Magnesium in PDB 6or7: Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dna and (-)Ftc-Tp

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dna 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 Dna and (-)Ftc-Tp, PDB code: 6or7 was solved by N.Bertoletti, A.H.Chan, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.57 / 2.53
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	166.499, 169.825, 103.283, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.9

The structure of Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dna 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 Dna and (-)Ftc-Tp (pdb code 6or7). 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 Dna and (-)Ftc-Tp, PDB code: 6or7:
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 Dna 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 Dna and (-)Ftc-Tp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:43.0 occ:1.00 OD1 A:ASP110 2.0 77.4 1.0 O A:VAL111 2.3 49.5 1.0 OD2 A:ASP185 2.3 59.3 1.0 OAQ A:1RY601 2.6 0.8 1.0 OAD A:1RY601 2.7 79.9 1.0 CG A:ASP110 3.0 71.2 1.0 OAI A:1RY601 3.1 0.1 1.0 PBB A:1RY601 3.3 0.1 1.0 OD2 A:ASP110 3.3 76.3 1.0 CG A:ASP185 3.4 57.4 1.0 C A:VAL111 3.4 51.6 1.0 PAZ A:1RY601 3.5 0.1 1.0 OAF A:1RY601 3.7 0.5 1.0 OAC A:1RY601 3.8 0.4 1.0 PBA A:1RY601 3.8 83.5 1.0 OAR A:1RY601 3.9 92.8 1.0 N A:VAL111 4.0 44.4 1.0 OD1 A:ASP185 4.1 57.5 1.0 CAL A:1RY601 4.2 76.5 1.0 CA A:VAL111 4.3 39.0 1.0 CB A:ASP185 4.3 52.0 1.0 CB A:ASP110 4.3 60.9 1.0 N A:GLY112 4.3 50.1 1.0 NZ A:LYS220 4.4 71.3 1.0 CA A:GLY112 4.4 48.9 1.0 OAO A:1RY601 4.4 81.9 1.0 C A:ASP110 4.5 46.8 1.0 OAE A:1RY601 4.7 0.6 1.0 CB A:ALA114 4.7 44.2 1.0 N A:ASP113 4.7 52.2 1.0 CA A:ASP110 4.9 50.2 1.0 OAG A:1RY601 4.9 0.8 1.0 CB A:VAL111 4.9 51.5 1.0 C A:GLY112 4.9 50.9 1.0 N A:ALA114 4.9 47.3 1.0

Magnesium binding site 2 out of 2 in the Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Dna 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 Dna and (-)Ftc-Tp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:39.9 occ:1.00 OD2 A:ASP498 2.0 76.6 1.0 OD1 A:ASP443 2.1 63.9 1.0 OE2 A:GLU478 2.2 66.5 1.0 CG A:ASP498 2.5 69.8 1.0 CB A:ASP498 2.9 68.5 1.0 CG A:ASP443 3.1 58.9 1.0 CD A:GLU478 3.2 63.0 1.0 OD2 A:ASP443 3.3 62.8 1.0 OD1 A:ASP498 3.5 68.5 1.0 OE1 A:GLU478 3.6 65.4 1.0 O A:GLY444 3.9 49.3 1.0 CA A:ASP498 4.3 63.7 1.0 CB A:ASP443 4.4 51.0 1.0 N A:GLY444 4.5 38.5 1.0 OP1 T:DC723 4.5 86.7 1.0 CG A:GLU478 4.5 56.8 1.0 C A:ASP498 4.5 56.4 1.0 CA A:ASP443 4.8 44.3 1.0 CB A:ALA538 4.8 41.7 1.0 O A:ASP498 4.9 53.2 1.0 C A:GLY444 4.9 44.9 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