Magnesium in PDB 4be2: Pfv Intasome with Inhibitor Xz-259

The structure of Pfv Intasome with Inhibitor Xz-259, PDB code: 4be2 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)	38.72 / 2.38
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	159.420, 159.420, 123.680, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.3

The structure of Pfv Intasome with Inhibitor Xz-259 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-259 (pdb code 4be2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Pfv Intasome with Inhibitor Xz-259, PDB code: 4be2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Pfv Intasome with Inhibitor Xz-259


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-259 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1380 b:43.1 occ:1.00 OAF D:XZ21018 1.8 45.3 1.0 OD1 A:ASP128 2.0 39.2 1.0 O A:HOH2070 2.0 39.5 1.0 O A:HOH2069 2.1 32.7 1.0 OD2 A:ASP185 2.1 39.1 1.0 OAG D:XZ21018 2.3 44.8 1.0 CAQ D:XZ21018 2.7 47.3 1.0 CAS D:XZ21018 2.9 48.6 1.0 CG A:ASP128 3.1 36.8 1.0 CG A:ASP185 3.2 42.5 1.0 OD2 A:ASP128 3.4 36.6 1.0 OD1 A:ASP185 3.6 41.4 1.0 MG A:MG1381 3.9 39.3 1.0 O A:HOH2096 4.0 48.0 1.0 CAL D:XZ21018 4.0 48.3 1.0 N6 D:DA17 4.2 86.2 0.8 N A:TYR129 4.2 37.2 1.0 O A:TYR129 4.2 39.7 1.0 CAX D:XZ21018 4.3 48.5 1.0 O A:HOH2068 4.3 43.9 1.0 CB A:ASP128 4.4 35.5 1.0 O A:HOH2009 4.4 42.5 1.0 OE2 A:GLU221 4.4 33.9 1.0 O A:HOH2071 4.5 34.8 1.0 CB A:ASP185 4.5 41.9 1.0 CA A:ASP128 4.6 36.0 1.0 N7 D:DA17 4.9 68.0 0.8 C A:ASP128 4.9 36.0 1.0

Magnesium binding site 2 out of 3 in the Pfv Intasome with Inhibitor Xz-259


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-259 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1381 b:39.3 occ:1.00 OAG D:XZ21018 1.9 44.8 1.0 OE2 A:GLU221 1.9 33.9 1.0 OD2 A:ASP128 2.0 36.6 1.0 OE1 A:GLU221 2.1 42.0 1.0 OAC D:XZ21018 2.2 46.6 1.0 O A:HOH2071 2.3 34.8 1.0 CD A:GLU221 2.3 36.3 1.0 CAS D:XZ21018 3.0 48.6 1.0 CAP D:XZ21018 3.0 45.8 1.0 CG A:ASP128 3.2 36.8 1.0 CAX D:XZ21018 3.3 48.5 1.0 ND2 A:ASN224 3.6 35.7 1.0 OD1 A:ASP128 3.7 39.2 1.0 CG A:GLU221 3.8 33.0 1.0 MG A:MG1380 3.9 43.1 1.0 O A:HOH2096 4.1 48.0 1.0 O A:TYR129 4.2 39.7 1.0 CAQ D:XZ21018 4.3 47.3 1.0 O A:HOH2070 4.3 39.5 1.0 NAZ D:XZ21018 4.3 45.5 1.0 OP1 D:DA17 4.4 41.2 0.8 CB A:ASP128 4.4 35.5 1.0 O3' D:DC16 4.4 39.3 1.0 CAV D:XZ21018 4.7 47.0 1.0 OAF D:XZ21018 4.7 45.3 1.0 CB A:GLU221 4.7 35.3 1.0 N7 D:DA17 4.7 68.0 0.8 C2' D:DC16 4.7 35.9 1.0 OD2 A:ASP185 4.8 39.1 1.0 CA A:GLU221 4.9 36.9 1.0 CG A:ASN224 4.9 39.5 1.0

Magnesium binding site 3 out of 3 in the Pfv Intasome with Inhibitor Xz-259


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pfv Intasome with Inhibitor Xz-259 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1302 b:97.5 occ:1.00 O B:HOH2031 2.1 70.1 1.0 O B:HOH2012 2.2 60.4 1.0 OD1 B:ASP128 2.2 68.3 1.0 O B:HOH2013 2.5 73.9 1.0 OD2 B:ASP185 2.5 55.1 1.0 CG B:ASP128 3.3 64.8 1.0 CG B:ASP185 3.4 52.5 1.0 OD1 B:ASP185 3.6 57.1 1.0 O B:HOH2002 3.7 59.9 1.0 OD2 B:ASP128 3.7 66.7 1.0 O B:HOH2011 3.8 51.8 1.0 N B:TYR129 3.9 45.0 1.0 O B:TYR129 4.2 53.6 1.0 CE2 B:PHE190 4.5 46.7 1.0 CB B:ASP128 4.5 57.5 1.0 CA B:ASP128 4.6 48.6 1.0 CA B:TYR129 4.8 47.7 1.0 C B:ASP128 4.8 47.7 1.0 CB B:ASP185 4.8 42.4 1.0 CB B:TYR129 4.8 48.4 1.0 C B:TYR129 5.0 49.5 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