Sodium in PDB 7zzo: HDAC2 in Complex with An Inhibitor

All present enzymatic activity of HDAC2 in Complex with An Inhibitor:
3.5.1.98;

The structure of HDAC2 in Complex with An Inhibitor, PDB code: 7zzo 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)	79.80 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.079, 97.444, 139.049, 90, 90, 90
R / Rfree (%)	17.2 / 22.5

The structure of HDAC2 in Complex with An Inhibitor also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the HDAC2 in Complex with An Inhibitor (pdb code 7zzo). 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 An Inhibitor, PDB code: 7zzo:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the HDAC2 in Complex with An Inhibitor


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 An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:21.4 occ:1.00 O A:PHE192 2.4 17.4 1.0 O A:VAL198 2.4 17.2 1.0 O A:HOH769 2.4 16.3 1.0 O A:THR195 2.5 18.4 1.0 O A:HOH826 2.7 25.7 1.0 C A:PHE192 3.5 17.8 1.0 C A:VAL198 3.6 17.2 1.0 O A:TYR227 3.6 17.1 1.0 C A:THR195 3.7 19.6 1.0 CB A:TYR227 3.8 19.6 1.0 CB A:PHE192 4.0 16.1 1.0 C A:TYR227 4.1 18.0 1.0 N A:THR195 4.2 20.1 1.0 CG2 A:THR195 4.3 18.8 1.0 C A:TYR193 4.3 19.2 1.0 N A:TYR193 4.3 18.0 1.0 CA A:TYR193 4.3 18.5 1.0 CA A:PHE192 4.3 17.0 1.0 O A:TYR193 4.4 19.1 1.0 N A:MET199 4.5 17.2 1.0 CA A:THR195 4.5 20.1 1.0 CA A:VAL198 4.5 16.6 1.0 CA A:MET199 4.5 17.6 1.0 CA A:GLY224 4.5 23.0 1.0 CA A:TYR227 4.5 19.1 1.0 N A:VAL198 4.6 17.4 1.0 O A:GLY224 4.6 21.3 1.0 CB A:VAL198 4.7 15.8 1.0 N A:ASP196 4.7 20.2 1.0 N A:THR194 4.9 19.7 1.0 CA A:ASP196 4.9 20.7 1.0 N A:ALA228 4.9 17.9 1.0 N A:THR200 4.9 15.1 1.0 CG A:TYR227 5.0 20.8 1.0

Sodium binding site 2 out of 3 in the HDAC2 in Complex with An Inhibitor


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 An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:17.3 occ:1.00 O B:PHE192 2.3 15.9 1.0 O B:HOH760 2.3 11.9 1.0 O B:VAL198 2.4 16.3 1.0 O B:HOH870 2.5 19.1 1.0 O B:THR195 2.5 17.5 1.0 C B:PHE192 3.4 16.6 1.0 O B:TYR227 3.6 19.1 1.0 C B:VAL198 3.6 16.3 1.0 C B:THR195 3.7 18.8 1.0 CB B:TYR227 3.9 19.4 1.0 CB B:PHE192 4.1 16.2 1.0 N B:THR195 4.1 19.1 1.0 C B:TYR227 4.1 18.7 1.0 C B:TYR193 4.2 18.6 1.0 CG2 B:THR195 4.2 17.2 1.0 O B:TYR193 4.2 19.2 1.0 CA B:TYR193 4.2 17.6 1.0 N B:TYR193 4.3 17.0 1.0 CA B:PHE192 4.3 16.4 1.0 CA B:THR195 4.4 19.2 1.0 N B:MET199 4.5 16.6 1.0 O B:GLY224 4.5 18.8 1.0 CA B:GLY224 4.5 21.3 1.0 CA B:VAL198 4.6 16.5 1.0 CA B:TYR227 4.6 19.6 1.0 CA B:MET199 4.6 17.1 1.0 N B:VAL198 4.7 17.3 1.0 N B:ASP196 4.7 19.8 1.0 N B:THR194 4.7 19.3 1.0 CB B:VAL198 4.8 16.3 1.0 N B:ALA228 4.9 18.7 1.0 CA B:ASP196 4.9 20.2 1.0 N B:THR200 5.0 14.2 1.0 CB B:THR195 5.0 18.6 1.0

Sodium binding site 3 out of 3 in the HDAC2 in Complex with An Inhibitor


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 An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Na603 b:22.0 occ:1.00 O C:PHE192 2.3 17.2 1.0 O C:VAL198 2.3 20.1 1.0 O C:THR195 2.4 18.6 1.0 O C:HOH742 2.4 14.3 1.0 O C:HOH719 3.2 28.7 1.0 C C:PHE192 3.5 17.3 1.0 C C:VAL198 3.6 20.8 1.0 C C:THR195 3.6 19.4 1.0 O C:TYR227 3.6 20.8 1.0 CB C:TYR227 3.8 21.1 1.0 CB C:PHE192 4.0 18.2 1.0 N C:THR195 4.1 19.0 1.0 C C:TYR227 4.2 20.8 1.0 CG2 C:THR195 4.2 18.2 1.0 C C:TYR193 4.3 18.5 1.0 O C:TYR193 4.3 18.7 1.0 CA C:PHE192 4.4 17.5 1.0 N C:TYR193 4.4 17.5 1.0 CA C:THR195 4.4 19.2 1.0 CA C:TYR193 4.4 17.7 1.0 CA C:MET199 4.4 21.3 1.0 CA C:GLY224 4.5 21.9 1.0 N C:MET199 4.5 20.9 1.0 CA C:VAL198 4.5 20.1 1.0 CA C:TYR227 4.6 21.5 1.0 O C:GLY224 4.6 21.4 1.0 N C:ASP196 4.6 20.2 1.0 N C:VAL198 4.6 19.9 1.0 CB C:VAL198 4.7 19.3 1.0 CA C:ASP196 4.8 21.3 1.0 N C:THR194 4.9 18.0 1.0 CB C:THR195 4.9 18.7 1.0 N C:THR200 4.9 18.8 1.0 N C:ALA228 4.9 20.6 1.0 CG C:TYR227 4.9 22.0 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