Chlorine in PDB 6ayc: Naegleria Fowleri CYP51-Itraconazole Complex

The structure of Naegleria Fowleri CYP51-Itraconazole Complex, PDB code: 6ayc 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)	71.15 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.300, 55.190, 72.390, 90.00, 100.62, 90.00
R / Rfree (%)	21.8 / 29

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

Iron

(Fe)

1 atom

The binding sites of Chlorine atom in the Naegleria Fowleri CYP51-Itraconazole Complex (pdb code 6ayc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Naegleria Fowleri CYP51-Itraconazole Complex, PDB code: 6ayc:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Naegleria Fowleri CYP51-Itraconazole Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Naegleria Fowleri CYP51-Itraconazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:87.3 occ:0.50 CL8 A:1YN502 0.0 87.3 0.5 CL8 A:1YN502 0.5 99.7 0.5 C45 A:1YN502 1.8 68.9 0.5 C45 A:1YN502 2.1 88.3 0.5 C44 A:1YN502 2.7 64.3 0.5 C46 A:1YN502 2.8 65.5 0.5 C46 A:1YN502 2.9 82.0 0.5 C44 A:1YN502 3.2 88.2 0.5 O A:ALA289 3.4 88.4 1.0 CB A:ALA289 3.4 78.7 1.0 C A:ALA289 3.4 78.7 1.0 N A:GLY290 3.7 79.6 1.0 CMD A:HEM501 3.9 67.7 1.0 CA A:ALA289 4.0 75.5 1.0 C43 A:1YN502 4.0 65.3 0.5 C47 A:1YN502 4.1 63.5 0.5 CA A:GLY290 4.2 79.0 1.0 CG2 A:VAL119 4.2 81.9 1.0 C47 A:1YN502 4.3 82.7 0.5 C43 A:1YN502 4.4 87.7 0.5 CB A:ALA293 4.5 87.9 1.0 CG1 A:VAL119 4.5 88.0 1.0 C42 A:1YN502 4.6 59.9 0.5 C2D A:HEM501 4.7 71.5 1.0 C42 A:1YN502 4.9 78.5 0.5 CB A:VAL119 5.0 84.4 1.0

Chlorine binding site 2 out of 4 in the Naegleria Fowleri CYP51-Itraconazole Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Naegleria Fowleri CYP51-Itraconazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:99.7 occ:0.50 CL8 A:1YN502 0.0 99.7 0.5 CL8 A:1YN502 0.5 87.3 0.5 C45 A:1YN502 1.5 68.9 0.5 C45 A:1YN502 1.8 88.3 0.5 C46 A:1YN502 2.4 65.5 0.5 C44 A:1YN502 2.6 64.3 0.5 C46 A:1YN502 2.7 82.0 0.5 C44 A:1YN502 2.8 88.2 0.5 CB A:ALA289 3.5 78.7 1.0 C47 A:1YN502 3.7 63.5 0.5 O A:ALA289 3.7 88.4 1.0 C43 A:1YN502 3.8 65.3 0.5 C A:ALA289 3.8 78.7 1.0 CMD A:HEM501 3.9 67.7 1.0 CG2 A:VAL119 4.0 81.9 1.0 C47 A:1YN502 4.0 82.7 0.5 CG1 A:VAL119 4.0 88.0 1.0 C43 A:1YN502 4.1 87.7 0.5 N A:GLY290 4.2 79.6 1.0 CA A:ALA289 4.2 75.5 1.0 C42 A:1YN502 4.3 59.9 0.5 CB A:VAL119 4.6 84.4 1.0 C42 A:1YN502 4.6 78.5 0.5 C2D A:HEM501 4.6 71.5 1.0 CA A:GLY290 4.7 79.0 1.0 CB A:ALA293 4.7 87.9 1.0 CE2 A:PHE114 4.9 87.8 1.0

