Magnesium in PDB 2yng: Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK560

All present enzymatic activity of Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK560:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13;

The structure of Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK560, PDB code: 2yng was solved by P.Chong, P.Sebahar, M.Youngman, D.Garrido, H.Zhang, E.L.Stewart, R.T.Nolte, L.Wang, R.G.Ferris, M.Edelstein, K.Weaver, A.Mathis, A.Peat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	78.57 / 2.12
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	118.876, 154.627, 156.958, 90.00, 90.00, 90.00
R / Rfree (%)	19.607 / 24.071

The structure of Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK560 also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Bromine	(Br)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK560 (pdb code 2yng). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK560, PDB code: 2yng:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK560


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK560 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1559 b:36.2 occ:1.00 OD1 A:ASP443 2.0 40.3 1.0 OE2 A:GLU478 2.1 33.8 0.5 OD1 A:ASP498 2.3 35.3 1.0 OD2 A:ASP498 2.7 37.7 1.0 CG A:ASP498 2.9 36.1 1.0 CG A:ASP443 2.9 38.2 1.0 MG A:MG1560 3.1 40.2 0.5 CD A:GLU478 3.1 31.3 0.5 MG A:MG1561 3.2 45.6 0.5 OD2 A:ASP443 3.2 42.1 1.0 OE1 A:GLU478 3.4 29.9 0.5 O A:HOH2336 3.5 44.6 1.0 O A:HOH2359 3.9 44.7 1.0 O A:GLY444 4.0 35.0 1.0 CB A:ASP443 4.3 35.5 1.0 NH2 A:ARG557 4.3 64.9 1.0 OE2 A:GLU478 4.3 36.0 0.5 CB A:ASP498 4.4 34.4 1.0 N A:GLY444 4.4 32.6 1.0 CG A:GLU478 4.5 30.9 0.5 CG A:GLU478 4.5 31.1 0.5 CA A:ASP443 4.6 32.8 1.0 CD A:GLU478 4.8 33.6 0.5 C A:ASP498 4.9 30.3 1.0

Magnesium binding site 2 out of 3 in the Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK560


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK560 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1560 b:40.2 occ:0.50 OD2 A:ASP443 2.5 42.1 1.0 OD2 A:ASP498 2.5 37.7 1.0 MG A:MG1559 3.1 36.2 1.0 CG A:ASP443 3.4 38.2 1.0 CG A:ASP498 3.6 36.1 1.0 OD1 A:ASP549 3.6 49.5 1.0 NH2 A:ARG557 3.6 64.9 1.0 OD1 A:ASP443 3.6 40.3 1.0 CG A:ASP549 3.9 48.5 1.0 CB A:ALA538 3.9 46.0 1.0 CB A:ASP549 4.0 44.5 1.0 NE2 A:HIS539 4.0 62.0 1.0 CE1 A:HIS539 4.1 60.4 1.0 OD1 A:ASP498 4.1 35.3 1.0 OD1 A:ASN545 4.3 39.4 1.0 ND2 A:ASN545 4.5 42.8 1.0 CA A:ALA538 4.5 46.7 1.0 CD2 A:HIS539 4.6 63.3 1.0 OD2 A:ASP549 4.6 54.7 1.0 ND1 A:HIS539 4.7 61.7 1.0 CB A:ASP443 4.7 35.5 1.0 CA A:ASP549 4.7 41.9 1.0 CB A:ASP498 4.8 34.4 1.0 CG A:ASN545 4.8 41.1 1.0 CZ A:ARG557 4.8 67.5 1.0 N A:HIS539 4.8 55.9 1.0 CG A:HIS539 5.0 63.1 1.0

Magnesium binding site 3 out of 3 in the Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK560


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK560 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1561 b:45.6 occ:0.50 OE2 A:GLU478 2.3 33.8 0.5 O A:GLY444 2.7 35.0 1.0 OE2 A:GLU478 2.8 36.0 0.5 MG A:MG1559 3.2 36.2 1.0 CD A:GLU478 3.3 31.3 0.5 NH1 A:ARG557 3.5 69.4 1.0 CG A:GLU478 3.6 30.9 0.5 CD A:GLU478 3.6 33.6 0.5 CG A:GLU478 3.6 31.1 0.5 C A:GLY444 3.8 34.3 1.0 OD1 A:ASN474 3.9 45.8 1.0 OD1 A:ASP443 3.9 40.3 1.0 NH2 A:ARG557 4.2 64.9 1.0 OE1 A:GLU478 4.3 29.9 0.5 CZ A:ARG557 4.3 67.5 1.0 CB A:ASN474 4.4 41.9 1.0 O A:HOH2359 4.4 44.7 1.0 CG A:ASN474 4.5 45.8 1.0 O A:ASN474 4.5 33.0 1.0 CA A:ALA445 4.5 37.1 1.0 N A:ALA445 4.6 35.9 1.0 OG1 A:THR477 4.6 34.4 1.0 N A:GLY444 4.7 32.6 1.0 CA A:GLY444 4.7 33.1 1.0 OE1 A:GLU478 4.8 33.5 0.5 CA A:ASN474 4.9 39.5 1.0 OD1 A:ASP498 4.9 35.3 1.0 CG A:ASP443 5.0 38.2 1.0 C A:ASN474 5.0 35.6 1.0

P.Chong, P.Sebahar, M.Youngman, D.Garrido, H.Zhang, E.L.Stewart, R.T.Nolte, L.Wang, R.G.Ferris, M.Edelstein, K.Weaver, A.Mathis, A.Peat. Rational Design of Potent Non-Nucleoside Inhibitors of Hiv- 1 Reverse Transcriptase. J.Med.Chem. V. 55 10601 2012.
ISSN: ISSN 0022-2623
PubMed: 23137340
DOI: 10.1021/JM301294G