Atomistry » Zinc » PDB 7jo3-7k36 » 7jvv
Atomistry »
  Zinc »
    PDB 7jo3-7k36 »
      7jvv »

Zinc in PDB 7jvv: Crystal Structure of Human Histone Deacetylase 8 (HDAC8) E66D/Y306F Double Mutation Complexed with A Tetrapeptide Substrate

Enzymatic activity of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) E66D/Y306F Double Mutation Complexed with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) E66D/Y306F Double Mutation Complexed with A Tetrapeptide Substrate:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) E66D/Y306F Double Mutation Complexed with A Tetrapeptide Substrate, PDB code: 7jvv was solved by J.D.Osko, D.W.Christianson, C.Decroos, N.J.Porter, M.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.97 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.048, 97.470, 104.254, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.7

Other elements in 7jvv:

The structure of Crystal Structure of Human Histone Deacetylase 8 (HDAC8) E66D/Y306F Double Mutation Complexed with A Tetrapeptide Substrate also contains other interesting chemical elements:

Potassium (K) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) E66D/Y306F Double Mutation Complexed with A Tetrapeptide Substrate (pdb code 7jvv). 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 Human Histone Deacetylase 8 (HDAC8) E66D/Y306F Double Mutation Complexed with A Tetrapeptide Substrate, PDB code: 7jvv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7jvv

Go back to Zinc Binding Sites List in 7jvv
Zinc binding site 1 out of 2 in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) E66D/Y306F Double Mutation Complexed 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 Human Histone Deacetylase 8 (HDAC8) E66D/Y306F Double Mutation Complexed with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn804

b:10.8
occ:1.00
 OD2 A:ASP178 2.0 11.5 1.0
OD2 A:ASP267 2.0 7.8 1.0
ND1 A:HIS180 2.1 9.2 1.0
OH C:ALY5 2.2 7.6 1.0
O A:HOH911 2.2 10.2 1.0
CG A:ASP178 2.8 6.7 1.0
CE1 A:HIS180 2.9 10.7 1.0
OD1 A:ASP178 3.0 8.6 1.0
CH C:ALY5 3.0 13.2 1.0
CG A:ASP267 3.1 12.4 1.0
CG A:HIS180 3.2 9.7 1.0
OD1 A:ASP267 3.5 9.3 1.0
CB A:HIS180 3.6 6.6 1.0
NZ C:ALY5 3.7 9.9 1.0
N A:HIS180 3.8 9.1 1.0
CE C:ALY5 3.8 11.6 1.0
CH3 C:ALY5 4.0 10.6 1.0
NE2 A:HIS180 4.1 9.8 1.0
CA A:GLY304 4.1 8.8 1.0
CD2 A:HIS180 4.2 10.0 1.0
CB A:ASP178 4.2 10.7 1.0
N A:LEU179 4.3 7.7 1.0
NE2 A:HIS142 4.3 11.0 1.0
CA A:HIS180 4.4 10.8 1.0
N A:GLY304 4.4 9.2 1.0
CB A:ASP267 4.4 11.4 1.0
CB A:LEU179 4.6 12.2 1.0
NE2 A:HIS143 4.6 9.4 1.0
C A:LEU179 4.7 9.3 1.0
CE2 A:PHE306 4.7 9.2 1.0
CA A:LEU179 4.8 8.3 1.0
CE1 A:HIS142 4.8 10.6 1.0
C A:ASP178 4.9 10.6 1.0
CA A:ASP178 5.0 11.5 1.0

Zinc binding site 2 out of 2 in 7jvv

Go back to Zinc Binding Sites List in 7jvv
Zinc binding site 2 out of 2 in the Crystal Structure of Human Histone Deacetylase 8 (HDAC8) E66D/Y306F Double Mutation Complexed 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 Human Histone Deacetylase 8 (HDAC8) E66D/Y306F Double Mutation Complexed with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:11.3
occ:1.00
 OD2 B:ASP178 2.0 12.6 1.0
OD2 B:ASP267 2.1 6.2 1.0
ND1 B:HIS180 2.1 10.0 1.0
O B:HOH521 2.2 9.2 1.0
OH D:ALY5 2.2 8.4 1.0
CG B:ASP178 2.9 12.0 1.0
CE1 B:HIS180 2.9 8.4 1.0
CH D:ALY5 3.1 12.4 1.0
CG B:ASP267 3.1 12.4 1.0
OD1 B:ASP178 3.1 10.5 1.0
CG B:HIS180 3.2 8.6 1.0
OD1 B:ASP267 3.5 9.9 1.0
CB B:HIS180 3.6 7.2 1.0
NZ D:ALY5 3.8 14.4 1.0
N B:HIS180 3.8 10.1 1.0
CE D:ALY5 3.9 11.5 1.0
CH3 D:ALY5 4.0 12.4 1.0
CA B:GLY304 4.1 9.5 1.0
NE2 B:HIS180 4.1 10.2 1.0
CD2 B:HIS180 4.2 9.2 1.0
CB B:ASP178 4.3 10.8 1.0
N B:LEU179 4.3 9.9 1.0
CA B:HIS180 4.4 9.3 1.0
N B:GLY304 4.4 10.3 1.0
NE2 B:HIS142 4.4 11.5 1.0
CB B:ASP267 4.4 7.3 1.0
NE2 B:HIS143 4.6 9.4 1.0
CB B:LEU179 4.6 11.6 1.0
C B:LEU179 4.7 11.6 1.0
CA B:LEU179 4.8 8.3 1.0
CE2 B:PHE306 4.8 8.3 1.0
C B:ASP178 4.9 12.8 1.0
CE1 B:HIS142 5.0 11.6 1.0

Reference:

J.D.Osko, N.J.Porter, C.Decroos, M.Lee, P.Watson, M.Deardorff, D.W.Christianson. Structural Analysis of Histone Deacetylase 8 Mutants Associated with Cornelia De Lange Syndrome Spectrum Disorders J.Struct.Biol. 2020.
ISSN: ESSN 1095-8657
Page generated: Tue Oct 29 21:08:58 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy