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

The structure of Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Lamivudine 5'- Triphosphate Ternary Complex, PDB code: 6kdj 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)	48.79 / 2.51
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	285.114, 285.114, 96.004, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 23

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Lamivudine 5'- Triphosphate Ternary Complex (pdb code 6kdj). 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:Lamivudine 5'- Triphosphate Ternary Complex, PDB code: 6kdj:
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:Lamivudine 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:Lamivudine 5'- Triphosphate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:0.6 occ:1.00 O1G A:1RZ601 2.0 0.6 1.0 O1A A:1RZ601 2.0 90.1 1.0 O A:VAL111 2.3 57.7 1.0 O2B A:1RZ601 2.3 0.6 1.0 OD2 A:ASP185 2.8 62.2 1.0 PG A:1RZ601 3.2 0.0 1.0 PA A:1RZ601 3.4 91.5 1.0 PB A:1RZ601 3.4 0.5 1.0 C A:VAL111 3.4 50.2 1.0 O3G A:1RZ601 3.6 92.7 1.0 O3B A:1RZ601 3.7 0.2 1.0 CG A:ASP185 3.7 61.2 1.0 O A:HOH702 3.7 83.2 1.0 O3A A:1RZ601 3.8 0.1 1.0 CA A:GLY112 3.9 53.5 1.0 C5' A:1RZ601 3.9 91.7 1.0 N A:GLY112 4.0 50.8 1.0 O5' A:1RZ601 4.2 94.9 1.0 CB A:ASP185 4.2 54.5 1.0 N A:ASP113 4.3 52.5 1.0 C A:GLY112 4.4 56.6 1.0 O2C A:1RZ601 4.4 0.1 1.0 O2A A:1RZ601 4.4 93.0 1.0 N A:VAL111 4.4 52.9 1.0 CB A:ASP110 4.4 66.9 1.0 OD2 A:ASP110 4.5 88.4 1.0 CA A:VAL111 4.5 53.2 1.0 OD1 A:ASP185 4.6 55.9 1.0 CB A:ALA114 4.6 51.1 1.0 O1B A:1RZ601 4.7 0.5 1.0 N A:ALA114 4.7 50.0 1.0 CG A:ASP110 4.7 76.4 1.0 C A:ASP110 4.9 59.6 1.0

Magnesium binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Lamivudine 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:Lamivudine 5'- Triphosphate Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:74.8 occ:1.00 O C:VAL111 1.9 0.3 1.0 O2A C:1RZ601 2.1 98.2 1.0 OD2 C:ASP185 2.3 57.2 1.0 OD2 C:ASP110 2.3 79.7 0.5 O3G C:1RZ601 2.6 0.6 1.0 O1B C:1RZ601 2.7 0.9 1.0 C C:VAL111 3.2 78.6 1.0 CG C:ASP185 3.4 56.7 1.0 CG C:ASP110 3.4 78.5 0.5 PA C:1RZ601 3.5 0.5 1.0 PG C:1RZ601 3.7 0.1 1.0 OD1 C:ASP110 3.8 76.8 0.5 CB C:ASP185 3.8 63.2 1.0 C5' C:1RZ601 3.8 96.8 1.0 PB C:1RZ601 3.9 0.1 1.0 O1G C:1RZ601 3.9 0.3 1.0 CA C:GLY112 4.0 66.5 1.0 N C:GLY112 4.0 77.7 1.0 N C:VAL111 4.1 68.7 1.0 O5' C:1RZ601 4.2 0.7 1.0 CA C:VAL111 4.2 67.7 1.0 O3A C:1RZ601 4.2 0.2 1.0 CB C:ALA114 4.2 56.0 1.0 O3B C:1RZ601 4.3 0.5 1.0 OD2 C:ASP110 4.3 77.2 0.5 C C:GLY112 4.3 67.4 1.0 N C:ASP113 4.3 72.2 1.0 N C:ALA114 4.4 63.0 1.0 OD1 C:ASP185 4.5 55.5 1.0 O1A C:1RZ601 4.5 0.9 1.0 CB C:ASP110 4.7 76.5 0.5 CB C:ASP110 4.7 76.4 0.5 C C:ASP110 4.7 71.6 0.5 CB C:VAL111 4.7 62.5 1.0 CG C:ASP110 4.8 76.5 0.5 C C:ASP110 4.8 71.6 0.5 O C:ASP185 4.9 67.8 1.0 CA C:ALA114 4.9 60.1 1.0 O2C C:1RZ601 5.0 0.1 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