Fluorine in PDB 6ay6: Naegleria Fowleri CYP51-Voriconazole Complex

Protein crystallography data

The structure of Naegleria Fowleri CYP51-Voriconazole Complex, PDB code: 6ay6 was solved by A.Debnath, C.M.Calvet, G.Jennings, W.Zhou, A.Aksenov, M.Luth, R.Abagyan, W.D.Nes, J.H.Mckerrow, L.M.Podust, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.92 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.180, 55.340, 73.220, 90.00, 100.80, 90.00
R / Rfree (%) 21.9 / 29

Other elements in 6ay6:

The structure of Naegleria Fowleri CYP51-Voriconazole Complex also contains other interesting chemical elements:

Iron (Fe) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Naegleria Fowleri CYP51-Voriconazole Complex (pdb code 6ay6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Naegleria Fowleri CYP51-Voriconazole Complex, PDB code: 6ay6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6ay6

Go back to Fluorine Binding Sites List in 6ay6
Fluorine binding site 1 out of 3 in the Naegleria Fowleri CYP51-Voriconazole Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Naegleria Fowleri CYP51-Voriconazole Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:76.7
occ:1.00
F1 A:VOR501 0.0 76.7 1.0
C16 A:VOR501 1.3 66.5 1.0
C19 A:VOR501 2.4 66.5 1.0
C13 A:VOR501 2.4 61.1 1.0
C10 A:VOR501 2.8 64.6 1.0
C12 A:VOR501 2.9 66.0 1.0
C11 A:VOR501 2.9 69.2 1.0
CD1 A:PHE292 3.0 66.0 1.0
CE1 A:PHE292 3.3 65.5 1.0
C22 A:VOR501 3.6 71.6 1.0
C17 A:VOR501 3.6 60.3 1.0
N5 A:VOR501 3.7 66.6 1.0
C14 A:VOR501 3.8 65.6 1.0
CZ A:PHE114 3.8 68.6 1.0
N7 A:VOR501 3.9 72.1 1.0
F2 A:VOR501 4.1 80.1 1.0
C20 A:VOR501 4.1 60.5 1.0
N A:ALA293 4.1 66.8 1.0
C15 A:VOR501 4.1 69.4 1.0
CG A:PHE292 4.2 63.9 1.0
O4 A:VOR501 4.2 70.2 1.0
CE A:MET110 4.3 94.8 1.0
CA A:ALA293 4.4 61.5 1.0
CZ A:PHE292 4.6 66.3 1.0
C18 A:VOR501 4.6 73.5 1.0
CE2 A:PHE114 4.6 68.1 1.0
CB A:PHE292 4.7 62.5 1.0
CE1 A:PHE114 4.7 70.3 1.0
F3 A:VOR501 4.7 76.3 1.0
CB A:ALA293 4.7 58.4 1.0
C A:PHE292 4.8 64.0 1.0
C21 A:VOR501 4.9 72.0 1.0

Fluorine binding site 2 out of 3 in 6ay6

Go back to Fluorine Binding Sites List in 6ay6
Fluorine binding site 2 out of 3 in the Naegleria Fowleri CYP51-Voriconazole Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Naegleria Fowleri CYP51-Voriconazole Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:80.1
occ:1.00
F2 A:VOR501 0.0 80.1 1.0
C18 A:VOR501 1.3 73.5 1.0
C23 A:VOR501 2.4 76.5 1.0
C15 A:VOR501 2.4 69.4 1.0
C11 A:VOR501 2.9 69.2 1.0
N9 A:VOR501 3.6 65.1 1.0
N6 A:VOR501 3.6 75.5 1.0
CG A:LEU467 3.8 90.1 1.0
C12 A:VOR501 3.9 66.0 1.0
C14 A:VOR501 4.0 65.6 1.0
C10 A:VOR501 4.0 64.6 1.0
F1 A:VOR501 4.1 76.7 1.0
C24 A:VOR501 4.1 70.7 1.0
CD2 A:LEU358 4.1 65.2 1.0
CD2 A:LEU467 4.1 91.6 1.0
CE1 A:PHE292 4.2 65.5 1.0
CB A:LEU467 4.4 88.6 1.0
CE A:MET110 4.6 94.8 1.0
CG2 A:VAL468 4.7 72.9 1.0
O A:LEU467 4.7 87.5 1.0
CZ A:PHE292 4.8 66.3 1.0
C A:LEU467 4.8 82.2 1.0
O4 A:VOR501 4.9 70.2 1.0
SD A:MET110 4.9 97.0 1.0
CD1 A:LEU467 4.9 83.4 1.0
C16 A:VOR501 5.0 66.5 1.0

Fluorine binding site 3 out of 3 in 6ay6

Go back to Fluorine Binding Sites List in 6ay6
Fluorine binding site 3 out of 3 in the Naegleria Fowleri CYP51-Voriconazole Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Naegleria Fowleri CYP51-Voriconazole Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:76.3
occ:1.00
F3 A:VOR501 0.0 76.3 1.0
C22 A:VOR501 1.3 71.6 1.0
C20 A:VOR501 2.4 60.5 1.0
C19 A:VOR501 2.4 66.5 1.0
O A:ALA289 3.2 65.2 1.0
CB A:ALA289 3.5 59.9 1.0
C16 A:VOR501 3.6 66.5 1.0
C A:ALA289 3.6 63.1 1.0
C17 A:VOR501 3.6 60.3 1.0
CA A:ALA289 4.1 63.4 1.0
C13 A:VOR501 4.1 61.1 1.0
CMD A:HEM502 4.2 56.6 1.0
CB A:ALA293 4.3 58.4 1.0
N A:GLY290 4.4 71.0 1.0
CZ A:PHE114 4.4 68.6 1.0
CE2 A:PHE114 4.5 68.1 1.0
CG1 A:VAL119 4.5 67.7 1.0
F1 A:VOR501 4.7 76.7 1.0
CA A:GLY290 4.8 68.6 1.0
CG2 A:VAL119 4.8 70.4 1.0
C2D A:HEM502 4.9 57.0 1.0

Reference:

A.Debnath, C.M.Calvet, G.Jennings, W.Zhou, A.Aksenov, M.R.Luth, R.Abagyan, W.D.Nes, J.H.Mckerrow, L.M.Podust. CYP51 Is An Essential Drug Target For the Treatment of Primary Amoebic Meningoencephalitis (Pam). Plos Negl Trop Dis V. 11 06104 2017.
ISSN: ESSN 1935-2735
PubMed: 29284029
DOI: 10.1371/JOURNAL.PNTD.0006104
Page generated: Sun Dec 13 12:44:44 2020

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