Atomistry » Sodium » PDB 7zyq-8acy » 8a0b
Atomistry »
  Sodium »
    PDB 7zyq-8acy »
      8a0b »

Sodium in PDB 8a0b: Inhibitor Binding to HDAC2

Enzymatic activity of Inhibitor Binding to HDAC2

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

Protein crystallography data

The structure of Inhibitor Binding to HDAC2, PDB code: 8a0b 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) 67.17 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.221, 98.018, 139.402, 90, 90, 90
R / Rfree (%) 16.5 / 18.8

Other elements in 8a0b:

The structure of Inhibitor 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 Inhibitor Binding to HDAC2 (pdb code 8a0b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Inhibitor Binding to HDAC2, PDB code: 8a0b:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8a0b

Go back to Sodium Binding Sites List in 8a0b
Sodium binding site 1 out of 3 in the Inhibitor 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 Inhibitor Binding to HDAC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:27.8
occ:1.00
 O A:PHE192 2.2 25.2 1.0
O A:VAL198 2.3 26.8 1.0
O A:HOH799 2.4 27.6 1.0
O A:THR195 2.4 27.7 1.0
O A:HOH821 3.0 36.4 1.0
C A:PHE192 3.3 24.9 1.0
C A:VAL198 3.6 26.3 1.0
O A:TYR227 3.6 26.0 1.0
C A:THR195 3.6 29.0 1.0
CB A:TYR227 3.7 26.2 1.0
CB A:PHE192 3.9 25.4 1.0
C A:TYR227 4.2 26.2 1.0
N A:THR195 4.2 29.8 1.0
CG2 A:THR195 4.2 28.7 1.0
CA A:PHE192 4.2 24.6 1.0
N A:TYR193 4.3 25.6 1.0
CA A:TYR193 4.3 26.2 1.0
C A:TYR193 4.3 27.4 1.0
CA A:THR195 4.4 29.5 1.0
O A:TYR193 4.4 27.7 1.0
N A:MET199 4.5 24.8 1.0
CA A:VAL198 4.5 24.3 1.0
CA A:MET199 4.5 22.8 1.0
CA A:TYR227 4.6 25.7 1.0
N A:VAL198 4.6 24.7 1.0
CA A:GLY224 4.6 29.5 1.0
CB A:VAL198 4.6 23.4 1.0
N A:ASP196 4.7 30.1 1.0
O A:GLY224 4.7 26.0 1.0
N A:THR194 4.9 27.3 1.0
CA A:ASP196 4.9 29.1 1.0
N A:THR200 4.9 23.3 1.0
CB A:THR195 4.9 31.1 1.0
N A:ALA228 4.9 25.5 1.0
CG A:TYR227 4.9 27.7 1.0

Sodium binding site 2 out of 3 in 8a0b

Go back to Sodium Binding Sites List in 8a0b
Sodium binding site 2 out of 3 in the Inhibitor 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 Inhibitor Binding to HDAC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:26.5
occ:1.00
 O B:PHE192 2.3 24.9 1.0
O B:VAL198 2.3 25.1 1.0
O B:HOH803 2.4 23.1 1.0
O B:THR195 2.4 26.0 1.0
O B:HOH795 2.8 31.9 1.0
C B:PHE192 3.4 24.3 1.0
O B:TYR227 3.5 26.6 1.0
C B:VAL198 3.6 24.1 1.0
C B:THR195 3.7 26.1 1.0
CB B:TYR227 3.7 25.6 1.0
CB B:PHE192 4.0 24.1 1.0
C B:TYR227 4.1 26.3 1.0
N B:THR195 4.2 27.2 1.0
CG2 B:THR195 4.2 27.4 1.0
N B:TYR193 4.3 24.6 1.0
CA B:PHE192 4.3 23.6 1.0
CA B:TYR193 4.3 24.2 1.0
C B:TYR193 4.3 25.8 1.0
O B:TYR193 4.3 26.7 1.0
CA B:THR195 4.4 26.6 1.0
N B:MET199 4.5 22.3 1.0
CA B:MET199 4.5 22.0 1.0
CA B:VAL198 4.5 22.9 1.0
CA B:TYR227 4.5 25.2 1.0
N B:VAL198 4.6 24.4 1.0
CA B:GLY224 4.6 28.8 1.0
O B:GLY224 4.7 26.5 1.0
CB B:VAL198 4.7 22.5 1.0
N B:ASP196 4.7 24.7 1.0
N B:THR194 4.8 26.6 1.0
N B:ALA228 4.9 24.1 1.0
N B:THR200 4.9 21.1 1.0
CA B:ASP196 4.9 26.0 1.0
CG B:TYR227 4.9 25.9 1.0
CB B:THR195 5.0 27.7 1.0

Sodium binding site 3 out of 3 in 8a0b

Go back to Sodium Binding Sites List in 8a0b
Sodium binding site 3 out of 3 in the Inhibitor 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 Inhibitor Binding to HDAC2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na603

b:30.3
occ:1.00
 O C:VAL198 2.3 29.4 1.0
O C:PHE192 2.3 26.9 1.0
O C:THR195 2.3 29.4 1.0
O C:HOH772 2.3 27.0 1.0
O C:HOH788 2.9 41.3 1.0
C C:PHE192 3.4 26.1 1.0
C C:VAL198 3.5 28.7 1.0
C C:THR195 3.5 29.6 1.0
O C:TYR227 3.6 31.1 1.0
CB C:TYR227 3.7 31.3 1.0
CB C:PHE192 4.0 25.8 1.0
N C:THR195 4.1 29.3 1.0
C C:TYR227 4.1 31.9 1.0
CG2 C:THR195 4.2 28.3 1.0
CA C:PHE192 4.3 25.4 1.0
CA C:THR195 4.3 28.8 1.0
C C:TYR193 4.4 28.0 1.0
N C:TYR193 4.4 25.4 1.0
CA C:TYR193 4.4 26.1 1.0
O C:TYR193 4.4 29.0 1.0
N C:MET199 4.4 27.8 1.0
CA C:MET199 4.4 27.7 0.5
CA C:MET199 4.4 27.2 0.5
CA C:VAL198 4.5 27.4 1.0
CA C:TYR227 4.5 30.7 1.0
N C:VAL198 4.5 28.1 1.0
CA C:GLY224 4.5 29.6 1.0
N C:ASP196 4.6 28.9 1.0
O C:GLY224 4.6 29.0 1.0
CB C:VAL198 4.7 26.5 1.0
CA C:ASP196 4.8 30.1 1.0
CG C:TYR227 4.8 32.6 1.0
N C:THR194 4.9 26.5 1.0
CB C:THR195 4.9 29.9 1.0
N C:ALA228 4.9 31.1 1.0
N C:THR200 4.9 26.5 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: Wed Oct 9 10:21:41 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