Fluorine in PDB 8x1z: Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y:Dna:E-Cfcp-Tp Ternary Complex

The structure of Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y:Dna:E-Cfcp-Tp Ternary Complex, PDB code: 8x1z 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)	44.47 / 2.62
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	283.141, 283.141, 95.442, 90, 90, 120
R / Rfree (%)	17.9 / 22.3

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

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y:Dna:E-Cfcp-Tp Ternary Complex (pdb code 8x1z). 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:Dna:E-Cfcp-Tp Ternary Complex, PDB code: 8x1z:
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: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:Dna:E-Cfcp-Tp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:95.0 occ:0.82 F46 A:XTE603 0.0 95.0 0.8 C44 A:XTE603 1.3 92.4 0.8 C6' A:XTE603 2.2 91.8 0.8 C2' E:DC33 2.6 52.2 1.0 C4' A:XTE603 2.6 95.9 0.8 C5' A:XTE603 2.7 101.2 0.8 C7' A:XTE603 2.8 102.0 0.8 OD1 A:ASP185 3.2 63.4 1.0 CE A:MET184 3.4 78.3 1.0 N47 A:XTE603 3.4 105.0 0.8 C1' E:DC33 3.4 53.3 1.0 O5' A:XTE603 3.4 108.7 0.8 C1' A:XTE603 3.5 87.4 0.8 O2 E:DC33 3.5 53.6 1.0 CB A:MET184 3.6 55.5 1.0 CG A:ASP185 3.8 63.2 1.0 C3' E:DC33 3.8 54.7 1.0 O3' E:DC33 3.9 66.9 1.0 C8 A:XTE603 3.9 80.2 0.8 C3' A:XTE603 4.0 90.7 0.8 N9 A:XTE603 4.1 82.2 0.8 C2 E:DC33 4.2 55.4 1.0 CG A:MET184 4.2 71.8 1.0 N1 E:DC33 4.2 56.4 1.0 OD2 A:ASP185 4.2 72.0 1.0 N A:ASP185 4.3 48.4 1.0 C2' A:XTE603 4.4 88.6 0.8 O2A A:XTE603 4.5 114.1 0.8 SD A:MET184 4.5 84.0 1.0 PA A:XTE603 4.5 115.6 0.8 O4' E:DC33 4.5 55.8 1.0 C4' E:DC33 4.6 49.3 1.0 CB A:ASP185 4.6 57.5 1.0 CA A:MET184 4.8 50.8 1.0 CE1 A:PHE115 4.9 47.1 1.0 N2 E:DG1 4.9 60.1 1.0 O3' A:XTE603 5.0 87.2 0.8

Fluorine binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y: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:Dna:E-Cfcp-Tp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F602 b:107.6 occ:1.00 F46 C:XTE602 0.0 107.6 1.0 C44 C:XTE602 1.3 106.4 1.0 C6' C:XTE602 2.2 106.1 1.0 C4' C:XTE602 2.7 108.3 1.0 C7' C:XTE602 2.8 111.3 1.0 C2' F:DC33 2.8 69.4 1.0 C5' C:XTE602 2.9 110.9 1.0 CB C:MET184 3.3 77.7 1.0 N47 C:XTE602 3.3 111.8 1.0 CG C:MET184 3.4 89.1 1.0 O2 F:DC33 3.5 72.4 1.0 C1' F:DC33 3.5 61.6 1.0 C1' C:XTE602 3.5 101.0 1.0 SD C:MET184 3.7 93.7 1.0 CE C:MET184 3.9 88.6 1.0 O5' C:XTE602 3.9 116.2 1.0 OD1 C:ASP185 4.0 98.5 1.0 C3' C:XTE602 4.1 103.4 1.0 C3' F:DC33 4.2 70.8 1.0 N9 C:XTE602 4.3 93.3 1.0 C2 F:DC33 4.3 67.6 1.0 N1 F:DC33 4.3 64.1 1.0 N C:ASP185 4.3 75.0 1.0 C8 C:XTE602 4.3 91.1 1.0 O3' F:DC33 4.4 86.1 1.0 CG C:ASP185 4.4 97.8 1.0 C2' C:XTE602 4.4 102.4 1.0 CE2 C:PHE115 4.5 69.4 1.0 CA C:MET184 4.6 67.8 1.0 O4' F:DC33 4.7 63.1 1.0 N2 F:DG1 4.7 72.0 1.0 C4' F:DC33 4.8 65.2 1.0 OD2 C:ASP185 4.9 111.9 1.0 CB C:ASP185 4.9 90.0 1.0 C C:MET184 5.0 74.5 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