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Zinc in PDB 5eek: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A, PDB code: 5eek was solved by Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.01 / 1.59
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.881, 94.429, 51.698, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 16.3

Other elements in 5eek:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A also contains other interesting chemical elements:

Potassium (K) 2 atoms
Iodine (I) 31 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A (pdb code 5eek). 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 6 Catalytic Domain 2 in Complex with Trichostatin A, PDB code: 5eek:

Zinc binding site 1 out of 1 in 5eek

Go back to Zinc Binding Sites List in 5eek
Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


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 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:14.3
occ:0.85
 OD2 A:ASP705 2.0 10.2 1.0
OD1 A:ASP612 2.0 9.3 1.0
ND1 A:HIS614 2.1 8.2 1.0
O1 A:TSN2004 2.2 22.1 1.0
O2 A:TSN2004 2.4 20.8 1.0
CG A:ASP612 2.7 8.3 1.0
OD2 A:ASP612 2.7 8.9 1.0
N1 A:TSN2004 2.7 24.6 1.0
C13 A:TSN2004 2.8 22.6 1.0
CE1 A:HIS614 3.0 8.9 1.0
CG A:ASP705 3.0 10.3 1.0
CG A:HIS614 3.2 8.9 1.0
OD1 A:ASP705 3.4 10.4 1.0
CB A:HIS614 3.6 8.7 1.0
N A:HIS614 3.9 7.9 1.0
CB A:ASP612 4.1 8.5 1.0
NE2 A:HIS614 4.1 10.0 1.0
NE2 A:HIS573 4.1 12.1 1.0
CG1 A:VAL613 4.2 8.8 1.0
C12 A:TSN2004 4.2 21.2 1.0
CD2 A:HIS614 4.2 9.7 1.0
CB A:ASP705 4.3 9.8 1.0
CA A:GLY743 4.3 11.0 1.0
N A:VAL613 4.4 7.9 1.0
CA A:HIS614 4.4 8.2 1.0
OH A:TYR745 4.5 15.4 1.0
CE1 A:HIS573 4.6 11.8 1.0
C11 A:TSN2004 4.6 20.5 1.0
N A:GLY743 4.7 9.8 1.0
CE2 A:TYR745 4.7 12.8 1.0
NE2 A:HIS574 4.7 10.9 1.0
C A:VAL613 4.8 8.6 1.0
C A:ASP612 4.8 8.0 1.0
CA A:ASP612 4.9 8.1 1.0
CA A:VAL613 5.0 8.1 1.0

Reference:

Y.Hai, D.W.Christianson. Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134
Page generated: Sun Oct 27 15:13:04 2024

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