Fluorine in PDB 5j2m: Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor

The structure of Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor, PDB code: 5j2m was solved by Z.L.Salie, K.A.Kirby, S.G.Sarafianos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.23 / 2.43
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	167.468, 169.758, 101.951, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.3

The structure of Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Fluorine atom in the Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor (pdb code 5j2m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor, PDB code: 5j2m:

Fluorine binding site 1 out of 1 in the Hiv-1 Reverse Transcriptase in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor


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 in Complex with Dna and Efda-Triphosphate, A Translocation-Defective Rt Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F604 b:37.6 occ:1.00 F32 A:6FN604 0.0 37.6 1.0 C2 A:6FN604 1.4 35.7 1.0 N3 A:6FN604 2.3 35.0 1.0 N1 A:6FN604 2.3 34.8 1.0 O2 T:DT705 2.9 53.9 1.0 O T:HOH802 3.0 30.4 1.0 C2 T:DC706 3.2 39.2 1.0 O2 T:DC706 3.3 40.7 1.0 N1 T:DC706 3.4 35.7 1.0 C4 A:6FN604 3.5 32.1 1.0 C6 A:6FN604 3.6 35.4 1.0 N A:GLY152 3.6 32.3 1.0 N3 T:DC706 3.7 40.6 1.0 C2 T:DT705 3.7 48.6 1.0 C1' T:DC706 3.7 41.1 1.0 N3 T:DT705 3.7 39.9 1.0 O A:HOH761 3.8 34.3 1.0 C6 T:DC706 4.0 42.9 1.0 C A:GLN151 4.0 43.2 1.0 C5 A:6FN604 4.0 34.1 1.0 CB A:GLN151 4.2 33.8 1.0 CA A:GLN151 4.2 39.3 1.0 CA A:GLY152 4.2 34.4 1.0 C4 T:DC706 4.3 44.1 1.0 O4' T:DC706 4.3 38.3 1.0 CD2 A:LEU74 4.4 41.7 1.0 C5 T:DC706 4.4 35.9 1.0 N9 A:6FN604 4.7 38.0 1.0 N2 P:DG822 4.7 37.0 1.0 N6 A:6FN604 4.8 27.1 1.0 O A:GLN151 4.8 39.7 1.0 OE1 A:GLN151 4.8 42.6 1.0 N1 T:DT705 5.0 47.7 1.0 C4 T:DT705 5.0 43.7 1.0 CE2 A:TYR115 5.0 35.4 1.0

Z.L.Salie, K.A.Kirby, E.Michailidis, B.Marchand, K.Singh, L.C.Rohan, E.N.Kodama, H.Mitsuya, M.A.Parniak, S.G.Sarafianos. Structural Basis of Hiv Inhibition By Translocation-Defective Rt Inhibitor 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine (Efda). Proc.Natl.Acad.Sci.Usa V. 113 9274 2016.
ISSN: ESSN 1091-6490
PubMed: 27489345
DOI: 10.1073/PNAS.1605223113