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

The structure of Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Dctp Ternary Complex, PDB code: 6kdk 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)	48.74 / 2.56
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	284.852, 284.852, 95.926, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 23.4

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Dctp Ternary Complex (pdb code 6kdk). 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:Dctp Ternary Complex, PDB code: 6kdk:
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:Dctp 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:Dctp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:63.7 occ:1.00 O A:VAL111 2.0 79.2 1.0 O1B A:DCP601 2.0 63.6 1.0 O1G A:DCP601 2.1 68.5 1.0 OD1 A:ASP110 2.2 78.7 1.0 O2A A:DCP601 2.3 60.4 1.0 OD2 A:ASP185 2.4 74.6 1.0 PB A:DCP601 3.0 66.9 1.0 C A:VAL111 3.1 59.0 1.0 PG A:DCP601 3.1 63.3 1.0 CG A:ASP110 3.4 78.0 1.0 O3B A:DCP601 3.4 72.4 1.0 PA A:DCP601 3.5 67.6 1.0 O3A A:DCP601 3.5 74.9 1.0 CG A:ASP185 3.6 67.5 1.0 O3G A:DCP601 3.7 69.0 1.0 CA A:GLY112 3.8 61.6 1.0 N A:GLY112 3.9 61.5 1.0 OD2 A:ASP110 3.9 77.4 1.0 N A:ASP113 4.1 64.3 1.0 N A:VAL111 4.2 54.9 1.0 C5' A:DCP601 4.2 57.1 1.0 CA A:VAL111 4.2 53.1 1.0 C A:GLY112 4.3 65.0 1.0 OD1 A:ASP185 4.3 69.3 1.0 NZ A:LYS220 4.3 82.1 1.0 O2B A:DCP601 4.3 60.8 1.0 O2G A:DCP601 4.4 72.2 1.0 O5' A:DCP601 4.4 66.7 1.0 O1A A:DCP601 4.6 83.8 1.0 CB A:ASP185 4.6 60.5 1.0 CB A:ASP110 4.6 68.1 1.0 N A:ALA114 4.6 59.0 1.0 C A:ASP110 4.6 59.4 1.0 CB A:ALA114 4.8 43.1 1.0 CE A:LYS220 4.9 83.2 1.0 CB A:VAL111 5.0 53.5 1.0

Magnesium binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Dctp 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:Dctp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:58.1 occ:1.00 O C:VAL111 1.9 90.4 1.0 OD2 C:ASP110 2.1 94.0 1.0 OD2 C:ASP185 2.2 88.4 1.0 O2B C:DCP601 2.2 66.8 1.0 O2G C:DCP601 2.2 70.6 1.0 O2A C:DCP601 2.3 66.4 1.0 C C:VAL111 3.1 75.2 1.0 CG C:ASP110 3.2 86.3 1.0 PB C:DCP601 3.3 70.0 1.0 CG C:ASP185 3.4 77.2 1.0 PG C:DCP601 3.5 79.1 1.0 PA C:DCP601 3.5 68.0 1.0 OD1 C:ASP110 3.7 88.1 1.0 O3A C:DCP601 3.8 81.1 1.0 O3B C:DCP601 3.8 69.7 1.0 N C:VAL111 3.8 64.4 1.0 OD1 C:ASP185 4.0 77.1 1.0 CA C:VAL111 4.0 63.8 1.0 O1G C:DCP601 4.1 83.8 1.0 N C:GLY112 4.1 72.5 1.0 C5' C:DCP601 4.1 62.8 1.0 CA C:GLY112 4.2 67.6 1.0 NZ C:LYS220 4.3 84.4 1.0 O5' C:DCP601 4.4 63.1 1.0 C C:ASP110 4.4 65.4 1.0 CB C:ASP110 4.4 76.6 1.0 N C:ASP113 4.5 75.2 1.0 CB C:ASP185 4.5 70.8 1.0 C C:GLY112 4.6 70.8 1.0 CB C:VAL111 4.6 57.9 1.0 O3G C:DCP601 4.6 85.1 1.0 O1A C:DCP601 4.6 79.5 1.0 O1B C:DCP601 4.6 73.9 1.0 N C:ALA114 4.6 70.9 1.0 CB C:ALA114 4.7 61.5 1.0 CD C:LYS220 4.7 88.0 1.0 CE C:LYS220 4.9 85.7 1.0 CA C:ASP110 4.9 69.3 1.0 O C:ASP110 4.9 63.8 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