Magnesium in PDB 6kdn: Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Dgtp Ternary Complex

The structure of Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Dgtp Ternary Complex, PDB code: 6kdn 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)	48.60 / 2.30
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	284.167, 284.167, 95.521, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 22.1

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Dgtp Ternary Complex (pdb code 6kdn). 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:Dgtp Ternary Complex, PDB code: 6kdn:
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: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/Y115F/F116Y:Dna:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:49.3 occ:1.00 OD2 A:ASP185 2.1 62.2 1.0 O1B A:DGT602 2.1 49.7 1.0 OD1 A:ASP110 2.1 73.7 1.0 O A:VAL111 2.1 54.1 1.0 O2G A:DGT602 2.1 51.8 1.0 O1A A:DGT602 2.2 54.0 1.0 CG A:ASP110 3.1 64.5 1.0 CG A:ASP185 3.2 49.2 1.0 PB A:DGT602 3.3 53.9 1.0 C A:VAL111 3.3 48.6 1.0 PG A:DGT602 3.4 55.9 1.0 PA A:DGT602 3.4 54.5 1.0 OD2 A:ASP110 3.5 63.3 1.0 OD1 A:ASP185 3.6 49.4 1.0 O3A A:DGT602 3.8 57.7 1.0 O3B A:DGT602 3.8 58.1 1.0 C5' A:DGT602 4.0 52.9 1.0 N A:VAL111 4.1 43.5 1.0 O1G A:DGT602 4.1 56.6 1.0 NZ A:LYS220 4.1 77.4 1.0 N A:GLY112 4.2 50.0 1.0 CA A:GLY112 4.2 44.7 1.0 O5' A:DGT602 4.2 55.9 1.0 CA A:VAL111 4.3 43.5 1.0 CB A:ASP110 4.4 53.2 1.0 N A:ASP113 4.4 46.9 1.0 CB A:ASP185 4.5 39.6 1.0 C A:ASP110 4.5 42.7 1.0 O2B A:DGT602 4.5 54.9 1.0 O3G A:DGT602 4.5 64.8 1.0 CE A:LYS220 4.5 81.0 1.0 O2A A:DGT602 4.6 63.2 1.0 C A:GLY112 4.6 47.7 1.0 CB A:ALA114 4.6 30.3 1.0 N A:ALA114 4.7 44.1 1.0 CB A:VAL111 4.9 42.8 1.0 O A:ASP110 4.9 51.8 1.0 CA A:ASP110 4.9 40.0 1.0

Magnesium binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y: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/Y115F/F116Y:Dna:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:56.4 occ:1.00 O1B C:DGT602 2.1 63.6 1.0 O C:VAL111 2.1 69.7 1.0 OD2 C:ASP185 2.1 70.2 1.0 OD2 C:ASP110 2.1 87.8 1.0 O1A C:DGT602 2.3 67.0 1.0 O1G C:DGT602 2.4 70.5 1.0 CG C:ASP185 3.3 56.2 1.0 PB C:DGT602 3.3 70.3 1.0 CG C:ASP110 3.3 81.5 1.0 C C:VAL111 3.3 60.3 1.0 PA C:DGT602 3.5 67.5 1.0 PG C:DGT602 3.5 73.6 1.0 OD1 C:ASP185 3.8 54.2 1.0 O3B C:DGT602 3.8 73.3 1.0 O3A C:DGT602 3.8 75.8 1.0 OD1 C:ASP110 4.0 82.2 1.0 C5' C:DGT602 4.1 56.9 1.0 O3G C:DGT602 4.1 75.6 1.0 CA C:GLY112 4.1 60.2 1.0 N C:GLY112 4.2 64.0 1.0 N C:VAL111 4.2 54.3 1.0 N C:ASP113 4.3 64.7 1.0 CA C:VAL111 4.3 57.1 1.0 O5' C:DGT602 4.4 62.9 1.0 CB C:ASP110 4.4 70.9 1.0 NZ C:LYS220 4.5 77.8 1.0 CB C:ASP185 4.5 46.1 1.0 C C:ASP110 4.5 56.0 1.0 CD C:LYS220 4.5 77.1 1.0 C C:GLY112 4.5 59.4 1.0 O2B C:DGT602 4.5 64.4 1.0 N C:ALA114 4.6 49.6 1.0 CB C:ALA114 4.6 44.5 1.0 O2A C:DGT602 4.7 75.3 1.0 O2G C:DGT602 4.8 81.6 1.0 O C:HOH791 4.8 66.7 1.0 O C:ASP110 4.9 57.6 1.0 CA C:ASP110 4.9 58.1 1.0 CB C:VAL111 5.0 52.4 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