Atomistry » Zinc » PDB 4q8r-4qhg » 4qa5
Atomistry »
  Zinc »
    PDB 4q8r-4qhg »
      4qa5 »

Zinc in PDB 4qa5: Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate

Enzymatic activity of Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 4qa5 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) 46.42 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.830, 97.760, 105.485, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 19.4

Other elements in 4qa5:

The structure of Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Potassium (K) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 4qa5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 4qa5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4qa5

Go back to Zinc Binding Sites List in 4qa5
Zinc binding site 1 out of 2 in the Crystal Structure of A188T/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 A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:16.4
occ:1.00
OD2 A:ASP178 1.9 14.9 1.0
OD2 A:ASP267 2.0 13.2 1.0
OH C:ALY505 2.1 16.1 1.0
ND1 A:HIS180 2.1 15.1 1.0
O A:HOH501 2.1 14.7 1.0
CG A:ASP178 2.8 17.2 1.0
CE1 A:HIS180 3.0 15.2 1.0
CH C:ALY505 3.0 18.7 1.0
OD1 A:ASP178 3.1 15.2 1.0
CG A:ASP267 3.1 15.2 1.0
CG A:HIS180 3.2 15.1 1.0
OD1 A:ASP267 3.4 15.0 1.0
CB A:HIS180 3.7 14.5 1.0
N A:HIS180 3.8 14.1 1.0
NZ C:ALY505 3.8 15.4 1.0
CE C:ALY505 3.9 13.7 1.0
CH3 C:ALY505 4.0 14.8 1.0
CA A:GLY304 4.1 14.1 1.0
NE2 A:HIS180 4.1 14.2 1.0
CB A:ASP178 4.2 15.9 1.0
N A:LEU179 4.3 13.0 1.0
CD2 A:HIS180 4.3 15.9 1.0
NE2 A:HIS142 4.3 17.2 1.0
CA A:HIS180 4.3 11.9 1.0
N A:GLY304 4.4 14.6 1.0
CB A:ASP267 4.4 11.2 1.0
CB A:LEU179 4.5 14.6 1.0
NE2 A:HIS143 4.7 16.5 1.0
C A:LEU179 4.7 16.1 1.0
CA A:LEU179 4.7 13.6 1.0
CE2 A:PHE306 4.8 14.9 1.0
CE1 A:HIS142 4.9 15.5 1.0
C A:ASP178 4.9 16.2 1.0
CA A:ASP178 5.0 14.0 1.0

Zinc binding site 2 out of 2 in 4qa5

Go back to Zinc Binding Sites List in 4qa5
Zinc binding site 2 out of 2 in the Crystal Structure of A188T/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 2 of Crystal Structure of A188T/Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:17.3
occ:1.00
OD2 B:ASP178 2.0 15.0 1.0
OD2 B:ASP267 2.0 14.9 1.0
ND1 B:HIS180 2.1 11.8 1.0
OH D:ALY505 2.1 14.0 1.0
O B:HOH501 2.2 14.9 1.0
CG B:ASP178 2.8 13.8 1.0
CE1 B:HIS180 3.0 15.6 1.0
OD1 B:ASP178 3.0 14.2 1.0
CH D:ALY505 3.0 15.0 1.0
CG B:ASP267 3.1 17.1 1.0
CG B:HIS180 3.2 14.2 1.0
OD1 B:ASP267 3.4 15.9 1.0
CB B:HIS180 3.6 13.6 1.0
NZ D:ALY505 3.8 14.0 1.0
N B:HIS180 3.8 14.8 1.0
CE D:ALY505 3.9 13.9 1.0
CH3 D:ALY505 3.9 14.1 1.0
NE2 B:HIS180 4.1 16.3 1.0
CA B:GLY304 4.1 12.2 1.0
CD2 B:HIS180 4.2 15.6 1.0
CB B:ASP178 4.3 15.9 1.0
N B:LEU179 4.3 13.1 1.0
NE2 B:HIS142 4.3 18.3 1.0
N B:GLY304 4.4 13.6 1.0
CA B:HIS180 4.4 13.1 1.0
CB B:ASP267 4.4 14.3 1.0
CB B:LEU179 4.5 15.1 1.0
NE2 B:HIS143 4.6 15.0 1.0
C B:LEU179 4.7 16.4 1.0
CA B:LEU179 4.8 14.4 1.0
CE2 B:PHE306 4.8 15.3 1.0
CE1 B:HIS142 4.9 17.9 1.0
C B:ASP178 4.9 12.1 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 Dec 16 05:43:09 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy