Zinc in PDB 5vi6: Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A

Enzymatic activity of Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A

All present enzymatic activity of Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A, PDB code: 5vi6 was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.29 / 1.24
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 50.980, 50.980, 116.517, 90.00, 90.00, 120.00
R / Rfree (%) 12.1 / 14.3

Other elements in 5vi6:

The structure of Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin A (pdb code 5vi6). 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 Histone Deacetylase 8 in Complex with Trapoxin A, PDB code: 5vi6:

Zinc binding site 1 out of 1 in 5vi6

Go back to Zinc Binding Sites List in 5vi6
Zinc binding site 1 out of 1 in the Crystal Structure of Histone Deacetylase 8 in Complex with Trapoxin 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 Histone Deacetylase 8 in Complex with Trapoxin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:9.2
occ:1.00
 H1 B:5OM4 1.8 11.2 1.0
O01 B:5OM4 1.9 9.3 1.0
OD2 A:ASP178 2.0 8.4 1.0
OD2 A:ASP267 2.0 9.6 1.0
ND1 A:HIS180 2.1 8.8 1.0
O02 B:5OM4 2.5 9.3 1.0
C02 B:5OM4 2.7 9.1 1.0
CG A:ASP178 2.9 8.4 1.0
CE1 A:HIS180 2.9 9.0 1.0
CG A:ASP267 3.0 9.7 1.0
HE1 A:HIS180 3.0 10.8 1.0
H A:HIS180 3.1 9.9 1.0
HB2 A:HIS180 3.2 10.7 1.0
OD1 A:ASP178 3.2 8.9 1.0
CG A:HIS180 3.2 8.7 1.0
HA3 A:GLY304 3.3 11.2 1.0
OD1 A:ASP267 3.3 9.1 1.0
H16 B:5OM4 3.3 11.1 1.0
H4 B:5OM4 3.5 11.8 1.0
HB3 A:LEU179 3.5 10.7 1.0
HH A:TYR306 3.5 12.1 1.0
H17 B:5OM4 3.6 12.0 1.0
HE1 A:TYR306 3.6 12.4 1.0
CB A:HIS180 3.6 8.9 1.0
C30 B:5OM4 3.7 10.0 1.0
H5 B:5OM4 3.7 11.8 1.0
HE2 A:HIS142 3.8 10.4 1.0
H A:LEU179 3.8 10.8 1.0
N A:HIS180 3.8 8.3 1.0
C03 B:5OM4 3.8 9.6 1.0
C04 B:5OM4 3.9 9.9 1.0
NE2 A:HIS180 4.1 10.1 1.0
H A:GLY304 4.1 11.5 1.0
N A:LEU179 4.2 9.0 1.0
CA A:GLY304 4.2 9.3 1.0
CD2 A:HIS180 4.2 9.5 1.0
CB A:ASP178 4.3 8.6 1.0
CB A:ASP267 4.3 9.8 1.0
OH A:TYR306 4.3 10.1 1.0
H2 B:5OM4 4.3 11.5 1.0
CA A:HIS180 4.4 8.7 1.0
CB A:LEU179 4.4 8.9 1.0
HB3 A:ASP178 4.4 10.3 1.0
HB3 A:ASP267 4.5 11.8 1.0
HB3 A:HIS180 4.5 10.7 1.0
CE1 A:TYR306 4.5 10.3 1.0
HB2 A:ASP267 4.5 11.8 1.0
NE2 A:HIS142 4.5 8.7 1.0
N A:GLY304 4.6 9.6 1.0
HA2 A:GLY304 4.6 11.2 1.0
H3 B:5OM4 4.6 11.5 1.0
C A:LEU179 4.6 8.6 1.0
CA A:LEU179 4.6 8.4 1.0
HE1 A:HIS142 4.7 10.8 1.0
HD23 A:LEU179 4.7 11.8 1.0
HE3 A:MET274 4.8 20.9 1.0
HB2 A:LEU179 4.8 10.7 1.0
HE2 A:HIS180 4.8 12.1 1.0
HG3 A:MET274 4.9 15.7 1.0
C A:ASP178 4.9 8.1 1.0
HB2 A:ASP178 4.9 10.3 1.0
CZ A:TYR306 4.9 9.8 1.0
HA A:ASP178 4.9 9.9 1.0
CE1 A:HIS142 5.0 9.0 1.0
CA A:ASP178 5.0 8.2 1.0
O32 B:5OM4 5.0 10.0 1.0

Reference:

N.J.Porter, D.W.Christianson. Binding of the Microbial Cyclic Tetrapeptide Trapoxin A to the Class I Histone Deacetylase HDAC8. Acs Chem. Biol. V. 12 2281 2017.
ISSN: ESSN 1554-8937
PubMed: 28846375
DOI: 10.1021/ACSCHEMBIO.7B00330
Page generated: Wed Dec 16 11:09:29 2020

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