Magnesium in PDB 4be1: Pfv Intasome with Inhibitor Xz-116

The structure of Pfv Intasome with Inhibitor Xz-116, PDB code: 4be1 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)	50.92 / 2.71
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	161.030, 161.030, 123.940, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.3

The structure of Pfv Intasome with Inhibitor Xz-116 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-116 (pdb code 4be1). 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-116, PDB code: 4be1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Pfv Intasome with Inhibitor Xz-116


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-116 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1381 b:47.4 occ:1.00 O A:HOH2053 1.9 55.1 1.0 OAD A:CI41383 2.0 51.6 1.0 O A:HOH2052 2.0 46.6 1.0 OAC A:CI41383 2.2 48.3 1.0 OD2 A:ASP185 2.2 51.5 1.0 OD1 A:ASP128 2.2 48.8 1.0 CAO A:CI41383 2.9 54.7 1.0 CAM A:CI41383 2.9 55.2 1.0 CG A:ASP185 3.2 52.9 1.0 CG A:ASP128 3.3 48.5 1.0 OD1 A:ASP185 3.6 57.6 1.0 OD2 A:ASP128 3.7 51.2 1.0 MG A:MG1382 3.8 53.4 1.0 O A:HOH2073 4.1 59.3 1.0 CAU A:CI41383 4.2 52.7 1.0 CAG A:CI41383 4.3 50.1 1.0 O A:HOH2008 4.3 47.8 1.0 O A:TYR129 4.4 50.9 1.0 O A:HOH2054 4.4 34.6 1.0 N A:TYR129 4.4 45.0 1.0 O A:HOH2051 4.5 62.5 1.0 CB A:ASP128 4.5 45.5 1.0 CB A:ASP185 4.6 49.7 1.0 OE2 A:GLU221 4.6 50.8 1.0 CA A:ASP128 4.9 41.1 1.0

Magnesium binding site 2 out of 3 in the Pfv Intasome with Inhibitor Xz-116


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-116 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1382 b:53.4 occ:1.00 OE2 A:GLU221 1.9 50.8 1.0 OAB A:CI41383 2.1 52.1 1.0 O A:HOH2054 2.1 34.6 1.0 OD2 A:ASP128 2.2 51.2 1.0 OE1 A:GLU221 2.2 50.9 1.0 OAD A:CI41383 2.3 51.6 1.0 CD A:GLU221 2.4 47.7 1.0 CAS A:CI41383 3.0 52.1 1.0 CG A:ASP128 3.2 48.5 1.0 CAO A:CI41383 3.2 54.7 1.0 CAU A:CI41383 3.4 52.7 1.0 OD1 A:ASP128 3.6 48.8 1.0 ND2 A:ASN224 3.8 42.8 1.0 MG A:MG1381 3.8 47.4 1.0 CG A:GLU221 3.9 44.2 1.0 O A:HOH2073 4.0 59.3 1.0 O A:HOH2053 4.2 55.1 1.0 NAV A:CI41383 4.2 51.2 1.0 O A:TYR129 4.3 50.9 1.0 CB A:ASP128 4.4 45.5 1.0 FAE A:CI41383 4.4 53.0 1.0 CAM A:CI41383 4.5 55.2 1.0 OP1 D:DA17 4.6 51.9 1.0 OD2 A:ASP185 4.7 51.5 1.0 CB A:GLU221 4.8 45.6 1.0 CAT A:CI41383 4.8 50.1 1.0 CA0 A:CI41383 4.8 43.9 1.0 CA A:GLU221 4.9 44.2 1.0 O3' D:DC16 4.9 53.7 1.0

Magnesium binding site 3 out of 3 in the Pfv Intasome with Inhibitor Xz-116


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-116 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1302 b:88.8 occ:1.00 OD1 B:ASP128 2.2 81.1 1.0 OD2 B:ASP185 2.4 50.4 1.0 O B:HOH2006 2.5 75.1 1.0 O B:HOH2018 2.6 73.1 1.0 CG B:ASP128 3.1 69.5 1.0 OD2 B:ASP128 3.3 67.8 1.0 CG B:ASP185 3.3 52.1 1.0 OD1 B:ASP185 3.6 56.0 1.0 O B:HOH2005 3.9 50.4 1.0 O B:HOH2001 4.1 63.2 1.0 N B:TYR129 4.3 57.8 1.0 O B:TYR129 4.4 65.3 1.0 CB B:ASP128 4.5 62.1 1.0 CB B:ASP185 4.6 45.8 1.0 CE2 B:PHE190 4.8 55.5 1.0 CA B:ASP128 4.9 59.0 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