Fluorine in PDB 6bsj: Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Sequence Non- Preferred For Rna Hydrolysis

The structure of Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Sequence Non- Preferred For Rna Hydrolysis, PDB code: 6bsj 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)	41.20 / 2.89
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.240, 163.240, 129.400, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 25.1

The structure of Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Sequence Non- Preferred For Rna Hydrolysis also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Sequence Non- Preferred For Rna Hydrolysis (pdb code 6bsj). 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 Sequence Non- Preferred For Rna Hydrolysis, PDB code: 6bsj:
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 Sequence Non- Preferred For Rna Hydrolysis


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 Sequence Non- Preferred For Rna Hydrolysis within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:82.7 occ:1.00 F1 A:EFZ601 0.0 82.7 1.0 C13 A:EFZ601 1.3 77.4 1.0 F2 A:EFZ601 2.2 77.2 1.0 F3 A:EFZ601 2.2 77.8 1.0 C7 A:EFZ601 2.3 77.4 1.0 O2 A:EFZ601 2.7 89.8 1.0 C6 A:EFZ601 3.0 65.3 1.0 CA A:GLY190 3.3 70.2 1.0 N A:GLY190 3.3 65.1 1.0 C14 A:EFZ601 3.3 83.9 1.0 C8 A:EFZ601 3.6 78.3 1.0 N A:EFZ601 3.7 79.1 1.0 C1 A:EFZ601 3.7 68.9 1.0 C A:VAL189 3.8 69.4 1.0 O A:VAL179 3.8 76.5 1.0 C5 A:EFZ601 3.8 71.1 1.0 CG1 A:VAL179 4.0 71.2 1.0 CG1 A:VAL106 4.1 75.1 1.0 O1 A:EFZ601 4.1 84.0 1.0 O A:VAL189 4.3 72.8 1.0 CG A:LYS103 4.3 74.6 1.0 CB A:VAL179 4.3 73.8 1.0 C A:GLY190 4.4 72.3 1.0 O A:TYR188 4.5 71.5 1.0 CA A:VAL189 4.5 66.5 1.0 N A:VAL189 4.7 69.1 1.0 C A:TYR188 4.7 70.2 1.0 C9 A:EFZ601 4.7 74.3 1.0 C A:VAL179 4.8 73.5 1.0 C4 A:EFZ601 4.8 75.3 1.0 NZ A:LYS103 4.8 82.5 1.0 C2 A:EFZ601 4.8 75.5 1.0 O A:GLY190 4.8 72.9 1.0

Fluorine binding site 2 out of 3 in the Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Sequence Non- Preferred For Rna Hydrolysis


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 Sequence Non- Preferred For Rna Hydrolysis within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:77.2 occ:1.00 F2 A:EFZ601 0.0 77.2 1.0 C13 A:EFZ601 1.4 77.4 1.0 F1 A:EFZ601 2.2 82.7 1.0 F3 A:EFZ601 2.2 77.8 1.0 C7 A:EFZ601 2.4 77.4 1.0 C8 A:EFZ601 2.7 78.3 1.0 O2 A:EFZ601 2.9 89.8 1.0 O A:TYR188 3.1 71.5 1.0 C9 A:EFZ601 3.5 74.3 1.0 O A:VAL179 3.5 76.5 1.0 C A:TYR188 3.7 70.2 1.0 CG1 A:VAL179 3.7 71.2 1.0 CB A:TYR181 3.7 66.5 1.0 C6 A:EFZ601 3.8 65.3 1.0 CB A:TYR188 3.9 66.7 1.0 N A:TYR181 4.0 68.7 1.0 C14 A:EFZ601 4.0 83.9 1.0 N A:VAL189 4.2 69.1 1.0 N A:GLY190 4.3 65.1 1.0 C A:VAL179 4.4 73.5 1.0 CA A:TYR188 4.4 67.8 1.0 CA A:TYR181 4.5 61.5 1.0 CA A:VAL189 4.5 66.5 1.0 C A:VAL189 4.5 69.4 1.0 C5 A:EFZ601 4.5 71.1 1.0 CB A:VAL179 4.6 73.8 1.0 O1 A:EFZ601 4.6 84.0 1.0 C A:ILE180 4.7 70.0 1.0 N A:EFZ601 4.8 79.1 1.0 CA A:GLY190 4.9 70.2 1.0 C10 A:EFZ601 4.9 74.2 1.0 C1 A:EFZ601 4.9 68.9 1.0 CA A:ILE180 4.9 72.7 1.0 CG A:TYR181 5.0 82.7 1.0

Fluorine binding site 3 out of 3 in the Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Sequence Non- Preferred For Rna Hydrolysis


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 Sequence Non- Preferred For Rna Hydrolysis within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:77.8 occ:1.00 F3 A:EFZ601 0.0 77.8 1.0 C13 A:EFZ601 1.3 77.4 1.0 F2 A:EFZ601 2.2 77.2 1.0 F1 A:EFZ601 2.2 82.7 1.0 C7 A:EFZ601 2.3 77.4 1.0 C8 A:EFZ601 2.7 78.3 1.0 C6 A:EFZ601 2.9 65.3 1.0 C5 A:EFZ601 3.0 71.1 1.0 CB A:TYR188 3.4 66.7 1.0 O2 A:EFZ601 3.5 89.8 1.0 C9 A:EFZ601 3.5 74.3 1.0 C A:TYR188 3.6 70.2 1.0 N A:VAL189 3.7 69.1 1.0 O A:TYR188 3.7 71.5 1.0 C A:VAL189 3.9 69.4 1.0 CA A:TYR188 4.0 67.8 1.0 O A:VAL189 4.1 72.8 1.0 C4 A:EFZ601 4.1 75.3 1.0 N A:GLY190 4.1 65.1 1.0 CG1 A:VAL106 4.1 75.1 1.0 CA A:VAL189 4.3 66.5 1.0 C1 A:EFZ601 4.3 68.9 1.0 CG A:TYR188 4.4 68.5 1.0 CD2 A:TYR188 4.5 68.9 1.0 CA A:GLY190 4.5 70.2 1.0 C14 A:EFZ601 4.6 83.9 1.0 CB A:VAL106 4.6 76.9 1.0 O A:VAL179 4.8 76.5 1.0 N A:EFZ601 4.9 79.1 1.0 C10 A:EFZ601 5.0 74.2 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