Zinc 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:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 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 N-Methylpiperazine Benzhydroxamic Acid, PDB code: 7u3m:

Zinc binding site 1 out of 1 in 7u3m

Go back to Zinc Binding Sites List in 7u3m
Zinc binding site 1 out of 1 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 Zinc with other atoms in the Zn 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:Zn702

b:37.7
occ:1.00
 OD2 A:ASP174 1.9 30.9 1.0
O16 A:L8C701 2.0 52.6 1.0
OD2 A:ASP267 2.1 34.6 1.0
O A:HOH816 2.1 36.1 1.0
ND1 A:HIS176 2.2 38.5 1.0
CG A:ASP174 2.7 37.4 1.0
N15 A:L8C701 2.7 47.1 1.0
OD1 A:ASP174 2.7 35.6 1.0
CG A:ASP267 3.1 29.9 1.0
CE1 A:HIS176 3.1 37.1 1.0
CG A:HIS176 3.2 32.5 1.0
OD1 A:ASP267 3.4 30.9 1.0
CB A:HIS176 3.5 28.7 1.0
C13 A:L8C701 3.5 49.2 1.0
O14 A:L8C701 3.6 56.9 1.0
N A:HIS176 3.8 31.1 1.0
CB A:ASP174 4.1 27.7 1.0
NE2 A:HIS136 4.2 34.0 1.0
NE2 A:HIS176 4.2 38.9 1.0
CA A:HIS176 4.3 27.5 1.0
CD2 A:HIS176 4.3 39.1 1.0
CG1 A:VAL175 4.3 34.7 1.0
N A:VAL175 4.3 33.0 1.0
CB A:ASP267 4.4 34.6 1.0
OH A:TYR307 4.5 45.0 1.0
CA A:GLY305 4.5 39.5 1.0
CE1 A:HIS136 4.5 28.6 1.0
NE2 A:HIS137 4.6 36.2 1.0
CE2 A:TYR307 4.7 39.3 1.0
C10 A:L8C701 4.7 44.1 1.0
C A:VAL175 4.7 33.5 1.0
N A:GLY305 4.8 35.1 1.0
C A:ASP174 4.9 33.4 1.0
CA A:ASP174 4.9 29.6 1.0
CA A:VAL175 4.9 33.5 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 Oct 30 11:50:32 2024

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