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Fluorine in PDB 3l4d: Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole

Enzymatic activity of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole

All present enzymatic activity of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole:
1.14.13.70;

Protein crystallography data

The structure of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole, PDB code: 3l4d was solved by G.I.Lepesheva, T.Y.Hargrove, Z.Wawrzak, M.R.Waterman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.80 / 2.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.891, 118.509, 100.960, 90.00, 104.82, 90.00
R / Rfree (%) 21.9 / 26.7

Other elements in 3l4d:

The structure of Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole (pdb code 3l4d). 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 Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole, PDB code: 3l4d:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3l4d

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Fluorine binding site 1 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole


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 (CYP51) From Leishmania Infantum in Complex with Fluconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F490

b:71.5
occ:1.00
 F1 A:TPF490 0.0 71.5 1.0
C11 A:TPF490 1.3 64.3 1.0
C10 A:TPF490 2.4 61.4 1.0
C12 A:TPF490 2.4 58.4 1.0
CB A:ALA286 3.4 50.8 1.0
CMD A:HEM481 3.5 46.4 1.0
C13 A:TPF490 3.6 56.5 1.0
C9 A:TPF490 3.6 55.8 1.0
CZ A:PHE109 3.9 69.8 1.0
CE2 A:PHE109 4.0 74.5 1.0
C8 A:TPF490 4.1 54.3 1.0
C2D A:HEM481 4.2 51.7 1.0
CA A:ALA286 4.3 52.1 1.0
CD2 A:LEU126 4.3 66.9 1.0
C A:ALA286 4.4 52.6 1.0
O A:ALA286 4.4 53.5 1.0
CE1 A:TYR115 4.5 48.3 1.0
CE1 A:PHE109 4.7 66.3 1.0
CAD A:HEM481 4.7 35.3 1.0
F2 A:TPF490 4.7 60.5 1.0
C3D A:HEM481 4.8 48.2 1.0
OH A:TYR115 4.8 49.9 1.0
CE A:MET283 4.8 58.2 1.0
CD2 A:PHE109 4.9 72.6 1.0

Fluorine binding site 2 out of 8 in 3l4d

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Fluorine binding site 2 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole


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 (CYP51) From Leishmania Infantum in Complex with Fluconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F490

b:60.5
occ:1.00
 F2 A:TPF490 0.0 60.5 1.0
C13 A:TPF490 1.3 56.5 1.0
C12 A:TPF490 2.4 58.4 1.0
C8 A:TPF490 2.4 54.3 1.0
C5 A:TPF490 2.5 49.5 1.0
C1 A:TPF490 2.8 54.7 1.0
CD2 A:PHE289 3.1 49.0 1.0
C2 A:TPF490 3.3 60.5 1.0
CE2 A:PHE289 3.4 51.2 1.0
CB A:ALA290 3.5 45.0 1.0
CA A:ALA290 3.6 48.1 1.0
C11 A:TPF490 3.6 64.3 1.0
C9 A:TPF490 3.6 55.8 1.0
N4 A:TPF490 3.8 40.3 1.0
N A:ALA290 3.9 48.0 1.0
CE A:MET105 4.1 55.6 1.0
N6 A:TPF490 4.1 33.1 1.0
C10 A:TPF490 4.1 61.4 1.0
O A:TPF490 4.2 54.0 1.0
O A:ALA286 4.2 53.5 1.0
CG A:PHE289 4.3 50.3 1.0
N1 A:TPF490 4.5 74.3 1.0
C6 A:TPF490 4.5 35.1 1.0
C A:PHE289 4.5 49.3 1.0
CZ A:PHE109 4.7 69.8 1.0
F1 A:TPF490 4.7 71.5 1.0
CB A:PHE289 4.8 49.6 1.0
CZ A:PHE289 4.8 48.5 1.0
SD A:MET105 4.9 67.6 1.0
CE2 A:PHE109 4.9 74.5 1.0
C7 A:TPF490 4.9 31.3 1.0
O A:PHE289 5.0 48.7 1.0
C A:ALA290 5.0 50.7 1.0
C3 A:TPF490 5.0 73.4 1.0

Fluorine binding site 3 out of 8 in 3l4d

Go back to Fluorine Binding Sites List in 3l4d
Fluorine binding site 3 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole


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 (CYP51) From Leishmania Infantum in Complex with Fluconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F490

b:70.0
occ:1.00
 F1 B:TPF490 0.0 70.0 1.0
C11 B:TPF490 1.3 67.4 1.0
C12 B:TPF490 2.4 64.5 1.0
C10 B:TPF490 2.4 65.8 1.0
CB B:ALA286 3.4 54.6 1.0
C13 B:TPF490 3.6 65.0 1.0
C9 B:TPF490 3.6 60.3 1.0
CMD B:HEM481 3.9 58.6 1.0
C8 B:TPF490 4.1 59.6 1.0
CZ B:PHE109 4.2 76.4 1.0
O B:ALA286 4.3 56.1 1.0
CA B:ALA286 4.4 54.7 1.0
C B:ALA286 4.4 55.2 1.0
CE2 B:PHE109 4.4 76.9 1.0
C2D B:HEM481 4.4 56.7 1.0
CE1 B:TYR115 4.5 60.8 1.0
OH B:TYR115 4.6 67.0 1.0
CE1 B:PHE109 4.7 75.9 1.0
CD2 B:LEU126 4.7 59.7 1.0
F2 B:TPF490 4.7 72.4 1.0
C3D B:HEM481 4.9 55.8 1.0
CAD B:HEM481 5.0 48.4 1.0
CZ B:TYR115 5.0 64.1 1.0

