Atomistry » Calcium » PDB 7zei-8a29 » 7zzt
Atomistry »
  Calcium »
    PDB 7zei-8a29 »
      7zzt »

Calcium 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:

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

Calcium Binding Sites:

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 7zzt

Go back to Calcium Binding Sites List in 7zzt
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 7zzt

Go back to Calcium Binding Sites List in 7zzt
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 7zzt

Go back to Calcium Binding Sites List in 7zzt
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

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: Thu Jul 10 03:00:24 2025

Last articles

Mg in 9MF6
Mg in 9MED
Mg in 9MEC
Mg in 9MDY
Mg in 9MDW
Mg in 9M84
Mg in 9M7M
Mg in 9M7L
Mg in 9M5O
Mg in 9M56
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy