Zinc in PDB 4lxz: Structure of Human HDAC2 in Complex with Saha (Vorinostat)

All present enzymatic activity of Structure of Human HDAC2 in Complex with Saha (Vorinostat):
3.5.1.98;

The structure of Structure of Human HDAC2 in Complex with Saha (Vorinostat), PDB code: 4lxz was solved by R.Fong, P.J.Lupardus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.09 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.967, 97.603, 138.833, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.2

The structure of Structure of Human HDAC2 in Complex with Saha (Vorinostat) also contains other interesting chemical elements:

Calcium	(Ca)	3 atoms
Sodium	(Na)	3 atoms

The binding sites of Zinc atom in the Structure of Human HDAC2 in Complex with Saha (Vorinostat) (pdb code 4lxz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Human HDAC2 in Complex with Saha (Vorinostat), PDB code: 4lxz:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Human HDAC2 in Complex with Saha (Vorinostat)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human HDAC2 in Complex with Saha (Vorinostat) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:11.4 occ:1.00 OD2 A:ASP269 1.9 9.5 1.0 O1 A:SHH407 2.0 9.9 1.0 OD2 A:ASP181 2.0 11.9 1.0 ND1 A:HIS183 2.1 11.4 1.0 O2 A:SHH407 2.3 11.8 1.0 N1 A:SHH407 2.7 12.9 1.0 CG A:ASP181 2.8 11.9 1.0 C1 A:SHH407 2.8 11.9 1.0 CG A:ASP269 2.9 11.5 1.0 OD1 A:ASP181 2.9 11.9 1.0 CE1 A:HIS183 3.0 11.5 1.0 CG A:HIS183 3.2 11.4 1.0 OD1 A:ASP269 3.2 10.1 1.0 CB A:HIS183 3.6 9.5 1.0 N A:HIS183 3.9 9.5 1.0 CA A:GLY306 4.0 10.1 1.0 CG2 A:ILE182 4.1 10.4 1.0 NE2 A:HIS183 4.2 12.1 1.0 CB A:ASP269 4.2 9.3 1.0 CB A:ASP181 4.2 11.6 1.0 NE2 A:HIS145 4.3 10.7 1.0 CD2 A:HIS183 4.3 12.0 1.0 C2 A:SHH407 4.3 8.5 1.0 N A:GLY306 4.3 9.2 1.0 CA A:HIS183 4.3 8.9 1.0 O A:HOH791 4.3 31.3 1.0 N A:ILE182 4.4 8.6 1.0 OH A:TYR308 4.6 11.3 1.0 CE1 A:TYR308 4.7 12.1 1.0 CE1 A:HIS145 4.7 10.1 1.0 C3 A:SHH407 4.8 11.0 1.0 C A:ILE182 4.9 11.3 1.0 NE2 A:HIS146 4.9 12.5 1.0 C A:ASP181 5.0 12.2 1.0 C A:GLY306 5.0 12.6 1.0 CA A:ASP181 5.0 9.7 1.0

