Fluorine in PDB 1ikw: Wild Type Hiv-1 Reverse Transcriptase in Complex with Efavirenz

All present enzymatic activity of Wild Type Hiv-1 Reverse Transcriptase in Complex with Efavirenz:
2.7.7.49;

The structure of Wild Type Hiv-1 Reverse Transcriptase in Complex with Efavirenz, PDB code: 1ikw was solved by J.Lindberg, T.Unge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.69 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	119.546, 157.310, 157.171, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 27.2

The structure of Wild Type Hiv-1 Reverse Transcriptase in Complex with Efavirenz also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Wild Type Hiv-1 Reverse Transcriptase in Complex with Efavirenz (pdb code 1ikw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Wild Type Hiv-1 Reverse Transcriptase in Complex with Efavirenz, PDB code: 1ikw:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Wild Type Hiv-1 Reverse Transcriptase in Complex with Efavirenz


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Wild Type Hiv-1 Reverse Transcriptase in Complex with Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ A:F2000 b:43.4 occ:1.00 F1 A:EFZ2000 0.0 43.4 1.0 C13 A:EFZ2000 1.4 46.1 1.0 F2 A:EFZ2000 2.2 45.4 1.0 F3 A:EFZ2000 2.3 47.8 1.0 C7 A:EFZ2000 2.4 47.6 1.0 O2 A:EFZ2000 2.8 49.4 1.0 C8 A:EFZ2000 2.9 49.1 1.0 CG2 A:VAL179 3.0 57.8 1.0 O A:TYR188 3.5 53.3 1.0 C14 A:EFZ2000 3.7 49.9 1.0 C9 A:EFZ2000 3.7 51.4 1.0 C6 A:EFZ2000 3.8 46.3 1.0 CB A:TYR181 4.0 49.5 1.0 O A:VAL179 4.0 61.0 1.0 N A:TYR181 4.1 53.0 1.0 C A:TYR188 4.1 53.2 1.0 CB A:TYR188 4.1 50.4 1.0 O1 A:EFZ2000 4.3 53.2 1.0 N A:GLY190 4.3 55.8 1.0 C A:VAL179 4.4 60.6 1.0 CB A:VAL179 4.5 59.5 1.0 N A:EFZ2000 4.6 47.1 1.0 C1 A:EFZ2000 4.7 47.3 1.0 C5 A:EFZ2000 4.7 46.5 1.0 CA A:TYR181 4.7 52.4 1.0 N A:VAL189 4.7 54.0 1.0 N A:ILE180 4.8 58.1 1.0 C A:ILE180 4.8 55.1 1.0 CA A:TYR188 4.8 52.4 1.0 C A:VAL189 4.8 55.9 1.0 CA A:ILE180 4.8 56.5 1.0 CA A:GLY190 4.8 58.8 1.0 CA A:VAL189 4.9 55.8 1.0 C10 A:EFZ2000 4.9 52.3 1.0

Fluorine binding site 2 out of 3 in the Wild Type Hiv-1 Reverse Transcriptase in Complex with Efavirenz


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Wild Type Hiv-1 Reverse Transcriptase in Complex with Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ A:F2000 b:45.4 occ:1.00 F2 A:EFZ2000 0.0 45.4 1.0 C13 A:EFZ2000 1.4 46.1 1.0 F1 A:EFZ2000 2.2 43.4 1.0 F3 A:EFZ2000 2.3 47.8 1.0 C7 A:EFZ2000 2.4 47.6 1.0 C6 A:EFZ2000 3.0 46.3 1.0 O2 A:EFZ2000 3.0 49.4 1.0 C14 A:EFZ2000 3.1 49.9 1.0 N A:EFZ2000 3.3 47.1 1.0 C1 A:EFZ2000 3.4 47.3 1.0 CG2 A:VAL179 3.4 57.8 1.0 CA A:GLY190 3.4 58.8 1.0 N A:GLY190 3.5 55.8 1.0 C8 A:EFZ2000 3.7 49.1 1.0 CG A:LYS103 3.8 65.4 1.0 O1 A:EFZ2000 3.8 53.2 1.0 C5 A:EFZ2000 3.9 46.5 1.0 C A:GLY190 4.3 61.7 1.0 C A:VAL189 4.3 55.9 1.0 O A:VAL179 4.5 61.0 1.0 C2 A:EFZ2000 4.5 50.6 1.0 CB A:LYS103 4.6 64.3 1.0 O A:GLY190 4.6 61.2 1.0 CB A:VAL179 4.6 59.5 1.0 CG2 A:VAL106 4.7 65.5 1.0 CG1 A:VAL179 4.8 59.1 1.0 O A:VAL189 4.9 55.6 1.0 CB A:VAL106 4.9 66.7 1.0 CE A:LYS103 4.9 69.8 1.0 CD A:LYS103 4.9 67.7 1.0 O A:TYR188 4.9 53.3 1.0 C9 A:EFZ2000 4.9 51.4 1.0 C4 A:EFZ2000 5.0 49.9 1.0

Fluorine binding site 3 out of 3 in the Wild Type Hiv-1 Reverse Transcriptase in Complex with Efavirenz


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Wild Type Hiv-1 Reverse Transcriptase in Complex with Efavirenz within 5.0Å range: probe atom residue distance (Å) B Occ A:F2000 b:47.8 occ:1.00 F3 A:EFZ2000 0.0 47.8 1.0 C13 A:EFZ2000 1.4 46.1 1.0 F1 A:EFZ2000 2.3 43.4 1.0 F2 A:EFZ2000 2.3 45.4 1.0 C7 A:EFZ2000 2.5 47.6 1.0 C8 A:EFZ2000 2.9 49.1 1.0 C6 A:EFZ2000 3.0 46.3 1.0 C5 A:EFZ2000 3.3 46.5 1.0 CB A:TYR188 3.4 50.4 1.0 CG2 A:VAL106 3.5 65.5 1.0 C A:TYR188 3.7 53.2 1.0 O2 A:EFZ2000 3.7 49.4 1.0 C9 A:EFZ2000 3.8 51.4 1.0 O A:TYR188 3.8 53.3 1.0 N A:GLY190 3.9 55.8 1.0 N A:VAL189 3.9 54.0 1.0 C A:VAL189 4.0 55.9 1.0 CA A:TYR188 4.1 52.4 1.0 C1 A:EFZ2000 4.2 47.3 1.0 CA A:GLY190 4.3 58.8 1.0 O A:VAL189 4.3 55.6 1.0 CA A:VAL189 4.3 55.8 1.0 CB A:VAL106 4.4 66.7 1.0 CG A:TYR188 4.5 47.8 1.0 C4 A:EFZ2000 4.5 49.9 1.0 C14 A:EFZ2000 4.5 49.9 1.0 CD2 A:TYR188 4.6 47.2 1.0 N A:EFZ2000 4.7 47.1 1.0 CG2 A:VAL179 4.8 57.8 1.0 C10 A:EFZ2000 5.0 52.3 1.0

J.Lindberg, S.Sigurdsson, S.Lowgren, H.O.Andersson, C.Sahlberg, R.Noreen, K.Fridborg, H.Zhang, T.Unge. Structural Basis For the Inhibitory Efficacy of Efavirenz (Dmp-266), MSC194 and PNU142721 Towards the Hiv-1 Rt K103N Mutant. Eur.J.Biochem. V. 269 1670 2002.
ISSN: ISSN 0014-2956
PubMed: 11895437
DOI: 10.1046/J.1432-1327.2002.02811.X