Magnesium in PDB 7dbm: Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/M184V:Dna:Dgtp Ternary Complex

All present enzymatic activity of Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/M184V:Dna:Dgtp Ternary Complex:
2.7.7.49; 3.1.26.13;

The structure of Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/M184V:Dna:Dgtp Ternary Complex, PDB code: 7dbm 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)	48.47 / 2.43
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	283.514, 283.514, 95.132, 90, 90, 120
R / Rfree (%)	18.1 / 22.4

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/M184V:Dna:Dgtp Ternary Complex (pdb code 7dbm). 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 Mutant Q151M/Y115F/F116Y/M184V:Dna:Dgtp Ternary Complex, PDB code: 7dbm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/M184V: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 Mutant Q151M/Y115F/F116Y/M184V:Dna:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:47.7 occ:1.00 O2B A:DGT601 2.0 49.0 1.0 O1A A:DGT601 2.1 46.3 1.0 O A:VAL111 2.1 62.8 1.0 O1G A:DGT601 2.1 58.6 1.0 OD2 A:ASP185 2.2 56.0 1.0 OD1 A:ASP110 2.2 61.8 1.0 PB A:DGT601 3.1 75.1 1.0 CG A:ASP110 3.2 58.7 1.0 CG A:ASP185 3.2 49.1 1.0 PA A:DGT601 3.3 48.5 1.0 C A:VAL111 3.3 50.4 1.0 PG A:DGT601 3.4 61.6 1.0 O3A A:DGT601 3.5 58.5 1.0 O3B A:DGT601 3.7 69.1 1.0 OD1 A:ASP185 3.7 50.5 1.0 OD2 A:ASP110 3.7 52.9 1.0 C5' A:DGT601 3.9 42.7 1.0 NZ A:LYS220 4.0 94.7 1.0 N A:VAL111 4.0 41.5 1.0 O3G A:DGT601 4.1 55.5 1.0 O5' A:DGT601 4.1 46.2 1.0 CA A:VAL111 4.2 46.1 1.0 N A:GLY112 4.3 49.4 1.0 CA A:GLY112 4.4 50.4 1.0 O1B A:DGT601 4.4 58.1 1.0 O2A A:DGT601 4.4 56.4 1.0 CB A:ASP110 4.5 51.9 1.0 CB A:ALA114 4.5 48.9 1.0 O2G A:DGT601 4.5 67.1 1.0 CB A:ASP185 4.5 39.4 1.0 C A:ASP110 4.6 47.1 1.0 N A:ASP113 4.6 56.9 1.0 CE A:LYS220 4.6 83.0 1.0 CD A:LYS220 4.7 77.6 1.0 N A:ALA114 4.7 53.2 1.0 C A:GLY112 4.8 56.4 1.0 CB A:VAL111 4.8 48.4 1.0

Magnesium binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase Mutant Q151M/Y115F/F116Y/M184V: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 Mutant Q151M/Y115F/F116Y/M184V:Dna:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:48.6 occ:1.00 OD2 C:ASP110 2.1 74.7 1.0 O C:VAL111 2.1 75.4 1.0 O1G C:DGT601 2.1 61.7 1.0 OD2 C:ASP185 2.2 74.0 1.0 O2B C:DGT601 2.2 47.8 1.0 O2A C:DGT601 2.3 53.2 1.0 CG C:ASP110 3.1 69.1 1.0 CG C:ASP185 3.2 65.1 1.0 C C:VAL111 3.3 66.2 1.0 PB C:DGT601 3.3 55.8 1.0 PG C:DGT601 3.4 61.6 1.0 OD1 C:ASP110 3.5 69.7 1.0 PA C:DGT601 3.5 55.7 1.0 OD1 C:ASP185 3.6 61.5 1.0 O3B C:DGT601 3.8 56.7 1.0 NZ C:LYS220 3.8 94.1 1.0 O3A C:DGT601 3.8 63.2 1.0 N C:VAL111 3.9 56.0 1.0 C5' C:DGT601 4.0 57.2 1.0 O3G C:DGT601 4.1 68.2 1.0 CA C:VAL111 4.2 61.2 1.0 N C:GLY112 4.2 64.9 1.0 CE C:LYS220 4.3 92.2 1.0 O5' C:DGT601 4.3 55.7 1.0 CA C:GLY112 4.3 59.8 1.0 CB C:ASP110 4.4 62.0 1.0 N C:ASP113 4.4 61.8 1.0 C C:ASP110 4.4 61.1 1.0 CB C:ASP185 4.5 59.2 1.0 O2G C:DGT601 4.5 69.8 1.0 O1B C:DGT601 4.6 58.6 1.0 CB C:ALA114 4.6 56.9 1.0 C C:GLY112 4.6 57.3 1.0 N C:ALA114 4.6 56.4 1.0 CD C:LYS220 4.7 89.2 1.0 O1A C:DGT601 4.7 65.8 1.0 CB C:VAL111 4.8 56.5 1.0 O C:HOH782 4.8 73.3 1.0 CA C:ASP110 4.9 61.2 1.0

S.Nakajima, K.Watashi, T.Kato, M.Muramatsu, T.Wakita, N.Tamura, S.I.Hattori, K.Maeda, H.Mitsuya, Y.Yasutake, T.Toyoda. Biochemical and Structural Properties of Entecavir-Resistant Hepatitis B Virus Polymerase with L180M/M204V Mutations. J.Virol. V. 95 40120 2021.
ISSN: ESSN 1098-5514
PubMed: 34076480
DOI: 10.1128/JVI.02401-20