Fluorine in PDB 6bsg: Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off Mode

The structure of Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off Mode, PDB code: 6bsg 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)	40.51 / 2.44
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	162.040, 162.040, 129.180, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 22.4

The structure of Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off 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 An Rna Hydrolysis-Off Mode (pdb code 6bsg). 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 An Rna Hydrolysis-Off Mode, PDB code: 6bsg:
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 An Rna Hydrolysis-Off 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 An Rna Hydrolysis-Off Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:62.0 occ:1.00 F1 A:EFZ601 0.0 62.0 1.0 C13 A:EFZ601 1.3 61.9 1.0 F3 A:EFZ601 2.1 66.5 1.0 F2 A:EFZ601 2.2 59.9 1.0 C7 A:EFZ601 2.3 64.5 1.0 O2 A:EFZ601 2.7 70.3 1.0 C6 A:EFZ601 3.0 58.2 1.0 C14 A:EFZ601 3.1 65.9 1.0 CA A:GLY190 3.3 49.8 1.0 N A:GLY190 3.4 43.7 1.0 N A:EFZ601 3.4 65.0 1.0 C1 A:EFZ601 3.5 50.2 1.0 C8 A:EFZ601 3.6 56.3 1.0 CB A:VAL179 3.8 63.8 1.0 C5 A:EFZ601 3.8 55.7 1.0 O1 A:EFZ601 3.9 66.3 1.0 CG1 A:VAL179 3.9 62.3 1.0 CG A:LYS103 4.1 57.0 1.0 C A:VAL189 4.1 51.2 1.0 O A:VAL179 4.2 54.9 1.0 CE A:LYS103 4.3 63.3 1.0 C A:GLY190 4.3 52.3 1.0 CD A:LYS103 4.6 59.1 1.0 O A:GLY190 4.6 56.3 1.0 CG2 A:VAL179 4.6 62.5 1.0 C2 A:EFZ601 4.7 56.2 1.0 CG1 A:VAL106 4.7 56.8 1.0 C A:VAL179 4.7 57.3 1.0 O A:VAL189 4.8 54.3 1.0 C4 A:EFZ601 4.8 54.3 1.0 C9 A:EFZ601 4.8 59.5 1.0 CA A:VAL189 4.8 46.1 1.0 CD2 A:TYR181 4.8 61.7 0.5 O A:TYR188 4.8 52.8 1.0 CA A:VAL179 4.8 57.1 1.0 CE2 A:TYR181 4.9 61.4 0.5 N A:VAL189 4.9 49.2 1.0 C A:TYR188 5.0 53.4 1.0

Fluorine binding site 2 out of 3 in the Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off 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 An Rna Hydrolysis-Off Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:59.9 occ:1.00 F2 A:EFZ601 0.0 59.9 1.0 C13 A:EFZ601 1.3 61.9 1.0 F3 A:EFZ601 2.2 66.5 1.0 F1 A:EFZ601 2.2 62.0 1.0 C7 A:EFZ601 2.4 64.5 1.0 C8 A:EFZ601 2.7 56.3 1.0 O2 A:EFZ601 3.0 70.3 1.0 O A:TYR188 3.2 52.8 1.0 CD2 A:TYR181 3.4 61.7 0.5 C9 A:EFZ601 3.5 59.5 1.0 C A:TYR188 3.5 53.4 1.0 CB A:TYR188 3.6 49.8 1.0 C6 A:EFZ601 3.8 58.2 1.0 CG A:TYR181 3.8 61.1 0.5 CG1 A:VAL179 3.9 62.3 1.0 CB A:TYR181 4.0 56.8 0.5 O A:VAL179 4.0 54.9 1.0 CB A:TYR181 4.0 56.9 0.5 N A:VAL189 4.0 49.2 1.0 N A:TYR181 4.0 50.6 1.0 CE2 A:TYR181 4.1 61.4 0.5 C14 A:EFZ601 4.1 65.9 1.0 N A:GLY190 4.1 43.7 1.0 CA A:TYR188 4.2 47.9 1.0 CA A:VAL189 4.4 46.1 1.0 CB A:VAL179 4.4 63.8 1.0 C5 A:EFZ601 4.4 55.7 1.0 C A:VAL189 4.4 51.2 1.0 C A:VAL179 4.4 57.3 1.0 CA A:TYR181 4.6 53.9 0.5 CA A:TYR181 4.7 54.0 0.5 CA A:GLY190 4.7 49.8 1.0 C A:ILE180 4.7 57.9 1.0 O1 A:EFZ601 4.7 66.3 1.0 CD1 A:TYR181 4.8 57.4 0.5 CA A:ILE180 4.8 56.3 1.0 N A:EFZ601 4.8 65.0 1.0 C1 A:EFZ601 4.9 50.2 1.0 N A:ILE180 4.9 57.6 1.0 C10 A:EFZ601 4.9 57.3 1.0 CZ A:TYR181 4.9 67.1 0.5 CG A:TYR188 5.0 53.2 1.0

Fluorine binding site 3 out of 3 in the Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in An Rna Hydrolysis-Off 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 An Rna Hydrolysis-Off Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:66.5 occ:1.00 F3 A:EFZ601 0.0 66.5 1.0 C13 A:EFZ601 1.3 61.9 1.0 F1 A:EFZ601 2.1 62.0 1.0 F2 A:EFZ601 2.2 59.9 1.0 C7 A:EFZ601 2.3 64.5 1.0 C6 A:EFZ601 2.8 58.2 1.0 C5 A:EFZ601 2.9 55.7 1.0 C8 A:EFZ601 2.9 56.3 1.0 O2 A:EFZ601 3.6 70.3 1.0 CB A:TYR188 3.7 49.8 1.0 N A:GLY190 3.7 43.7 1.0 N A:VAL189 3.7 49.2 1.0 C A:VAL189 3.8 51.2 1.0 C A:TYR188 3.8 53.4 1.0 C9 A:EFZ601 3.8 59.5 1.0 C4 A:EFZ601 3.9 54.3 1.0 CA A:GLY190 3.9 49.8 1.0 O A:VAL189 4.0 54.3 1.0 CG1 A:VAL106 4.1 56.8 1.0 C1 A:EFZ601 4.1 50.2 1.0 O A:TYR188 4.1 52.8 1.0 CA A:VAL189 4.2 46.1 1.0 CA A:TYR188 4.3 47.9 1.0 C14 A:EFZ601 4.5 65.9 1.0 CB A:VAL106 4.5 61.4 1.0 N A:EFZ601 4.6 65.0 1.0 C3 A:EFZ601 4.7 53.4 1.0 CG A:TYR188 4.7 53.2 1.0 CD2 A:TYR188 4.8 55.6 1.0 C2 A:EFZ601 4.8 56.2 1.0 CL A:EFZ601 4.9 63.4 1.0 O A:THR107 4.9 54.4 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