Magnesium in PDB 2ynf: Hiv-1 Reverse Transcriptase Y188L Mutant in Complex with Inhibitor GSK560

All present enzymatic activity of Hiv-1 Reverse Transcriptase Y188L Mutant 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 Y188L Mutant in Complex with Inhibitor GSK560, PDB code: 2ynf 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)	47.57 / 2.36
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	119.578, 154.508, 157.026, 90.00, 90.00, 90.00
R / Rfree (%)	19.722 / 23.631

The structure of Hiv-1 Reverse Transcriptase Y188L Mutant 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 Y188L Mutant in Complex with Inhibitor GSK560 (pdb code 2ynf). 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 Y188L Mutant in Complex with Inhibitor GSK560, PDB code: 2ynf:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Hiv-1 Reverse Transcriptase Y188L Mutant 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 Y188L Mutant in Complex with Inhibitor GSK560 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1559 b:55.4 occ:1.00 OD1 A:ASP443 2.5 36.4 1.0 OE2 A:GLU478 2.5 31.8 0.5 MG A:MG1561 2.6 43.7 0.5 OD1 A:ASP498 2.6 33.5 1.0 MG A:MG1560 2.9 34.9 0.5 OD2 A:ASP498 3.3 34.6 1.0 CG A:ASP498 3.3 33.3 1.0 CG A:ASP443 3.4 35.5 1.0 OD2 A:ASP443 3.5 36.9 1.0 O A:HOH2207 3.7 36.5 1.0 CD A:GLU478 3.8 31.2 0.5 NH2 A:ARG557 3.8 65.0 1.0 O A:GLY444 3.9 33.8 1.0 OE2 A:GLU478 4.0 29.6 0.5 O A:HOH2191 4.3 39.4 1.0 NH1 A:ARG557 4.4 67.0 1.0 OE1 A:GLU478 4.5 32.1 0.5 CZ A:ARG557 4.6 66.4 1.0 CG A:GLU478 4.8 30.6 0.5 CB A:ASP498 4.8 32.3 1.0 CB A:ASP443 4.8 34.2 1.0 CB A:ALA538 4.8 43.4 1.0 N A:GLY444 4.9 33.1 1.0 CD A:GLU478 4.9 29.1 0.5

Magnesium binding site 2 out of 3 in the Hiv-1 Reverse Transcriptase Y188L Mutant 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 Y188L Mutant in Complex with Inhibitor GSK560 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1560 b:34.9 occ:0.50 OD2 A:ASP443 2.3 36.9 1.0 OD2 A:ASP498 2.7 34.6 1.0 MG A:MG1559 2.9 55.4 1.0 O A:HOH2235 3.0 54.8 1.0 OD1 A:ASP549 3.0 47.4 1.0 CG A:ASP443 3.0 35.5 1.0 OD1 A:ASP443 3.2 36.4 1.0 NH2 A:ARG557 3.7 65.0 1.0 CG A:ASP498 3.7 33.3 1.0 CG A:ASP549 3.7 48.1 1.0 CB A:ASP549 3.9 46.2 1.0 OD1 A:ASP498 4.0 33.5 1.0 CB A:ASP443 4.3 34.2 1.0 CB A:ALA538 4.3 43.4 1.0 OD1 A:ASN545 4.4 46.2 1.0 CA A:ASP549 4.5 44.4 1.0 ND2 A:ASN545 4.5 42.3 1.0 NE2 A:HIS539 4.5 55.0 1.0 OD2 A:ASP549 4.8 52.3 1.0 CZ A:ARG557 4.8 66.4 1.0 CE1 A:HIS539 4.8 54.0 1.0 CG A:ASN545 4.9 44.6 1.0 OE2 A:GLU478 4.9 31.8 0.5 CB A:ASP498 5.0 32.3 1.0 O A:HOH2191 5.0 39.4 1.0 CA A:ALA538 5.0 44.4 1.0

Magnesium binding site 3 out of 3 in the Hiv-1 Reverse Transcriptase Y188L Mutant 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 Y188L Mutant in Complex with Inhibitor GSK560 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1561 b:43.7 occ:0.50 O A:GLY444 2.5 33.8 1.0 MG A:MG1559 2.6 55.4 1.0 OE2 A:GLU478 2.6 31.8 0.5 OE2 A:GLU478 2.7 29.6 0.5 CD A:GLU478 3.4 31.2 0.5 CG A:GLU478 3.6 30.6 0.5 CD A:GLU478 3.6 29.1 0.5 NH1 A:ARG557 3.6 67.0 1.0 CG A:GLU478 3.6 29.5 0.5 C A:GLY444 3.7 33.8 1.0 OD1 A:ASP443 3.7 36.4 1.0 NH2 A:ARG557 4.2 65.0 1.0 O A:HOH2207 4.2 36.5 1.0 OD1 A:ASN474 4.4 40.7 1.0 CZ A:ARG557 4.4 66.4 1.0 OE1 A:GLU478 4.5 32.1 0.5 N A:ALA445 4.5 34.4 1.0 N A:GLY444 4.6 33.1 1.0 CA A:ALA445 4.6 34.6 1.0 CA A:GLY444 4.6 33.5 1.0 OD1 A:ASP498 4.6 33.5 1.0 CG A:ASP443 4.7 35.5 1.0 CB A:ASN474 4.7 37.6 1.0 O A:ASN474 4.7 33.9 1.0 OE1 A:GLU478 4.8 28.5 0.5 CG A:ASN474 4.8 40.0 1.0 OG1 A:THR477 4.9 31.6 1.0 OD2 A:ASP443 4.9 36.9 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