Zinc binding site 2 out of 3 in the Structure of Human HDAC2 in Complex with Saha (Vorinostat)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human HDAC2 in Complex with Saha (Vorinostat) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:10.0 occ:1.00 OD1 B:ASP269 1.9 11.1 1.0 O1 B:SHH408 2.0 13.4 1.0 OD2 B:ASP181 2.0 8.9 1.0 ND1 B:HIS183 2.1 10.9 1.0 O2 B:SHH408 2.4 9.8 1.0 N1 B:SHH408 2.7 10.3 1.0 CG B:ASP181 2.8 6.4 1.0 CG B:ASP269 2.9 14.0 1.0 C1 B:SHH408 2.9 11.8 1.0 OD1 B:ASP181 2.9 8.6 1.0 CE1 B:HIS183 3.0 10.1 1.0 CG B:HIS183 3.2 10.0 1.0 OD2 B:ASP269 3.2 11.0 1.0 CB B:HIS183 3.6 7.5 1.0 N B:HIS183 3.9 7.5 1.0 CA B:GLY306 4.0 6.8 1.0 NE2 B:HIS145 4.2 8.9 1.0 NE2 B:HIS183 4.2 10.0 1.0 CG2 B:ILE182 4.2 7.2 1.0 CB B:ASP269 4.2 8.6 1.0 CB B:ASP181 4.2 7.5 1.0 CD2 B:HIS183 4.3 10.8 1.0 N B:GLY306 4.3 7.1 1.0 C2 B:SHH408 4.3 11.6 1.0 CA B:HIS183 4.4 7.6 1.0 N B:ILE182 4.4 5.8 1.0 OH B:TYR308 4.6 8.8 1.0 CE1 B:TYR308 4.6 6.5 1.0 CE1 B:HIS145 4.7 7.6 1.0 O B:HOH776 4.7 30.6 1.0 C3 B:SHH408 4.8 14.6 1.0 C B:ILE182 4.9 10.2 1.0 NE2 B:HIS146 4.9 10.2 1.0 C B:GLY306 4.9 10.6 1.0 C B:ASP181 5.0 8.9 1.0 CA B:ASP181 5.0 6.0 1.0

Zinc binding site 3 out of 3 in the Structure of Human HDAC2 in Complex with Saha (Vorinostat)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human HDAC2 in Complex with Saha (Vorinostat) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:13.9 occ:1.00 OD2 C:ASP269 2.0 12.5 1.0 ND1 C:HIS183 2.0 13.8 1.0 O1 C:SHH406 2.0 14.0 1.0 OD2 C:ASP181 2.1 10.4 1.0 O2 C:SHH406 2.4 13.3 1.0 N1 C:SHH406 2.8 15.8 1.0 CG C:ASP181 2.8 14.3 1.0 CE1 C:HIS183 2.8 14.3 1.0 C1 C:SHH406 2.9 18.8 1.0 CG C:ASP269 2.9 14.2 1.0 OD1 C:ASP181 2.9 13.8 1.0 CG C:HIS183 3.1 13.0 1.0 OD1 C:ASP269 3.2 12.1 1.0 CB C:HIS183 3.6 10.5 1.0 N C:HIS183 3.9 11.3 1.0 CA C:GLY306 4.0 11.7 1.0 NE2 C:HIS183 4.1 15.1 1.0 CG2 C:ILE182 4.1 13.5 1.0 CD2 C:HIS183 4.2 15.0 1.0 NE2 C:HIS145 4.2 12.1 1.0 CB C:ASP269 4.3 13.2 1.0 CB C:ASP181 4.3 13.6 1.0 C2 C:SHH406 4.3 17.2 1.0 N C:GLY306 4.3 11.3 1.0 CA C:HIS183 4.4 10.0 1.0 N C:ILE182 4.4 11.2 1.0 O C:HOH755 4.5 23.6 1.0 OH C:TYR308 4.5 17.4 1.0 CE1 C:TYR308 4.6 16.6 1.0 CE1 C:HIS145 4.7 12.0 1.0 C3 C:SHH406 4.8 16.6 1.0 C C:ILE182 4.8 13.3 1.0 NE2 C:HIS146 4.9 13.0 1.0 C C:GLY306 4.9 14.8 1.0 C C:ASP181 5.0 15.9 1.0 CA C:ILE182 5.0 10.7 1.0 CA C:ASP181 5.0 12.9 1.0

B.E.Lauffer, R.Mintzer, R.Fong, S.Mukund, C.Tam, I.Zilberleyb, B.Flicke, A.Ritscher, G.Fedorowicz, R.Vallero, D.F.Ortwine, J.Gunzner, Z.Modrusan, L.Neumann, C.M.Koth, P.J.Lupardus, J.S.Kaminker, C.E.Heise, P.Steiner. Histone Deacetylase (Hdac) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation But Not Transcription and Cell Viability. J.Biol.Chem. V. 288 26926 2013.
ISSN: ISSN 0021-9258
PubMed: 23897821
DOI: 10.1074/JBC.M113.490706