Magnesium in PDB 4bdy: Pfv Intasome with Inhibitor Xz-89

The structure of Pfv Intasome with Inhibitor Xz-89, PDB code: 4bdy was solved by S.Hare, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.12 / 2.52
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	159.410, 159.410, 124.030, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.8

The structure of Pfv Intasome with Inhibitor Xz-89 also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Zinc	(Zn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Pfv Intasome with Inhibitor Xz-89 (pdb code 4bdy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pfv Intasome with Inhibitor Xz-89, PDB code: 4bdy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pfv Intasome with Inhibitor Xz-89


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pfv Intasome with Inhibitor Xz-89 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1380 b:38.9 occ:1.00 OAC A:CIJ1382 2.0 39.0 1.0 O A:HOH2064 2.0 37.2 1.0 O A:HOH2063 2.1 31.1 1.0 OAD A:CIJ1382 2.1 45.8 1.0 OD2 A:ASP185 2.1 40.2 1.0 OD1 A:ASP128 2.2 39.3 1.0 CAM A:CIJ1382 2.8 42.4 1.0 CAO A:CIJ1382 2.8 45.5 1.0 CG A:ASP185 3.2 40.2 1.0 CG A:ASP128 3.3 41.8 1.0 OD1 A:ASP185 3.6 44.3 1.0 OD2 A:ASP128 3.7 43.6 1.0 MG A:MG1381 3.8 40.9 1.0 O A:HOH2085 3.8 43.8 1.0 CAG A:CIJ1382 4.2 41.4 1.0 CAU A:CIJ1382 4.2 46.2 1.0 O A:HOH2062 4.4 41.7 1.0 N A:TYR129 4.4 39.8 1.0 O A:HOH2065 4.4 30.9 1.0 O A:TYR129 4.5 41.0 1.0 CB A:ASP185 4.5 41.8 1.0 CB A:ASP128 4.6 38.9 1.0 OE2 A:GLU221 4.6 40.6 1.0 O A:HOH2019 4.7 53.6 1.0 CA A:ASP128 4.9 37.5 1.0 OAB A:CIJ1382 5.0 46.5 1.0

Magnesium binding site 2 out of 2 in the Pfv Intasome with Inhibitor Xz-89


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pfv Intasome with Inhibitor Xz-89 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1381 b:40.9 occ:1.00 OE2 A:GLU221 2.0 40.6 1.0 OAB A:CIJ1382 2.0 46.5 1.0 OE1 A:GLU221 2.1 36.5 1.0 OAD A:CIJ1382 2.1 45.8 1.0 OD2 A:ASP128 2.1 43.6 1.0 O A:HOH2065 2.3 30.9 1.0 CD A:GLU221 2.3 37.1 1.0 CAS A:CIJ1382 2.9 45.7 1.0 CAO A:CIJ1382 3.1 45.5 1.0 CG A:ASP128 3.1 41.8 1.0 CAU A:CIJ1382 3.3 46.2 1.0 OD1 A:ASP128 3.5 39.3 1.0 O A:HOH2085 3.7 43.8 1.0 MG A:MG1380 3.8 38.9 1.0 CG A:GLU221 3.8 33.6 1.0 ND2 A:ASN224 3.9 37.0 1.0 O A:HOH2064 4.2 37.2 1.0 NAV A:CIJ1382 4.2 47.9 1.0 CAM A:CIJ1382 4.3 42.4 1.0 O A:TYR129 4.4 41.0 1.0 CB A:ASP128 4.4 38.9 1.0 CAT A:CIJ1382 4.6 46.0 1.0 OD2 A:ASP185 4.7 40.2 1.0 OP1 D:DA17 4.7 50.3 1.0 CB A:GLU221 4.7 36.0 1.0 OAC A:CIJ1382 4.8 39.0 1.0 CA A:GLU221 4.9 38.0 1.0 CAL A:CIJ1382 4.9 37.2 1.0 O3' D:DC16 5.0 42.7 1.0

M.Metifiot, K.Maddali, B.C.Johnson, S.Hare, S.J.Smith, X.Z.Zhao, C.Marchand, T.R.Burke, S.H.Hughes, P.Cherepanov, Y.Pommier. Activities, Crystal Structures and Molecular Dynamics of Dihydro-1H-Isoindole Derivatives, Inhibitors of Hiv-1 Integrase. Acs Chem.Biol. V. 8 209 2013.
ISSN: ISSN 1554-8929
PubMed: 23075516
DOI: 10.1021/CB300471N