Potassium in PDB 7u59: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Piperidine-4-Hydroxamic Acid Inhibitor

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Piperidine-4-Hydroxamic Acid Inhibitor

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Piperidine-4-Hydroxamic Acid Inhibitor:
3.5.1.48; 3.5.1.62;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Piperidine-4-Hydroxamic Acid Inhibitor, PDB code: 7u59 was solved by C.J.Herbst-Gervasoni, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.94 / 2.18
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.849, 80.849, 247.467, 90, 90, 120
R / Rfree (%) 17.9 / 21

Other elements in 7u59:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Piperidine-4-Hydroxamic Acid Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Sodium (Na) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Piperidine-4-Hydroxamic Acid Inhibitor (pdb code 7u59). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Piperidine-4-Hydroxamic Acid Inhibitor, PDB code: 7u59:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 7u59

Go back to Potassium Binding Sites List in 7u59
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Piperidine-4-Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Piperidine-4-Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K706

b:26.5
occ:1.00
 O A:ASP174 2.6 25.7 1.0
O A:HIS176 2.6 24.6 1.0
O A:TRP196 2.7 23.8 1.0
OD2 A:ASP172 2.8 28.1 1.0
OG A:SER195 2.9 22.9 1.0
O A:ASP172 2.9 28.7 1.0
CG A:ASP172 3.1 28.5 1.0
C A:ASP174 3.5 32.1 1.0
C A:ASP172 3.6 31.0 1.0
OD1 A:ASP172 3.6 31.9 1.0
C A:HIS176 3.7 23.2 1.0
CB A:ASP172 3.8 24.3 1.0
C A:TRP196 3.8 28.9 1.0
N A:ASP174 3.9 26.2 1.0
CB A:SER195 3.9 26.2 1.0
N A:TRP196 4.0 25.1 1.0
CA A:ASP174 4.1 29.8 1.0
CB A:ASP174 4.1 25.6 1.0
CA A:SER195 4.3 19.2 1.0
C A:TRP173 4.3 28.0 1.0
CA A:ASP172 4.3 22.6 1.0
N A:TRP173 4.3 29.2 1.0
N A:HIS176 4.3 26.0 1.0
CA A:HIS177 4.3 25.5 1.0
N A:HIS177 4.4 25.6 1.0
CA A:TRP173 4.5 25.1 1.0
CB A:HIS197 4.5 22.8 1.0
C A:SER195 4.5 27.5 1.0
N A:GLY178 4.5 26.0 1.0
ND1 A:HIS197 4.6 22.4 1.0
N A:VAL175 4.6 27.8 1.0
CD1 A:TRP196 4.6 22.7 1.0
CA A:TRP196 4.6 26.2 1.0
C A:VAL175 4.6 27.4 1.0
CA A:HIS176 4.7 24.3 1.0
CE1 A:HIS136 4.7 22.0 1.0
CA A:HIS197 4.8 23.6 1.0
OH A:TYR193 4.8 29.2 1.0
N A:HIS197 4.8 24.7 1.0
C A:HIS177 4.8 27.5 1.0
ND1 A:HIS136 4.9 24.8 1.0
CA A:VAL175 4.9 29.6 1.0
O A:TRP173 4.9 27.9 1.0

Potassium binding site 2 out of 2 in 7u59

Go back to Potassium Binding Sites List in 7u59
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Piperidine-4-Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Piperidine-4-Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K707

b:44.1
occ:1.00
 O A:HOH923 2.3 30.0 0.7
O A:VAL191 2.5 31.7 1.0
O A:HOH836 2.6 27.7 1.0
O A:PHE185 2.6 29.5 1.0
O A:ASP188 2.6 34.4 1.0
O A:PHE224 3.2 30.9 1.0
CB A:PHE224 3.6 26.0 1.0
C A:PHE185 3.6 31.7 1.0
C A:ASP188 3.7 34.7 1.0
CB A:PHE185 3.7 28.4 1.0
C A:VAL191 3.7 33.0 1.0
O A:HOH890 3.7 29.9 1.0
C A:PHE224 3.9 28.6 1.0
N A:ASP188 4.2 41.4 1.0
CA A:PHE185 4.3 28.8 1.0
CA A:ASP188 4.3 37.1 1.0
CA A:PHE224 4.3 31.8 1.0
CB A:ASP188 4.5 37.1 1.0
O A:GLU186 4.5 33.4 1.0
CA A:VAL191 4.5 33.2 1.0
CB A:VAL191 4.6 30.9 1.0
N A:GLU186 4.6 32.9 1.0
N A:VAL191 4.6 29.7 1.0
C A:GLU186 4.6 35.6 1.0
N A:LEU192 4.7 30.7 1.0
N A:PRO189 4.7 34.1 1.0
N A:ASN225 4.7 27.4 1.0
CA A:LEU192 4.7 33.2 1.0
O A:GLY221 4.8 34.0 1.0
N A:TYR193 4.8 28.3 1.0
CA A:GLU186 4.8 35.9 1.0
CG A:PHE224 4.8 29.8 1.0
CA A:PRO189 4.9 27.5 1.0
CG A:PHE185 5.0 29.1 1.0

Reference:

D.Herp, J.Ridinger, D.Robaa, S.A.Shinsky, K.Schmidtkunz, T.Z.Yesiloglu, T.Bayer, R.R.Steimbach, C.J.Herbst-Gervasoni, A.Merz, C.Romier, P.Sehr, N.Gunkel, A.K.Miller, D.W.Christianson, I.Oehme, W.Sippl, M.Jung. First Fluorescent Acetylspermidine Deacetylation Assay For HDAC10 Identifies Selective Inhibitors with Cellular Target Engagement. Chembiochem V. 23 00180 2022.
ISSN: ESSN 1439-7633
PubMed: 35608330
DOI: 10.1002/CBIC.202200180
Page generated: Wed Apr 5 10:20:49 2023

Last articles

Cl in 6COG
Cl in 6CST
Cl in 6CTW
Cl in 6CTZ
Cl in 6CTT
Cl in 6CSP
Cl in 6CU9
Cl in 6CTX
Cl in 6CTU
Cl in 6CTP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy