Atomistry » Zinc » PDB 5d88-5dro » 5dc6
Atomistry »
  Zinc »
    PDB 5d88-5dro »
      5dc6 »

Zinc in PDB 5dc6: Crystal Structure of D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate

Enzymatic activity of Crystal Structure of D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5dc6 was solved by C.Decroos, M.S.Lee, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.10 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.332, 98.206, 104.281, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 16.6

Other elements in 5dc6:

The structure of Crystal Structure of D176N-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 D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 5dc6). 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 D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5dc6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5dc6

Go back to Zinc Binding Sites List in 5dc6
Zinc binding site 1 out of 2 in the Crystal Structure of D176N-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 D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:17.5
occ:1.00
OD2 A:ASP178 1.9 15.7 1.0
OD2 A:ASP267 1.9 16.4 1.0
OH C:ALY5 2.0 17.1 1.0
ND1 A:HIS180 2.1 14.9 1.0
CG A:ASP178 2.8 17.0 1.0
O A:HOH507 2.8 29.4 0.4
CG A:ASP267 2.9 15.2 1.0
CE1 A:HIS180 2.9 14.8 1.0
OD1 A:ASP178 3.0 17.6 1.0
CH C:ALY5 3.1 16.5 1.0
CG A:HIS180 3.2 13.5 1.0
OD1 A:ASP267 3.2 14.7 1.0
CB A:HIS180 3.6 13.6 1.0
N A:HIS180 3.7 14.1 1.0
NZ C:ALY5 3.9 15.9 1.0
CE C:ALY5 3.9 16.1 1.0
CA A:GLY304 4.0 14.0 1.0
CH3 C:ALY5 4.0 19.5 1.0
N A:LEU179 4.1 14.2 1.0
NE2 A:HIS180 4.1 13.9 1.0
CB A:ASP178 4.2 18.3 1.0
CB A:ASP267 4.2 13.6 1.0
CD2 A:HIS180 4.2 14.6 1.0
N A:GLY304 4.3 14.3 1.0
CB A:LEU179 4.3 14.2 1.0
CA A:HIS180 4.3 14.0 1.0
CA A:LEU179 4.5 13.4 1.0
C A:LEU179 4.6 14.5 1.0
CE2 A:PHE306 4.7 17.0 1.0
C A:ASP178 4.8 17.7 1.0
NE2 A:HIS143 4.8 15.9 1.0
CA A:ASP178 4.9 16.9 1.0

Zinc binding site 2 out of 2 in 5dc6

Go back to Zinc Binding Sites List in 5dc6
Zinc binding site 2 out of 2 in the Crystal Structure of D176N-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 D176N-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:18.0
occ:1.00
OD2 B:ASP267 1.9 16.9 1.0
OD2 B:ASP178 1.9 16.1 1.0
OH D:ALY5 2.0 17.1 1.0
ND1 B:HIS180 2.1 15.2 1.0
O B:HOH510 2.6 13.1 0.2
CG B:ASP178 2.8 17.9 1.0
CE1 B:HIS180 2.9 13.5 1.0
CG B:ASP267 2.9 17.2 1.0
OD1 B:ASP178 3.0 18.0 1.0
CH D:ALY5 3.0 17.9 1.0
CG B:HIS180 3.2 13.2 1.0
OD1 B:ASP267 3.3 16.4 1.0
CB B:HIS180 3.6 13.7 1.0
N B:HIS180 3.7 15.2 1.0
NZ D:ALY5 3.9 15.1 1.0
CE D:ALY5 4.0 15.1 1.0
CH3 D:ALY5 4.0 23.4 1.0
CA B:GLY304 4.0 16.8 1.0
NE2 B:HIS180 4.1 13.5 1.0
N B:LEU179 4.1 15.6 1.0
CB B:ASP178 4.2 18.3 1.0
CD2 B:HIS180 4.2 12.8 1.0
CB B:ASP267 4.3 13.8 1.0
N B:GLY304 4.3 17.3 1.0
CA B:HIS180 4.3 14.9 1.0
CB B:LEU179 4.3 15.0 1.0
C B:LEU179 4.6 17.4 1.0
CA B:LEU179 4.6 14.2 1.0
NE2 B:HIS143 4.7 18.4 1.0
CE2 B:PHE306 4.8 16.7 1.0
C B:ASP178 4.8 16.2 1.0
CA B:ASP178 4.9 16.5 1.0

Reference:

S.M.Gantt, C.Decroos, M.S.Lee, L.E.Gullett, C.M.Bowman, D.W.Christianson, C.A.Fierke. General Base-General Acid Catalysis in Human Histone Deacetylase 8. Biochemistry V. 55 820 2016.
ISSN: ISSN 0006-2960
PubMed: 26806311
DOI: 10.1021/ACS.BIOCHEM.5B01327
Page generated: Wed Dec 16 06:08:14 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy