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Potassium in PDB 5eek: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A

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

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

Protein crystallography data

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

Resolution Low / High (Å) 44.01 / 1.59
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.881, 94.429, 51.698, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 16.3

Other elements in 5eek:

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

Zinc (Zn) 1 atom
Iodine (I) 31 atoms
Chlorine (Cl) 1 atom

Potassium Binding Sites:

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

Potassium binding site 1 out of 2 in 5eek

Go back to Potassium Binding Sites List in 5eek
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio 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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2002

b:12.5
occ:1.00
O A:ASP612 2.5 9.0 1.0
OD1 A:ASP610 2.6 11.3 1.0
O A:LEU634 2.6 9.2 1.0
O A:HIS614 2.7 10.4 1.0
OG A:SER633 2.7 9.5 1.0
O A:ASP610 2.8 8.9 1.0
CG A:ASP610 3.2 9.9 1.0
C A:ASP610 3.5 7.6 1.0
C A:ASP612 3.6 8.0 1.0
C A:LEU634 3.7 7.9 1.0
C A:HIS614 3.7 8.7 1.0
CB A:ASP610 3.8 8.9 1.0
N A:ASP612 3.8 7.6 1.0
OD2 A:ASP610 3.9 10.6 1.0
N A:LEU634 3.9 8.4 1.0
CB A:SER633 3.9 9.4 1.0
CB A:HIS635 4.0 7.2 1.0
CA A:ASP612 4.1 8.1 1.0
N A:TRP611 4.2 7.6 1.0
C A:TRP611 4.2 7.5 1.0
CA A:ASP610 4.2 7.9 1.0
CB A:ASP612 4.2 8.5 1.0
CA A:SER633 4.3 8.7 1.0
CA A:TRP611 4.3 8.0 1.0
CA A:HIS615 4.3 8.9 1.0
ND1 A:HIS635 4.3 8.9 1.0
N A:HIS615 4.4 8.7 1.0
N A:HIS614 4.4 7.9 1.0
C A:SER633 4.5 8.3 1.0
CA A:LEU634 4.5 8.4 1.0
CA A:HIS635 4.5 7.4 1.0
N A:GLY616 4.5 8.8 1.0
N A:HIS635 4.5 7.6 1.0
O A:HOH2124 4.5 11.5 1.0
CG A:HIS635 4.6 7.6 1.0
C A:VAL613 4.7 8.6 1.0
CA A:HIS614 4.7 8.2 1.0
N A:VAL613 4.7 7.9 1.0
CE1 A:HIS573 4.7 11.8 1.0
OH A:TYR631 4.8 9.4 1.0
C A:HIS615 4.8 9.5 1.0
O A:TRP611 4.9 9.2 1.0
ND1 A:HIS573 4.9 11.0 1.0

Potassium binding site 2 out of 2 in 5eek

Go back to Potassium Binding Sites List in 5eek
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio 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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2003

b:21.8
occ:0.58
O A:VAL629 2.8 13.3 1.0
O A:PHE623 2.8 10.8 1.0
O A:HOH2131 2.8 13.0 1.0
O A:HOH2219 2.9 11.4 1.0
O A:TYR662 2.9 10.1 1.0
O A:ASP626 3.2 15.6 1.0
C A:TYR662 3.6 9.3 1.0
C A:PHE623 3.7 10.2 1.0
CB A:PHE623 3.7 9.2 1.0
CB A:TYR662 3.8 10.8 1.0
C A:VAL629 4.0 11.3 1.0
N A:TYR631 4.3 7.6 1.0
C A:ASP626 4.3 14.2 1.0
CA A:TYR662 4.3 10.1 1.0
CA A:PHE623 4.4 9.7 1.0
N A:ASN663 4.4 9.1 1.0
N A:GLU624 4.6 10.8 1.0
CA A:GLU624 4.6 11.9 1.0
CB A:ASP626 4.6 15.2 0.5
CB A:TYR631 4.6 7.4 1.0
N A:ASP626 4.6 14.1 1.0
CA A:LEU630 4.6 9.2 1.0
CA A:ASN663 4.7 9.1 1.0
CB A:ASN663 4.7 8.5 1.0
C A:GLU624 4.7 12.2 1.0
O A:GLU624 4.7 12.4 1.0
CB A:ASP626 4.7 16.4 0.5
CA A:ASP626 4.8 14.4 0.5
N A:LEU630 4.8 9.8 1.0
CA A:ASP626 4.8 14.7 0.5
OD1 A:ASN663 4.8 11.2 1.0
O A:GLY659 4.9 13.5 1.0
C A:LEU630 4.9 9.5 1.0
CG A:PHE623 5.0 8.5 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: Sun Dec 13 23:56:53 2020

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