Magnesium in PDB 6otz: Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (+)Ftc-Tp

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (+)Ftc-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 (+)Ftc-Tp, PDB code: 6otz 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)	29.82 / 2.86
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	167.069, 170.368, 103.188, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.1

The structure of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (+)Ftc-Tp also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Magnesium atom in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (+)Ftc-Tp (pdb code 6otz). 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 (+)Ftc-Tp, PDB code: 6otz:
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 (+)Ftc-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 (+)Ftc-Tp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:30.9 occ:1.00 OD1 A:ASP443 2.0 58.5 1.0 OE1 A:GLU478 2.1 56.8 1.0 OD2 A:ASP498 2.3 52.1 1.0 OD1 A:ASP498 2.8 54.5 1.0 CG A:ASP498 2.9 49.0 1.0 CG A:ASP443 2.9 56.2 1.0 CD A:GLU478 3.1 57.1 1.0 OD2 A:ASP443 3.1 60.5 1.0 OE2 A:GLU478 3.4 57.9 1.0 O A:GLY444 3.6 56.8 1.0 N A:GLY444 4.3 43.9 1.0 CB A:ASP443 4.3 49.3 1.0 CB A:ASP498 4.4 42.2 1.0 CG A:GLU478 4.4 53.6 1.0 OP1 T:DC723 4.5 96.3 1.0 C A:GLY444 4.7 50.3 1.0 CA A:ASP443 4.7 42.3 1.0 CB A:ALA538 5.0 39.5 1.0

Magnesium binding site 2 out of 2 in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and (+)Ftc-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 (+)Ftc-Tp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:22.1 occ:1.00 OAD A:N8G604 2.1 36.8 1.0 O A:VAL111 2.1 52.6 1.0 OD2 A:ASP110 2.1 56.6 1.0 OD2 A:ASP185 2.4 38.8 1.0 OAQ A:N8G604 2.6 49.8 1.0 OAC A:N8G604 3.0 57.2 1.0 CG A:ASP110 3.1 50.5 1.0 OAI A:N8G604 3.3 52.1 1.0 C A:VAL111 3.3 46.5 1.0 PAZ A:N8G604 3.4 55.0 1.0 OD1 A:ASP110 3.4 55.0 1.0 PBB A:N8G604 3.5 44.7 1.0 PBA A:N8G604 3.5 42.3 1.0 CG A:ASP185 3.6 36.8 1.0 OAR A:N8G604 3.7 45.5 1.0 N A:VAL111 4.0 45.9 1.0 OD1 A:ASP185 4.1 38.3 1.0 CA A:VAL111 4.2 44.4 1.0 CAL A:N8G604 4.3 38.0 1.0 OAO A:N8G604 4.3 36.5 1.0 N A:GLY112 4.3 44.0 1.0 CB A:ASP110 4.4 47.4 1.0 CA A:GLY112 4.4 42.9 1.0 OAF A:N8G604 4.4 51.6 1.0 NZ A:LYS220 4.4 58.4 1.0 OAG A:N8G604 4.5 55.1 1.0 OAH A:N8G604 4.5 32.8 1.0 C A:ASP110 4.5 47.1 1.0 N A:ASP113 4.6 55.0 1.0 CB A:ALA114 4.7 41.2 1.0 CB A:ASP185 4.7 35.6 1.0 N A:ALA114 4.8 49.3 1.0 C A:GLY112 4.8 48.5 1.0 OAE A:N8G604 4.8 48.4 1.0 CB A:VAL111 4.8 40.4 1.0 CA A:ASP110 4.9 45.5 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