Magnesium in PDB 6kdm: Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Entecavir 5'- Triphosphate Ternary Complex

The structure of Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Entecavir 5'- Triphosphate Ternary Complex, PDB code: 6kdm 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)	48.67 / 2.32
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	284.447, 284.447, 95.773, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 22.3

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Entecavir 5'- Triphosphate Ternary Complex (pdb code 6kdm). 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/Y115F/F116Y:Dna:Entecavir 5'- Triphosphate Ternary Complex, PDB code: 6kdm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Entecavir 5'- 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/Y115F/F116Y:Dna:Entecavir 5'- Triphosphate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:55.4 occ:1.00 O1B A:ET9603 1.9 57.7 1.0 O A:VAL111 1.9 59.5 1.0 O1G A:ET9603 2.1 60.6 1.0 OD1 A:ASP110 2.1 61.8 0.6 OD2 A:ASP185 2.1 60.2 1.0 O1A A:ET9603 2.3 66.9 1.0 PB A:ET9603 3.0 61.1 1.0 PG A:ET9603 3.1 66.0 1.0 C A:VAL111 3.2 47.8 1.0 CG A:ASP110 3.2 45.8 0.6 CG A:ASP185 3.2 50.2 1.0 PA A:ET9603 3.3 65.3 1.0 O3A A:ET9603 3.4 68.4 1.0 O3B A:ET9603 3.5 68.5 1.0 OD1 A:ASP185 3.7 48.4 1.0 OD2 A:ASP110 3.7 41.7 0.6 O3G A:ET9603 3.8 68.2 1.0 N A:VAL111 4.0 43.7 1.0 N A:GLY112 4.0 48.5 1.0 C5' A:ET9603 4.0 61.7 1.0 CA A:GLY112 4.1 46.2 1.0 NZ A:LYS220 4.1 73.5 1.0 O5' A:ET9603 4.1 66.2 1.0 CA A:VAL111 4.1 45.4 1.0 O2B A:ET9603 4.3 57.1 1.0 O2G A:ET9603 4.4 68.5 1.0 N A:ASP113 4.4 45.7 1.0 CB A:ASP110 4.4 43.7 0.4 CB A:ASP110 4.4 43.5 0.6 CB A:ASP185 4.5 45.3 1.0 C A:GLY112 4.5 46.6 1.0 C A:ASP110 4.5 43.0 1.0 CB A:ALA114 4.5 28.8 1.0 O2A A:ET9603 4.6 67.5 1.0 N A:ALA114 4.6 40.4 1.0 CB A:VAL111 4.8 42.2 1.0 CE A:LYS220 4.9 77.9 1.0 CD A:LYS220 5.0 71.5 1.0 CA A:ASP110 5.0 41.9 0.4 CA A:ASP110 5.0 41.6 0.6

Magnesium binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Entecavir 5'- 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/Y115F/F116Y:Dna:Entecavir 5'- Triphosphate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:65.5 occ:1.00 O C:VAL111 1.9 81.8 1.0 OD2 C:ASP110 1.9 91.7 1.0 O2B C:ET9602 2.1 68.5 1.0 OD2 C:ASP185 2.1 75.0 1.0 O2G C:ET9602 2.3 78.7 1.0 O1A C:ET9602 2.4 76.1 1.0 CG C:ASP110 3.1 77.7 1.0 C C:VAL111 3.1 63.8 1.0 CG C:ASP185 3.2 59.4 1.0 PB C:ET9602 3.3 70.5 1.0 PA C:ET9602 3.4 74.2 1.0 PG C:ET9602 3.5 79.3 1.0 O3A C:ET9602 3.7 78.4 1.0 OD1 C:ASP185 3.7 58.4 1.0 OD1 C:ASP110 3.7 76.5 1.0 O3B C:ET9602 3.8 73.7 1.0 N C:VAL111 3.9 54.4 1.0 NZ C:LYS220 4.0 77.3 1.0 N C:GLY112 4.0 63.2 1.0 CA C:VAL111 4.1 56.6 1.0 O1G C:ET9602 4.1 80.8 1.0 CA C:GLY112 4.1 59.7 1.0 C5' C:ET9602 4.2 65.2 1.0 CB C:ASP110 4.2 67.5 1.0 O5' C:ET9602 4.3 71.5 1.0 C C:ASP110 4.3 55.0 1.0 N C:ASP113 4.4 62.3 1.0 CB C:ASP185 4.5 52.0 1.0 C C:GLY112 4.6 57.1 1.0 O1B C:ET9602 4.6 71.3 1.0 O2A C:ET9602 4.7 76.1 1.0 CB C:VAL111 4.7 51.4 1.0 CB C:ALA114 4.7 49.0 1.0 O3G C:ET9602 4.7 83.9 1.0 N C:ALA114 4.7 55.2 1.0 O C:ASP110 4.8 55.1 1.0 CA C:ASP110 4.8 57.3 1.0

Y.Yasutake, S.I.Hattori, N.Tamura, K.Matsuda, S.Kohgo, K.Maeda, H.Mitsuya. Structural Features in Common of Hbv and Hiv-1 Resistance Against Chirally-Distinct Nucleoside Analogues Entecavir and Lamivudine. Sci Rep V. 10 3021 2020.
ISSN: ESSN 2045-2322
PubMed: 32080249
DOI: 10.1038/S41598-020-59775-W