Calcium in PDB 7zzu: Inhibitory Ligand Binding to HDAC2

Enzymatic activity of Inhibitory Ligand Binding to HDAC2

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

Protein crystallography data

The structure of Inhibitory Ligand Binding to HDAC2, PDB code: 7zzu 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) 48.45 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.35, 98.352, 139.291, 90, 90, 90
R / Rfree (%) 15.4 / 18.2

Other elements in 7zzu:

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

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

Calcium Binding Sites:

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

Calcium binding site 1 out of 3 in 7zzu

Go back to Calcium Binding Sites List in 7zzu
Calcium binding site 1 out of 3 in the Inhibitory 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 Inhibitory Ligand Binding to HDAC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca611

b:11.2
occ:1.00
 OD1 A:ASP179 2.6 9.7 1.0
O A:ASP181 2.6 8.0 1.0
O A:PHE203 2.7 9.5 1.0
O A:HIS183 2.8 9.9 1.0
OG A:SER202 2.9 11.3 1.0
O A:ASP179 2.9 9.2 1.0
CG A:ASP179 3.3 9.6 1.0
C A:ASP179 3.5 9.3 1.0
C A:ASP181 3.6 8.8 1.0
C A:PHE203 3.6 10.6 1.0
N A:ASP181 3.7 8.2 1.0
C A:HIS183 3.7 9.9 1.0
CB A:ASP179 3.8 9.5 1.0
CB A:HIS204 3.8 10.6 1.0
N A:PHE203 3.9 10.8 1.0
CA A:ASP181 4.0 8.0 1.0
CB A:ASP181 4.0 7.8 1.0
CB A:SER202 4.1 11.1 1.0
N A:ILE180 4.1 8.8 1.0
C A:ILE180 4.1 8.9 1.0
OD2 A:ASP179 4.2 10.5 1.0
CA A:ILE180 4.3 9.2 1.0
CA A:ASP179 4.3 9.1 1.0
CA A:SER202 4.3 10.7 1.0
CA A:HIS204 4.3 11.0 1.0
ND1 A:HIS204 4.3 12.1 1.0
CA A:HIS184 4.4 10.2 1.0
N A:HIS184 4.4 10.2 1.0
N A:GLY185 4.4 11.0 1.0
N A:HIS204 4.4 10.6 1.0
N A:HIS183 4.4 9.2 1.0
CA A:PHE203 4.4 11.2 1.0
C A:SER202 4.4 10.8 1.0
O A:HOH759 4.6 12.3 1.0
CG A:HIS204 4.6 11.4 1.0
C A:ILE182 4.6 9.5 1.0
N A:ILE182 4.7 8.4 1.0
C A:HIS184 4.7 11.2 1.0
CA A:HIS183 4.7 9.8 1.0
O A:ILE180 4.9 9.8 1.0
O A:ILE182 5.0 10.9 1.0
CE1 A:HIS145 5.0 9.8 1.0
CA A:ILE182 5.0 9.8 1.0

Calcium binding site 2 out of 3 in 7zzu

Go back to Calcium Binding Sites List in 7zzu
Calcium binding site 2 out of 3 in the Inhibitory 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 Inhibitory Ligand Binding to HDAC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca608

