Magnesium in PDB 1t05: Hiv-1 Reverse Transcriptase Crosslinked to Template-Primer with Tenofovir-Diphosphate Bound As the Incoming Nucleotide Substrate

All present enzymatic activity of Hiv-1 Reverse Transcriptase Crosslinked to Template-Primer with Tenofovir-Diphosphate Bound As the Incoming Nucleotide Substrate:
2.7.7.49;

The structure of Hiv-1 Reverse Transcriptase Crosslinked to Template-Primer with Tenofovir-Diphosphate Bound As the Incoming Nucleotide Substrate, PDB code: 1t05 was solved by S.Tuske, S.G.Sarafianos, J.Ding, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	171.570, 171.570, 156.270, 90.00, 90.00, 120.00
R / Rfree (%)	25.3 / 29.2

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase Crosslinked to Template-Primer with Tenofovir-Diphosphate Bound As the Incoming Nucleotide Substrate (pdb code 1t05). 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 Crosslinked to Template-Primer with Tenofovir-Diphosphate Bound As the Incoming Nucleotide Substrate, PDB code: 1t05:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Hiv-1 Reverse Transcriptase Crosslinked to Template-Primer with Tenofovir-Diphosphate Bound As the Incoming Nucleotide Substrate


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 Crosslinked to Template-Primer with Tenofovir-Diphosphate Bound As the Incoming Nucleotide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg600 b:16.2 occ:1.00 OD1 A:ASP110 2.2 0.3 1.0 O2B A:TNV823 2.3 37.7 1.0 O A:VAL111 2.3 43.6 1.0 O1A A:TNV823 2.4 34.6 1.0 O1G A:TNV823 2.5 61.8 1.0 OD2 A:ASP185 2.5 49.6 1.0 CG A:ASP110 2.9 89.5 1.0 C A:VAL111 3.1 49.2 1.0 N A:VAL111 3.2 47.7 1.0 OD2 A:ASP110 3.4 96.1 1.0 PB A:TNV823 3.5 48.4 1.0 PG A:TNV823 3.6 58.0 1.0 CG A:ASP185 3.6 31.9 1.0 PA A:TNV823 3.7 56.3 1.0 CA A:VAL111 3.7 48.4 1.0 CB A:ASP110 3.7 64.0 1.0 NZ A:LYS219 3.8 69.5 1.0 O3B A:TNV823 3.9 53.6 1.0 O3A A:TNV823 4.0 41.2 1.0 O3G A:TNV823 4.0 44.7 1.0 N A:GLY112 4.1 47.8 1.0 C A:ASP110 4.1 48.4 1.0 C9' A:TNV823 4.2 43.1 1.0 OD1 A:ASP185 4.3 28.1 1.0 CA A:ASP110 4.4 45.5 1.0 CA A:GLY112 4.4 51.9 1.0 CB A:ASP185 4.6 17.2 1.0 CB A:VAL111 4.6 39.6 1.0 O9' A:TNV823 4.6 49.4 1.0 N A:ASP113 4.7 57.9 1.0 O1B A:TNV823 4.8 51.8 1.0 O2G A:TNV823 4.8 55.4 1.0 C A:GLY112 4.9 55.1 1.0 CB A:ALA114 4.9 20.9 1.0 O2A A:TNV823 4.9 62.9 1.0 N A:ALA114 5.0 44.3 1.0

Magnesium binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase Crosslinked to Template-Primer with Tenofovir-Diphosphate Bound As the Incoming Nucleotide Substrate


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 Crosslinked to Template-Primer with Tenofovir-Diphosphate Bound As the Incoming Nucleotide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:73.6 occ:1.00 OD2 A:ASP443 2.5 0.7 1.0 OD2 A:ASP498 2.6 91.1 1.0 OD1 A:ASP443 2.7 95.5 1.0 CG A:ASP443 2.9 0.2 1.0 CG A:ASP498 3.4 0.9 1.0 OD1 A:ASP498 3.4 95.6 1.0 OE1 A:GLU478 3.9 0.0 1.0 O A:GLY444 4.3 92.2 1.0 CB A:ASP443 4.4 97.9 1.0 OP1 T:DC723 4.6 0.8 1.0 N A:GLY444 4.7 96.6 1.0 CB A:ASP498 4.9 0.8 1.0 CB A:ALA538 4.9 0.4 1.0 CA A:ASP443 5.0 94.3 1.0

S.Tuske, S.G.Sarafianos, A.D.Clark Jr., J.Ding, L.K.Naeger, K.L.White, M.D.Miller, C.S.Gibbs, P.L.Boyer, P.Clark, G.Wang, B.L.Gaffney, R.A.Jones, D.M.Jerina, S.H.Hughes, E.Arnold. Structures of Hiv-1 Rt-Dna Complexes Before and After Incorporation of the Anti-Aids Drug Tenofovir Nat.Struct.Mol.Biol. V. 11 469 2004.
ISSN: ISSN 1545-9993
PubMed: 15107837
DOI: 10.1038/NSMB760