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Zinc 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:

Potassium (K) 2 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Piperidine-4-Hydroxamic Acid Inhibitor, PDB code: 7u59:

Zinc binding site 1 out of 1 in 7u59

Go back to Zinc Binding Sites List in 7u59
Zinc binding site 1 out of 1 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 Zinc with other atoms in the Zn 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:Zn705

b:31.9
occ:1.00
OD2 A:ASP174 1.9 24.1 1.0
OD2 A:ASP267 2.0 27.6 1.0
O01 A:LDI704 2.2 33.6 1.0
O04 A:LDI704 2.3 38.0 1.0
ND1 A:HIS176 2.3 28.8 1.0
CG A:ASP174 2.6 30.4 1.0
OD1 A:ASP174 2.7 27.5 1.0
N02 A:LDI704 2.9 34.6 1.0
C03 A:LDI704 2.9 41.0 1.0
CG A:ASP267 3.0 28.4 1.0
OD1 A:ASP267 3.2 27.9 1.0
CG A:HIS176 3.2 29.4 1.0
CE1 A:HIS176 3.3 31.1 1.0
CB A:HIS176 3.5 27.5 1.0
N A:HIS176 3.8 26.0 1.0
CB A:ASP174 4.1 25.6 1.0
NE2 A:HIS136 4.2 29.8 1.0
N A:VAL175 4.3 27.8 1.0
CA A:HIS176 4.3 24.3 1.0
CG1 A:VAL175 4.3 29.0 1.0
CB A:ASP267 4.3 29.4 1.0
C05 A:LDI704 4.4 37.2 1.0
NE2 A:HIS176 4.4 29.8 1.0
CD2 A:HIS176 4.4 31.5 1.0
CA A:GLY305 4.5 31.4 1.0
OH A:TYR307 4.6 31.7 1.0
CE1 A:HIS136 4.6 22.0 1.0
CE2 A:TYR307 4.6 32.3 1.0
N A:GLY305 4.7 30.7 1.0
C06 A:LDI704 4.7 38.6 1.0
C A:VAL175 4.8 27.4 1.0
NE2 A:HIS137 4.8 31.9 1.0
C A:ASP174 4.9 32.1 1.0
CA A:ASP174 4.9 29.8 1.0
CA A:VAL175 4.9 29.6 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: Sat Apr 8 03:53:11 2023

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