Fluorine in PDB 1fk9: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Dmp- 266(Efavirenz)

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Dmp- 266(Efavirenz):
2.7.7.49;

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Dmp- 266(Efavirenz), PDB code: 1fk9 was solved by J.Ren, J.Milton, K.L.Weaver, S.A.Short, D.I.Stuart, D.K.Stammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	139.800, 115.000, 65.400, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 30.1

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Dmp- 266(Efavirenz) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Dmp- 266(Efavirenz) (pdb code 1fk9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Dmp- 266(Efavirenz), PDB code: 1fk9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Dmp- 266(Efavirenz)


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 Hiv-1 Reverse Transcriptase in Complex with Dmp- 266(Efavirenz) within 5.0Å range: probe atom residue distance (Å) B Occ A:F999 b:49.8 occ:1.00 F1 A:EFZ999 0.0 49.8 1.0 C13 A:EFZ999 1.3 47.3 1.0 F2 A:EFZ999 2.1 48.6 1.0 F3 A:EFZ999 2.1 53.9 1.0 C7 A:EFZ999 2.4 44.2 1.0 O2 A:EFZ999 2.7 42.3 1.0 C8 A:EFZ999 2.9 47.1 1.0 CG1 A:VAL179 2.9 43.4 1.0 O A:VAL179 3.5 45.1 1.0 O A:TYR188 3.6 53.6 1.0 C14 A:EFZ999 3.6 39.8 1.0 C9 A:EFZ999 3.7 47.9 1.0 C6 A:EFZ999 3.7 37.3 1.0 C A:VAL179 3.9 44.2 1.0 CB A:VAL179 3.9 46.5 1.0 N A:TYR181 4.0 49.9 1.0 O1 A:EFZ999 4.2 35.2 1.0 CB A:TYR181 4.2 51.4 1.0 N A:GLY190 4.3 45.6 1.0 N A:EFZ999 4.3 38.6 1.0 C A:TYR188 4.3 50.0 1.0 N A:ILE180 4.4 45.3 1.0 CB A:TYR188 4.4 52.1 1.0 CA A:ILE180 4.5 46.1 1.0 C1 A:EFZ999 4.5 35.2 1.0 C A:ILE180 4.5 48.6 1.0 C5 A:EFZ999 4.6 35.7 1.0 CA A:VAL179 4.6 46.3 1.0 CA A:TYR181 4.7 50.6 1.0 CA A:GLY190 4.8 45.1 1.0 C A:VAL189 4.9 47.9 1.0 N A:VAL189 4.9 48.7 1.0 CA A:VAL189 4.9 47.4 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Dmp- 266(Efavirenz)


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 Hiv-1 Reverse Transcriptase in Complex with Dmp- 266(Efavirenz) within 5.0Å range: probe atom residue distance (Å) B Occ A:F999 b:48.6 occ:1.00 F2 A:EFZ999 0.0 48.6 1.0 C13 A:EFZ999 1.3 47.3 1.0 F3 A:EFZ999 2.1 53.9 1.0 F1 A:EFZ999 2.1 49.8 1.0 C7 A:EFZ999 2.4 44.2 1.0 C8 A:EFZ999 2.8 47.1 1.0 C6 A:EFZ999 3.0 37.3 1.0 C5 A:EFZ999 3.3 35.7 1.0 CB A:TYR188 3.4 52.1 1.0 O A:TYR188 3.5 53.6 1.0 C9 A:EFZ999 3.5 47.9 1.0 C A:TYR188 3.5 50.0 1.0 O2 A:EFZ999 3.6 42.3 1.0 N A:GLY190 3.7 45.6 1.0 N A:VAL189 3.8 48.7 1.0 C A:VAL189 3.9 47.9 1.0 CA A:TYR188 4.0 49.3 1.0 CG2 A:VAL106 4.1 44.9 1.0 C1 A:EFZ999 4.1 35.2 1.0 CA A:GLY190 4.2 45.1 1.0 CA A:VAL189 4.2 47.4 1.0 O A:VAL179 4.4 45.1 1.0 O A:VAL189 4.4 50.2 1.0 C4 A:EFZ999 4.5 41.4 1.0 CB A:VAL106 4.5 47.1 1.0 C14 A:EFZ999 4.5 39.8 1.0 CG A:TYR188 4.6 54.4 1.0 N A:EFZ999 4.6 38.6 1.0 CD1 A:TYR188 4.8 52.3 1.0 C10 A:EFZ999 4.9 48.0 1.0 CG1 A:VAL179 4.9 43.4 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with Dmp- 266(Efavirenz)


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 Hiv-1 Reverse Transcriptase in Complex with Dmp- 266(Efavirenz) within 5.0Å range: probe atom residue distance (Å) B Occ A:F999 b:53.9 occ:1.00 F3 A:EFZ999 0.0 53.9 1.0 C13 A:EFZ999 1.3 47.3 1.0 F2 A:EFZ999 2.1 48.6 1.0 F1 A:EFZ999 2.1 49.8 1.0 C7 A:EFZ999 2.4 44.2 1.0 C6 A:EFZ999 2.8 37.3 1.0 O2 A:EFZ999 3.0 42.3 1.0 N A:EFZ999 3.1 38.6 1.0 C1 A:EFZ999 3.2 35.2 1.0 C14 A:EFZ999 3.2 39.8 1.0 CA A:GLY190 3.4 45.1 1.0 N A:GLY190 3.5 45.6 1.0 C8 A:EFZ999 3.6 47.1 1.0 CG1 A:VAL179 3.8 43.4 1.0 C5 A:EFZ999 3.8 35.7 1.0 CG A:LYS103 3.8 38.5 1.0 O1 A:EFZ999 4.0 35.2 1.0 O A:VAL179 4.0 45.1 1.0 CB A:VAL179 4.1 46.5 1.0 CE A:LYS103 4.2 41.3 1.0 C2 A:EFZ999 4.2 37.2 1.0 C A:GLY190 4.3 47.4 1.0 C A:VAL189 4.3 47.9 1.0 CD A:LYS103 4.6 38.8 1.0 C4 A:EFZ999 4.7 41.4 1.0 O A:GLY190 4.7 47.2 1.0 C9 A:EFZ999 4.7 47.9 1.0 C A:VAL179 4.7 44.2 1.0 CB A:VAL106 4.8 47.1 1.0 O A:TYR188 4.8 53.6 1.0 C3 A:EFZ999 4.9 42.2 1.0 CB A:LYS103 4.9 42.5 1.0 O A:VAL189 5.0 50.2 1.0

J.Ren, J.Milton, K.L.Weaver, S.A.Short, D.I.Stuart, D.K.Stammers. Structural Basis For the Resilience of Efavirenz (Dmp-266) to Drug Resistance Mutations in Hiv-1 Reverse Transcriptase. Structure Fold.Des. V. 8 1089 2000.
ISSN: ISSN 0969-2126
PubMed: 11080630
DOI: 10.1016/S0969-2126(00)00513-X