Zinc 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
Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Pfv Intasome with Inhibitor Xz-89 (pdb code 4bdy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Pfv Intasome with Inhibitor Xz-89, PDB code: 4bdy:

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pfv Intasome with Inhibitor Xz-89 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn393 b:45.4 occ:1.00 NE2 A:HIS62 1.9 38.6 1.0 ND1 A:HIS66 2.0 36.8 1.0 SG A:CYS96 2.3 49.2 1.0 SG A:CYS99 2.3 44.8 1.0 CE1 A:HIS62 2.8 40.8 1.0 CE1 A:HIS66 2.9 40.4 1.0 CG A:HIS66 3.0 37.9 1.0 CD2 A:HIS62 3.0 39.4 1.0 CB A:CYS96 3.3 45.3 1.0 CB A:CYS99 3.3 41.5 1.0 CB A:HIS66 3.4 35.6 1.0 N A:CYS99 3.8 39.3 1.0 CA A:HIS66 4.0 39.4 1.0 ND1 A:HIS62 4.0 39.5 1.0 CA A:CYS99 4.0 40.9 1.0 NE2 A:HIS66 4.1 39.9 1.0 CG A:HIS62 4.1 40.0 1.0 CD2 A:HIS66 4.2 38.6 1.0 O A:HOH2014 4.2 54.2 1.0 C A:HIS66 4.5 41.3 1.0 O A:HIS66 4.6 42.8 1.0 CA A:CYS96 4.7 46.5 1.0 C A:GLN98 4.7 44.4 1.0 CB A:GLN98 4.8 45.6 1.0 OD1 A:ASN63 4.9 49.1 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