Potassium in PDB 7u3m: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with N-Methylpiperazine Benzhydroxamic Acid

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with N-Methylpiperazine Benzhydroxamic Acid

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with N-Methylpiperazine Benzhydroxamic Acid:
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 N-Methylpiperazine Benzhydroxamic Acid, PDB code: 7u3m 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) 60.96 / 2.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.75, 80.75, 248.874, 90, 90, 120
R / Rfree (%) 19.6 / 23.3

Other elements in 7u3m:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with N-Methylpiperazine Benzhydroxamic Acid also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with N-Methylpiperazine Benzhydroxamic Acid (pdb code 7u3m). 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 N-Methylpiperazine Benzhydroxamic Acid, PDB code: 7u3m:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 7u3m

Go back to Potassium Binding Sites List in 7u3m
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with N-Methylpiperazine Benzhydroxamic Acid


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 N-Methylpiperazine Benzhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K703

b:29.6
occ:1.00
 O A:ASP174 2.6 28.7 1.0
O A:TRP196 2.7 28.7 1.0
O A:HIS176 2.7 31.0 1.0
OD2 A:ASP172 2.8 30.3 1.0
OG A:SER195 2.9 24.1 1.0
O A:ASP172 2.9 31.8 1.0
CG A:ASP172 3.1 28.4 1.0
C A:ASP172 3.5 33.5 1.0
C A:ASP174 3.5 33.4 1.0
CB A:ASP172 3.7 26.9 1.0
OD1 A:ASP172 3.7 35.5 1.0
C A:HIS176 3.8 26.5 1.0
N A:ASP174 3.8 27.3 1.0
C A:TRP196 3.9 32.1 1.0
CB A:SER195 4.0 30.8 1.0
CA A:ASP174 4.0 29.6 1.0
CB A:ASP174 4.0 27.7 1.0
N A:TRP196 4.1 32.9 1.0
CA A:ASP172 4.2 29.6 1.0
N A:TRP173 4.2 33.4 1.0
C A:TRP173 4.3 27.3 1.0
CA A:SER195 4.3 23.5 1.0
N A:HIS176 4.4 31.1 1.0
CB A:HIS197 4.4 25.8 1.0
CA A:TRP173 4.4 26.9 1.0
CA A:HIS177 4.4 30.0 1.0
N A:HIS177 4.5 29.4 1.0
C A:SER195 4.5 34.5 1.0
CD1 A:TRP196 4.5 29.1 1.0
N A:GLY178 4.6 29.7 1.0
ND1 A:HIS197 4.6 26.1 1.0
CA A:TRP196 4.6 31.4 1.0
N A:VAL175 4.6 33.0 1.0
CE1 A:HIS136 4.7 28.6 1.0
C A:VAL175 4.7 33.5 1.0
CA A:HIS176 4.8 27.5 1.0
OH A:TYR193 4.8 30.4 1.0
CA A:HIS197 4.8 25.2 1.0
N A:HIS197 4.8 26.4 1.0
C A:HIS177 4.9 29.1 1.0
ND1 A:HIS136 4.9 27.9 1.0
O A:TRP173 5.0 30.7 1.0

Potassium binding site 2 out of 2 in 7u3m

Go back to Potassium Binding Sites List in 7u3m
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with N-Methylpiperazine Benzhydroxamic Acid


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 N-Methylpiperazine Benzhydroxamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K704

b:50.6
occ:1.00
 O A:HOH885 2.4 34.2 0.7
O A:VAL191 2.5 35.7 1.0
O A:PHE185 2.5 29.3 1.0
O A:ASP188 2.6 39.2 1.0
O A:HOH867 2.6 34.2 1.0
O A:PHE224 3.3 31.8 1.0
C A:PHE185 3.6 34.4 1.0
CB A:PHE224 3.6 33.7 1.0
C A:VAL191 3.7 37.0 1.0
C A:ASP188 3.7 37.9 1.0
CB A:PHE185 3.7 30.3 1.0
O A:HOH837 3.9 33.3 1.0
C A:PHE224 4.0 35.8 1.0
N A:ASP188 4.1 36.8 1.0
CA A:PHE185 4.2 30.8 1.0
CA A:ASP188 4.3 38.9 1.0
CA A:PHE224 4.4 37.5 1.0
CA A:VAL191 4.4 33.5 1.0
CB A:ASP188 4.5 41.0 1.0
CB A:VAL191 4.5 33.1 1.0
N A:VAL191 4.5 33.8 1.0
N A:GLU186 4.6 33.7 1.0
N A:LEU192 4.7 32.7 1.0
C A:GLU186 4.7 39.0 1.0
CA A:GLU186 4.7 39.5 1.0
N A:PRO189 4.7 38.5 1.0
O A:GLU186 4.7 43.8 1.0
CA A:LEU192 4.8 32.1 1.0
N A:ASN225 4.8 34.2 1.0
CA A:PRO189 4.8 36.0 1.0
CG A:PHE224 4.8 30.5 1.0
N A:TYR193 4.8 29.6 1.0
O A:GLY221 4.9 33.8 1.0
CG A:PHE185 4.9 30.4 1.0
CG1 A:VAL191 5.0 31.7 1.0

Reference:

P.Zeyen, Y.Zeyn, D.Herp, F.Mahmoudi, T.Z.Yesiloglu, F.Erdmann, M.Schmidt, D.Robaa, C.Romier, J.Ridinger, C.J.Herbst-Gervasoni, D.W.Christianson, I.Oehme, M.Jung, O.H.Kramer, W.Sippl. Identification of Histone Deacetylase 10 (HDAC10) Inhibitors That Modulate Autophagy in Transformed Cells. Eur.J.Med.Chem. V. 234 14272 2022.
ISSN: ISSN 0223-5234
PubMed: 35306288
DOI: 10.1016/J.EJMECH.2022.114272
Page generated: Wed Apr 5 10:20:54 2023

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