b:12.9
occ:1.00
 O B:ASP181 2.6 10.7 1.0
OD1 B:ASP179 2.6 10.0 1.0
O B:PHE203 2.6 11.9 1.0
O B:HIS183 2.8 10.2 1.0
O B:ASP179 2.8 10.4 1.0
OG B:SER202 2.9 11.9 1.0
CG B:ASP179 3.3 10.0 1.0
C B:ASP179 3.4 10.6 1.0
C B:ASP181 3.6 10.1 1.0
C B:PHE203 3.6 12.2 1.0
N B:ASP181 3.7 9.6 1.0
C B:HIS183 3.8 11.2 1.0
CB B:ASP179 3.8 9.5 1.0
N B:PHE203 3.8 11.4 1.0
CB B:HIS204 3.9 11.4 1.0
CA B:ASP181 4.0 9.8 1.0
CB B:ASP181 4.0 9.9 1.0
N B:ILE180 4.1 9.7 1.0
OD2 B:ASP179 4.1 12.1 1.0
C B:ILE180 4.1 9.6 1.0
CB B:SER202 4.1 12.4 1.0
CA B:ILE180 4.2 10.2 1.0
CA B:ASP179 4.3 9.4 1.0
ND1 B:HIS204 4.3 11.4 1.0
CA B:HIS204 4.4 11.8 1.0
CA B:PHE203 4.4 12.0 1.0
CA B:SER202 4.4 11.7 1.0
N B:HIS204 4.4 12.3 1.0
N B:HIS183 4.4 11.4 1.0
N B:GLY185 4.4 12.8 1.0
CA B:HIS184 4.4 12.6 1.0
N B:HIS184 4.5 12.4 1.0
C B:SER202 4.5 12.5 1.0
O B:HOH744 4.6 15.3 1.0
CG B:HIS204 4.6 11.5 1.0
C B:ILE182 4.6 11.4 1.0
N B:ILE182 4.7 10.4 1.0
CA B:HIS183 4.7 11.3 1.0
C B:HIS184 4.8 12.6 1.0
O B:ILE180 4.9 10.3 1.0
O B:ILE182 5.0 12.0 1.0
CE1 B:HIS145 5.0 10.8 1.0

Calcium binding site 3 out of 3 in 7zzu

Go back to Calcium Binding Sites List in 7zzu
Calcium binding site 3 out of 3 in the Inhibitory 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 Inhibitory Ligand Binding to HDAC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca604

b:19.3
occ:1.00
 O C:ASP181 2.6 17.9 1.0
O C:PHE203 2.6 17.9 1.0
OD1 C:ASP179 2.7 17.8 1.0
O C:HIS183 2.8 16.7 1.0
O C:ASP179 2.9 17.6 1.0
OG C:SER202 3.0 18.6 1.0
CG C:ASP179 3.4 17.9 1.0
C C:ASP179 3.5 17.9 1.0
C C:ASP181 3.5 18.2 1.0
C C:PHE203 3.6 19.6 1.0
C C:HIS183 3.7 17.3 1.0
N C:ASP181 3.7 18.5 1.0
CB C:ASP179 3.8 17.5 1.0
N C:PHE203 3.8 18.9 1.0
CB C:HIS204 3.8 20.1 1.0
CA C:ASP181 4.0 18.6 1.0
CB C:ASP181 4.1 17.8 1.0
N C:ILE180 4.1 18.0 1.0
C C:ILE180 4.1 19.1 1.0
CB C:SER202 4.2 18.5 1.0
OD2 C:ASP179 4.2 18.2 1.0
CA C:ILE180 4.3 18.6 1.0
CA C:ASP179 4.3 17.1 1.0
ND1 C:HIS204 4.3 20.0 1.0
CA C:HIS204 4.4 20.6 1.0
N C:HIS183 4.4 17.8 1.0
CA C:PHE203 4.4 19.7 1.0
CA C:HIS184 4.4 18.1 1.0
N C:HIS204 4.4 20.2 1.0
CA C:SER202 4.4 18.8 1.0
N C:HIS184 4.4 17.9 1.0
N C:GLY185 4.4 18.2 1.0
C C:SER202 4.5 19.2 1.0
O C:HOH731 4.5 19.1 1.0
C C:ILE182 4.6 18.2 1.0
CG C:HIS204 4.6 20.2 1.0
N C:ILE182 4.6 18.2 1.0
CA C:HIS183 4.7 17.6 1.0
C C:HIS184 4.8 18.4 1.0
O C:ILE180 4.9 19.3 1.0
O C:ILE182 5.0 18.1 1.0
CE1 C:HIS145 5.0 16.5 1.0
CA C:ILE182 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: Tue Apr 4 19:22:48 2023

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