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Fluorine in PDB 4uym: Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole

Enzymatic activity of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole

All present enzymatic activity of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole:
1.14.13.70;

Protein crystallography data

The structure of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole, PDB code: 4uym was solved by T.Y.Hargrove, Z.Wawrzak, G.I.Lepesheva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.55
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 109.193, 109.193, 90.211, 90.00, 90.00, 120.00
R / Rfree (%) 20.959 / 23.891

Other elements in 4uym:

The structure of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole (pdb code 4uym). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole, PDB code: 4uym:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4uym

Go back to Fluorine Binding Sites List in 4uym
Fluorine binding site 1 out of 6 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole


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 Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F590

b:68.4
occ:1.00
 F1 A:VOR590 0.0 68.4 1.0
C16 A:VOR590 1.3 58.9 1.0
C19 A:VOR590 2.4 57.6 1.0
C13 A:VOR590 2.5 48.9 1.0
C10 A:VOR590 2.9 66.3 1.0
C11 A:VOR590 2.9 61.7 1.0
C12 A:VOR590 3.0 67.4 1.0
CZ A:PHE504 3.4 51.2 1.0
C14 A:VOR590 3.5 57.4 1.0
C22 A:VOR590 3.6 67.5 1.0
N5 A:VOR590 3.7 72.2 1.0
C17 A:VOR590 3.7 52.8 1.0
CE1 A:PHE504 3.9 57.1 1.0
N7 A:VOR590 4.1 73.2 1.0
F2 A:VOR590 4.1 80.2 1.0
C20 A:VOR590 4.1 54.9 1.0
C15 A:VOR590 4.3 62.7 1.0
CZ A:PHE130 4.3 59.4 1.0
O4 A:VOR590 4.3 62.8 1.0
CE2 A:PHE504 4.4 59.3 1.0
CD2 A:LEU503 4.5 83.6 1.0
C21 A:VOR590 4.5 73.8 1.0
C18 A:VOR590 4.7 59.1 1.0
F3 A:VOR590 4.7 58.1 1.0
CZ A:PHE229 4.8 88.8 1.0
CE2 A:PHE130 4.9 63.1 1.0
CB A:ALA307 5.0 82.4 1.0

Fluorine binding site 2 out of 6 in 4uym

Go back to Fluorine Binding Sites List in 4uym
Fluorine binding site 2 out of 6 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole


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 Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F590

b:80.2
occ:1.00
 F2 A:VOR590 0.0 80.2 1.0
C18 A:VOR590 1.3 59.1 1.0
C23 A:VOR590 2.4 57.7 1.0
C15 A:VOR590 2.5 62.7 1.0
CG A:LEU503 2.9 81.5 1.0
C11 A:VOR590 2.9 61.7 1.0
C12 A:VOR590 3.3 67.4 1.0
CD2 A:LEU503 3.3 83.6 1.0
CD1 A:LEU503 3.3 79.7 1.0
N9 A:VOR590 3.6 68.8 1.0
N6 A:VOR590 3.7 58.9 1.0
C10 A:VOR590 3.7 66.3 1.0
CE1 A:PHE504 3.7 57.1 1.0
CZ A:PHE504 3.8 51.2 1.0
O A:LEU503 3.8 74.2 1.0
CD1 A:PHE504 4.0 59.2 1.0
CE2 A:PHE504 4.0 59.3 1.0
C24 A:VOR590 4.1 71.5 1.0
C A:LEU503 4.1 73.9 1.0
F1 A:VOR590 4.1 68.4 1.0
CG1 A:ILE373 4.2 70.5 1.0
CB A:LEU503 4.2 76.7 1.0
C14 A:VOR590 4.2 57.4 1.0
CG A:PHE504 4.2 59.1 1.0
CD2 A:PHE504 4.3 58.4 1.0
N A:PHE504 4.5 63.4 1.0
O4 A:VOR590 4.5 62.8 1.0
N5 A:VOR590 4.7 72.2 1.0
CA A:LEU503 4.7 74.5 1.0
CD1 A:ILE373 4.7 78.7 1.0
CA A:PHE504 4.8 59.7 1.0
C13 A:VOR590 4.9 48.9 1.0
C16 A:VOR590 5.0 58.9 1.0

Fluorine binding site 3 out of 6 in 4uym

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Fluorine binding site 3 out of 6 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole


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 Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F590

b:58.1
occ:1.00
 F3 A:VOR590 0.0 58.1 1.0
C22 A:VOR590 1.3 67.5 1.0
C19 A:VOR590 2.4 57.6 1.0
C20 A:VOR590 2.4 54.9 1.0
C16 A:VOR590 3.6 58.9 1.0
C17 A:VOR590 3.6 52.8 1.0
CG1 A:VAL135 4.0 61.4 1.0
CE2 A:PHE130 4.1 63.1 1.0
C13 A:VOR590 4.1 48.9 1.0
CMD A:HEM580 4.2 49.9 1.0
CB A:ALA307 4.3 82.4 1.0
CZ A:PHE130 4.3 59.4 1.0
CG2 A:VAL135 4.4 57.5 1.0
CB A:ALA303 4.5 56.0 1.0
C2D A:HEM580 4.5 48.9 1.0
O A:ALA303 4.5 57.7 1.0
F1 A:VOR590 4.7 68.4 1.0
CD2 A:PHE130 4.8 53.9 1.0
C1D A:HEM580 4.9 46.4 1.0
CB A:VAL135 4.9 59.9 1.0
C A:ALA303 4.9 51.9 1.0
CHD A:HEM580 5.0 46.4 1.0

