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Zinc in PDB 6vnq: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Bishydroxamic Acid Based Inhibitor

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Bishydroxamic Acid Based Inhibitor

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Bishydroxamic Acid Based 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 Bishydroxamic Acid Based Inhibitor, PDB code: 6vnq 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 / 2.05
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.549, 80.549, 245.370, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 23.1

Other elements in 6vnq:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Bishydroxamic Acid Based Inhibitor 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 Bishydroxamic Acid Based Inhibitor (pdb code 6vnq). 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 Bishydroxamic Acid Based Inhibitor, PDB code: 6vnq:

Zinc binding site 1 out of 1 in 6vnq

Go back to Zinc Binding Sites List in 6vnq
Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with Bishydroxamic Acid Based 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 Bishydroxamic Acid Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:32.7
occ:1.00
 OD2 A:ASP174 2.0 24.9 1.0
OD2 A:ASP267 2.1 33.4 1.0
O01 A:R5G701 2.1 44.4 0.7
O A:HOH801 2.2 31.7 0.7
ND1 A:HIS176 2.3 30.0 1.0
O01 A:R5G701 2.4 34.7 0.3
N02 A:R5G701 2.4 37.5 0.7
N02 A:R5G701 2.6 32.8 0.3
CG A:ASP174 2.7 34.7 1.0
OD1 A:ASP174 2.7 31.8 1.0
O24 A:R5G701 2.8 40.6 0.3
C03 A:R5G701 2.8 37.4 0.3
CG A:ASP267 3.1 29.5 1.0
CG A:HIS176 3.2 30.4 1.0
CE1 A:HIS176 3.3 32.3 1.0
C03 A:R5G701 3.3 37.1 0.7
OD1 A:ASP267 3.4 28.4 1.0
CB A:HIS176 3.4 26.8 1.0
N A:HIS176 3.8 30.4 1.0
O24 A:R5G701 3.8 38.3 0.7
C04 A:R5G701 3.9 36.2 0.3
CB A:ASP174 4.2 24.6 1.0
NE2 A:HIS136 4.2 28.5 1.0
CA A:HIS176 4.3 30.9 1.0
C04 A:R5G701 4.3 35.7 0.7
N A:VAL175 4.3 28.6 1.0
CD2 A:HIS176 4.3 33.6 1.0
NE2 A:HIS176 4.4 33.3 1.0
CG1 A:VAL175 4.4 29.0 1.0
C23 A:R5G701 4.4 37.9 0.3
CB A:ASP267 4.4 29.3 1.0
CA A:GLY305 4.4 27.7 1.0
NE2 A:HIS137 4.5 31.2 1.0
CE2 A:TYR307 4.6 36.6 1.0
CE1 A:HIS136 4.7 24.2 1.0
OH A:TYR307 4.7 39.3 1.0
N A:GLY305 4.7 32.8 1.0
C A:VAL175 4.7 35.2 1.0
C23 A:R5G701 4.8 38.1 0.7
C05 A:R5G701 4.9 36.1 0.3
CA A:VAL175 4.9 30.4 1.0
C A:ASP174 5.0 34.0 1.0
CA A:ASP174 5.0 25.2 1.0

Reference:

A.K.Miller, M.Morgen, R.R.Steimbach, M.Geraldy, L.Hellweg, P.Sehr, J.Ridinger, O.Witt, I.Oehme, C.J.Herbst-Gervasoni, J.D.Osko, N.J.Porter, D.W.Christianson, N.Gunkel. Design and Synthesis of Dihydroxamic Acids As HDAC6/8/10 Inhibitors. Chemmedchem 2020.
ISSN: ESSN 1860-7187
PubMed: 32348628
DOI: 10.1002/CMDC.202000149
Page generated: Tue Oct 29 09:05:09 2024

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