Fluorine binding site 4 out of 8 in 3l4d

Go back to Fluorine Binding Sites List in 3l4d
Fluorine binding site 4 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole


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 (CYP51) From Leishmania Infantum in Complex with Fluconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F490

b:72.4
occ:1.00
 F2 B:TPF490 0.0 72.4 1.0
C13 B:TPF490 1.3 65.0 1.0
C12 B:TPF490 2.4 64.5 1.0
C8 B:TPF490 2.4 59.6 1.0
C5 B:TPF490 2.4 50.6 1.0
C1 B:TPF490 2.8 57.3 1.0
CD2 B:PHE289 3.0 51.4 1.0
CE2 B:PHE289 3.2 49.5 1.0
C2 B:TPF490 3.3 62.9 1.0
CB B:ALA290 3.4 55.1 1.0
N4 B:TPF490 3.6 40.3 1.0
CA B:ALA290 3.6 57.0 1.0
C11 B:TPF490 3.6 67.4 1.0
C9 B:TPF490 3.6 60.3 1.0
N6 B:TPF490 3.8 35.1 1.0
N B:ALA290 3.9 57.0 1.0
CE B:MET105 3.9 68.6 1.0
C10 B:TPF490 4.1 65.8 1.0
O B:TPF490 4.1 56.7 1.0
N1 B:TPF490 4.2 77.3 1.0
C6 B:TPF490 4.3 41.0 1.0
CG B:PHE289 4.3 56.5 1.0
O B:ALA286 4.4 56.1 1.0
CZ B:PHE289 4.5 47.9 1.0
C7 B:TPF490 4.6 30.0 1.0
C3 B:TPF490 4.6 73.5 1.0
C B:PHE289 4.7 56.9 1.0
F1 B:TPF490 4.7 70.0 1.0
CZ B:PHE109 4.8 76.4 1.0
SD B:MET105 4.8 71.9 1.0
N5 B:TPF490 4.9 31.7 1.0
CB B:PHE289 4.9 55.8 1.0

Fluorine binding site 5 out of 8 in 3l4d

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Fluorine binding site 5 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole


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 (CYP51) From Leishmania Infantum in Complex with Fluconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F490

b:60.5
occ:1.00
 F1 C:TPF490 0.0 60.5 1.0
C11 C:TPF490 1.3 60.2 1.0
C12 C:TPF490 2.4 52.8 1.0
C10 C:TPF490 2.4 56.9 1.0
CMD C:HEM481 3.2 59.0 1.0
CB C:ALA286 3.4 51.6 1.0
C13 C:TPF490 3.6 51.7 1.0
C9 C:TPF490 3.6 52.5 1.0
CE2 C:PHE109 3.9 82.1 1.0
CZ C:PHE109 3.9 80.1 1.0
C2D C:HEM481 4.0 56.1 1.0
C8 C:TPF490 4.1 50.7 1.0
O C:ALA286 4.2 53.7 1.0
CA C:ALA286 4.3 51.7 1.0
C C:ALA286 4.3 52.9 1.0
CD2 C:LEU126 4.5 39.9 1.0
C3D C:HEM481 4.6 60.2 1.0
CAD C:HEM481 4.7 64.2 1.0
F2 C:TPF490 4.7 58.1 1.0
CD2 C:PHE109 4.8 76.2 1.0
CE1 C:PHE109 4.9 79.0 1.0
CE1 C:TYR115 4.9 54.0 1.0

Fluorine binding site 6 out of 8 in 3l4d

Go back to Fluorine Binding Sites List in 3l4d
Fluorine binding site 6 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole


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 (CYP51) From Leishmania Infantum in Complex with Fluconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F490

