Magnesium in PDB 6p1x: Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and L-Ddctp

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and L-Ddctp:
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 L-Ddctp, PDB code: 6p1x 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)	29.75 / 2.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	169.213, 171.502, 107.306, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23

The binding sites of Magnesium atom in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and L-Ddctp (pdb code 6p1x). 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 L-Ddctp, PDB code: 6p1x:
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 L-Ddctp


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 L-Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:50.5 occ:1.00 OD1 A:ASP443 2.2 68.3 1.0 OE1 A:GLU478 2.7 60.7 1.0 OD2 A:ASP498 2.7 51.6 1.0 OD1 A:ASP498 2.8 53.4 1.0 CG A:ASP443 2.9 63.0 1.0 OD2 A:ASP443 2.9 68.2 1.0 CG A:ASP498 3.1 50.0 1.0 O A:GLY444 3.7 47.4 1.0 CD A:GLU478 3.8 57.4 1.0 OE2 A:GLU478 4.1 61.4 1.0 OP1 T:DC723 4.3 74.2 1.0 CB A:ASP443 4.4 51.1 1.0 OD1 A:ASP549 4.5 71.9 1.0 N A:GLY444 4.6 48.7 1.0 CB A:ASP498 4.6 45.5 1.0 CB A:ALA538 4.8 31.4 1.0 C A:GLY444 4.8 44.2 1.0 CE1 A:HIS539 4.9 61.2 1.0 CA A:ASP443 5.0 43.5 1.0

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


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 L-Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:30.2 occ:1.00 O A:VAL111 2.3 52.9 1.0 O4 A:NQ4603 2.4 71.0 1.0 OD1 A:ASP110 2.4 47.8 1.0 OD2 A:ASP185 2.4 52.5 1.0 O7 A:NQ4603 2.5 90.9 1.0 O1 A:NQ4603 2.5 59.6 1.0 P2 A:NQ4603 3.3 90.0 1.0 P1 A:NQ4603 3.3 71.6 1.0 O6 A:NQ4603 3.4 86.5 1.0 C A:VAL111 3.4 47.0 1.0 CG A:ASP110 3.5 50.4 1.0 CG A:ASP185 3.6 50.0 1.0 O9 A:NQ4603 3.6 89.6 1.0 P A:NQ4603 3.7 61.9 1.0 O3 A:NQ4603 3.9 66.0 1.0 OD2 A:ASP110 4.0 53.0 1.0 N A:VAL111 4.2 40.4 1.0 C7 A:NQ4603 4.2 59.0 1.0 CA A:GLY112 4.3 45.0 1.0 N A:GLY112 4.3 45.3 1.0 CA A:VAL111 4.4 40.5 1.0 OD1 A:ASP185 4.4 51.7 1.0 CB A:ASP185 4.4 46.4 1.0 O A:NQ4603 4.4 62.1 1.0 N A:ASP113 4.5 49.3 1.0 C A:ASP110 4.5 42.9 1.0 CB A:ALA114 4.6 48.9 1.0 C A:GLY112 4.7 47.9 1.0 CB A:ASP110 4.7 45.7 1.0 O5 A:NQ4603 4.7 69.4 1.0 N A:ALA114 4.7 46.1 1.0 O8 A:NQ4603 4.7 87.3 1.0 O A:ASP110 5.0 49.2 1.0 CB A:VAL111 5.0 34.3 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