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Zinc in PDB 5bwz: Crystal Structure of S39E HDAC8 in Complex with Droxinostat

Enzymatic activity of Crystal Structure of S39E HDAC8 in Complex with Droxinostat

All present enzymatic activity of Crystal Structure of S39E HDAC8 in Complex with Droxinostat:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of S39E HDAC8 in Complex with Droxinostat, PDB code: 5bwz was solved by C.Decroos, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.98 / 1.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.379, 84.390, 94.639, 90.00, 99.37, 90.00
R / Rfree (%) 14.2 / 16

Other elements in 5bwz:

The structure of Crystal Structure of S39E HDAC8 in Complex with Droxinostat also contains other interesting chemical elements:

Potassium (K) 4 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of S39E HDAC8 in Complex with Droxinostat (pdb code 5bwz). 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 S39E HDAC8 in Complex with Droxinostat, PDB code: 5bwz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5bwz

Go back to Zinc Binding Sites List in 5bwz
Zinc binding site 1 out of 2 in the Crystal Structure of S39E HDAC8 in Complex with Droxinostat


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 S39E HDAC8 in Complex with Droxinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:14.1
occ:1.00
OD1 A:ASP178 2.0 12.3 1.0
OD2 A:ASP267 2.0 14.9 1.0
O2 A:XCH404 2.0 18.4 1.0
ND1 A:HIS180 2.1 13.4 1.0
O1 A:XCH404 2.2 16.4 1.0
N1 A:XCH404 2.8 16.0 1.0
C1 A:XCH404 2.8 17.7 1.0
CG A:ASP178 2.9 14.3 1.0
CE1 A:HIS180 3.0 14.3 1.0
CG A:ASP267 3.0 14.1 1.0
OD2 A:ASP178 3.1 13.4 1.0
CG A:HIS180 3.2 12.7 1.0
OD1 A:ASP267 3.4 12.6 1.0
CB A:HIS180 3.6 11.9 1.0
N A:HIS180 3.8 11.4 1.0
CA A:GLY304 4.1 12.1 1.0
NE2 A:HIS180 4.1 14.6 1.0
C2 A:XCH404 4.2 21.1 1.0
CD2 A:HIS180 4.2 14.1 1.0
CB A:ASP178 4.3 13.3 1.0
N A:LEU179 4.3 12.4 1.0
CB A:ASP267 4.3 11.7 1.0
NE2 A:HIS142 4.3 15.7 1.0
N A:GLY304 4.4 14.3 1.0
CA A:HIS180 4.4 11.3 1.0
CB A:LEU179 4.5 12.9 1.0
OH A:TYR306 4.6 21.4 1.0
C3 A:XCH404 4.6 37.7 1.0
C A:LEU179 4.7 12.7 1.0
CE1 A:HIS142 4.7 14.9 1.0
CA A:LEU179 4.8 13.3 1.0
CE2 A:TYR306 4.8 15.3 1.0
C A:ASP178 5.0 12.2 1.0

Zinc binding site 2 out of 2 in 5bwz

Go back to Zinc Binding Sites List in 5bwz
Zinc binding site 2 out of 2 in the Crystal Structure of S39E HDAC8 in Complex with Droxinostat


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 S39E HDAC8 in Complex with Droxinostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:14.3
occ:1.00
OD2 B:ASP267 2.0 14.4 1.0
OD1 B:ASP178 2.0 13.0 1.0
O2 B:XCH404 2.0 19.0 1.0
ND1 B:HIS180 2.1 13.9 1.0
O1 B:XCH404 2.2 17.3 1.0
N1 B:XCH404 2.8 19.1 1.0
C1 B:XCH404 2.8 19.5 1.0
CG B:ASP178 2.9 14.6 1.0
CG B:ASP267 3.0 12.9 1.0
CE1 B:HIS180 3.0 13.9 1.0
OD2 B:ASP178 3.1 13.4 1.0
CG B:HIS180 3.2 12.0 1.0
OD1 B:ASP267 3.3 13.0 1.0
CB B:HIS180 3.6 11.7 1.0
N B:HIS180 3.9 11.4 1.0
CA B:GLY304 4.1 14.0 1.0
NE2 B:HIS180 4.1 15.1 1.0
CD2 B:HIS180 4.3 13.5 1.0
CB B:ASP178 4.3 14.5 1.0
C2 B:XCH404 4.3 21.8 1.0
N B:LEU179 4.3 13.7 1.0
CB B:ASP267 4.3 12.8 1.0
NE2 B:HIS142 4.4 16.4 1.0
N B:GLY304 4.4 16.5 1.0
CA B:HIS180 4.4 12.6 1.0
CB B:LEU179 4.4 13.0 1.0
O B:HOH758 4.5 34.2 1.0
OH B:TYR306 4.6 24.0 1.0
C3 B:XCH404 4.7 34.2 1.0
CA B:LEU179 4.7 12.4 1.0
C B:LEU179 4.7 13.1 1.0
CE1 B:HIS142 4.8 15.7 1.0
CE2 B:TYR306 4.8 18.0 1.0
C B:ASP178 4.9 13.8 1.0

Reference:

C.Decroos, D.W.Christianson. Structure of S39E HDAC8 in Complex with Droxinostat To Be Published.
Page generated: Wed Dec 16 06:05:26 2020

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