Zinc in PDB 7zzw: Ligand Binding to HDAC2

All present enzymatic activity of Ligand Binding to HDAC2:
3.5.1.98;

The structure of Ligand Binding to HDAC2, PDB code: 7zzw was solved by A.Cleasby, D.Tisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.41 / 1.73
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.149, 97.934, 139.538, 90, 90, 90
R / Rfree (%)	16.4 / 18.9

The structure of Ligand Binding to HDAC2 also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Ligand Binding to HDAC2 (pdb code 7zzw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Ligand Binding to HDAC2, PDB code: 7zzw:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Ligand Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn606 b:17.3 occ:1.00 OD2 A:ASP269 2.0 16.4 1.0 OD1 A:ASP181 2.0 16.0 1.0 ND1 A:HIS183 2.0 17.3 1.0 N23 A:KKW609 2.1 10.4 0.7 O27 A:KKW609 2.5 11.6 0.7 CG A:ASP181 2.9 14.2 1.0 CE1 A:HIS183 2.9 17.9 1.0 CG A:ASP269 3.0 18.2 1.0 C17 A:KKW609 3.0 10.0 0.7 C18 A:KKW609 3.0 10.2 0.7 C16 A:KKW609 3.1 10.5 0.7 OD2 A:ASP181 3.1 14.8 1.0 CG A:HIS183 3.1 17.4 1.0 OD1 A:ASP269 3.4 15.9 1.0 CB A:HIS183 3.6 18.2 1.0 N A:HIS183 4.0 16.6 1.0 NE2 A:HIS183 4.1 18.4 1.0 NE2 A:HIS145 4.2 17.7 1.0 CG2 A:ILE182 4.2 18.2 1.0 N24 A:KKW609 4.2 12.6 0.7 CD2 A:HIS183 4.2 19.5 1.0 C12 A:KKW609 4.3 10.0 0.7 CA A:GLY306 4.3 17.4 1.0 CB A:ASP269 4.3 16.1 1.0 C01 A:KKW609 4.3 10.8 0.7 CB A:ASP181 4.3 15.6 1.0 CA A:HIS183 4.4 18.1 1.0 N A:GLY306 4.5 15.5 1.0 N A:ILE182 4.5 16.5 1.0 CE1 A:HIS145 4.6 17.4 1.0 OH A:TYR308 4.7 20.1 1.0 NE2 A:HIS146 4.8 20.3 1.0 CE2 A:TYR308 4.9 18.4 1.0 C04 A:KKW609 4.9 13.8 0.7 C A:ILE182 4.9 18.2 1.0

Zinc binding site 2 out of 3 in the Ligand Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn607 b:19.6 occ:1.00 OD2 B:ASP269 1.8 18.4 1.0 OD1 B:ASP181 2.0 19.4 1.0 N23 B:KKW610 2.1 14.0 0.8 ND1 B:HIS183 2.1 18.5 1.0 O27 B:KKW610 2.4 14.6 0.8 CG B:ASP181 2.8 18.4 1.0 CG B:ASP269 2.9 18.0 1.0 CE1 B:HIS183 3.0 20.4 1.0 C17 B:KKW610 3.0 13.0 0.8 C18 B:KKW610 3.0 14.5 0.8 C16 B:KKW610 3.0 13.7 0.8 OD2 B:ASP181 3.0 19.4 1.0 CG B:HIS183 3.2 20.9 1.0 OD1 B:ASP269 3.4 17.9 1.0 CB B:HIS183 3.6 19.1 1.0 N B:HIS183 4.0 18.3 1.0 NE2 B:HIS183 4.2 19.8 1.0 CG2 B:ILE182 4.2 20.7 1.0 NE2 B:HIS145 4.2 19.5 1.0 N24 B:KKW610 4.2 14.9 0.8 CA B:GLY306 4.2 18.9 1.0 CB B:ASP269 4.2 19.1 1.0 C12 B:KKW610 4.2 12.1 0.8 CD2 B:HIS183 4.3 21.6 1.0 C01 B:KKW610 4.3 14.2 0.8 CB B:ASP181 4.3 18.1 1.0 CA B:HIS183 4.4 19.7 1.0 N B:GLY306 4.4 18.0 1.0 N B:ILE182 4.5 18.7 1.0 CE1 B:HIS145 4.6 20.4 1.0 OH B:TYR308 4.7 22.5 1.0 NE2 B:HIS146 4.8 20.5 1.0 C07 B:KKW610 4.9 15.6 0.8 CE2 B:TYR308 4.9 21.7 1.0 C B:ILE182 5.0 19.0 1.0

Zinc binding site 3 out of 3 in the Ligand Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn605 b:23.3 occ:1.00 OD1 C:ASP181 1.9 21.2 1.0 ND1 C:HIS183 2.0 23.9 1.0 OD2 C:ASP269 2.1 21.6 1.0 N23 C:KKW608 2.2 16.9 0.9 O27 C:KKW608 2.4 27.4 0.9 CG C:ASP181 2.8 22.2 1.0 CE1 C:HIS183 2.9 24.8 1.0 C17 C:KKW608 2.9 20.4 0.9 C18 C:KKW608 3.0 27.2 0.9 CG C:ASP269 3.0 24.6 1.0 OD2 C:ASP181 3.0 22.7 1.0 C16 C:KKW608 3.1 21.7 0.9 CG C:HIS183 3.2 24.9 1.0 OD1 C:ASP269 3.4 23.9 1.0 CB C:HIS183 3.6 25.1 1.0 N C:HIS183 3.9 23.4 1.0 NE2 C:HIS183 4.1 24.9 1.0 CG2 C:ILE182 4.1 23.6 1.0 N24 C:KKW608 4.2 25.7 0.9 NE2 C:HIS145 4.2 21.1 1.0 CA C:GLY306 4.2 23.5 1.0 CD2 C:HIS183 4.2 26.7 1.0 CB C:ASP181 4.2 21.1 1.0 C12 C:KKW608 4.2 19.5 0.9 C01 C:KKW608 4.3 19.9 0.9 CB C:ASP269 4.3 24.0 1.0 CA C:HIS183 4.4 24.0 1.0 N C:ILE182 4.5 23.6 1.0 N C:GLY306 4.5 23.3 1.0 CE1 C:HIS145 4.5 21.4 1.0 OH C:TYR308 4.8 28.1 1.0 NE2 C:HIS146 4.8 22.2 1.0 CE2 C:TYR308 4.9 27.8 1.0 C C:ILE182 4.9 22.5 1.0 C07 C:KKW608 4.9 26.7 0.9

E.Tamanini, S.Miyamura, I.M.Buck, B.D.Cons, L.Dawson, C.East, T.Futamura, S.Goto, C.Griffiths-Jones, T.Hashimoto, T.D.Heightman, S.Ishikawa, H.Ito, Y.Kaneko, T.Kawato, K.Kondo, N.Kurihara, J.M.Mccarthy, Y.Mori, T.Nagase, Y.Nakaishi, J.Reeks, A.Sato, P.Schopf, K.Tai, T.Tamai, D.Tisi, A.J.Woolford. Fragment-Based Discovery of A Novel, Brain Penetrant, Orally Active HDAC2 Inhibitor. Acs Med.Chem.Lett. V. 13 1591 2022.
ISSN: ISSN 1948-5875
PubMed: 36262388
DOI: 10.1021/ACSMEDCHEMLETT.2C00272