Sodium in PDB 7zzr: HDAC2 in Complex with Inhibitory Ligand

All present enzymatic activity of HDAC2 in Complex with Inhibitory Ligand:
3.5.1.98;

The structure of HDAC2 in Complex with Inhibitory Ligand, PDB code: 7zzr 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)	76.69 / 2.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.991, 97.7, 138.849, 90, 90, 90
R / Rfree (%)	18.8 / 24.7

The structure of HDAC2 in Complex with Inhibitory Ligand also contains other interesting chemical elements:

Calcium	(Ca)	3 atoms
Zinc	(Zn)	3 atoms

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

Sodium binding site 1 out of 3 in the HDAC2 in Complex with Inhibitory Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of HDAC2 in Complex with Inhibitory Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:21.2 occ:1.00 O A:VAL198 2.2 15.8 1.0 O A:PHE192 2.3 17.3 1.0 O A:HOH750 2.5 16.6 1.0 O A:THR195 2.6 17.4 1.0 O A:HOH842 2.7 20.8 1.0 C A:VAL198 3.4 15.4 1.0 C A:PHE192 3.4 17.3 1.0 O A:TYR227 3.4 16.6 1.0 CB A:TYR227 3.7 18.2 1.0 C A:THR195 3.8 17.9 1.0 CB A:PHE192 3.9 14.6 1.0 C A:TYR227 4.0 16.2 1.0 N A:MET199 4.3 14.9 1.0 CA A:MET199 4.3 16.2 1.0 CA A:PHE192 4.3 16.2 1.0 CG2 A:THR195 4.3 21.3 1.0 N A:TYR193 4.3 17.4 1.0 N A:THR195 4.4 17.7 1.0 CA A:TYR193 4.4 17.9 1.0 CA A:VAL198 4.4 15.0 1.0 C A:TYR193 4.5 17.9 1.0 O A:TYR193 4.5 16.3 1.0 CA A:TYR227 4.5 17.5 1.0 N A:VAL198 4.6 16.8 1.0 CA A:THR195 4.6 18.1 1.0 CB A:VAL198 4.6 13.5 1.0 N A:THR200 4.7 14.7 1.0 O A:GLY224 4.7 22.0 1.0 N A:ALA228 4.7 16.3 1.0 CA A:GLY224 4.8 21.9 1.0 N A:ASP196 4.8 18.5 1.0 C A:MET199 4.9 16.9 1.0 CG2 A:THR200 4.9 12.9 1.0 OG1 A:THR200 4.9 12.6 1.0 CG A:TYR227 4.9 19.4 1.0

Sodium binding site 2 out of 3 in the HDAC2 in Complex with Inhibitory Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of HDAC2 in Complex with Inhibitory Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:15.1 occ:1.00 O B:PHE192 2.3 16.3 1.0 O B:VAL198 2.3 13.5 1.0 O B:HOH777 2.3 8.5 1.0 O B:THR195 2.5 15.4 1.0 O B:HOH794 2.7 20.5 1.0 C B:PHE192 3.4 16.3 1.0 O B:TYR227 3.5 16.9 1.0 C B:VAL198 3.5 12.9 1.0 CB B:TYR227 3.7 18.4 1.0 C B:THR195 3.7 15.5 1.0 CB B:PHE192 4.0 16.0 1.0 C B:TYR227 4.0 16.7 1.0 N B:THR195 4.2 17.9 1.0 CG2 B:THR195 4.3 17.2 1.0 CA B:PHE192 4.3 16.8 1.0 N B:TYR193 4.3 16.4 1.0 CA B:TYR193 4.3 17.5 1.0 C B:TYR193 4.3 19.3 1.0 O B:TYR193 4.4 20.9 1.0 N B:MET199 4.4 11.1 1.0 CA B:MET199 4.4 11.5 1.0 CA B:VAL198 4.5 15.5 1.0 CA B:THR195 4.5 16.6 1.0 CA B:TYR227 4.5 17.8 1.0 N B:VAL198 4.6 16.1 1.0 O B:GLY224 4.6 22.4 1.0 CA B:GLY224 4.6 23.2 1.0 CB B:VAL198 4.7 18.0 1.0 N B:ASP196 4.7 14.9 1.0 N B:ALA228 4.7 16.4 1.0 N B:THR200 4.8 11.3 1.0 CG B:TYR227 4.9 19.3 1.0 N B:THR194 4.9 18.2 1.0 CA B:ASP196 5.0 14.9 1.0

Sodium binding site 3 out of 3 in the HDAC2 in Complex with Inhibitory Ligand


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of HDAC2 in Complex with Inhibitory Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Na603 b:30.7 occ:1.00 O C:HOH762 2.3 11.0 1.0 O C:PHE192 2.3 17.7 1.0 O C:THR195 2.4 18.8 1.0 O C:VAL198 2.4 21.1 1.0 O C:HOH796 2.9 21.5 1.0 C C:PHE192 3.4 18.0 1.0 O C:TYR227 3.6 20.9 1.0 C C:THR195 3.6 18.8 1.0 C C:VAL198 3.6 20.1 1.0 CB C:TYR227 3.6 22.2 1.0 CB C:PHE192 4.1 19.1 1.0 C C:TYR227 4.1 21.2 1.0 N C:THR195 4.1 18.4 1.0 CG2 C:THR195 4.2 21.9 1.0 C C:TYR193 4.3 18.3 1.0 O C:TYR193 4.3 18.3 1.0 CA C:TYR193 4.3 18.9 1.0 N C:TYR193 4.3 17.7 1.0 CA C:THR195 4.3 19.5 1.0 CA C:PHE192 4.4 18.6 1.0 CA C:GLY224 4.4 22.0 1.0 CA C:TYR227 4.5 22.8 1.0 O C:GLY224 4.5 23.5 1.0 N C:MET199 4.5 19.6 1.0 CA C:MET199 4.5 20.8 1.0 CA C:VAL198 4.5 18.0 1.0 N C:VAL198 4.6 18.6 1.0 N C:ASP196 4.6 18.6 1.0 N C:ALA228 4.8 20.4 1.0 CG C:TYR227 4.8 22.1 1.0 CB C:VAL198 4.8 16.2 1.0 CA C:ASP196 4.8 21.1 1.0 N C:THR194 4.9 17.4 1.0 CB C:THR195 4.9 21.9 1.0 N C:THR200 4.9 20.1 1.0 C C:GLY224 5.0 22.6 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