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

The structure of Hiv-1 Reverse Transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:Dna:Entecavir-Triphosphate Ternary Complex, PDB code: 6ika 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)	48.87 / 2.60
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	285.405, 285.405, 96.346, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 23.2

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:Dna:Entecavir-Triphosphate Ternary Complex (pdb code 6ika). 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:Entecavir-Triphosphate Ternary Complex, PDB code: 6ika:
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:Entecavir-Triphosphate 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:Entecavir-Triphosphate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:0.4 occ:1.00 O1B A:ET9601 1.9 0.4 1.0 O1G A:ET9601 1.9 0.9 1.0 O A:VAL111 2.0 0.6 1.0 OD2 A:ASP185 2.2 0.2 1.0 O1A A:ET9601 2.2 0.4 1.0 PB A:ET9601 3.0 0.4 1.0 C A:VAL111 3.1 74.2 1.0 PG A:ET9601 3.2 0.7 1.0 PA A:ET9601 3.3 0.1 1.0 CG A:ASP185 3.3 89.2 1.0 O3A A:ET9601 3.5 0.5 1.0 O3B A:ET9601 3.6 0.8 1.0 OD1 A:ASP110 3.6 82.9 1.0 CA A:SER112 3.6 64.2 1.0 N A:SER112 3.7 67.5 1.0 N A:ALA113 4.0 54.4 1.0 C5' A:ET9601 4.0 0.9 1.0 O2G A:ET9601 4.0 0.2 1.0 C A:SER112 4.1 58.7 1.0 N A:VAL111 4.1 55.5 1.0 CB A:ASP185 4.2 68.5 1.0 CA A:VAL111 4.2 59.9 1.0 OD1 A:ASP185 4.2 97.8 1.0 O3G A:ET9601 4.2 0.0 1.0 O5' A:ET9601 4.2 0.7 1.0 O2B A:ET9601 4.3 0.1 1.0 O2A A:ET9601 4.4 0.6 1.0 CG A:ASP110 4.5 81.1 1.0 CB A:ASP110 4.6 69.1 1.0 C A:ASP110 4.6 56.1 1.0 N A:ALA114 4.7 53.3 1.0 CB A:ALA114 4.9 48.0 1.0 CB A:VAL111 4.9 50.0 1.0 CB A:SER112 4.9 65.8 1.0

Magnesium binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase with Q151M/G112S/D113A/Y115F/F116Y/F160L/I159L:Dna:Entecavir-Triphosphate 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:Entecavir-Triphosphate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:96.7 occ:1.00 O2B C:ET9601 1.8 0.6 1.0 O C:VAL111 2.2 0.7 1.0 O2G C:ET9601 2.4 0.6 1.0 OD2 C:ASP110 2.4 85.9 1.0 OD2 C:ASP185 2.4 73.6 1.0 O2A C:ET9601 2.4 0.6 1.0 PB C:ET9601 3.1 0.5 1.0 C C:VAL111 3.2 85.1 1.0 CG C:ASP185 3.3 68.8 1.0 O3A C:ET9601 3.5 0.8 1.0 PA C:ET9601 3.5 0.9 1.0 PG C:ET9601 3.6 1.0 1.0 CG C:ASP110 3.6 83.2 1.0 O3B C:ET9601 3.7 0.0 1.0 N C:VAL111 3.9 64.9 1.0 OD1 C:ASP185 3.9 64.7 1.0 N C:SER112 4.0 78.4 1.0 CA C:SER112 4.1 74.2 1.0 CA C:VAL111 4.1 68.7 1.0 O1B C:ET9601 4.2 0.6 1.0 OD1 C:ASP110 4.4 84.4 1.0 CB C:ASP185 4.4 67.0 1.0 C5' C:ET9601 4.4 0.9 1.0 O3G C:ET9601 4.4 0.2 1.0 C C:ASP110 4.4 64.6 1.0 O1A C:ET9601 4.5 0.8 1.0 O5' C:ET9601 4.5 1.0 1.0 CB C:ASP110 4.5 74.6 1.0 N C:ALA113 4.5 77.9 1.0 C C:SER112 4.6 75.0 1.0 O1G C:ET9601 4.6 0.6 1.0 CB C:VAL111 4.9 61.2 1.0 CA C:ASP110 4.9 66.2 1.0 O C:ASP185 5.0 65.5 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