Zinc in PDB 3max: Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide

All present enzymatic activity of Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide:
3.5.1.98;

The structure of Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide, PDB code: 3max was solved by R.J.Skene, A.J.Jennings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.311, 97.227, 138.849, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.4

The structure of Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide (pdb code 3max). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide, PDB code: 3max:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn379 b:25.1 occ:1.00 OD2 A:ASP181 2.0 26.9 1.0 OD2 A:ASP269 2.1 27.0 1.0 N1 A:LLX400 2.1 24.6 1.0 ND1 A:HIS183 2.2 26.2 1.0 O10 A:LLX400 2.5 25.9 1.0 CG A:ASP181 2.8 26.5 1.0 CG A:ASP269 3.0 26.5 1.0 OD1 A:ASP181 3.0 24.5 1.0 CE1 A:HIS183 3.1 26.1 1.0 C2 A:LLX400 3.1 28.0 1.0 CG A:HIS183 3.2 27.1 1.0 OD1 A:ASP269 3.3 23.2 1.0 C9 A:LLX400 3.5 28.7 1.0 CB A:HIS183 3.6 24.1 1.0 C3 A:LLX400 3.8 27.3 1.0 N A:HIS183 3.9 24.7 1.0 C7 A:LLX400 4.0 28.1 1.0 CA A:GLY306 4.1 24.9 1.0 N8 A:LLX400 4.1 29.3 1.0 NE2 A:HIS145 4.2 24.5 1.0 CG2 A:ILE182 4.2 24.1 1.0 NE2 A:HIS183 4.3 25.0 1.0 CB A:ASP269 4.3 22.4 1.0 CB A:ASP181 4.3 25.8 1.0 N A:GLY306 4.3 24.8 1.0 CD2 A:HIS183 4.3 26.4 1.0 CA A:HIS183 4.4 25.0 1.0 C11 A:LLX400 4.4 30.6 1.0 N A:ILE182 4.5 25.4 1.0 NE2 A:HIS146 4.5 26.4 1.0 OH A:TYR308 4.7 24.8 1.0 CE1 A:HIS145 4.7 23.9 1.0 CE1 A:TYR308 4.8 26.4 1.0 C A:ILE182 4.9 26.5 1.0 C16 A:LLX400 4.9 30.2 1.0 C A:ASP181 5.0 26.0 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn379 b:23.6 occ:1.00 OD1 B:ASP269 1.9 26.0 1.0 OD2 B:ASP181 1.9 24.7 1.0 N1 B:LLX400 2.1 23.3 1.0 ND1 B:HIS183 2.1 23.6 1.0 O10 B:LLX400 2.7 19.7 1.0 CG B:ASP181 2.7 20.5 1.0 OD1 B:ASP181 2.8 19.5 1.0 CG B:ASP269 2.9 25.7 1.0 CE1 B:HIS183 3.0 22.7 1.0 C2 B:LLX400 3.1 25.2 1.0 CG B:HIS183 3.2 24.0 1.0 OD2 B:ASP269 3.2 27.0 1.0 C9 B:LLX400 3.5 26.6 1.0 CB B:HIS183 3.6 23.0 1.0 C3 B:LLX400 3.9 25.6 1.0 C7 B:LLX400 4.0 23.6 1.0 N B:HIS183 4.0 22.1 1.0 N8 B:LLX400 4.0 26.9 1.0 NE2 B:HIS145 4.1 25.6 1.0 CA B:GLY306 4.1 27.2 1.0 NE2 B:HIS183 4.1 24.7 1.0 CB B:ASP181 4.2 20.4 1.0 CB B:ASP269 4.3 24.9 1.0 CD2 B:HIS183 4.3 26.7 1.0 CG2 B:ILE182 4.3 20.8 1.0 N B:GLY306 4.4 25.3 1.0 CA B:HIS183 4.4 24.0 1.0 N B:ILE182 4.5 23.0 1.0 NE2 B:HIS146 4.5 20.8 1.0 C11 B:LLX400 4.5 24.2 1.0 CE1 B:HIS145 4.7 20.9 1.0 OH B:TYR308 4.7 23.9 1.0 CE1 B:TYR308 4.8 24.3 1.0 CA B:ASP181 4.9 22.0 1.0 C B:ILE182 4.9 24.3 1.0 C B:ASP181 5.0 23.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn379 b:32.7 occ:1.00 OD2 C:ASP269 2.0 36.8 1.0 ND1 C:HIS183 2.0 32.8 1.0 N1 C:LLX400 2.1 27.2 1.0 OD2 C:ASP181 2.1 32.8 1.0 O10 C:LLX400 2.6 28.6 1.0 CG C:ASP181 2.9 32.4 1.0 CE1 C:HIS183 2.9 34.9 1.0 OD1 C:ASP181 3.0 33.8 1.0 CG C:ASP269 3.0 37.3 1.0 C2 C:LLX400 3.1 30.7 1.0 CG C:HIS183 3.1 33.1 1.0 OD1 C:ASP269 3.3 32.1 1.0 C9 C:LLX400 3.4 32.0 1.0 CB C:HIS183 3.6 34.1 1.0 C3 C:LLX400 3.9 29.2 1.0 C7 C:LLX400 3.9 31.2 1.0 N8 C:LLX400 4.0 31.5 1.0 N C:HIS183 4.0 33.5 1.0 NE2 C:HIS183 4.1 32.0 1.0 CA C:GLY306 4.1 34.5 1.0 NE2 C:HIS145 4.1 35.3 1.0 CG2 C:ILE182 4.1 35.6 1.0 CD2 C:HIS183 4.2 35.5 1.0 CB C:ASP269 4.3 35.8 1.0 CB C:ASP181 4.4 32.5 1.0 N C:GLY306 4.4 32.7 1.0 C11 C:LLX400 4.4 33.2 1.0 CA C:HIS183 4.4 32.8 1.0 NE2 C:HIS146 4.4 33.2 1.0 N C:ILE182 4.5 35.2 1.0 CE1 C:HIS145 4.6 34.7 1.0 OH C:TYR308 4.8 35.5 1.0 CE1 C:TYR308 4.9 33.1 1.0 C16 C:LLX400 4.9 34.7 1.0 C C:ILE182 4.9 33.2 1.0

J.C.Bressi, A.J.Jennings, R.Skene, Y.Wu, R.Melkus, R.De Jong, S.O'connell, C.E.Grimshaw, M.Navre, A.R.Gangloff. Exploration of the HDAC2 Foot Pocket: Synthesis and Sar of Substituted N-(2-Aminophenyl)Benzamides. Bioorg.Med.Chem.Lett. V. 20 3142 2010.
ISSN: ISSN 0960-894X
PubMed: 20392638
DOI: 10.1016/J.BMCL.2010.03.091