Magnesium in PDB 6wpf: 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: 6wpf 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)	47.68 / 2.53
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	165.569, 170.468, 103.343, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 23.1

The binding sites of Magnesium atom in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and D4T (pdb code 6wpf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dsdna and D4T, PDB code: 6wpf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 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 P:Mg903 b:43.3 occ:1.00 OP1 P:D4M901 2.2 40.4 1.0 OD1 A:ASP110 2.3 50.6 1.0 O2A A:D4T603 2.4 38.1 1.0 O3' P:DG822 2.5 45.2 1.0 OD1 A:ASP185 2.6 49.9 1.0 OD2 A:ASP110 2.8 52.6 1.0 P P:D4M901 2.9 49.1 1.0 CG A:ASP110 2.9 48.1 1.0 OD2 A:ASP185 3.1 33.0 1.0 CG A:ASP185 3.2 46.4 1.0 MG A:MG602 3.3 32.0 1.0 PA A:D4T603 3.5 45.5 1.0 C3' P:DG822 3.7 41.9 1.0 O5' A:D4T603 3.8 44.4 1.0 NZ A:LYS220 3.8 45.7 1.0 O5' P:D4M901 3.8 53.9 1.0 C5' A:D4T603 3.9 48.1 1.0 O1A A:D4T603 4.0 43.3 1.0 C2' P:DG822 4.0 44.7 1.0 OP2 P:D4M901 4.1 48.6 1.0 CB A:ASP110 4.4 42.4 1.0 O2C A:D4T603 4.4 48.3 1.0 C4' P:DG822 4.5 39.0 1.0 CB A:ASP186 4.6 46.5 1.0 N A:ASP186 4.6 36.0 1.0 CB A:ASP185 4.6 46.0 1.0 OD2 A:ASP186 4.6 51.6 1.0 C A:ASP185 4.7 39.8 1.0 CE A:LYS220 4.7 46.3 1.0 O2B A:D4T603 4.8 44.7 1.0 O A:ASP185 4.8 35.2 1.0 O6' A:D4T603 4.8 51.1 1.0 CA A:ASP186 4.9 39.9 1.0 O A:VAL111 5.0 43.4 1.0

Magnesium binding site 2 out of 3 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:Mg601 b:24.7 occ:1.00 OD1 A:ASP443 2.0 51.5 1.0 OD1 A:ASP498 2.1 46.8 1.0 OE2 A:GLU478 2.1 51.1 1.0 OD2 A:ASP498 2.5 47.2 1.0 CG A:ASP498 2.6 44.0 1.0 O A:HOH709 2.8 48.3 1.0 CG A:ASP443 3.0 48.5 1.0 CD A:GLU478 3.1 46.9 1.0 OD2 A:ASP443 3.2 49.6 1.0 OE1 A:GLU478 3.5 51.2 1.0 O A:GLY444 3.9 41.6 1.0 CB A:ASP498 4.1 39.0 1.0 CB A:ASP443 4.3 44.1 1.0 N A:GLY444 4.4 34.5 1.0 CG A:GLU478 4.5 38.0 1.0 OP1 T:DC723 4.7 86.5 1.0 CA A:ASP443 4.7 35.3 1.0 CB A:ALA538 4.7 30.9 1.0 C A:ASP498 4.8 35.0 1.0 CA A:ASP498 4.9 35.7 1.0 C A:GLY444 4.9 35.9 1.0

Magnesium binding site 3 out of 3 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 3 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:32.0 occ:1.00 O A:VAL111 2.0 43.4 1.0 OD2 A:ASP110 2.1 52.6 1.0 O2C A:D4T603 2.2 48.3 1.0 O2A A:D4T603 2.3 38.1 1.0 O2B A:D4T603 2.4 44.7 1.0 OD2 A:ASP185 2.5 33.0 1.0 C A:VAL111 3.2 39.7 1.0 CG A:ASP110 3.2 48.1 1.0 MG P:MG903 3.3 43.3 1.0 PC A:D4T603 3.4 45.2 1.0 PB A:D4T603 3.4 50.1 1.0 PA A:D4T603 3.6 45.5 1.0 O7' A:D4T603 3.6 49.9 1.0 CG A:ASP185 3.6 46.4 1.0 NZ A:LYS220 3.7 45.7 1.0 N A:VAL111 3.8 34.6 1.0 O6' A:D4T603 3.9 51.1 1.0 OD1 A:ASP110 3.9 50.6 1.0 CA A:VAL111 4.0 33.6 1.0 O1C A:D4T603 4.1 43.8 1.0 N A:GLY112 4.2 37.8 1.0 OD1 A:ASP185 4.2 49.9 1.0 C5' A:D4T603 4.3 48.1 1.0 CB A:ASP110 4.3 42.4 1.0 CA A:GLY112 4.4 35.0 1.0 OP1 P:D4M901 4.4 40.4 1.0 N A:ASP113 4.5 35.9 1.0 O5' A:D4T603 4.5 44.4 1.0 C A:ASP110 4.5 36.7 1.0 CB A:ALA114 4.6 34.9 1.0 CB A:VAL111 4.6 31.3 1.0 O3C A:D4T603 4.6 44.2 1.0 O1A A:D4T603 4.6 43.3 1.0 N A:ALA114 4.6 36.6 1.0 C A:GLY112 4.7 38.0 1.0 CE A:LYS220 4.7 46.3 1.0 O1B A:D4T603 4.7 51.5 1.0 CB A:ASP185 4.8 46.0 1.0 CD A:LYS220 4.8 44.7 1.0 CA A:ASP110 4.9 36.2 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