Magnesium in PDB 6ik9: Hiv-1 Reverse Transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:Dna:Dgtp Ternary Complex

The structure of Hiv-1 Reverse Transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:Dna:Dgtp Ternary Complex, PDB code: 6ik9 was solved by Y.Yasutake, S.I.Hattori, N.Tamura, K.Maeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.74 / 2.44
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	284.869, 284.869, 95.892, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 22.5

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:Dna:Dgtp Ternary Complex (pdb code 6ik9). 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 with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:Dna:Dgtp Ternary Complex, PDB code: 6ik9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Hiv-1 Reverse Transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:Dna:Dgtp 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 with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:Dna:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:60.0 occ:0.63 OD2 A:ASP185 2.4 79.0 1.0 O A:VAL111 2.5 55.3 1.0 O1B A:DGT601 2.6 0.1 1.0 N A:ALA113 2.9 52.6 1.0 N A:ALA114 3.0 50.8 1.0 O1G A:DGT601 3.3 0.4 1.0 CG A:ASP185 3.3 72.9 1.0 C A:SER112 3.4 55.6 1.0 C A:VAL111 3.5 56.3 1.0 O3A A:DGT601 3.6 0.7 1.0 CA A:ALA113 3.6 61.8 1.0 PB A:DGT601 3.6 0.2 1.0 CA A:SER112 3.7 64.1 1.0 CB A:ALA114 3.8 55.8 1.0 C A:ALA113 3.8 57.7 1.0 CB A:ASP185 3.9 58.1 1.0 C5' A:DGT601 3.9 93.5 1.0 O3' A:DGT601 3.9 70.8 1.0 N A:SER112 4.0 63.4 1.0 CA A:ALA114 4.0 51.5 1.0 O A:SER112 4.2 56.6 1.0 OD1 A:ASP185 4.3 76.5 1.0 C4' A:DGT601 4.3 85.7 1.0 O3B A:DGT601 4.3 0.8 1.0 O5' A:DGT601 4.3 0.3 1.0 PA A:DGT601 4.4 0.4 1.0 PG A:DGT601 4.4 0.2 1.0 C3' A:DGT601 4.5 79.9 1.0 O2A A:DGT601 4.5 0.3 1.0 NZ A:LYS220 4.6 82.9 1.0 CA A:VAL111 4.7 55.2 1.0 O2B A:DGT601 4.9 1.0 1.0 CB A:VAL111 5.0 52.2 1.0

Magnesium binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:Dna:Dgtp 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 with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:Dna:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:97.6 occ:0.98 O C:VAL111 2.5 53.0 1.0 O2B F:DGT701 2.8 0.1 1.0 OD2 C:ASP185 2.9 74.9 1.0 N C:ALA114 3.2 67.3 1.0 CG C:ASP185 3.3 69.7 1.0 N C:ALA113 3.3 67.8 1.0 CB C:ASP185 3.6 62.7 1.0 C C:VAL111 3.6 54.3 1.0 O3A F:DGT701 3.6 0.5 1.0 CB C:ALA114 3.6 73.9 1.0 NZ C:LYS220 3.7 95.0 1.0 PB F:DGT701 3.7 0.9 1.0 C C:SER112 3.7 63.4 1.0 O1G F:DGT701 3.8 0.1 1.0 O3' F:DGT701 3.9 79.2 1.0 CA C:SER112 3.9 60.7 1.0 C5' F:DGT701 4.0 84.8 1.0 CA C:ALA113 4.0 67.8 1.0 CA C:ALA114 4.0 72.3 1.0 OD1 C:ASP185 4.1 68.9 1.0 C C:ALA113 4.1 69.3 1.0 O5' F:DGT701 4.1 94.3 1.0 N C:SER112 4.2 57.1 1.0 PA F:DGT701 4.3 0.4 1.0 C4' F:DGT701 4.3 83.0 1.0 O3B F:DGT701 4.5 0.8 1.0 O1A F:DGT701 4.5 95.6 1.0 C3' F:DGT701 4.5 80.3 1.0 O C:SER112 4.6 61.0 1.0 PG F:DGT701 4.7 0.9 1.0 CA C:VAL111 4.8 58.3 1.0 O1B F:DGT701 4.9 0.5 1.0 CB C:VAL111 5.0 58.1 1.0

Y.Yasutake, S.I.Hattori, N.Tamura, K.Matsuda, S.Kohgo, K.Maeda, H.Mitsuya. Active-Site Deformation in the Structure of Hiv-1 Rt with Hbv-Associated Septuple Amino Acid Substitutions Rationalizes the Differential Susceptibility of Hiv-1 and Hbv Against 4'-Modified Nucleoside Rt Inhibitors. Biochem. Biophys. Res. V. 509 943 2019COMMUN..
ISSN: ESSN 1090-2104
PubMed: 30648556
DOI: 10.1016/J.BBRC.2019.01.026