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Potassium in PDB 5edu: Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A

Enzymatic activity of Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A

All present enzymatic activity of Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A, PDB code: 5edu was solved by Y.Hai, D.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.54 / 2.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.262, 149.032, 216.333, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 27.5

Other elements in 5edu:

The structure of Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A (pdb code 5edu). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A, PDB code: 5edu:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5edu

Go back to Potassium Binding Sites List in 5edu
Potassium binding site 1 out of 4 in the Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2503

b:0.3
occ:1.00
 O B:PHE699 2.8 45.2 1.0
O B:PHE660 2.8 59.0 1.0
O B:VAL666 2.9 42.9 1.0
O B:ASP663 3.2 47.2 1.0
CB B:PHE699 3.2 46.6 1.0
C B:PHE699 3.4 45.0 1.0
OG1 B:THR700 3.7 44.6 1.0
CA B:PHE699 3.9 46.5 1.0
C B:PHE660 3.9 55.5 1.0
C B:VAL666 4.1 41.3 1.0
N B:THR700 4.2 39.6 1.0
C B:ASP663 4.3 42.7 1.0
N B:TYR668 4.3 41.0 1.0
CB B:PHE660 4.3 38.0 1.0
O B:GLY696 4.4 49.5 1.0
CG B:PHE699 4.5 49.1 1.0
CB B:TYR668 4.6 33.7 1.0
O B:GLU661 4.6 50.6 1.0
CA B:THR700 4.7 39.2 1.0
CA B:LEU667 4.7 35.2 1.0
C B:GLU661 4.7 50.0 1.0
CA B:GLU661 4.7 49.0 1.0
N B:ASP663 4.8 43.4 1.0
N B:GLU661 4.8 45.2 1.0
CB B:THR700 4.8 43.4 1.0
CA B:PHE660 4.8 51.6 1.0
N B:LEU667 4.9 35.2 1.0
N B:PHE699 4.9 46.1 1.0
C B:LEU667 5.0 34.1 1.0

Potassium binding site 2 out of 4 in 5edu

Go back to Potassium Binding Sites List in 5edu
Potassium binding site 2 out of 4 in the Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2504

b:0.8
occ:1.00
 O B:ASP647 2.8 43.9 1.0
OG B:SER670 2.8 37.4 1.0
O B:HIS651 2.8 37.3 1.0
O B:ASP649 2.8 37.7 1.0
OD1 B:ASP647 2.8 51.2 1.0
O B:LEU671 3.0 52.6 1.0
CG B:ASP647 3.3 48.7 1.0
C B:ASP647 3.6 40.7 1.0
C B:ASP649 3.7 31.6 1.0
C B:HIS651 3.7 32.7 1.0
CB B:ASP647 3.7 46.8 1.0
N B:ASP649 3.8 29.3 1.0
C B:LEU671 3.8 50.4 1.0
ND1 B:HIS672 3.8 49.2 1.0
N B:LEU671 3.8 49.1 1.0
CB B:HIS672 3.9 45.3 1.0
CB B:SER670 3.9 39.4 1.0
CA B:HIS652 4.1 32.4 1.0
CA B:ASP649 4.1 29.3 1.0
OD2 B:ASP647 4.1 46.6 1.0
CB B:ASP649 4.2 46.3 1.0
CA B:ASP647 4.3 39.8 1.0
CA B:SER670 4.3 48.7 1.0
N B:HIS652 4.3 32.1 1.0
CG B:HIS672 4.3 48.0 1.0
N B:TRP648 4.4 41.9 1.0
C B:TRP648 4.4 37.4 1.0
N B:GLY653 4.4 31.7 1.0
C B:SER670 4.4 50.6 1.0
CA B:LEU671 4.5 49.8 1.0
CA B:TRP648 4.5 39.8 1.0
N B:HIS651 4.5 30.9 1.0
N B:HIS672 4.6 34.9 1.0
CA B:HIS672 4.6 35.0 1.0
C B:HIS652 4.7 32.0 1.0
CA B:HIS651 4.8 31.4 1.0
N B:VAL650 4.8 36.1 1.0
C B:VAL650 4.9 35.5 1.0
OH B:TYR668 4.9 31.8 1.0

