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

Protein crystallography data

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

Other elements in 8x1z:

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

Fluorine Binding Sites:

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 8x1z

Go back to Fluorine Binding Sites List in 8x1z
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 8x1z

Go back to Fluorine Binding Sites List in 8x1z
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

Reference:

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
Page generated: Wed Jul 16 10:08:20 2025

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