.2 1.0
C15 B:VOR506 3.3 45.1 1.0
CE1 B:PHE121 3.5 21.6 1.0
CZ B:PHE121 3.5 21.2 1.0
C24 B:VOR506 3.5 45.7 1.0
C22 B:VOR506 3.7 45.5 1.0
C17 B:VOR506 3.7 45.1 1.0
C11 B:VOR506 3.7 44.6 1.0
C18 B:VOR506 3.8 45.5 1.0
N5 B:VOR506 3.9 41.9 1.0
N9 B:VOR506 4.0 46.0 1.0
C23 B:VOR506 4.1 45.6 1.0
C20 B:VOR506 4.2 45.3 1.0
CD1 B:PHE121 4.2 21.4 1.0
O4 B:VOR506 4.3 43.5 1.0
CE2 B:PHE121 4.3 21.1 1.0
N7 B:VOR506 4.4 41.6 1.0
F2 B:VOR506 4.5 45.6 1.0
CB B:ALA302 4.5 13.4 1.0
F3 B:VOR506 4.7 46.4 1.0
CG2 B:ILE301 4.9 14.2 1.0
C14 B:VOR506 4.9 45.3 1.0
CA B:ALA302 4.9 13.4 1.0
N B:ALA302 4.9 13.8 1.0
CG B:PHE121 4.9 21.6 1.0
CD2 B:PHE121 5.0 21.2 1.0

Fluorine binding site 5 out of 6 in 3mdt

Go back to Fluorine Binding Sites List in 3mdt
Fluorine binding site 5 out of 6 in the Voriconazole Complex of Cytochrome P450 46A1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Voriconazole Complex of Cytochrome P450 46A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F506

b:45.6
occ:1.00
 F2 B:VOR506 0.0 45.6 1.0
C18 B:VOR506 1.3 45.5 1.0
C23 B:VOR506 2.4 45.6 1.0
C15 B:VOR506 2.4 45.1 1.0
C11 B:VOR506 2.8 44.6 1.0
O B:HOH605 2.9 24.0 1.0
C13 B:VOR506 3.2 44.6 1.0
C17 B:VOR506 3.3 45.1 1.0
O B:HOH644 3.3 12.3 1.0
C10 B:VOR506 3.5 44.2 1.0
N6 B:VOR506 3.6 45.2 1.0
N9 B:VOR506 3.6 46.0 1.0
O B:HOH617 3.8 16.6 1.0
C16 B:VOR506 3.8 44.6 1.0
CD1 B:LEU112 3.9 26.0 1.0
C20 B:VOR506 4.0 45.3 1.0
O B:ALA474 4.0 17.2 1.0
C14 B:VOR506 4.0 45.3 1.0
C24 B:VOR506 4.1 45.7 1.0
O4 B:VOR506 4.1 43.5 1.0
C19 B:VOR506 4.4 45.1 1.0
CD2 B:LEU112 4.5 26.1 1.0
C22 B:VOR506 4.5 45.5 1.0
F1 B:VOR506 4.5 44.6 1.0
C12 B:VOR506 4.8 43.0 1.0
CG B:LEU112 4.8 26.1 1.0

Fluorine binding site 6 out of 6 in 3mdt

Go back to Fluorine Binding Sites List in 3mdt
Fluorine binding site 6 out of 6 in the Voriconazole Complex of Cytochrome P450 46A1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Voriconazole Complex of Cytochrome P450 46A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F506

b:46.4
occ:1.00
 F3 B:VOR506 0.0 46.4 1.0
C22 B:VOR506 1.3 45.5 1.0
C20 B:VOR506 2.4 45.3 1.0
C19 B:VOR506 2.4 45.1 1.0
CB B:LEU112 3.2 25.9 1.0
CB B:SER127 3.5 22.4 1.0
CD1 B:LEU112 3.5 26.0 1.0
C17 B:VOR506 3.7 45.1 1.0
C16 B:VOR506 3.7 44.6 1.0
CG B:LEU112 3.8 26.1 1.0
CA B:SER127 4.0 22.4 1.0
CG B:PHE121 4.2 21.6 1.0
CB B:PHE121 4.2 21.9 1.0
N B:SER127 4.2 22.1 1.0
CD2 B:LEU112 4.2 26.1 1.0
C13 B:VOR506 4.2 44.6 1.0
CD2 B:PHE121 4.3 21.2 1.0
OG B:SER127 4.4 22.6 1.0
CA B:LEU112 4.5 25.9 1.0
CD2 B:TYR109 4.5 25.8 1.0
C B:LEU112 4.5 25.9 1.0
O B:LEU112 4.5 26.0 1.0
C B:VAL126 4.6 21.9 1.0
CD1 B:PHE121 4.6 21.4 1.0
F1 B:VOR506 4.7 44.6 1.0
O B:VAL126 4.8 21.9 1.0
O B:TYR109 4.8 25.5 1.0
CB B:VAL126 4.8 21.6 1.0
CE2 B:PHE121 4.9 21.1 1.0

Reference:

N.Mast, C.Charvet, I.A.Pikuleva, C.D.Stout. Structural Basis of Drug Binding to CYP46A1, An Enzyme That Controls Cholesterol Turnover in the Brain. J.Biol.Chem. V. 285 31783 2010.
ISSN: ISSN 0021-9258
PubMed: 20667828
DOI: 10.1074/JBC.M110.143313
Page generated: Sun Dec 13 11:50:55 2020

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