Fluorine in PDB 6bsi: Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence

The structure of Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence, PDB code: 6bsi was solved by L.Tian, M.Kim, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.30 / 3.25
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.850, 163.850, 129.570, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 24.1

The structure of Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence (pdb code 6bsi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence, PDB code: 6bsi:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:93.5 occ:1.00 F1 A:EFZ601 0.0 93.5 1.0 C13 A:EFZ601 1.3 91.4 1.0 F2 A:EFZ601 2.2 86.0 1.0 F3 A:EFZ601 2.2 86.7 1.0 C7 A:EFZ601 2.3 93.5 1.0 C6 A:EFZ601 2.6 82.7 1.0 O2 A:EFZ601 3.0 0.6 1.0 C5 A:EFZ601 3.1 80.7 1.0 CA A:GLY190 3.3 86.2 1.0 C8 A:EFZ601 3.5 93.1 1.0 C1 A:EFZ601 3.5 89.2 1.0 N A:GLY190 3.6 78.9 1.0 C14 A:EFZ601 3.7 96.9 1.0 C A:VAL189 3.8 74.9 1.0 N A:EFZ601 3.9 97.4 1.0 O A:VAL189 3.9 79.4 1.0 CG2 A:VAL179 4.0 86.3 1.0 C4 A:EFZ601 4.1 93.3 1.0 CG1 A:VAL106 4.2 86.1 1.0 C2 A:EFZ601 4.4 91.3 1.0 CG A:LYS103 4.5 95.0 1.0 N A:VAL189 4.5 80.1 1.0 O A:TYR188 4.5 84.6 1.0 C A:TYR188 4.6 82.1 1.0 C3 A:EFZ601 4.6 95.2 1.0 CA A:VAL189 4.6 76.7 1.0 C A:GLY190 4.6 89.9 1.0 C9 A:EFZ601 4.6 92.1 1.0 O1 A:EFZ601 4.6 97.9 1.0 CB A:VAL106 4.7 80.7 1.0 O A:VAL179 4.9 90.5 1.0 CB A:TYR188 5.0 71.3 1.0

Fluorine binding site 2 out of 3 in the Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:86.0 occ:1.00 F2 A:EFZ601 0.0 86.0 1.0 C13 A:EFZ601 1.3 91.4 1.0 F3 A:EFZ601 2.1 86.7 1.0 F1 A:EFZ601 2.2 93.5 1.0 C7 A:EFZ601 2.4 93.5 1.0 O2 A:EFZ601 2.6 0.6 1.0 CG2 A:VAL179 3.0 86.3 1.0 C8 A:EFZ601 3.2 93.1 1.0 O A:TYR188 3.4 84.6 1.0 C14 A:EFZ601 3.6 96.9 1.0 O A:VAL179 3.7 90.5 1.0 C6 A:EFZ601 3.7 82.7 1.0 N A:GLY190 3.9 78.9 1.0 C A:TYR188 4.0 82.1 1.0 C9 A:EFZ601 4.1 92.1 1.0 CB A:VAL179 4.1 81.7 1.0 O1 A:EFZ601 4.2 97.9 1.0 CA A:GLY190 4.2 86.2 1.0 C A:VAL179 4.2 88.2 1.0 C A:VAL189 4.3 74.9 1.0 N A:TYR181 4.4 83.8 1.0 N A:EFZ601 4.4 97.4 1.0 N A:VAL189 4.4 80.1 1.0 CA A:VAL189 4.5 76.7 1.0 CB A:TYR188 4.5 71.3 1.0 C5 A:EFZ601 4.5 80.7 1.0 CB A:TYR181 4.5 89.3 1.0 C1 A:EFZ601 4.6 89.2 1.0 CA A:VAL179 4.8 88.6 1.0 N A:ILE180 4.8 86.2 1.0 O A:VAL189 4.9 79.4 1.0 CA A:ILE180 4.9 78.6 1.0 CA A:TYR188 4.9 72.6 1.0 C A:ILE180 5.0 84.8 1.0

Fluorine binding site 3 out of 3 in the Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:86.7 occ:1.00 F3 A:EFZ601 0.0 86.7 1.0 C13 A:EFZ601 1.3 91.4 1.0 F2 A:EFZ601 2.1 86.0 1.0 F1 A:EFZ601 2.2 93.5 1.0 C7 A:EFZ601 2.3 93.5 1.0 C8 A:EFZ601 2.4 93.1 1.0 CB A:TYR188 2.8 71.3 1.0 C9 A:EFZ601 3.1 92.1 1.0 O A:TYR188 3.2 84.6 1.0 C A:TYR188 3.2 82.1 1.0 C6 A:EFZ601 3.3 82.7 1.0 O2 A:EFZ601 3.4 0.6 1.0 C5 A:EFZ601 3.5 80.7 1.0 CA A:TYR188 3.5 72.6 1.0 N A:VAL189 3.7 80.1 1.0 CG A:TYR188 3.9 76.7 1.0 CD2 A:TYR188 4.1 75.3 1.0 C A:VAL189 4.3 74.9 1.0 CA A:VAL189 4.4 76.7 1.0 C10 A:EFZ601 4.5 79.0 1.0 N A:GLY190 4.5 78.9 1.0 O A:VAL189 4.6 79.4 1.0 C14 A:EFZ601 4.6 96.9 1.0 C4 A:EFZ601 4.6 93.3 1.0 C11 A:EFZ601 4.7 79.1 1.0 C1 A:EFZ601 4.8 89.2 1.0 CB A:TYR181 4.8 89.3 1.0 N A:TYR188 4.8 77.5 1.0 CA A:GLY190 4.9 86.2 1.0 N A:TYR181 5.0 83.8 1.0

L.Tian, M.S.Kim, H.Li, J.Wang, W.Yang. Structure of Hiv-1 Reverse Transcriptase Cleaving Rna in An Rna/Dna Hybrid. Proc. Natl. Acad. Sci. V. 115 507 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29295939
DOI: 10.1073/PNAS.1719746115