Fluorine in PDB 6wph: Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc:
2.7.7.49; 2.7.7.7; 3.1.26.13;

The structure of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc, PDB code: 6wph was solved by N.Bertoletti, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.52 / 2.72
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	165.980, 168.054, 101.916, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 25.7

The structure of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc (pdb code 6wph). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc, PDB code: 6wph:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc


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 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc within 5.0Å range: probe atom residue distance (Å) B Occ P:F901 b:85.0 occ:0.60 F5 P:43X901 0.0 85.0 0.6 C2' P:43X901 0.9 84.6 0.4 C1' P:43X901 1.2 86.3 0.4 C5 P:43X901 1.3 84.1 0.6 S3' P:43X901 1.4 84.5 0.4 O4' P:43X901 1.7 84.8 0.4 C4' P:43X901 1.8 84.4 0.4 N1 P:43X901 2.3 80.1 0.4 C6 P:43X901 2.3 85.0 0.6 C4 P:43X901 2.4 84.1 0.6 N4 P:43X901 2.8 83.1 0.6 C6 P:43X901 3.1 86.1 0.4 C5' P:43X901 3.1 83.3 0.4 C2 P:43X901 3.3 86.2 0.4 O2 P:43X901 3.5 82.4 0.4 O5' P:43X901 3.6 83.8 0.4 N1 P:43X901 3.6 86.0 0.6 N3 P:43X901 3.6 84.2 0.6 C2' P:DG822 4.1 55.7 1.0 C2 P:43X901 4.1 81.4 0.6 N3 P:DG822 4.1 47.0 1.0 OE1 A:GLN151 4.3 78.3 1.0 C5 P:43X901 4.3 79.4 0.4 O3A P:43X901 4.3 83.0 0.6 C2 P:DG822 4.4 47.1 1.0 C4 P:DG822 4.5 46.3 1.0 N3 P:43X901 4.5 81.9 0.4 N2 P:DG822 4.6 44.8 1.0 CZ A:TYR115 4.6 63.2 1.0 OH A:TYR115 4.7 70.8 1.0 O4' P:43X901 4.8 85.2 0.6 NE A:ARG72 4.8 68.1 1.0 C1' P:43X901 4.8 84.1 0.6 NH2 A:ARG72 4.8 61.7 1.0 CE1 A:TYR115 4.9 57.9 1.0 CE2 A:TYR115 4.9 64.0 1.0 N9 P:DG822 4.9 50.4 1.0 C4 P:43X901 5.0 83.1 0.4 C1' P:DG822 5.0 53.7 1.0

Fluorine binding site 2 out of 2 in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc


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 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)-Ftc within 5.0Å range: probe atom residue distance (Å) B Occ P:F901 b:84.8 occ:0.40 F5 P:43X901 0.0 84.8 0.4 C1' P:43X901 0.6 84.1 0.6 C2' P:43X901 0.9 85.4 0.6 C5 P:43X901 1.3 79.4 0.4 O4' P:43X901 1.8 85.2 0.6 N1 P:43X901 1.9 86.0 0.6 S3' P:43X901 2.3 86.0 0.6 C6 P:43X901 2.3 86.1 0.4 C4 P:43X901 2.4 83.1 0.4 C4' P:43X901 2.4 84.5 0.6 O2 P:43X901 2.6 82.9 0.6 C2 P:43X901 2.6 81.4 0.6 N4 P:43X901 2.7 79.9 0.4 C6 P:43X901 3.0 85.0 0.6 N1 P:43X901 3.6 80.1 0.4 N3 P:43X901 3.6 81.9 0.4 NH2 A:ARG72 3.7 61.7 1.0 C5' P:43X901 3.8 82.4 0.6 N7 P:DG822 3.8 46.3 1.0 CZ A:ARG72 3.9 73.3 1.0 NH1 A:ARG72 3.9 76.1 1.0 N3 P:43X901 4.0 84.2 0.6 O P:HOH1003 4.0 51.4 1.0 O5' P:43X901 4.0 82.5 0.6 C2 P:43X901 4.1 86.2 0.4 C8 P:DG822 4.1 48.6 1.0 C5 P:43X901 4.2 84.1 0.6 C5 P:DG822 4.3 43.6 1.0 O2A P:43X901 4.4 81.7 0.4 C4 P:43X901 4.6 84.1 0.6 NE A:ARG72 4.7 68.1 1.0 O5' P:43X901 4.7 83.8 0.4 O4' P:43X901 4.7 84.8 0.4 N9 P:DG822 4.8 50.4 1.0 C1' P:43X901 4.8 86.3 0.4 C6 P:DG822 4.8 45.5 1.0 C4 P:DG822 4.9 46.3 1.0 O6 P:DG822 5.0 52.0 1.0

N.Bertoletti, A.H.Chan, R.F.Schinazi, K.S.Anderson. Post-Catalytic Complexes with Emtricitabine or Stavudine and Hiv-1 Reverse Transcriptase Reveal New Mechanistic Insights For Nucleotide Incorporation and Drug Resistance. Molecules V. 25 2020.
ISSN: ESSN 1420-3049
PubMed: 33096918
DOI: 10.3390/MOLECULES25204868