Calcium in PDB 7zzt: 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: 7zzt 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)	48.39 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.208, 98.023, 139.275, 90, 90, 90
R / Rfree (%)	14.8 / 17.3

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

Sodium	(Na)	3 atoms
Zinc	(Zn)	3 atoms

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:21.8 occ:1.00 OD1 A:ASP179 2.4 15.6 1.0 O A:ASP181 2.4 13.7 1.0 O A:PHE203 2.5 14.8 1.0 O A:HIS183 2.6 15.5 1.0 O A:ASP179 2.9 14.8 1.0 OG A:SER202 3.0 16.0 1.0 CG A:ASP179 3.2 16.0 1.0 C A:ASP181 3.4 13.8 1.0 C A:PHE203 3.5 15.4 1.0 C A:ASP179 3.5 13.9 1.0 C A:HIS183 3.6 14.6 1.0 N A:ASP181 3.7 13.7 1.0 CB A:ASP179 3.8 14.5 1.0 N A:PHE203 3.8 15.0 1.0 CB A:HIS204 3.9 14.8 1.0 CA A:ASP181 4.0 13.4 1.0 CB A:ASP181 4.0 13.1 1.0 C A:ILE180 4.0 13.4 1.0 OD2 A:ASP179 4.1 16.3 1.0 N A:ILE180 4.1 13.4 1.0 CB A:SER202 4.2 16.3 1.0 CA A:ILE180 4.2 13.6 1.0 N A:HIS183 4.3 14.8 1.0 CA A:ASP179 4.3 13.4 1.0 CA A:HIS204 4.3 15.2 1.0 CA A:PHE203 4.3 15.9 1.0 ND1 A:HIS204 4.3 15.1 1.0 N A:HIS204 4.4 15.1 1.0 N A:HIS184 4.4 15.3 1.0 CA A:HIS184 4.4 16.1 1.0 O A:HOH794 4.4 16.4 1.0 C A:ILE182 4.5 14.4 1.0 CA A:SER202 4.5 14.9 1.0 N A:GLY185 4.5 15.9 1.0 C A:SER202 4.5 14.9 1.0 N A:ILE182 4.6 13.5 1.0 CG A:HIS204 4.6 15.1 1.0 CA A:HIS183 4.6 14.3 1.0 C A:HIS184 4.8 16.0 1.0 O A:ILE180 4.8 14.5 1.0 O A:ILE182 4.9 14.8 1.0 CA A:ILE182 4.9 15.0 1.0 CE1 A:HIS145 4.9 16.2 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:21.7 occ:1.00 OD1 B:ASP179 2.4 14.9 1.0 O B:ASP181 2.4 13.1 1.0 O B:PHE203 2.5 13.2 1.0 O B:HIS183 2.6 14.3 1.0 O B:ASP179 2.9 13.3 1.0 OG B:SER202 2.9 15.5 1.0 CG B:ASP179 3.2 14.3 1.0 C B:ASP181 3.4 13.3 1.0 C B:ASP179 3.5 13.4 1.0 C B:PHE203 3.5 13.2 1.0 C B:HIS183 3.6 13.5 1.0 N B:ASP181 3.6 12.5 1.0 CB B:ASP179 3.8 13.3 1.0 CB B:HIS204 3.9 14.2 1.0 N B:PHE203 3.9 13.3 1.0 CA B:ASP181 3.9 12.8 1.0 CB B:ASP181 4.0 12.0 1.0 C B:ILE180 4.0 12.7 1.0 N B:ILE180 4.1 12.0 1.0 OD2 B:ASP179 4.1 14.2 1.0 CB B:SER202 4.2 14.5 1.0 CA B:ILE180 4.2 13.0 1.0 CA B:ASP179 4.2 12.9 1.0 CA B:HIS204 4.3 14.1 1.0 N B:HIS183 4.3 13.1 1.0 ND1 B:HIS204 4.4 14.8 1.0 N B:HIS204 4.4 13.4 1.0 CA B:PHE203 4.4 13.6 1.0 O B:HOH851 4.4 15.7 1.0 N B:HIS184 4.4 14.2 1.0 CA B:HIS184 4.4 13.7 1.0 CA B:SER202 4.4 14.4 1.0 C B:ILE182 4.5 13.8 1.0 N B:ILE182 4.5 12.5 1.0 N B:GLY185 4.5 14.9 1.0 C B:SER202 4.5 13.7 1.0 CA B:HIS183 4.6 13.7 1.0 CG B:HIS204 4.6 14.9 1.0 O B:ILE180 4.8 12.8 1.0 C B:HIS184 4.8 14.6 1.0 CA B:ILE182 4.8 13.5 1.0 O B:ILE182 4.9 14.4 1.0 CE1 B:HIS145 5.0 13.3 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ligand Binding to HDAC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca602 b:26.1 occ:1.00 OD1 C:ASP179 2.4 19.4 1.0 O C:ASP181 2.4 18.4 1.0 O C:PHE203 2.5 19.3 1.0 O C:HIS183 2.6 18.5 1.0 O C:ASP179 2.9 17.3 1.0 OG C:SER202 2.9 19.7 1.0 CG C:ASP179 3.2 18.9 1.0 C C:ASP181 3.4 17.6 1.0 C C:ASP179 3.5 18.2 1.0 C C:PHE203 3.5 18.0 1.0 C C:HIS183 3.6 17.2 1.0 N C:ASP181 3.7 17.3 1.0 CB C:ASP179 3.8 18.7 1.0 N C:PHE203 3.8 18.4 1.0 CB C:HIS204 3.9 18.6 1.0 CA C:ASP181 4.0 17.7 1.0 CB C:ASP181 4.0 16.5 1.0 N C:ILE180 4.1 17.9 1.0 C C:ILE180 4.1 18.3 1.0 OD2 C:ASP179 4.1 19.2 1.0 CB C:SER202 4.2 19.6 1.0 CA C:ILE180 4.3 18.6 1.0 CA C:ASP179 4.3 17.4 1.0 N C:HIS183 4.3 17.0 1.0 CA C:HIS204 4.3 18.7 1.0 CA C:PHE203 4.3 19.3 1.0 ND1 C:HIS204 4.4 18.5 1.0 O C:HOH783 4.4 20.6 1.0 N C:HIS204 4.4 18.2 1.0 N C:HIS184 4.4 17.5 1.0 CA C:HIS184 4.4 18.3 1.0 CA C:SER202 4.4 19.3 1.0 C C:ILE182 4.4 17.9 1.0 C C:SER202 4.5 19.7 1.0 N C:ILE182 4.5 17.7 1.0 N C:GLY185 4.5 19.7 1.0 CA C:HIS183 4.6 17.0 1.0 CG C:HIS204 4.6 18.4 1.0 O C:ILE180 4.8 19.9 1.0 CA C:ILE182 4.8 18.1 1.0 C C:HIS184 4.8 18.1 1.0 O C:ILE182 4.8 17.6 1.0 CE1 C:HIS145 5.0 18.5 1.0

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