Fluorine in PDB 5j2q: Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated A Mismatched Efda-Mp at the N-(Pre-Translocation) Site

The structure of Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated A Mismatched Efda-Mp at the N-(Pre-Translocation) Site, PDB code: 5j2q 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)	64.33 / 2.79
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	165.557, 170.512, 102.235, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.2

The structure of Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated A Mismatched 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 A Mismatched Efda-Mp at the N-(Pre-Translocation) Site (pdb code 5j2q). 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 A Mismatched Efda-Mp at the N-(Pre-Translocation) Site, PDB code: 5j2q:
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 A Mismatched 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 A Mismatched Efda-Mp at the N-(Pre-Translocation) Site within 5.0Å range: probe atom residue distance (Å) B Occ P:F901 b:79.9 occ:1.00 F32 P:6FM901 0.0 79.9 1.0 C2 P:6FM901 1.4 78.1 1.0 N3 P:6FM901 2.3 81.5 1.0 N1 P:6FM901 2.3 83.9 1.0 O2 T:DT706 2.8 70.0 1.0 N3 T:DT706 3.4 69.4 1.0 C2 T:DT706 3.5 71.0 1.0 N3 T:6FM801 3.5 0.3 1.0 C4 P:6FM901 3.5 75.0 1.0 C6 P:6FM901 3.6 76.1 1.0 C4 T:6FM801 3.6 93.8 1.0 C2 T:DG707 3.7 60.1 1.0 N3 T:DG707 3.8 63.0 1.0 N1 T:DG707 3.8 57.2 1.0 C4 T:DG707 3.8 66.9 1.0 N9 T:6FM801 3.9 83.0 1.0 C5 T:DG707 3.9 62.1 1.0 C6 T:DG707 3.9 58.4 1.0 C2 T:6FM801 4.0 0.4 1.0 CE A:MET184 4.0 66.5 1.0 C5 P:6FM901 4.0 74.7 1.0 C5 T:6FM801 4.1 93.1 1.0 C1' T:6FM801 4.2 82.7 1.0 N2 T:DG707 4.3 66.1 1.0 N1 T:6FM801 4.4 95.4 1.0 OH A:TYR115 4.4 55.4 1.0 N9 T:DG707 4.5 56.3 1.0 C6 T:6FM801 4.5 94.4 1.0 C8 T:6FM801 4.5 84.8 1.0 O4' T:6FM801 4.5 85.4 1.0 F32 T:6FM801 4.5 99.3 1.0 O6 T:DG707 4.6 70.0 1.0 N7 T:DG707 4.6 62.6 1.0 N7 T:6FM801 4.7 89.3 1.0 N9 P:6FM901 4.7 82.0 1.0 C4 T:DT706 4.7 75.0 1.0 N6 P:6FM901 4.8 75.8 1.0 N1 T:DT706 4.9 71.2 1.0 C8 T:DG707 4.9 57.8 1.0 CG A:PRO157 4.9 50.5 1.0

Fluorine binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated A Mismatched 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 A Mismatched Efda-Mp at the N-(Pre-Translocation) Site within 5.0Å range: probe atom residue distance (Å) B Occ T:F801 b:99.3 occ:1.00 F32 T:6FM801 0.0 99.3 1.0 C2 T:6FM801 1.4 0.4 1.0 N3 T:6FM801 2.3 0.3 1.0 N1 T:6FM801 2.3 95.4 1.0 C2 T:DT706 3.0 71.0 1.0 O2 T:DT706 3.0 70.0 1.0 N1 T:DT706 3.2 71.2 1.0 N A:GLY152 3.4 68.9 1.0 C4 T:6FM801 3.5 93.8 1.0 C1' T:DT706 3.5 68.7 1.0 C6 T:6FM801 3.6 94.4 1.0 N3 T:DT706 3.6 69.4 1.0 C8 T:DA705 3.8 0.4 1.0 CA A:GLY152 4.0 73.3 1.0 C6 T:DT706 4.0 72.4 1.0 C5 T:6FM801 4.0 93.1 1.0 N7 T:DA705 4.1 0.7 1.0 O4' T:DT706 4.1 74.3 1.0 C4 T:DT706 4.3 75.0 1.0 C A:GLN151 4.4 69.0 1.0 CD2 A:LEU74 4.4 77.1 0.7 CB A:GLN151 4.4 75.2 1.0 C5 T:DT706 4.5 74.2 1.0 CA A:GLN151 4.5 67.0 1.0 F32 P:6FM901 4.5 79.9 1.0 N9 T:6FM801 4.7 83.0 1.0 N6 T:6FM801 4.8 91.8 1.0 OE1 A:GLN151 4.8 84.9 1.0 CE2 A:TYR115 4.9 53.1 1.0 C2' T:DT706 4.9 63.0 1.0 N9 T:DA705 4.9 0.2 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