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Potassium in PDB 7u6a: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 3-Thienylmethyl Benzhydroxamic Acid Inhibitor

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 3-Thienylmethyl Benzhydroxamic Acid Inhibitor

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 3-Thienylmethyl Benzhydroxamic 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 3-Thienylmethyl Benzhydroxamic Acid Inhibitor, PDB code: 7u6a 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) 60.97 / 2.25
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.748, 80.748, 248.919, 90, 90, 120
R / Rfree (%) 19.5 / 22.7

Other elements in 7u6a:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 3-Thienylmethyl Benzhydroxamic Acid Inhibitor 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 3-Thienylmethyl Benzhydroxamic Acid Inhibitor (pdb code 7u6a). 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 3-Thienylmethyl Benzhydroxamic Acid Inhibitor, PDB code: 7u6a:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 7u6a

Go back to Potassium Binding Sites List in 7u6a
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 3-Thienylmethyl Benzhydroxamic 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 3-Thienylmethyl Benzhydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K703

b:37.7
occ:1.00
 O A:ASP174 2.7 37.0 1.0
O A:HIS176 2.7 39.6 1.0
O A:TRP196 2.7 33.5 1.0
OD2 A:ASP172 2.8 33.9 1.0
O A:ASP172 2.8 37.6 1.0
OG A:SER195 2.9 28.9 1.0
CG A:ASP172 3.1 32.1 1.0
C A:ASP174 3.5 43.3 1.0
C A:ASP172 3.6 42.1 1.0
OD1 A:ASP172 3.7 42.1 1.0
N A:ASP174 3.7 33.1 1.0
CB A:ASP172 3.8 31.9 1.0
C A:HIS176 3.8 32.8 1.0
C A:TRP196 3.9 36.7 1.0
CB A:SER195 4.0 35.6 1.0
CA A:ASP174 4.0 34.1 1.0
N A:TRP196 4.0 35.9 1.0
CB A:ASP174 4.0 33.6 1.0
C A:TRP173 4.3 33.0 1.0
CA A:SER195 4.3 27.9 1.0
CA A:ASP172 4.3 32.3 1.0
N A:TRP173 4.3 38.5 1.0
CA A:HIS177 4.4 34.4 1.0
CB A:HIS197 4.4 33.4 1.0
CA A:TRP173 4.5 29.6 1.0
N A:HIS176 4.5 39.6 1.0
C A:SER195 4.5 41.5 1.0
ND1 A:HIS197 4.5 34.8 1.0
N A:HIS177 4.5 34.6 1.0
N A:GLY178 4.5 33.8 1.0
N A:VAL175 4.6 41.4 1.0
CD1 A:TRP196 4.6 34.3 1.0
CA A:TRP196 4.6 35.0 1.0
C A:VAL175 4.7 39.7 1.0
OH A:TYR193 4.7 35.6 1.0
CE1 A:HIS136 4.8 35.1 1.0
CA A:HIS197 4.8 30.9 1.0
CA A:HIS176 4.8 35.3 1.0
N A:HIS197 4.9 31.8 1.0
C A:HIS177 4.9 38.3 1.0
ND1 A:HIS136 4.9 35.4 1.0
CA A:VAL175 5.0 38.0 1.0
CG A:HIS197 5.0 37.4 1.0

Potassium binding site 2 out of 2 in 7u6a

Go back to Potassium Binding Sites List in 7u6a
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 3-Thienylmethyl Benzhydroxamic 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 3-Thienylmethyl Benzhydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K704

b:59.1
occ:1.00
 O A:HOH931 2.4 40.0 0.7
O A:VAL191 2.5 45.4 1.0
O A:HOH877 2.5 41.6 1.0
O A:PHE185 2.5 37.5 1.0
O A:ASP188 2.6 43.5 1.0
O A:PHE224 3.3 40.9 1.0
C A:PHE185 3.6 38.6 1.0
CB A:PHE224 3.6 40.0 1.0
C A:ASP188 3.6 46.4 1.0
C A:VAL191 3.7 43.4 1.0
CB A:PHE185 3.7 41.2 1.0
O A:HOH825 3.9 37.0 1.0
C A:PHE224 3.9 39.6 1.0
N A:ASP188 4.1 52.1 1.0
CA A:PHE185 4.3 36.6 1.0
CA A:ASP188 4.3 46.3 1.0
CA A:PHE224 4.4 42.1 1.0
CB A:ASP188 4.5 45.5 1.0
CA A:VAL191 4.5 41.3 1.0
CB A:VAL191 4.5 44.2 1.0
N A:GLU186 4.5 39.0 1.0
N A:VAL191 4.6 38.0 1.0
CA A:GLU186 4.6 46.3 1.0
C A:GLU186 4.6 46.2 1.0
N A:LEU192 4.6 41.8 1.0
N A:PRO189 4.7 46.2 1.0
O A:GLU186 4.7 47.0 1.0
CA A:LEU192 4.7 37.1 1.0
N A:ASN225 4.8 37.8 1.0
O A:GLY221 4.8 43.6 1.0
CA A:PRO189 4.8 38.4 1.0
CG A:PHE224 4.8 37.9 1.0
N A:TYR193 4.8 35.5 1.0
CG A:PHE185 5.0 42.3 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: Mon Aug 12 21:19:06 2024

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