Magnesium in PDB 4bdz: Pfv Intasome with Inhibitor Xz-90

The structure of Pfv Intasome with Inhibitor Xz-90, PDB code: 4bdz 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)	39.87 / 2.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	160.170, 160.170, 123.490, 90.00, 90.00, 90.00
R / Rfree (%)	18.159 / 21.477

The structure of Pfv Intasome with Inhibitor Xz-90 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-90 (pdb code 4bdz). 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-90, PDB code: 4bdz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pfv Intasome with Inhibitor Xz-90


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-90 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1380 b:42.4 occ:1.00 OAC A:19C1382 2.0 75.4 1.0 OD2 A:ASP185 2.2 51.3 1.0 O A:HOH2047 2.2 47.7 1.0 OD1 A:ASP128 2.2 44.6 1.0 OAB A:19C1382 2.4 75.0 1.0 CAP A:19C1382 2.9 76.2 1.0 CAN A:19C1382 3.1 76.7 1.0 CG A:ASP185 3.2 51.7 1.0 CG A:ASP128 3.3 40.7 1.0 MG A:MG1381 3.6 47.1 1.0 OD1 A:ASP185 3.7 52.9 1.0 O A:HOH2067 3.7 53.5 1.0 OD2 A:ASP128 3.8 46.0 1.0 O A:TYR129 4.2 46.3 1.0 CAT A:19C1382 4.2 71.8 1.0 N A:TYR129 4.4 39.5 1.0 O A:HOH2048 4.5 40.6 1.0 CAF A:19C1382 4.5 73.9 1.0 CB A:ASP185 4.5 47.7 1.0 CB A:ASP128 4.6 39.1 1.0 O A:HOH2005 4.6 44.0 1.0 OE2 A:GLU221 4.7 45.2 1.0 O A:HOH2046 4.8 46.2 1.0 CA A:ASP128 4.9 40.5 1.0 OAA A:19C1382 4.9 63.3 1.0

Magnesium binding site 2 out of 2 in the Pfv Intasome with Inhibitor Xz-90


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-90 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1381 b:47.1 occ:1.00 OAA A:19C1382 2.0 63.3 1.0 OD2 A:ASP128 2.2 46.0 1.0 OE2 A:GLU221 2.2 45.2 1.0 OAC A:19C1382 2.3 75.4 1.0 O A:HOH2048 2.3 40.6 1.0 OE1 A:GLU221 2.4 39.0 1.0 CD A:GLU221 2.6 43.2 1.0 CAM A:19C1382 2.9 63.2 1.0 CG A:ASP128 3.2 40.7 1.0 CAP A:19C1382 3.2 76.2 1.0 CAT A:19C1382 3.3 71.8 1.0 OD1 A:ASP128 3.4 44.6 1.0 MG A:MG1380 3.6 42.4 1.0 O A:HOH2067 3.8 53.5 1.0 ND2 A:ASN224 3.9 40.6 1.0 O A:TYR129 4.1 46.3 1.0 NAU A:19C1382 4.1 56.7 1.0 CG A:GLU221 4.1 43.2 1.0 CAN A:19C1382 4.5 76.7 1.0 CB A:ASP128 4.5 39.1 1.0 OP1 D:DA17 4.6 56.4 1.0 OD2 A:ASP185 4.6 51.3 1.0 CAK A:19C1382 4.7 47.0 1.0 CAS A:19C1382 4.7 70.8 1.0 O3' D:DC16 4.9 51.8 1.0 O5' D:DA17 4.9 61.5 1.0 OAB A:19C1382 5.0 75.0 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