Magnesium 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:

Fluorine

(F)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y:Dna:E-Cfcp-Tp Ternary Complex, PDB code: 8x1z:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg602 b:83.5 occ:0.50 O A:VAL111 1.7 91.7 1.0 O1B A:XTE603 1.9 104.8 0.8 OD2 A:ASP185 2.3 72.0 1.0 O2G A:XTE603 2.5 125.4 0.8 C A:VAL111 2.9 67.1 1.0 PB A:XTE603 3.0 120.7 0.8 O2A A:XTE603 3.2 114.1 0.8 O3B A:XTE603 3.3 123.6 0.8 CG A:ASP185 3.4 63.2 1.0 PG A:XTE603 3.6 122.7 0.8 O3A A:XTE603 3.7 128.0 0.8 CA A:GLY112 3.7 58.5 1.0 N A:GLY112 3.7 59.4 1.0 CB A:ASP185 3.8 57.5 1.0 N A:ASP113 3.8 58.4 1.0 C5' A:XTE603 3.9 101.2 0.8 C A:GLY112 3.9 58.4 1.0 N A:ALA114 3.9 64.3 1.0 CB A:ALA114 4.0 57.1 1.0 PA A:XTE603 4.0 115.6 0.8 CA A:VAL111 4.0 66.7 1.0 OD1 A:ASP110 4.1 91.6 1.0 N A:VAL111 4.1 66.6 1.0 O2B A:XTE603 4.3 119.2 0.8 O1G A:XTE603 4.3 120.4 0.8 OD1 A:ASP185 4.4 63.4 1.0 O5' A:XTE603 4.5 108.7 0.8 CB A:VAL111 4.5 63.8 1.0 CA A:ALA114 4.5 57.1 1.0 O A:GLY112 4.7 59.5 1.0 CA A:ASP113 4.8 67.3 1.0 O3G A:XTE603 4.8 123.8 0.8 CG1 A:VAL111 4.8 66.9 1.0 NZ A:LYS220 4.8 105.3 1.0 C A:ASP113 4.9 66.3 1.0 C7' A:XTE603 4.9 102.0 0.8 C4' A:XTE603 4.9 95.9 0.8 C A:ASP110 4.9 66.6 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg601 b:90.2 occ:1.00 O2B C:XTE602 1.9 113.2 1.0 O C:VAL111 2.0 110.7 1.0 OD2 C:ASP185 2.1 111.9 1.0 O1G C:XTE602 2.1 112.4 1.0 OD2 C:ASP110 2.3 84.4 0.5 O2A C:XTE602 2.4 131.6 1.0 OD1 C:ASP110 2.8 82.1 0.5 CG C:ASP110 2.9 81.8 0.5 PB C:XTE602 3.2 125.8 1.0 C C:VAL111 3.2 88.7 1.0 CG C:ASP185 3.3 97.8 1.0 PG C:XTE602 3.4 128.3 1.0 PA C:XTE602 3.6 123.0 1.0 O3B C:XTE602 3.8 127.4 1.0 O3A C:XTE602 3.8 127.9 1.0 OD1 C:ASP185 4.0 98.5 1.0 N C:VAL111 4.1 81.7 1.0 N C:GLY112 4.1 82.0 1.0 CA C:GLY112 4.1 74.3 1.0 O2G C:XTE602 4.2 132.1 1.0 CA C:VAL111 4.2 81.0 1.0 C5' C:XTE602 4.2 110.9 1.0 CB C:ASP185 4.3 90.0 1.0 O1B C:XTE602 4.3 126.4 1.0 CB C:ASP110 4.4 79.3 0.5 CB C:ASP110 4.4 79.2 0.5 O5' C:XTE602 4.5 116.2 1.0 N C:ASP113 4.5 76.0 1.0 O3G C:XTE602 4.5 129.1 1.0 C C:GLY112 4.5 75.1 1.0 C C:ASP110 4.6 80.3 1.0 O1A C:XTE602 4.6 123.3 1.0 CB C:ALA114 4.7 74.9 1.0 N C:ALA114 4.7 72.8 1.0 CB C:VAL111 4.8 72.8 1.0 OD1 C:ASP110 5.0 80.2 0.5

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