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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: Fri Aug 22 00:56:10 2025

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