Magnesium in PDB 6oun: Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)3TC-Tp

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)3TC-Tp:
2.7.7.49; 2.7.7.7; 3.1.26.13;

The structure of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)3TC-Tp, PDB code: 6oun was solved by N.Bertoletti, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.57 / 2.66
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	167.011, 171.784, 105.885, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.9

The binding sites of Magnesium atom in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)3TC-Tp (pdb code 6oun). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)3TC-Tp, PDB code: 6oun:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)3TC-Tp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)3TC-Tp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:58.0 occ:1.00 OD1 A:ASP443 2.1 0.0 1.0 OE2 A:GLU478 2.2 92.3 1.0 OD2 A:ASP498 2.3 93.1 1.0 OD1 A:ASP498 2.3 86.8 1.0 CG A:ASP498 2.6 88.2 1.0 CG A:ASP443 3.0 92.2 1.0 CD A:GLU478 3.2 87.0 1.0 OD2 A:ASP443 3.2 96.8 1.0 OE1 A:GLU478 3.5 90.6 1.0 O A:GLY444 3.8 80.0 1.0 CB A:ASP498 4.0 82.5 1.0 CB A:ASP443 4.4 83.5 1.0 N A:GLY444 4.4 80.5 1.0 CG A:GLU478 4.5 77.7 1.0 CB A:ALA538 4.7 73.2 1.0 CA A:ASP443 4.8 75.2 1.0 C A:ASP498 4.8 73.7 1.0 C A:GLY444 4.9 79.8 1.0 CA A:ASP498 4.9 73.2 1.0 O A:ASP498 4.9 78.3 1.0

Magnesium binding site 2 out of 2 in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)3TC-Tp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (-)3TC-Tp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:78.3 occ:1.00 O A:VAL111 2.3 82.8 1.0 O3A A:1RZ604 2.6 0.5 1.0 OD2 A:ASP110 2.6 0.8 1.0 OD2 A:ASP185 2.6 92.5 1.0 O1B A:1RZ604 2.7 0.8 1.0 O3G A:1RZ604 2.9 0.8 1.0 PB A:1RZ604 3.2 0.0 1.0 C A:VAL111 3.5 74.5 1.0 CG A:ASP185 3.7 93.2 1.0 PA A:1RZ604 3.7 0.3 1.0 CG A:ASP110 3.7 99.0 1.0 O2A A:1RZ604 3.8 0.4 1.0 PG A:1RZ604 3.8 0.6 1.0 O3B A:1RZ604 3.9 0.8 1.0 C5' A:1RZ604 4.1 1.0 1.0 O2C A:1RZ604 4.2 0.8 1.0 N A:VAL111 4.2 73.1 1.0 OD1 A:ASP110 4.3 0.4 1.0 O5' A:1RZ604 4.3 0.2 1.0 CB A:ASP185 4.3 83.5 1.0 CA A:GLY112 4.3 64.7 1.0 N A:GLY112 4.3 68.7 1.0 CA A:VAL111 4.4 70.5 1.0 N A:ASP113 4.4 68.5 1.0 O2B A:1RZ604 4.5 0.1 1.0 OD1 A:ASP185 4.6 99.3 1.0 C A:ASP110 4.6 76.2 1.0 C A:GLY112 4.6 66.1 1.0 N A:ALA114 4.7 76.1 1.0 CB A:ALA114 4.7 83.0 1.0 CB A:ASP110 4.7 86.6 1.0 CB A:VAL111 5.0 64.0 1.0 O1A A:1RZ604 5.0 0.1 1.0

N.Bertoletti, A.H.Chan, R.F.Schinazi, Y.W.Yin, K.S.Anderson. Structural Insights Into the Recognition of Nucleoside Reverse Transcriptase Inhibitors By Hiv-1 Reverse Transcriptase: First Crystal Structures with Reverse Transcriptase and the Active Triphosphate Forms of Lamivudine and Emtricitabine. Protein Sci. V. 28 1664 2019.
ISSN: ESSN 1469-896X
PubMed: 31301259
DOI: 10.1002/PRO.3681