Magnesium in PDB 5xn2: Hiv-1 Reverse Transcriptase Q151M:Dna:Dgtp Ternary Complex

The structure of Hiv-1 Reverse Transcriptase Q151M:Dna:Dgtp Ternary Complex, PDB code: 5xn2 was solved by Y.Yasutake, N.Tamura, H.Hayashi, K.Maeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.90 / 2.38
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	285.694, 285.694, 96.325, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 22.3

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase Q151M:Dna:Dgtp Ternary Complex (pdb code 5xn2). 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 Q151M:Dna:Dgtp Ternary Complex, PDB code: 5xn2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Hiv-1 Reverse Transcriptase Q151M: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 Q151M:Dna:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:59.9 occ:1.00 OD1 A:ASP110 2.1 65.0 0.6 O2B A:DGT602 2.1 65.8 1.0 O A:VAL111 2.1 71.5 1.0 O3G A:DGT602 2.1 71.4 1.0 O1A A:DGT602 2.2 72.6 1.0 OD2 A:ASP185 2.2 60.0 1.0 CG A:ASP110 3.2 56.5 0.6 PB A:DGT602 3.2 73.3 1.0 C A:VAL111 3.3 57.1 1.0 PG A:DGT602 3.3 77.5 1.0 CG A:ASP185 3.4 54.9 1.0 PA A:DGT602 3.4 76.9 1.0 OD2 A:ASP110 3.7 57.8 0.6 O3B A:DGT602 3.7 80.7 1.0 O3A A:DGT602 3.7 78.1 1.0 O2G A:DGT602 3.9 76.6 1.0 OD1 A:ASP185 3.9 53.4 1.0 NZ A:LYS220 4.0 97.3 1.0 N A:VAL111 4.0 51.5 1.0 C5' A:DGT602 4.1 72.0 1.0 N A:GLY112 4.2 53.9 1.0 CA A:GLY112 4.2 58.4 1.0 CA A:VAL111 4.2 52.2 1.0 O5' A:DGT602 4.3 75.9 1.0 N A:ASP113 4.4 51.8 1.0 CB A:ASP110 4.4 54.3 0.4 CB A:ASP110 4.4 54.1 0.6 O1B A:DGT602 4.5 69.7 1.0 O1G A:DGT602 4.5 81.8 1.0 O2A A:DGT602 4.5 85.4 1.0 CB A:ASP185 4.6 50.3 1.0 C A:GLY112 4.6 59.2 1.0 C A:ASP110 4.6 54.9 1.0 CD A:LYS220 4.7 86.6 1.0 CB A:ALA114 4.7 36.9 1.0 N A:ALA114 4.7 52.0 1.0 CB A:VAL111 4.9 50.5 1.0 CE A:LYS220 4.9 91.2 1.0

Magnesium binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase Q151M: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 Q151M:Dna:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:60.1 occ:1.00 O C:VAL111 2.0 81.5 1.0 OD2 C:ASP110 2.1 89.5 1.0 O1B C:DGT602 2.3 74.6 1.0 OD2 C:ASP185 2.4 72.6 1.0 O1A C:DGT602 2.4 85.1 1.0 O2G C:DGT602 2.5 82.1 1.0 CG C:ASP110 3.2 82.3 1.0 C C:VAL111 3.2 68.8 1.0 PB C:DGT602 3.4 80.2 1.0 CG C:ASP185 3.5 67.2 1.0 PG C:DGT602 3.6 91.0 1.0 PA C:DGT602 3.7 84.3 1.0 O3A C:DGT602 3.8 89.6 1.0 OD1 C:ASP110 3.8 84.0 1.0 O3B C:DGT602 3.9 86.0 1.0 N C:VAL111 3.9 67.0 1.0 OD1 C:ASP185 4.0 65.8 1.0 N C:GLY112 4.1 69.1 1.0 CA C:VAL111 4.1 66.5 1.0 CA C:GLY112 4.2 68.3 1.0 CB C:ASP110 4.2 73.6 1.0 O3G C:DGT602 4.2 95.8 1.0 C C:ASP110 4.3 66.3 1.0 C5' C:DGT602 4.4 74.9 1.0 N C:ASP113 4.5 75.1 1.0 O5' C:DGT602 4.6 78.5 1.0 CB C:ASP185 4.7 65.8 1.0 C C:GLY112 4.7 70.7 1.0 O2B C:DGT602 4.7 78.2 1.0 O2A C:DGT602 4.7 92.1 1.0 O C:ASP110 4.8 69.4 1.0 CA C:ASP110 4.8 62.5 1.0 CB C:VAL111 4.8 63.6 1.0 O1G C:DGT602 4.8 97.7 1.0 N C:ALA114 4.9 64.8 1.0 CB C:ALA114 5.0 55.3 1.0

Y.Yasutake, S.I.Hattori, H.Hayashi, K.Matsuda, N.Tamura, S.Kohgo, K.Maeda, H.Mitsuya. Hiv-1 with Hbv-Associated Q151M Substitution in Rt Becomes Highly Susceptible to Entecavir: Structural Insights Into Hbv-Rt Inhibition By Entecavir. Sci Rep V. 8 1624 2018.
ISSN: ESSN 2045-2322
PubMed: 29374261
DOI: 10.1038/S41598-018-19602-9