Magnesium in PDB 8u6t: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy) Phenoxy)-2-Naphthonitrile (JLJ758), A Non-Nucleoside Inhibitor

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy) Phenoxy)-2-Naphthonitrile (JLJ758), A Non-Nucleoside Inhibitor, PDB code: 8u6t was solved by G.Prucha, S.Henry, W.L.Jorgensen, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.98 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	222.153, 67.265, 103.259, 90, 108.1, 90
R / Rfree (%)	24.7 / 28.7

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy) Phenoxy)-2-Naphthonitrile (JLJ758), A Non-Nucleoside Inhibitor (pdb code 8u6t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy) Phenoxy)-2-Naphthonitrile (JLJ758), A Non-Nucleoside Inhibitor, PDB code: 8u6t:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy) Phenoxy)-2-Naphthonitrile (JLJ758), A Non-Nucleoside Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy) Phenoxy)-2-Naphthonitrile (JLJ758), A Non-Nucleoside Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:30.0 occ:1.00 OD1 A:ASP498 2.5 60.3 1.0 OE2 A:GLU478 2.5 71.4 1.0 OD1 A:ASP443 2.6 68.8 1.0 OD2 A:ASP498 2.7 65.2 1.0 CG A:ASP498 2.9 62.6 1.0 OD2 A:ASP443 3.1 70.9 1.0 CG A:ASP443 3.2 68.0 1.0 CD A:GLU478 3.8 68.0 1.0 O A:GLY444 4.1 66.6 1.0 OD1 A:ASP549 4.2 83.3 1.0 OE1 A:GLU478 4.4 63.0 1.0 CB A:ASP498 4.5 53.1 1.0 CB A:ASP443 4.7 62.6 1.0 CG A:GLU478 4.9 67.3 1.0 N A:GLY444 5.0 63.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy) Phenoxy)-2-Naphthonitrile (JLJ758), A Non-Nucleoside Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5-(2- (2-(3-Acryloyl-2-Oxo-2,3-Dihydro-1H-Benzo[D]Imidazol-1-Yl)Ethoxy) Phenoxy)-2-Naphthonitrile (JLJ758), A Non-Nucleoside Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:30.0 occ:1.00 OE1 B:GLN23 2.6 56.9 1.0 O B:THR58 2.6 53.7 1.0 N B:THR131 2.7 49.4 1.0 O B:THR131 3.0 52.3 1.0 OD1 B:ASN57 3.1 52.1 1.0 ND2 B:ASN57 3.2 44.4 1.0 CB B:THR131 3.3 51.4 1.0 CA B:THR131 3.3 46.6 1.0 CB B:GLN23 3.4 51.1 1.0 CD B:GLN23 3.5 52.5 1.0 CG B:ASN57 3.5 50.4 1.0 OG1 B:THR131 3.6 52.3 1.0 C B:THR58 3.6 48.6 1.0 C B:THR131 3.6 49.1 1.0 C B:PHE130 3.7 51.3 1.0 CA B:PRO59 3.7 48.9 1.0 CA B:PHE130 3.8 46.7 1.0 CG B:GLN23 3.8 51.3 1.0 CB B:PHE130 4.0 46.1 1.0 N B:PRO59 4.1 47.4 1.0 N B:VAL60 4.1 46.1 1.0 C B:PRO59 4.3 46.4 1.0 CA B:GLN23 4.3 54.0 1.0 N B:THR58 4.5 48.6 1.0 CG2 B:VAL60 4.5 51.5 1.0 CG2 B:THR131 4.7 44.8 1.0 CA B:THR58 4.7 47.8 1.0 NE2 B:GLN23 4.7 52.1 1.0 CG1 B:VAL60 4.7 55.7 1.0 O B:PHE130 4.8 49.0 1.0 N B:GLN23 4.9 59.5 1.0 N B:ILE132 4.9 47.9 1.0 CB B:PRO59 4.9 40.9 1.0 CB B:ASN57 4.9 51.7 1.0

G.R.Prucha, S.Henry, K.Hollander, Z.J.Carter, K.A.Spasov, W.L.Jorgensen, K.S.Anderson. Covalent and Noncovalent Strategies For Targeting LYS102 in Hiv-1 Reverse Transcriptase. Eur.J.Med.Chem. V. 262 15894 2023.
ISSN: ISSN 0223-5234
PubMed: 37883896
DOI: 10.1016/J.EJMECH.2023.115894