Calcium in PDB 7zzw: 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: 7zzw 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) 48.41 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.149, 97.934, 139.538, 90, 90, 90
R / Rfree (%) 16.4 / 18.9

Other elements in 7zzw:

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

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Ligand Binding to HDAC2 (pdb code 7zzw). 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: 7zzw:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7zzw

Go back to Calcium Binding Sites List in 7zzw
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:Ca607

b:19.9
occ:1.00
 O A:ASP181 2.6 15.5 1.0
O A:PHE203 2.6 17.0 1.0
O A:HIS183 2.6 18.2 1.0
OD1 A:ASP179 2.6 15.7 1.0
OG A:SER202 2.9 17.4 1.0
O A:ASP179 3.0 16.8 1.0
CG A:ASP179 3.3 17.7 1.0
C A:ASP179 3.5 15.9 1.0
C A:PHE203 3.6 17.1 1.0
C A:ASP181 3.6 16.3 1.0
N A:ASP181 3.7 15.1 1.0
C A:HIS183 3.7 16.9 1.0
CB A:ASP179 3.8 16.4 1.0
CB A:HIS204 3.8 18.3 1.0
N A:PHE203 3.9 15.9 1.0
CA A:ASP181 4.0 15.7 1.0
N A:ILE180 4.0 16.4 1.0
CB A:ASP181 4.0 15.6 1.0
C A:ILE180 4.1 15.7 1.0
CB A:SER202 4.1 17.1 1.0
OD2 A:ASP179 4.2 17.7 1.0
CA A:ILE180 4.2 16.5 1.0
CA A:ASP179 4.3 15.8 1.0
CA A:HIS204 4.3 17.7 1.0
ND1 A:HIS204 4.3 19.2 1.0
N A:HIS204 4.3 16.6 1.0
CA A:SER202 4.4 16.6 1.0
CA A:PHE203 4.4 16.8 1.0
CA A:HIS184 4.4 16.4 1.0
N A:HIS184 4.4 17.3 1.0
N A:HIS183 4.4 16.6 1.0
N A:GLY185 4.4 17.8 1.0
C A:SER202 4.5 16.5 1.0
O A:HOH820 4.5 19.5 1.0
C A:ILE182 4.6 18.2 1.0
CG A:HIS204 4.6 18.8 1.0
N A:ILE182 4.7 16.5 1.0
CA A:HIS183 4.7 18.1 1.0
C A:HIS184 4.7 18.5 1.0
O A:ILE180 4.9 17.2 1.0
O A:ILE182 5.0 18.1 1.0
CA A:ILE182 5.0 16.5 1.0
CE1 A:HIS145 5.0 17.4 1.0

Calcium binding site 2 out of 3 in 7zzw

Go back to Calcium Binding Sites List in 7zzw
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:Ca608

b:21.0
occ:1.00
 O B:PHE203 2.5 20.4 1.0
OD1 B:ASP179 2.6 18.2 1.0
O B:ASP181 2.6 19.9 1.0
O B:HIS183 2.7 18.8 1.0
O B:ASP179 2.8 18.9 1.0
OG B:SER202 2.9 20.0 1.0
CG B:ASP179 3.3 18.1 1.0
C B:ASP179 3.5 20.3 1.0
C B:PHE203 3.5 20.1 1.0
C B:ASP181 3.6 19.8 1.0
N B:ASP181 3.7 19.1 1.0
C B:HIS183 3.7 20.0 1.0
N B:PHE203 3.8 19.4 1.0
CB B:HIS204 3.8 18.8 1.0
CB B:ASP179 3.9 18.0 1.0
CA B:ASP181 4.0 19.2 1.0
CB B:ASP181 4.0 18.1 1.0
N B:ILE180 4.1 18.1 1.0
OD2 B:ASP179 4.1 19.9 1.0
CB B:SER202 4.1 20.2 1.0
C B:ILE180 4.1 19.1 1.0
CA B:ILE180 4.2 18.7 1.0
CA B:ASP179 4.3 17.6 1.0
ND1 B:HIS204 4.3 19.6 1.0
CA B:HIS204 4.3 19.2 1.0
N B:HIS204 4.3 19.1 1.0
CA B:PHE203 4.3 19.7 1.0
CA B:SER202 4.3 20.1 1.0
CA B:HIS184 4.4 20.1 1.0
N B:GLY185 4.4 18.8 1.0
N B:HIS183 4.4 18.3 1.0
C B:SER202 4.4 20.6 1.0
N B:HIS184 4.4 19.6 1.0
O B:HOH754 4.5 21.2 1.0
CG B:HIS204 4.6 18.2 1.0
C B:ILE182 4.6 19.0 1.0
N B:ILE182 4.7 18.7 1.0
C B:HIS184 4.7 19.8 1.0
CA B:HIS183 4.7 19.7 1.0
O B:ILE180 4.9 18.5 1.0
CE1 B:HIS145 5.0 20.4 1.0
O B:ILE182 5.0 19.8 1.0

Calcium binding site 3 out of 3 in 7zzw

Go back to Calcium Binding Sites List in 7zzw
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:Ca606

b:24.9
occ:1.00
 O C:ASP181 2.6 23.5 1.0
O C:PHE203 2.6 20.8 1.0
OD1 C:ASP179 2.6 21.7 1.0
O C:HIS183 2.7 22.4 1.0
O C:ASP179 2.9 24.1 1.0
OG C:SER202 2.9 21.4 1.0
CG C:ASP179 3.3 21.7 1.0
C C:ASP179 3.5 22.1 1.0
C C:ASP181 3.6 22.9 1.0
C C:PHE203 3.6 22.5 1.0
C C:HIS183 3.7 23.8 1.0
N C:ASP181 3.8 24.3 1.0
CB C:ASP179 3.8 22.5 1.0
N C:PHE203 3.9 22.0 1.0
CB C:HIS204 3.9 23.2 1.0
CA C:ASP181 4.1 23.2 1.0
CB C:ASP181 4.1 21.1 1.0
N C:ILE180 4.1 21.9 1.0
CB C:SER202 4.1 22.2 1.0
C C:ILE180 4.2 24.4 1.0
OD2 C:ASP179 4.2 21.4 1.0
CA C:ASP179 4.3 21.8 1.0
CA C:ILE180 4.3 22.1 1.0
CA C:PHE203 4.4 23.1 1.0
ND1 C:HIS204 4.4 23.9 1.0
CA C:HIS204 4.4 23.3 1.0
CA C:SER202 4.4 24.1 1.0
CA C:HIS184 4.4 23.1 1.0
N C:GLY185 4.4 22.5 1.0
N C:HIS183 4.4 23.4 1.0
N C:HIS184 4.4 23.9 1.0
N C:HIS204 4.4 22.1 1.0
C C:SER202 4.5 23.7 1.0
O C:HOH751 4.5 24.3 1.0
C C:ILE182 4.6 22.5 1.0
CG C:HIS204 4.6 25.1 1.0
N C:ILE182 4.7 23.6 1.0
CA C:HIS183 4.7 24.0 1.0
C C:HIS184 4.7 23.1 1.0
O C:ILE180 4.9 23.9 1.0
CA C:ILE182 5.0 23.8 1.0
O C:ILE182 5.0 22.2 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 Jul 19 06:43:21 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy