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Zinc in PDB 4qa7: Crystal Structure of H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate

Enzymatic activity of Crystal Structure of H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 4qa7 was solved by C.Decroos, C.B.Bowman, J.-A.S.Moser, K.E.Christianson, M.A.Deardorff, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.19 / 2.31
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.406, 80.406, 106.063, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 24.1

Other elements in 4qa7:

The structure of Crystal Structure of H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 4qa7). 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 H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 4qa7:

Zinc binding site 1 out of 1 in 4qa7

Go back to Zinc Binding Sites List in 4qa7
Zinc binding site 1 out of 1 in the Crystal Structure of H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 H334R/Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:47.9
occ:1.00
 OH B:ALY505 2.0 47.7 1.0
OD1 A:ASP178 2.1 41.7 1.0
OD2 A:ASP267 2.1 48.9 1.0
ND1 A:HIS180 2.3 50.4 1.0
O A:HOH522 2.4 45.0 1.0
CG A:ASP178 2.8 45.3 1.0
OD2 A:ASP178 2.9 46.0 1.0
CH B:ALY505 3.0 46.0 1.0
CG A:ASP267 3.2 45.6 1.0
CE1 A:HIS180 3.2 48.3 1.0
CG A:HIS180 3.3 44.0 1.0
OD1 A:ASP267 3.6 46.2 1.0
CB A:HIS180 3.6 44.8 1.0
N A:HIS180 3.7 51.7 1.0
NZ B:ALY505 3.9 48.3 1.0
CE B:ALY505 4.0 44.1 1.0
CH3 B:ALY505 4.0 44.1 1.0
CA A:GLY304 4.0 43.5 1.0
CB A:ASP178 4.3 41.3 1.0
N A:LEU179 4.3 47.4 1.0
CA A:HIS180 4.3 44.9 1.0
NE2 A:HIS180 4.3 47.1 1.0
CD2 A:HIS180 4.4 46.1 1.0
N A:GLY304 4.4 45.7 1.0
NE2 A:HIS142 4.4 41.4 1.0
CB A:ASP267 4.5 49.7 1.0
CB A:LEU179 4.5 48.5 1.0
NE2 A:HIS143 4.5 48.0 1.0
C A:LEU179 4.7 50.6 1.0
CA A:LEU179 4.7 49.3 1.0
CE2 A:PHE306 4.8 45.8 1.0
CE1 A:HIS142 4.9 43.2 1.0
CZ A:PHE306 5.0 45.1 1.0
C A:ASP178 5.0 47.1 1.0

Reference:

C.Decroos, C.M.Bowman, J.A.Moser, K.E.Christianson, M.A.Deardorff, D.W.Christianson. Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia De Lange Syndrome Spectrum Disorders. Acs Chem.Biol. V. 9 2157 2014.
ISSN: ISSN 1554-8929
PubMed: 25075551
DOI: 10.1021/CB5003762
Page generated: Wed Aug 20 21:44:01 2025

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