Magnesium in PDB 6p1i: Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and Dctp

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and Dctp:
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 Dctp, PDB code: 6p1i 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)	28.93 / 2.74
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	166.417, 169.504, 103.063, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 23.7

The binding sites of Magnesium atom in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and Dctp (pdb code 6p1i). 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 Dctp, PDB code: 6p1i:
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 Dctp


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 Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:26.9 occ:1.00 OD1 A:ASP110 1.9 53.3 1.0 O2A A:DCP602 2.1 33.7 1.0 O A:VAL111 2.2 48.5 1.0 O3G A:DCP602 2.2 39.4 1.0 O2B A:DCP602 2.3 42.7 1.0 OD2 A:ASP185 2.3 38.8 1.0 CG A:ASP110 3.0 50.0 1.0 C A:VAL111 3.4 41.9 1.0 PB A:DCP602 3.4 36.4 1.0 PG A:DCP602 3.4 44.0 1.0 CG A:ASP185 3.5 39.9 1.0 PA A:DCP602 3.5 36.7 1.0 OD2 A:ASP110 3.6 60.6 1.0 O3B A:DCP602 3.6 36.0 1.0 O3A A:DCP602 3.8 39.6 1.0 OD1 A:ASP185 4.0 41.9 1.0 NZ A:LYS220 4.0 67.7 1.0 N A:VAL111 4.0 38.8 1.0 O2G A:DCP602 4.1 47.1 1.0 N A:GLY112 4.3 41.3 1.0 CB A:ASP110 4.3 39.8 1.0 CA A:VAL111 4.3 36.1 1.0 CA A:GLY112 4.3 31.4 1.0 C5' A:DCP602 4.3 36.8 1.0 O5' A:DCP602 4.4 36.0 1.0 N A:ASP113 4.5 38.0 1.0 C A:ASP110 4.5 41.0 1.0 O1A A:DCP602 4.6 38.7 1.0 CB A:ALA114 4.6 38.5 1.0 CB A:ASP185 4.6 38.0 1.0 O1G A:DCP602 4.6 42.4 1.0 C A:GLY112 4.7 35.9 1.0 O1B A:DCP602 4.8 34.5 1.0 N A:ALA114 4.8 40.0 1.0 CA A:ASP110 4.8 36.7 1.0 CE A:LYS220 4.9 62.2 1.0 CB A:VAL111 4.9 35.2 1.0

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


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 Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:47.1 occ:1.00 OD1 A:ASP498 2.1 68.8 1.0 OD1 A:ASP443 2.4 55.4 1.0 OE1 A:GLU478 2.6 57.7 1.0 CG A:ASP498 3.0 60.5 1.0 CG A:ASP443 3.2 54.0 1.0 OD2 A:ASP443 3.2 53.9 1.0 OD2 A:ASP498 3.2 69.5 1.0 CD A:GLU478 3.5 52.7 1.0 O A:GLY444 3.6 46.3 1.0 OE2 A:GLU478 3.6 55.1 1.0 OP1 T:DC723 3.9 79.5 1.0 CB A:ASP498 4.4 44.2 1.0 N A:GLY444 4.6 38.1 1.0 CB A:ASP443 4.7 48.3 1.0 C A:GLY444 4.7 42.4 1.0 CB A:ALA538 4.8 48.3 1.0 CG A:GLU478 4.8 44.8 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