Magnesium in PDB 6wpj: Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and D4T

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and D4T:
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 D4T, PDB code: 6wpj 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)	47.56 / 2.73
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	167.588, 170.061, 102.459, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 25.7

The binding sites of Magnesium atom in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and D4T (pdb code 6wpj). 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 D4T, PDB code: 6wpj:
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 D4T


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 D4T within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:35.5 occ:1.00 OD2 A:ASP110 1.9 41.2 1.0 O A:VAL111 2.0 42.2 1.0 O2A A:D4T601 2.1 32.8 1.0 O2C A:D4T601 2.1 40.7 1.0 O2B A:D4T601 2.4 37.4 1.0 OD2 A:ASP185 2.5 35.9 1.0 CG A:ASP110 2.8 42.1 1.0 OD1 A:ASP110 3.1 52.4 1.0 C A:VAL111 3.2 41.2 1.0 CG A:ASP185 3.5 42.0 1.0 PC A:D4T601 3.5 38.6 1.0 PA A:D4T601 3.5 38.6 1.0 PB A:D4T601 3.5 39.4 1.0 N A:VAL111 3.7 39.9 1.0 OD1 A:ASP185 3.8 46.9 1.0 NZ A:LYS220 3.9 46.6 1.0 O6' A:D4T601 3.9 44.9 1.0 O7' A:D4T601 3.9 42.9 1.0 CA A:VAL111 4.0 40.5 1.0 CB A:ASP110 4.1 38.3 1.0 O1C A:D4T601 4.1 38.0 1.0 N A:GLY112 4.2 36.3 1.0 C A:ASP110 4.3 39.1 1.0 C5' A:D4T601 4.3 37.2 1.0 CA A:GLY112 4.4 32.1 1.0 O5' A:D4T601 4.5 35.4 1.0 O1A A:D4T601 4.5 37.7 1.0 O3C A:D4T601 4.6 42.3 1.0 CB A:VAL111 4.6 43.5 1.0 CA A:ASP110 4.7 37.4 1.0 CB A:ALA114 4.7 38.0 1.0 N A:ASP113 4.7 38.8 1.0 CE A:LYS220 4.8 48.9 1.0 N A:ALA114 4.8 37.2 1.0 C A:GLY112 4.8 38.5 1.0 CB A:ASP185 4.8 38.6 1.0 O1B A:D4T601 4.8 42.8 1.0 O A:ASP110 5.0 41.4 1.0

Magnesium binding site 2 out of 2 in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and D4T


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 D4T within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:17.9 occ:1.00 OD1 A:ASP443 1.8 41.0 1.0 OE2 A:GLU478 1.9 36.7 1.0 OD1 A:ASP498 2.0 40.9 1.0 OD2 A:ASP498 2.0 48.1 1.0 CG A:ASP498 2.4 40.8 1.0 CG A:ASP443 2.8 46.7 1.0 CD A:GLU478 3.0 41.2 1.0 OD2 A:ASP443 3.1 44.2 1.0 OE1 A:GLU478 3.4 48.7 1.0 O A:GLY444 3.7 50.6 1.0 CB A:ASP498 3.9 31.7 1.0 CB A:ASP443 4.2 44.4 1.0 N A:GLY444 4.3 44.8 1.0 CG A:GLU478 4.3 43.9 1.0 CA A:ASP443 4.6 37.6 1.0 C A:ASP498 4.8 39.8 1.0 CA A:ASP498 4.8 36.8 1.0 C A:GLY444 4.8 46.1 1.0 CB A:ALA538 4.8 42.5 1.0 C A:ASP443 5.0 40.3 1.0

N.Bertoletti, A.H.Chan, R.F.Schinazi, K.S.Anderson. Post-Catalytic Complexes with Emtricitabine or Stavudine and Hiv-1 Reverse Transcriptase Reveal New Mechanistic Insights For Nucleotide Incorporation and Drug Resistance. Molecules V. 25 2020.
ISSN: ESSN 1420-3049
PubMed: 33096918
DOI: 10.3390/MOLECULES25204868