Fluorine in PDB 5j2n: Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) Site

The structure of Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) Site, PDB code: 5j2n 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)	53.62 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	166.827, 169.885, 102.656, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.2

The structure of Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) Site also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) Site (pdb code 5j2n). 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 That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) Site, PDB code: 5j2n:

Fluorine binding site 1 out of 1 in the Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) 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 in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and Dtmp at the N-(Pre- Translocation) Site within 5.0Å range: probe atom residue distance (Å) B Occ P:F822 b:54.8 occ:1.00 F32 P:6FM822 0.0 54.8 1.0 C2 P:6FM822 1.4 53.1 1.0 N3 P:6FM822 2.3 51.6 1.0 N1 P:6FM822 2.3 53.0 1.0 O2 T:DT706 2.7 49.4 1.0 O T:HOH801 3.3 33.5 1.0 N3 T:DT706 3.4 50.4 1.0 C2 T:DT706 3.5 50.2 1.0 C4 P:6FM822 3.5 58.9 1.0 C6 P:6FM822 3.6 51.5 1.0 N1 T:DG707 3.6 47.2 1.0 C2 T:DG707 3.6 52.1 1.0 C2 P:DT823 3.7 56.6 1.0 N3 T:DG707 3.8 54.7 1.0 C6 T:DG707 3.8 48.1 1.0 C4 T:DG707 3.9 55.7 1.0 O2 P:DT823 3.9 58.3 1.0 N3 P:DT823 3.9 56.0 1.0 C5 T:DG707 3.9 48.1 1.0 C5 P:6FM822 4.0 49.9 1.0 N1 P:DT823 4.1 55.1 1.0 N2 T:DG707 4.2 51.6 1.0 O6 T:DG707 4.4 48.8 1.0 C4 P:DT823 4.4 57.3 1.0 OH A:TYR115 4.5 35.7 1.0 N9 T:DG707 4.6 47.6 1.0 C6 P:DT823 4.6 53.3 1.0 N9 P:6FM822 4.7 58.5 1.0 N7 T:DG707 4.7 48.9 1.0 C4 T:DT706 4.7 51.4 1.0 C1' P:DT823 4.7 66.0 1.0 N6 P:6FM822 4.8 51.5 1.0 C5 P:DT823 4.8 52.7 1.0 N1 T:DT706 4.8 58.3 1.0 N1 T:DA705 4.8 54.0 1.0 CE A:MET184 4.9 52.2 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