b:58.1
occ:1.00
 F2 C:TPF490 0.0 58.1 1.0
C13 C:TPF490 1.3 51.7 1.0
C12 C:TPF490 2.4 52.8 1.0
C8 C:TPF490 2.4 50.7 1.0
C5 C:TPF490 2.5 47.1 1.0
C1 C:TPF490 2.8 52.0 1.0
C2 C:TPF490 3.3 56.3 1.0
CD2 C:PHE289 3.4 52.3 1.0
CE2 C:PHE289 3.5 50.0 1.0
C11 C:TPF490 3.6 60.2 1.0
C9 C:TPF490 3.6 52.5 1.0
N4 C:TPF490 3.7 40.7 1.0
CB C:ALA290 3.7 41.3 1.0
CA C:ALA290 3.8 43.8 1.0
CE C:MET105 4.0 70.0 1.0
N6 C:TPF490 4.0 37.4 1.0
C10 C:TPF490 4.1 56.9 1.0
O C:TPF490 4.2 51.1 1.0
N C:ALA290 4.2 43.3 1.0
C6 C:TPF490 4.3 37.3 1.0
N1 C:TPF490 4.4 66.6 1.0
O C:ALA286 4.5 53.7 1.0
CG C:PHE289 4.6 49.9 1.0
C3 C:TPF490 4.7 63.3 1.0
F1 C:TPF490 4.7 60.5 1.0
CZ C:PHE109 4.7 80.1 1.0
C7 C:TPF490 4.8 32.7 1.0
CZ C:PHE289 4.8 51.4 1.0
C C:PHE289 4.8 45.5 1.0
SD C:MET105 5.0 75.0 1.0
N5 C:TPF490 5.0 32.8 1.0

Fluorine binding site 7 out of 8 in 3l4d

Go back to Fluorine Binding Sites List in 3l4d
Fluorine binding site 7 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole


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 Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F490

b:62.6
occ:1.00
 F1 D:TPF490 0.0 62.6 1.0
C11 D:TPF490 1.3 56.7 1.0
C12 D:TPF490 2.4 54.5 1.0
C10 D:TPF490 2.4 55.6 1.0
CB D:ALA286 3.2 51.9 1.0
CMD D:HEM481 3.6 63.1 1.0
C13 D:TPF490 3.6 56.4 1.0
C9 D:TPF490 3.6 53.3 1.0
CE2 D:PHE109 3.9 81.8 1.0
CZ D:PHE109 4.0 81.7 1.0
O D:ALA286 4.1 53.4 1.0
C8 D:TPF490 4.1 54.1 1.0
CA D:ALA286 4.1 52.6 1.0
C D:ALA286 4.2 53.6 1.0
C2D D:HEM481 4.3 61.9 1.0
CB D:ALA290 4.7 49.6 1.0
F2 D:TPF490 4.7 64.0 1.0
CD2 D:PHE109 4.8 79.7 1.0
CD2 D:LEU126 4.9 51.1 1.0
N D:ALA287 4.9 54.8 1.0
C1D D:HEM481 5.0 60.1 1.0

Fluorine binding site 8 out of 8 in 3l4d

Go back to Fluorine Binding Sites List in 3l4d
Fluorine binding site 8 out of 8 in the Crystal Structure of Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole


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 Sterol 14-Alpha Demethylase (CYP51) From Leishmania Infantum in Complex with Fluconazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F490

b:64.0
occ:1.00
 F2 D:TPF490 0.0 64.0 1.0
C13 D:TPF490 1.3 56.4 1.0
C8 D:TPF490 2.4 54.1 1.0
C12 D:TPF490 2.4 54.5 1.0
C5 D:TPF490 2.5 56.6 1.0
C1 D:TPF490 2.8 56.8 1.0
CD2 D:PHE289 2.9 48.6 1.0
CE2 D:PHE289 3.0 50.5 1.0
C2 D:TPF490 3.2 59.8 1.0
CA D:ALA290 3.6 52.0 1.0
C9 D:TPF490 3.6 53.3 1.0
C11 D:TPF490 3.6 56.7 1.0
N4 D:TPF490 3.7 55.5 1.0
CB D:ALA290 3.8 49.6 1.0
N6 D:TPF490 3.9 54.9 1.0
N D:ALA290 4.0 52.7 1.0
CE D:MET105 4.1 65.4 1.0
C10 D:TPF490 4.1 55.6 1.0
O D:TPF490 4.1 56.5 1.0
CG D:PHE289 4.3 47.9 1.0
N1 D:TPF490 4.3 69.1 1.0
CZ D:PHE289 4.3 50.6 1.0
C6 D:TPF490 4.4 59.4 1.0
O D:ALA286 4.6 53.4 1.0
C D:PHE289 4.7 53.1 1.0
C7 D:TPF490 4.7 58.5 1.0
C3 D:TPF490 4.7 66.7 1.0
F1 D:TPF490 4.7 62.6 1.0
CZ D:PHE109 4.9 81.7 1.0
CB D:PHE289 4.9 51.2 1.0
C D:ALA290 4.9 52.4 1.0
N5 D:TPF490 4.9 55.9 1.0

Reference:

T.Y.Hargrove, Z.Wawrzak, J.Liu, W.D.Nes, M.R.Waterman, G.I.Lepesheva. Substrate Preferences and Catalytic Parameters Determined By Structural Characteristics of Sterol 14{Alpha}-Demethylase (CYP51) From Leishmania Infantum. J.Biol.Chem. V. 286 26838 2011.
ISSN: ISSN 0021-9258
PubMed: 21632531
DOI: 10.1074/JBC.M111.237099
Page generated: Wed Jul 31 20:21:56 2024

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