Fluorine in PDB 6bsh: Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in the Rna Hydrolysis Mode

All present enzymatic activity of Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in the Rna Hydrolysis Mode:
2.7.7.7;

The structure of Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in the Rna Hydrolysis Mode, PDB code: 6bsh 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)	37.20 / 2.65
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.792, 161.792, 128.773, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 22.7

The structure of Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in the Rna Hydrolysis Mode 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 Rna/Dna Hybrid in the Rna Hydrolysis Mode (pdb code 6bsh). 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 Rna/Dna Hybrid in the Rna Hydrolysis Mode, PDB code: 6bsh:
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 Rna/Dna Hybrid in the Rna Hydrolysis Mode


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 Rna/Dna Hybrid in the Rna Hydrolysis Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:60.7 occ:1.00 F1 A:EFZ601 0.0 60.7 1.0 C13 A:EFZ601 1.3 59.7 1.0 F2 A:EFZ601 2.2 58.8 1.0 F3 A:EFZ601 2.2 62.1 1.0 C7 A:EFZ601 2.3 65.8 1.0 O2 A:EFZ601 2.7 68.9 1.0 C6 A:EFZ601 2.9 50.5 1.0 CG2 A:VAL179 3.0 65.6 1.0 C14 A:EFZ601 3.1 65.7 1.0 CA A:GLY190 3.3 50.0 1.0 N A:EFZ601 3.4 61.5 1.0 C1 A:EFZ601 3.5 44.4 1.0 N A:GLY190 3.5 49.4 1.0 C8 A:EFZ601 3.6 54.9 1.0 C5 A:EFZ601 3.8 47.4 1.0 O1 A:EFZ601 3.9 64.1 1.0 CG A:LYS103 4.1 53.5 1.0 O A:VAL179 4.2 55.2 1.0 C A:VAL189 4.2 55.0 1.0 C A:GLY190 4.3 50.4 1.0 CB A:VAL179 4.4 61.0 1.0 CE A:LYS103 4.5 61.9 1.0 O A:TYR188 4.6 55.8 1.0 C2 A:EFZ601 4.6 55.4 1.0 CG1 A:VAL179 4.7 60.4 1.0 CG1 A:VAL106 4.7 48.3 1.0 C4 A:EFZ601 4.7 50.5 1.0 O A:GLY190 4.7 56.1 1.0 C9 A:EFZ601 4.7 53.2 1.0 CD A:LYS103 4.8 52.6 1.0 O A:VAL189 4.8 56.6 1.0 C A:VAL179 4.8 58.2 1.0 CD1 A:TYR181 4.8 60.0 0.5 C A:TYR188 4.9 53.1 1.0 CA A:VAL189 4.9 48.4 1.0 CE1 A:TYR181 5.0 61.2 0.5

Fluorine binding site 2 out of 3 in the Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in the Rna Hydrolysis Mode


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 Rna/Dna Hybrid in the Rna Hydrolysis Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:58.8 occ:1.00 F2 A:EFZ601 0.0 58.8 1.0 C13 A:EFZ601 1.3 59.7 1.0 F1 A:EFZ601 2.2 60.7 1.0 F3 A:EFZ601 2.2 62.1 1.0 C7 A:EFZ601 2.4 65.8 1.0 C8 A:EFZ601 2.8 54.9 1.0 O2 A:EFZ601 3.0 68.9 1.0 O A:TYR188 3.0 55.8 1.0 CG2 A:VAL179 3.2 65.6 1.0 CD1 A:TYR181 3.4 60.0 0.5 C A:TYR188 3.6 53.1 1.0 C9 A:EFZ601 3.6 53.2 1.0 CB A:TYR188 3.8 46.5 1.0 C6 A:EFZ601 3.8 50.5 1.0 O A:VAL179 3.9 55.2 1.0 CG A:TYR181 3.9 59.0 0.5 N A:TYR181 4.0 49.5 1.0 CB A:TYR181 4.0 56.6 0.5 C14 A:EFZ601 4.0 65.7 1.0 CB A:TYR181 4.0 56.7 0.5 CE1 A:TYR181 4.0 61.2 0.5 N A:GLY190 4.1 49.4 1.0 N A:VAL189 4.2 47.0 1.0 CA A:TYR188 4.3 50.9 1.0 C A:VAL179 4.3 58.2 1.0 C5 A:EFZ601 4.5 47.4 1.0 C A:VAL189 4.5 55.0 1.0 CA A:VAL189 4.5 48.4 1.0 CA A:TYR181 4.6 54.2 0.5 C A:ILE180 4.6 54.1 1.0 O1 A:EFZ601 4.6 64.1 1.0 CB A:VAL179 4.6 61.0 1.0 CA A:TYR181 4.6 54.0 0.5 CA A:GLY190 4.7 50.0 1.0 CA A:ILE180 4.7 59.6 1.0 N A:ILE180 4.8 59.5 1.0 N A:EFZ601 4.8 61.5 1.0 C1 A:EFZ601 4.8 44.4 1.0 CD2 A:TYR181 4.9 55.8 0.5 CZ A:TYR181 5.0 65.9 0.5

Fluorine binding site 3 out of 3 in the Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in the Rna Hydrolysis Mode


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 Rna/Dna Hybrid in the Rna Hydrolysis Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:62.1 occ:1.00 F3 A:EFZ601 0.0 62.1 1.0 C13 A:EFZ601 1.3 59.7 1.0 F1 A:EFZ601 2.2 60.7 1.0 F2 A:EFZ601 2.2 58.8 1.0 C7 A:EFZ601 2.3 65.8 1.0 C8 A:EFZ601 2.8 54.9 1.0 C6 A:EFZ601 2.8 50.5 1.0 C5 A:EFZ601 2.9 47.4 1.0 O2 A:EFZ601 3.5 68.9 1.0 CB A:TYR188 3.6 46.5 1.0 C A:TYR188 3.6 53.1 1.0 C9 A:EFZ601 3.7 53.2 1.0 O A:TYR188 3.8 55.8 1.0 N A:VAL189 3.8 47.0 1.0 N A:GLY190 3.9 49.4 1.0 C A:VAL189 3.9 55.0 1.0 C4 A:EFZ601 4.0 50.5 1.0 CA A:TYR188 4.1 50.9 1.0 CA A:GLY190 4.1 50.0 1.0 C1 A:EFZ601 4.1 44.4 1.0 O A:VAL189 4.2 56.6 1.0 CG1 A:VAL106 4.3 48.3 1.0 CA A:VAL189 4.3 48.4 1.0 C14 A:EFZ601 4.5 65.7 1.0 CG A:TYR188 4.5 52.6 1.0 CD2 A:TYR188 4.6 53.0 1.0 CB A:VAL106 4.7 57.1 1.0 N A:EFZ601 4.7 61.5 1.0 CG2 A:VAL179 4.7 65.6 1.0 C3 A:EFZ601 4.8 49.5 1.0 O A:THR107 4.9 53.3 1.0 CL A:EFZ601 4.9 64.2 1.0 C2 A:EFZ601 4.9 55.4 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