Fluorine in PDB 5j2p: Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp 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 A Second Efda-Mp at the N-(Pre-Translocation) Site, PDB code: 5j2p 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)	63.78 / 2.53
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	165.977, 170.183, 99.695, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.6

The structure of Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp 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 A Second Efda-Mp at the N-(Pre-Translocation) Site (pdb code 5j2p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp at the N-(Pre-Translocation) Site, PDB code: 5j2p:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp 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 A Second Efda-Mp at the N-(Pre-Translocation) Site within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:49.9 occ:1.00 F32 A:6FM602 0.0 49.9 1.0 C2 A:6FM602 1.4 44.6 1.0 N1 A:6FM602 2.3 43.9 1.0 N3 A:6FM602 2.3 52.6 1.0 O2 T:DT705 2.9 51.4 1.0 O T:HOH806 3.0 33.0 1.0 O2 T:DT706 3.0 37.9 1.0 C2 T:DT706 3.1 38.8 1.0 N1 T:DT706 3.4 48.8 1.0 N A:GLY152 3.4 36.3 1.0 O A:HOH796 3.4 34.5 1.0 C1' T:DT706 3.5 40.2 1.0 C4 A:6FM602 3.5 46.8 1.0 C6 A:6FM602 3.6 42.6 1.0 C2 T:DT705 3.8 47.0 1.0 N3 T:DT706 3.8 38.6 1.0 N3 T:DT705 3.9 40.5 1.0 C A:GLN151 4.0 36.7 1.0 C5 A:6FM602 4.0 48.2 1.0 CA A:GLN151 4.1 40.4 1.0 CA A:GLY152 4.1 36.9 1.0 CB A:GLN151 4.1 36.0 1.0 O4' T:DT706 4.2 46.3 1.0 C6 T:DT706 4.2 44.6 1.0 F32 P:6FM901 4.3 49.4 1.0 CD2 A:LEU74 4.6 37.2 1.0 C4 T:DT706 4.6 53.5 1.0 N9 A:6FM602 4.7 46.8 1.0 N6 A:6FM602 4.7 41.9 1.0 C2' T:DT706 4.8 40.0 1.0 C5 T:DT706 4.8 40.7 1.0 O A:GLN151 4.9 45.0 1.0 CE2 A:TYR115 4.9 39.2 1.0 OE1 A:GLN151 4.9 35.9 1.0 N1 P:6FM901 5.0 41.5 1.0

Fluorine binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp 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 2 of Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp at the N-(Pre-Translocation) Site within 5.0Å range: probe atom residue distance (Å) B Occ P:F901 b:49.4 occ:1.00 F32 P:6FM901 0.0 49.4 1.0 C2 P:6FM901 1.4 41.6 1.0 N3 P:6FM901 2.3 49.1 1.0 N1 P:6FM901 2.3 41.5 1.0 O2 T:DT706 2.8 37.9 1.0 O T:HOH806 3.1 33.0 1.0 N3 A:6FM602 3.3 52.6 1.0 C4 A:6FM602 3.4 46.8 1.0 C4 P:6FM901 3.5 57.6 1.0 C6 P:6FM901 3.6 40.3 1.0 C2 T:DT706 3.6 38.8 1.0 C2 T:DG707 3.7 34.8 1.0 C2 A:6FM602 3.7 44.6 1.0 N3 T:DT706 3.8 38.6 1.0 N9 A:6FM602 3.8 46.8 1.0 N1 T:DG707 3.8 35.4 1.0 CE A:MET184 3.8 30.9 1.0 N3 T:DG707 3.9 35.4 1.0 C5 A:6FM602 4.0 48.2 1.0 C4 T:DG707 4.0 36.5 1.0 C6 T:DG707 4.0 36.5 1.0 C5 P:6FM901 4.0 39.2 1.0 C1' A:6FM602 4.1 42.7 1.0 C5 T:DG707 4.1 44.6 1.0 N2 T:DG707 4.2 33.7 1.0 N1 A:6FM602 4.2 43.9 1.0 F32 A:6FM602 4.3 49.9 1.0 C6 A:6FM602 4.3 42.6 1.0 OH A:TYR115 4.4 32.1 1.0 C8 A:6FM602 4.4 42.2 1.0 O4' A:6FM602 4.5 41.4 1.0 N7 A:6FM602 4.6 42.8 1.0 N9 P:6FM901 4.6 58.8 1.0 O6 T:DG707 4.7 47.2 1.0 N9 T:DG707 4.7 37.3 1.0 N6 P:6FM901 4.8 40.3 1.0 N7 T:DG707 4.9 49.1 1.0 N1 T:DT706 4.9 48.8 1.0 SD A:MET184 5.0 30.2 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