Chlorine binding site 3 out of 4 in the Naegleria Fowleri CYP51-Itraconazole Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Naegleria Fowleri CYP51-Itraconazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:72.2 occ:0.50 CL9 A:1YN502 0.0 72.2 0.5 C47 A:1YN502 1.7 82.7 0.5 C43 A:1YN502 1.8 65.3 0.5 C46 A:1YN502 2.6 82.0 0.5 C44 A:1YN502 2.8 64.3 0.5 C42 A:1YN502 2.8 78.5 0.5 O33 A:1YN502 2.8 70.3 0.5 O33 A:1YN502 2.8 86.9 0.5 C42 A:1YN502 2.9 59.9 0.5 CD2 A:PHE292 3.0 0.0 1.0 C34 A:1YN502 3.1 79.1 0.5 C34 A:1YN502 3.1 62.0 0.5 C36 A:1YN502 3.1 58.4 0.5 C36 A:1YN502 3.2 73.7 0.5 CZ A:PHE114 3.2 91.2 1.0 CE2 A:PHE292 3.5 98.2 1.0 CE A:MET110 3.6 0.3 1.0 N37 A:1YN502 3.9 56.3 0.5 N37 A:1YN502 3.9 68.7 0.5 C45 A:1YN502 3.9 88.3 0.5 CG A:PHE292 4.0 92.6 1.0 CE1 A:PHE114 4.0 87.9 1.0 C45 A:1YN502 4.0 68.9 0.5 C32 A:1YN502 4.1 91.9 0.5 C43 A:1YN502 4.1 87.7 0.5 C47 A:1YN502 4.1 63.5 0.5 C32 A:1YN502 4.1 75.5 0.5 CE2 A:PHE114 4.1 87.8 1.0 N41 A:1YN502 4.2 58.5 0.5 N41 A:1YN502 4.2 69.4 0.5 CB A:PHE292 4.3 88.1 1.0 N A:ALA293 4.4 87.3 1.0 CA A:ALA293 4.4 89.9 1.0 O35 A:1YN502 4.5 87.2 0.5 C44 A:1YN502 4.5 88.2 0.5 O35 A:1YN502 4.5 71.7 0.5 CB A:ALA293 4.6 87.9 1.0 C46 A:1YN502 4.6 65.5 0.5 O A:ALA289 4.7 88.4 1.0 CZ A:PHE292 4.8 0.7 1.0 C38 A:1YN502 4.8 61.0 0.5 C A:PHE292 4.9 84.4 1.0 C38 A:1YN502 5.0 73.0 0.5

Chlorine binding site 4 out of 4 in the Naegleria Fowleri CYP51-Itraconazole Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Naegleria Fowleri CYP51-Itraconazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:1.0 occ:0.50 CL9 A:1YN502 0.0 1.0 0.5 C43 A:1YN502 1.8 87.7 0.5 C47 A:1YN502 2.1 63.5 0.5 O35 A:1YN502 2.1 71.7 0.5 OH A:TYR120 2.2 90.5 1.0 O35 A:1YN502 2.5 87.2 0.5 C42 A:1YN502 2.8 59.9 0.5 C44 A:1YN502 2.8 88.2 0.5 C42 A:1YN502 2.8 78.5 0.5 C34 A:1YN502 2.9 62.0 0.5 C31 A:1YN502 3.0 75.8 0.5 C34 A:1YN502 3.2 79.1 0.5 C46 A:1YN502 3.2 65.5 0.5 C31 A:1YN502 3.3 92.7 0.5 CHA A:HEM501 3.4 67.4 1.0 CZ A:TYR120 3.4 90.0 1.0 CAD A:HEM501 3.4 74.5 1.0 C4D A:HEM501 3.5 69.6 1.0 C3D A:HEM501 3.5 72.4 1.0 C38 A:1YN502 3.6 61.0 0.5 C38 A:1YN502 3.8 73.0 0.5 CE2 A:TYR120 3.8 79.0 1.0 O33 A:1YN502 3.8 70.3 0.5 C32 A:1YN502 3.8 75.5 0.5 C32 A:1YN502 4.0 91.9 0.5 CBA A:HEM501 4.0 85.7 1.0 C36 A:1YN502 4.0 58.4 0.5 C45 A:1YN502 4.1 88.3 0.5 N37 A:1YN502 4.1 56.3 0.5 C47 A:1YN502 4.1 82.7 0.5 O33 A:1YN502 4.1 86.9 0.5 C1A A:HEM501 4.1 71.8 1.0 C43 A:1YN502 4.2 65.3 0.5 ND A:HEM501 4.3 70.8 1.0 C36 A:1YN502 4.3 73.7 0.5 N37 A:1YN502 4.3 68.7 0.5 C30 A:1YN502 4.3 79.1 0.5 C2D A:HEM501 4.3 71.5 1.0 C45 A:1YN502 4.5 68.9 0.5 O1D A:HEM501 4.5 81.2 1.0 CE1 A:TYR120 4.6 84.9 1.0 C30 A:1YN502 4.6 97.0 0.5 C46 A:1YN502 4.6 82.0 0.5 C2A A:HEM501 4.6 79.4 1.0 CBD A:HEM501 4.6 82.0 1.0 C1D A:HEM501 4.7 74.2 1.0 CAA A:HEM501 4.7 80.6 1.0 CGA A:HEM501 4.8 89.6 1.0 N39 A:1YN502 4.8 59.7 0.5 N39 A:1YN502 4.8 68.5 0.5 C44 A:1YN502 4.9 64.3 0.5 NA A:HEM501 4.9 73.3 1.0

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