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

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