Fluorine binding site 4 out of 6 in 4uym

Go back to Fluorine Binding Sites List in 4uym
Fluorine binding site 4 out of 6 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole


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 Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F590

b:68.0
occ:1.00
 F1 B:VOR590 0.0 68.0 1.0
C16 B:VOR590 1.3 61.1 1.0
C19 B:VOR590 2.3 66.8 1.0
C13 B:VOR590 2.4 59.5 1.0
C10 B:VOR590 2.9 71.4 1.0
C11 B:VOR590 2.9 80.2 1.0
C12 B:VOR590 3.0 69.4 1.0
C14 B:VOR590 3.4 81.1 1.0
C22 B:VOR590 3.6 76.7 1.0
C17 B:VOR590 3.6 69.0 1.0
N5 B:VOR590 3.6 67.3 1.0
CZ B:PHE504 3.7 62.3 1.0
N7 B:VOR590 3.9 62.5 1.0
C20 B:VOR590 4.0 71.5 1.0
O4 B:VOR590 4.3 72.1 1.0
CZ B:PHE130 4.3 72.8 1.0
C15 B:VOR590 4.3 94.5 1.0
CE1 B:PHE504 4.3 66.8 1.0
F2 B:VOR590 4.5 0.8 1.0
C21 B:VOR590 4.5 69.8 1.0
CB B:ALA307 4.6 66.9 1.0
CE2 B:PHE504 4.6 61.6 1.0
F3 B:VOR590 4.7 69.1 1.0
CD2 B:LEU503 4.7 83.8 1.0
CE2 B:PHE130 4.7 74.8 1.0
C18 B:VOR590 4.9 97.6 1.0
C25 B:VOR590 4.9 59.2 1.0
CA B:ALA307 4.9 61.1 1.0

Fluorine binding site 5 out of 6 in 4uym

Go back to Fluorine Binding Sites List in 4uym
Fluorine binding site 5 out of 6 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole


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 Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F590

b:0.8
occ:1.00
 F2 B:VOR590 0.0 0.8 1.0
C18 B:VOR590 1.3 97.6 1.0
C23 B:VOR590 2.3 88.7 1.0
C15 B:VOR590 2.4 94.5 1.0
CG B:LEU503 2.8 81.6 1.0
C11 B:VOR590 3.0 80.2 1.0
CD1 B:LEU503 3.0 84.8 1.0
CD2 B:LEU503 3.3 83.8 1.0
N9 B:VOR590 3.5 99.0 1.0
C12 B:VOR590 3.6 69.4 1.0
N6 B:VOR590 3.6 0.6 1.0
O B:LEU503 3.8 81.0 1.0
C10 B:VOR590 3.9 71.4 1.0
C24 B:VOR590 4.0 99.5 1.0
CZ B:PHE504 4.0 62.3 1.0
CE1 B:PHE504 4.1 66.8 1.0
C14 B:VOR590 4.1 81.1 1.0
CB B:LEU503 4.2 74.8 1.0
C B:LEU503 4.2 73.1 1.0
CE2 B:PHE504 4.3 61.6 1.0
CD1 B:PHE504 4.3 63.2 1.0
CG1 B:ILE373 4.4 68.6 1.0
F1 B:VOR590 4.5 68.0 1.0
CD2 B:PHE504 4.6 60.6 1.0
O4 B:VOR590 4.6 72.1 1.0
CG B:PHE504 4.6 59.0 1.0
CA B:LEU503 4.7 73.9 1.0
N B:PHE504 4.8 72.7 1.0
N5 B:VOR590 4.9 67.3 1.0

Fluorine binding site 6 out of 6 in 4uym

Go back to Fluorine Binding Sites List in 4uym
Fluorine binding site 6 out of 6 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole


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 Sterol 14-Alpha Demethylase (CYP51B) From A Pathogenic Filamentous Fungus Aspergillus Fumigatus in Complex with Voriconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F590

b:69.1
occ:1.00
 F3 B:VOR590 0.0 69.1 1.0
C22 B:VOR590 1.3 76.7 1.0
C20 B:VOR590 2.3 71.5 1.0
C19 B:VOR590 2.3 66.8 1.0
C16 B:VOR590 3.6 61.1 1.0
C17 B:VOR590 3.6 69.0 1.0
CE2 B:PHE130 4.0 74.8 1.0
CMD B:HEM580 4.1 63.9 1.0
C13 B:VOR590 4.1 59.5 1.0
CB B:ALA307 4.2 66.9 1.0
CG1 B:VAL135 4.3 68.5 1.0
CZ B:PHE130 4.4 72.8 1.0
C2D B:HEM580 4.4 71.6 1.0
CB B:ALA303 4.5 61.9 1.0
O B:ALA303 4.5 61.5 1.0
CG2 B:VAL135 4.5 68.3 1.0
F1 B:VOR590 4.7 68.0 1.0
CD2 B:PHE130 4.8 75.5 1.0
OH B:TYR136 4.8 70.8 1.0
C1D B:HEM580 4.8 69.1 1.0
CHD B:HEM580 4.9 64.9 1.0
C B:ALA303 4.9 58.9 1.0

Reference:

T.Y.Hargrove, Z.Warwzak, D.C.Lamb, F.P.Guengerich, G.I.Lepesheva. Structure-Functional Characterization of Cytochrome P450 Sterol Alpha-Demethylase (CYP51B) From Aspergillus Fumigatus and Molecular Basis For the Development of Antifungal Drugs J.Biol.Chem. V. 290 23916 2015.
ISSN: ISSN 0021-9258
PubMed: 26269599
DOI: 10.1074/JBC.M115.677310
Page generated: Sun Dec 13 12:13:46 2020

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