Potassium binding site 3 out of 4 in 5edu

Go back to Potassium Binding Sites List in 5edu
Potassium binding site 3 out of 4 in the Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K902

b:68.8
occ:1.00
 OG A:SER670 2.8 36.6 1.0
O A:ASP649 2.8 39.4 1.0
OD1 A:ASP647 2.8 44.7 1.0
O A:ASP647 2.8 28.4 1.0
O A:HIS651 2.9 30.1 1.0
O A:LEU671 2.9 30.2 1.0
CG A:ASP647 3.3 42.9 1.0
C A:ASP647 3.5 28.2 1.0
CB A:ASP647 3.6 39.8 1.0
C A:LEU671 3.7 29.2 1.0
C A:HIS651 3.7 29.9 1.0
C A:ASP649 3.7 32.1 1.0
CB A:HIS672 3.8 35.6 1.0
N A:ASP649 3.8 28.7 1.0
N A:LEU671 3.8 26.2 1.0
CB A:SER670 4.0 35.6 1.0
ND1 A:HIS672 4.1 37.1 1.0
OD2 A:ASP647 4.1 43.8 1.0
CA A:ASP649 4.1 28.4 1.0
CA A:HIS652 4.1 26.2 1.0
CA A:ASP647 4.2 32.0 1.0
CB A:ASP649 4.2 29.1 1.0
N A:HIS652 4.3 26.0 1.0
N A:TRP648 4.3 31.6 1.0
CA A:SER670 4.3 30.6 1.0
C A:TRP648 4.3 30.7 1.0
C A:SER670 4.4 27.9 1.0
N A:GLY653 4.4 25.9 1.0
CG A:HIS672 4.4 36.2 1.0
N A:HIS672 4.4 34.3 1.0
CA A:LEU671 4.4 27.6 1.0
CA A:HIS672 4.4 35.3 1.0
CA A:TRP648 4.5 30.9 1.0
N A:HIS651 4.5 27.2 1.0
CA A:HIS651 4.8 31.2 1.0
C A:HIS652 4.8 26.1 1.0
C A:VAL650 4.8 25.1 1.0
N A:VAL650 4.8 24.3 1.0
OH A:TYR668 4.9 30.1 1.0

Potassium binding site 4 out of 4 in 5edu

Go back to Potassium Binding Sites List in 5edu
Potassium binding site 4 out of 4 in the Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Human Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K903

b:82.9
occ:1.00
 O A:PHE660 2.7 55.2 1.0
O A:PHE699 2.8 41.5 1.0
O A:VAL666 2.8 42.9 1.0
O A:HOH1003 3.1 60.1 1.0
O A:ASP663 3.1 42.8 1.0
C A:PHE699 3.5 40.8 1.0
CB A:PHE699 3.5 51.8 1.0
OG1 A:THR700 3.8 41.5 1.0
C A:PHE660 3.8 51.3 1.0
C A:VAL666 4.0 38.2 1.0
CA A:PHE699 4.1 41.6 1.0
N A:TYR668 4.1 41.6 1.0
CB A:PHE660 4.2 31.9 1.0
C A:ASP663 4.2 42.3 1.0
N A:THR700 4.3 35.8 1.0
CB A:TYR668 4.5 38.4 1.0
CA A:LEU667 4.5 43.0 1.0
O A:GLY696 4.5 61.7 1.0
CA A:PHE660 4.7 44.4 1.0
O A:GLU661 4.7 49.2 1.0
N A:ASP663 4.7 41.8 1.0
N A:GLU661 4.7 47.8 1.0
N A:LEU667 4.7 42.9 1.0
CA A:GLU661 4.7 51.3 1.0
CA A:THR700 4.7 35.1 1.0
C A:GLU661 4.8 49.6 1.0
C A:LEU667 4.8 45.8 1.0
CG A:PHE699 4.8 56.8 1.0
CB A:THR700 4.8 40.8 1.0
CA A:ASP663 4.9 42.4 1.0
CA A:TYR668 5.0 38.5 1.0

Reference:

Y.Hai, D.W.Christianson. Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134
Page generated: Mon Aug 12 13:22:53 2024

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