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Zinc in PDB 7sgk: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728:
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 Dkfz-728, PDB code: 7sgk 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) 69.76 / 2.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.548, 80.548, 243.35, 90, 90, 120
R / Rfree (%) 19.5 / 24.3

Other elements in 7sgk:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728 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 Dkfz-728 (pdb code 7sgk). 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 Dkfz-728, PDB code: 7sgk:

Zinc binding site 1 out of 1 in 7sgk

Go back to Zinc Binding Sites List in 7sgk
Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Dkfz-728


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 Dkfz-728 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:36.2
occ:1.00
 O09 A:9A9701 1.8 40.6 1.0
OD2 A:ASP174 1.9 30.9 1.0
OD2 A:ASP267 2.0 33.5 1.0
ND1 A:HIS176 2.3 34.4 1.0
O07 A:9A9701 2.5 44.3 1.0
N08 A:9A9701 2.6 35.4 1.0
CG A:ASP174 2.7 33.4 1.0
OD1 A:ASP174 2.8 34.3 1.0
C06 A:9A9701 2.9 44.4 1.0
CG A:ASP267 2.9 28.8 1.0
OD1 A:ASP267 3.2 28.9 1.0
CE1 A:HIS176 3.2 38.5 1.0
CG A:HIS176 3.2 35.2 1.0
CB A:HIS176 3.5 30.9 1.0
N A:HIS176 3.8 36.9 1.0
CB A:ASP174 4.1 29.4 1.0
CG1 A:VAL175 4.2 25.4 1.0
N A:VAL175 4.2 31.1 1.0
NE2 A:HIS136 4.2 25.9 1.0
CB A:ASP267 4.3 30.4 1.0
CA A:HIS176 4.3 30.4 1.0
C05 A:9A9701 4.3 36.7 1.0
OH A:TYR307 4.3 37.8 1.0
NE2 A:HIS176 4.4 38.3 1.0
CD2 A:HIS176 4.4 35.3 1.0
CA A:GLY305 4.4 34.8 1.0
CE1 A:HIS136 4.5 25.8 1.0
CE2 A:TYR307 4.5 33.6 1.0
N A:GLY305 4.7 38.2 1.0
C A:VAL175 4.7 34.2 1.0
NE2 A:HIS137 4.7 37.5 1.0
C A:ASP174 4.9 34.3 1.0
CA A:VAL175 4.9 34.0 1.0
CA A:ASP174 4.9 32.9 1.0
C04 A:9A9701 4.9 45.0 1.0
CZ A:TYR307 5.0 35.7 1.0

Reference:

R.R.Steimbach, C.J.Herbst-Gervasoni, S.Lechner, T.M.Stewart, G.Klinke, J.Ridinger, M.N.E.Geraldy, G.Tihanyi, J.R.Foley, U.Uhrig, B.Kuster, G.Poschet, R.A.Casero Jr., G.Medard, I.Oehme, D.W.Christianson, N.Gunkel, A.K.Miller. Aza-Saha Derivatives Are Selective Histone Deacetylase 10 Chemical Probes That Inhibit Polyamine Deacetylation and Phenocopy HDAC10 Knockout. J.Am.Chem.Soc. V. 144 18861 2022.
ISSN: ESSN 1520-5126
PubMed: 36200994
DOI: 10.1021/JACS.2C05030
Page generated: Fri Aug 22 04:41:44 2025

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