Sodium in PDB 7zzt: Ligand Binding to HDAC2

Enzymatic activity of Ligand Binding to HDAC2

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

Protein crystallography data

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

Other elements in 7zzt:

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

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

Sodium Binding Sites:

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

Sodium binding site 1 out of 3 in 7zzt

Go back to Sodium Binding Sites List in 7zzt
Sodium binding site 1 out of 3 in the Ligand Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ligand Binding to HDAC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:21.9
occ:1.00
 O A:VAL198 2.3 20.7 1.0
O A:PHE192 2.3 19.8 1.0
O A:HOH817 2.4 19.6 1.0
O A:THR195 2.4 21.5 1.0
O A:HOH823 3.1 28.4 1.0
C A:PHE192 3.5 18.9 1.0
C A:VAL198 3.5 19.0 1.0
C A:THR195 3.6 21.2 1.0
O A:TYR227 3.6 19.7 1.0
CB A:TYR227 3.7 20.7 1.0
CB A:PHE192 4.0 17.0 1.0
N A:THR195 4.1 22.0 1.0
C A:TYR227 4.2 19.3 1.0
CG2 A:THR195 4.2 21.5 1.0
CA A:PHE192 4.3 17.5 1.0
N A:TYR193 4.4 19.2 1.0
C A:TYR193 4.4 20.9 1.0
CA A:TYR193 4.4 19.6 1.0
CA A:THR195 4.4 23.0 1.0
O A:TYR193 4.5 20.8 1.0
N A:MET199 4.5 18.1 1.0
CA A:MET199 4.5 18.4 1.0
CA A:VAL198 4.5 18.5 1.0
N A:VAL198 4.5 18.6 1.0
CA A:TYR227 4.6 20.0 1.0
CA A:GLY224 4.6 22.6 1.0
CB A:VAL198 4.6 18.0 1.0
N A:ASP196 4.6 22.2 1.0
O A:GLY224 4.7 19.2 1.0
CA A:ASP196 4.8 22.6 1.0
N A:THR194 4.9 20.8 1.0
N A:THR200 4.9 16.0 1.0
CG A:TYR227 4.9 20.6 1.0
CB A:THR195 4.9 22.6 1.0
N A:ALA228 4.9 18.8 1.0

Sodium binding site 2 out of 3 in 7zzt

Go back to Sodium Binding Sites List in 7zzt
Sodium binding site 2 out of 3 in the Ligand Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ligand Binding to HDAC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:20.0
occ:1.00
 O B:VAL198 2.3 18.0 1.0
O B:PHE192 2.4 18.2 1.0
O B:HOH881 2.4 16.8 1.0
O B:THR195 2.5 20.1 1.0
O B:HOH867 2.8 26.8 1.0
O B:TYR227 3.5 20.9 1.0
C B:PHE192 3.5 18.4 1.0
C B:VAL198 3.5 18.1 1.0
C B:THR195 3.7 20.4 1.0
CB B:TYR227 3.7 20.5 1.0
CB B:PHE192 4.0 16.8 1.0
C B:TYR227 4.1 19.7 1.0
N B:THR195 4.2 20.4 1.0
CG2 B:THR195 4.3 20.6 1.0
CA B:PHE192 4.4 17.5 1.0
N B:TYR193 4.4 18.2 1.0
C B:TYR193 4.4 19.5 1.0
N B:MET199 4.4 16.4 1.0
CA B:TYR193 4.4 18.7 1.0
CA B:MET199 4.4 18.1 1.0
O B:TYR193 4.4 19.7 1.0
CA B:VAL198 4.4 17.6 1.0
CA B:THR195 4.5 21.2 1.0
N B:VAL198 4.5 17.7 1.0
CA B:TYR227 4.5 19.6 1.0
CB B:VAL198 4.6 16.6 1.0
CA B:GLY224 4.7 22.0 1.0
N B:ASP196 4.7 20.8 1.0
O B:GLY224 4.7 20.1 1.0
N B:THR200 4.8 15.9 1.0
N B:ALA228 4.9 18.7 1.0
CA B:ASP196 4.9 21.7 1.0
N B:THR194 4.9 20.2 1.0
CG B:TYR227 4.9 21.2 1.0
CB B:THR195 5.0 21.4 1.0

Sodium binding site 3 out of 3 in 7zzt

Go back to Sodium Binding Sites List in 7zzt
Sodium binding site 3 out of 3 in the Ligand Binding to HDAC2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ligand Binding to HDAC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na603

b:20.2
occ:1.00
 O C:VAL198 2.3 19.1 1.0
O C:PHE192 2.3 16.7 1.0
O C:THR195 2.4 19.6 1.0
O C:HOH845 2.4 18.1 1.0
O C:HOH799 3.0 30.9 1.0
C C:PHE192 3.4 17.3 1.0
C C:VAL198 3.5 19.7 1.0
C C:THR195 3.6 19.5 1.0
O C:TYR227 3.6 20.6 1.0
CB C:TYR227 3.7 19.7 1.0
CB C:PHE192 4.0 17.8 1.0
N C:THR195 4.1 18.3 1.0
CG2 C:THR195 4.1 19.4 1.0
C C:TYR227 4.2 20.0 1.0
CA C:PHE192 4.3 16.5 1.0
CA C:THR195 4.3 19.4 1.0
N C:TYR193 4.3 16.9 1.0
C C:TYR193 4.3 18.6 1.0
O C:TYR193 4.4 18.5 1.0
CA C:TYR193 4.4 17.4 1.0
CA C:MET199 4.4 19.5 1.0
N C:MET199 4.4 18.6 1.0
CA C:VAL198 4.5 18.3 1.0
N C:VAL198 4.5 19.1 1.0
CA C:TYR227 4.6 20.0 1.0
CA C:GLY224 4.6 19.8 1.0
N C:ASP196 4.6 20.3 1.0
CB C:VAL198 4.6 18.0 1.0
O C:GLY224 4.7 20.1 1.0
CB C:THR195 4.8 19.6 1.0
N C:THR194 4.8 17.8 1.0
CA C:ASP196 4.9 22.3 1.0
CG C:TYR227 4.9 20.7 1.0
N C:THR200 4.9 18.6 1.0
N C:ALA228 4.9 19.8 1.0

Reference:

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
Page generated: Fri Apr 7 17:44:48 2023

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