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Sodium 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
Calcium (Ca) 3 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 3 in 7zzw

Go back to Sodium Binding Sites List in 7zzw
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:Na608

b:16.6
occ:1.00
 O A:HOH789 2.5 21.9 1.0
O A:PHE192 2.5 24.6 1.0
O A:VAL198 2.5 25.0 1.0
O A:THR195 2.7 24.5 1.0
O A:HOH824 2.8 26.1 1.0
O A:TYR227 3.1 23.3 1.0
C A:PHE192 3.5 23.4 1.0
CB A:TYR227 3.7 25.1 1.0
C A:VAL198 3.7 22.8 1.0
C A:TYR227 3.8 23.8 1.0
C A:THR195 4.0 24.7 1.0
CB A:PHE192 4.1 21.7 1.0
CA A:TYR193 4.3 23.6 1.0
N A:TYR193 4.3 24.1 1.0
CA A:TYR227 4.3 24.2 1.0
C A:TYR193 4.4 23.2 1.0
O A:TYR193 4.4 23.8 1.0
CA A:PHE192 4.4 22.6 1.0
N A:THR195 4.4 23.8 1.0
CA A:MET199 4.5 22.8 1.0
CG2 A:THR195 4.5 25.2 1.0
N A:ALA228 4.6 22.1 1.0
N A:MET199 4.6 21.3 1.0
N A:THR200 4.7 19.6 1.0
CA A:VAL198 4.7 22.1 1.0
O A:GLY224 4.7 24.6 1.0
CA A:THR195 4.7 25.6 1.0
CA A:GLY224 4.8 27.2 1.0
N A:VAL198 4.8 23.2 1.0
OG1 A:THR200 4.8 19.8 1.0
CB A:VAL198 4.8 21.0 1.0
N A:ASP196 5.0 26.5 1.0
N A:THR194 5.0 26.6 1.0
CG A:TYR227 5.0 25.5 1.0

Sodium binding site 2 out of 3 in 7zzw

Go back to Sodium Binding Sites List in 7zzw
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:Na609

b:19.8
occ:1.00
 O B:PHE192 2.5 25.0 1.0
O B:HOH788 2.5 24.1 1.0
O B:VAL198 2.5 24.9 1.0
O B:THR195 2.8 27.6 1.0
O B:HOH822 2.9 27.9 1.0
O B:TYR227 3.1 23.3 1.0
C B:PHE192 3.5 25.6 1.0
CB B:TYR227 3.7 27.0 1.0
C B:VAL198 3.8 24.3 1.0
C B:TYR227 3.8 24.7 1.0
C B:THR195 4.0 26.8 1.0
CB B:PHE192 4.0 22.5 1.0
CA B:TYR193 4.3 25.0 1.0
CA B:TYR227 4.3 25.1 1.0
N B:TYR193 4.3 24.9 1.0
CA B:PHE192 4.4 23.4 1.0
C B:TYR193 4.4 26.2 1.0
O B:TYR193 4.4 27.3 1.0
N B:THR195 4.4 29.3 1.0
CA B:MET199 4.5 23.6 1.0
CG2 B:THR195 4.5 28.3 1.0
N B:ALA228 4.5 23.3 1.0
N B:MET199 4.6 23.7 1.0
N B:THR200 4.6 20.6 1.0
O B:GLY224 4.7 25.4 1.0
CA B:VAL198 4.7 22.7 1.0
CA B:GLY224 4.7 28.7 1.0
CA B:THR195 4.8 29.1 1.0
OG1 B:THR200 4.8 21.0 1.0
CB B:VAL198 4.8 21.3 1.0
N B:VAL198 4.9 23.4 1.0
CG B:TYR227 5.0 26.9 1.0
C B:MET199 5.0 22.5 1.0
N B:THR194 5.0 26.7 1.0

Sodium binding site 3 out of 3 in 7zzw

Go back to Sodium Binding Sites List in 7zzw
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:Na607

b:19.2
occ:1.00
 O C:HOH755 2.5 23.4 1.0
O C:VAL198 2.5 24.2 1.0
O C:PHE192 2.5 23.1 1.0
O C:THR195 2.8 24.7 1.0
O C:HOH750 2.9 27.3 1.0
O C:TYR227 3.1 26.2 1.0
C C:PHE192 3.6 22.0 1.0
CB C:TYR227 3.7 24.3 1.0
C C:VAL198 3.7 25.7 1.0
C C:TYR227 3.8 25.8 1.0
C C:THR195 4.0 23.9 1.0
CB C:PHE192 4.0 22.2 1.0
CA C:TYR227 4.3 24.8 1.0
CA C:TYR193 4.4 23.6 1.0
N C:TYR193 4.4 22.5 1.0
CA C:MET199 4.4 24.4 1.0
CA C:PHE192 4.4 21.1 1.0
C C:TYR193 4.4 23.7 1.0
O C:TYR193 4.4 23.6 1.0
N C:THR195 4.4 24.0 1.0
CG2 C:THR195 4.5 23.6 1.0
N C:MET199 4.5 24.8 1.0
N C:ALA228 4.6 25.0 1.0
N C:THR200 4.7 24.1 1.0
O C:GLY224 4.7 23.9 1.0
CA C:VAL198 4.7 24.7 1.0
CA C:THR195 4.8 24.7 1.0
OG1 C:THR200 4.8 20.0 1.0
CA C:GLY224 4.8 24.9 1.0
CB C:VAL198 4.9 22.0 1.0
N C:VAL198 4.9 23.1 1.0
C C:MET199 5.0 24.4 1.0
CB C:ALA228 5.0 24.4 1.0
CA C:ALA228 5.0 24.4 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: Wed Oct 9 10:21:41 2024

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