Fluorine in PDB 4ify: Hiv-1 Reverse Transcriptase with Bound Fragment at the Knuckles Site

All present enzymatic activity of Hiv-1 Reverse Transcriptase with Bound Fragment at the Knuckles Site:
2.7.7.49; 2.7.7.7; 3.1.26.13;

The structure of Hiv-1 Reverse Transcriptase with Bound Fragment at the Knuckles Site, PDB code: 4ify was solved by J.D.Bauman, D.Patel, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.31 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.946, 73.051, 108.755, 90.00, 100.47, 90.00
R / Rfree (%)	18.6 / 21.3

The structure of Hiv-1 Reverse Transcriptase with Bound Fragment at the Knuckles Site also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Hiv-1 Reverse Transcriptase with Bound Fragment at the Knuckles Site (pdb code 4ify). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Hiv-1 Reverse Transcriptase with Bound Fragment at the Knuckles Site, PDB code: 4ify:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Hiv-1 Reverse Transcriptase with Bound Fragment at the Knuckles Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv-1 Reverse Transcriptase with Bound Fragment at the Knuckles Site within 5.0Å range: probe atom residue distance (Å) B Occ A:F611 b:71.9 occ:1.00 F3 A:1FD611 0.0 71.9 1.0 C1 A:1FD611 1.3 73.2 1.0 F1 A:1FD611 2.2 73.6 1.0 F2 A:1FD611 2.2 70.6 1.0 O A:1FD611 2.2 77.4 1.0 C2 A:1FD611 2.6 76.9 1.0 C7 A:1FD611 3.0 77.1 1.0 CG2 A:VAL118 3.2 29.8 1.0 CB A:SER163 3.4 26.4 1.0 CG1 A:ILE5 3.5 55.7 1.0 C3 A:1FD611 3.5 78.2 1.0 C6 A:1FD611 4.1 79.0 1.0 CG1 A:VAL118 4.1 30.0 1.0 CB A:VAL118 4.2 31.6 1.0 CG2 A:ILE5 4.2 48.8 1.0 OG A:SER163 4.2 32.4 1.0 CD1 A:ILE5 4.3 59.9 1.0 CB A:ILE5 4.4 49.0 1.0 C A:SER163 4.4 27.1 1.0 C4 A:1FD611 4.5 80.2 1.0 CA A:SER163 4.6 25.9 1.0 N A:MET164 4.6 27.5 1.0 CA A:VAL118 4.7 31.0 1.0 C5 A:1FD611 4.7 80.6 1.0 O A:SER163 4.8 27.9 1.0 CD1 A:PHE160 5.0 41.1 1.0

Fluorine binding site 2 out of 3 in the Hiv-1 Reverse Transcriptase with Bound Fragment at the Knuckles Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hiv-1 Reverse Transcriptase with Bound Fragment at the Knuckles Site within 5.0Å range: probe atom residue distance (Å) B Occ A:F611 b:73.6 occ:1.00 F1 A:1FD611 0.0 73.6 1.0 C1 A:1FD611 1.3 73.2 1.0 F3 A:1FD611 2.2 71.9 1.0 F2 A:1FD611 2.2 70.6 1.0 O A:1FD611 2.2 77.4 1.0 CE1 A:PHE160 3.3 42.1 1.0 CD1 A:PHE160 3.4 41.1 1.0 C2 A:1FD611 3.4 76.9 1.0 CG2 A:VAL118 3.5 29.8 1.0 N A:MET164 3.6 27.5 1.0 CE A:MET164 3.7 30.3 1.0 O A:PHE160 3.7 23.9 1.0 CB A:SER163 3.8 26.4 1.0 CB A:MET164 3.9 26.4 1.0 C7 A:1FD611 3.9 77.1 1.0 CA A:MET164 3.9 27.7 1.0 C A:SER163 4.2 27.1 1.0 CZ A:PHE160 4.3 43.7 1.0 CG A:PHE160 4.3 38.7 1.0 C3 A:1FD611 4.5 78.2 1.0 CB A:ALA114 4.5 47.5 1.0 C A:PHE160 4.6 28.9 1.0 CA A:SER163 4.6 25.9 1.0 CA A:PHE160 4.7 30.2 1.0 SD A:MET164 4.7 39.1 1.0 O A:ALA114 4.8 43.6 1.0 O A:SER163 4.8 27.9 1.0 CG A:MET164 4.8 33.9 1.0 OG A:SER163 4.9 32.4 1.0 CB A:VAL118 4.9 31.6 1.0

Fluorine binding site 3 out of 3 in the Hiv-1 Reverse Transcriptase with Bound Fragment at the Knuckles Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hiv-1 Reverse Transcriptase with Bound Fragment at the Knuckles Site within 5.0Å range: probe atom residue distance (Å) B Occ A:F611 b:70.6 occ:1.00 F2 A:1FD611 0.0 70.6 1.0 C1 A:1FD611 1.3 73.2 1.0 F3 A:1FD611 2.2 71.9 1.0 F1 A:1FD611 2.2 73.6 1.0 O A:1FD611 2.2 77.4 1.0 C2 A:1FD611 3.2 76.9 1.0 CD1 A:ILE167 3.3 44.4 1.0 N A:MET164 3.5 27.5 1.0 C A:SER163 3.5 27.1 1.0 O A:SER163 3.5 27.9 1.0 CA A:MET164 3.5 27.7 1.0 C3 A:1FD611 3.7 78.2 1.0 CB A:SER163 3.8 26.4 1.0 CE A:MET164 4.0 30.3 1.0 CG1 A:ILE167 4.1 41.0 1.0 CB A:MET164 4.2 26.4 1.0 C7 A:1FD611 4.2 77.1 1.0 CG1 A:ILE5 4.3 55.7 1.0 CA A:SER163 4.3 25.9 1.0 CG2 A:ILE167 4.4 33.5 1.0 SD A:MET164 4.4 39.1 1.0 CD1 A:ILE5 4.7 59.9 1.0 O A:HOH884 4.8 40.5 1.0 C A:MET164 4.8 27.1 1.0 CB A:ILE167 4.9 38.2 1.0 CG A:MET164 4.9 33.9 1.0 C4 A:1FD611 5.0 80.2 1.0

J.D.Bauman, D.Patel, C.Dharia, M.W.Fromer, S.Ahmed, Y.Frenkel, R.S.Vijayan, J.T.Eck, W.C.Ho, K.Das, A.J.Shatkin, E.Arnold. Detecting Allosteric Sites of Hiv-1 Reverse Transcriptase By X-Ray Crystallographic Fragment Screening. J.Med.Chem. V. 56 2738 2013.
ISSN: ISSN 0022-2623
PubMed: 23342998
DOI: 10.1021/JM301271J