Fluorine in PDB 8x20: Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/L74V:Dna:E-Cfcp- Tp Ternary Complex

The structure of Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/L74V:Dna:E-Cfcp- Tp Ternary Complex, PDB code: 8x20 was solved by Y.Yasutake, S.I.Hattori, H.Mitsuya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.60 / 2.70
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	284.069, 284.069, 95.605, 90, 90, 120
R / Rfree (%)	17.4 / 23.1

The structure of Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/L74V:Dna:E-Cfcp- Tp Ternary Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/L74V:Dna:E-Cfcp- Tp Ternary Complex (pdb code 8x20). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/L74V:Dna:E-Cfcp- Tp Ternary Complex, PDB code: 8x20:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/L74V:Dna:E-Cfcp- Tp Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/L74V:Dna:E-Cfcp- Tp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:110.6 occ:1.00 F46 A:XTE601 0.0 110.6 1.0 C44 A:XTE601 1.3 109.7 1.0 C6' A:XTE601 2.3 110.2 1.0 C4' A:XTE601 2.9 112.0 1.0 C7' A:XTE601 3.0 120.2 1.0 C2' E:DC33 3.0 54.2 1.0 C5' A:XTE601 3.1 112.7 1.0 CB A:MET184 3.1 49.8 1.0 CE A:MET184 3.1 77.5 1.0 O2 E:DC33 3.4 54.4 1.0 C1' E:DC33 3.4 60.1 1.0 N47 A:XTE601 3.5 118.9 1.0 CG A:MET184 3.5 65.8 1.0 C1' A:XTE601 3.7 110.3 1.0 OD1 A:ASP185 3.9 57.5 1.0 O5' A:XTE601 4.1 112.7 1.0 SD A:MET184 4.1 80.3 1.0 C2 E:DC33 4.2 56.2 1.0 N1 E:DC33 4.3 59.8 1.0 C3' E:DC33 4.3 56.2 1.0 C3' A:XTE601 4.3 112.5 1.0 CA A:MET184 4.4 42.9 1.0 N A:ASP185 4.4 41.0 1.0 N9 A:XTE601 4.4 109.0 1.0 C8 A:XTE601 4.5 109.2 1.0 O4' E:DC33 4.5 64.8 1.0 CG A:ASP185 4.6 59.8 1.0 N2 E:DG1 4.6 66.2 1.0 O3' E:DC33 4.6 67.0 1.0 C2' A:XTE601 4.7 111.0 1.0 CE1 A:PHE115 4.7 52.4 1.0 C4' E:DC33 4.8 54.2 1.0 C A:MET184 4.8 44.5 1.0 CZ A:PHE115 4.8 47.3 1.0

Fluorine binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/L74V:Dna:E-Cfcp- Tp Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/L74V:Dna:E-Cfcp- Tp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F601 b:94.7 occ:1.00 F46 C:XTE601 0.0 94.7 1.0 C44 C:XTE601 1.3 91.4 1.0 C6' C:XTE601 2.3 92.4 1.0 C4' C:XTE601 2.9 96.8 1.0 CB C:MET184 3.0 72.7 1.0 C2' F:DC33 3.0 68.3 1.0 C5' C:XTE601 3.0 97.4 1.0 C7' C:XTE601 3.1 100.0 1.0 CG C:MET184 3.2 80.0 1.0 C1' F:DC33 3.4 65.3 1.0 O2 F:DC33 3.4 77.2 1.0 N47 C:XTE601 3.6 100.5 1.0 SD C:MET184 3.6 85.1 1.0 C1' C:XTE601 3.7 91.5 1.0 OD1 C:ASP185 3.8 103.5 1.0 O5' C:XTE601 3.8 97.0 1.0 C2 F:DC33 4.3 69.2 1.0 C3' F:DC33 4.3 71.9 1.0 N C:ASP185 4.3 70.1 1.0 N1 F:DC33 4.3 62.6 1.0 C3' C:XTE601 4.3 97.4 1.0 CA C:MET184 4.4 60.5 1.0 N9 C:XTE601 4.4 95.3 1.0 C8 C:XTE601 4.4 92.0 1.0 O4' F:DC33 4.5 68.8 1.0 O3' F:DC33 4.5 82.7 1.0 CG C:ASP185 4.5 95.0 1.0 CE C:MET184 4.5 80.0 1.0 C2' C:XTE601 4.7 93.8 1.0 C4' F:DC33 4.7 71.9 1.0 N2 F:DG1 4.8 69.5 1.0 C C:MET184 4.8 64.1 1.0 CE2 C:PHE115 5.0 67.8 1.0

Y.Yasutake, S.I.Hattori, H.Kumamoto, N.Tamura, K.Maeda, H.Mitsuya. Deviated Binding of Anti-Hbv Nucleoside Analog E-Cfcp-Tp to the Reverse Transcriptase Active Site Attenuates the Effect of Drug-Resistant Mutations. Sci Rep V. 14 15742 2024.
ISSN: ESSN 2045-2322
PubMed: 38977798
DOI: 10.1038/S41598-024-66505-Z