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Potassium in PDB 6uo2: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A, PDB code: 6uo2 was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.68 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.030, 124.261, 55.520, 90.00, 114.09, 90.00
R / Rfree (%) 18.7 / 22.2

Other elements in 6uo2:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed 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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A (pdb code 6uo2). 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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A, PDB code: 6uo2:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6uo2

Go back to Potassium Binding Sites List in 6uo2
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed 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 1 (CD1) Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:24.2
occ:1.00
 O A:VAL247 2.6 19.6 1.0
O A:PHE241 2.7 17.5 1.0
O A:HOH644 2.7 21.4 1.0
O A:ASP244 2.9 21.0 1.0
O A:TYR280 2.9 16.3 1.0
O A:HOH630 2.9 17.3 1.0
C A:PHE241 3.6 17.8 1.0
CB A:PHE241 3.7 18.2 1.0
C A:TYR280 3.7 18.6 1.0
CB A:TYR280 3.8 19.5 1.0
C A:VAL247 3.9 18.8 1.0
C A:ASP244 4.0 22.1 1.0
CA A:PHE241 4.3 18.1 1.0
N A:TYR249 4.4 16.9 1.0
CA A:TYR280 4.4 15.5 1.0
N A:ASN281 4.4 16.6 1.0
N A:ASP244 4.5 18.4 1.0
CA A:LEU248 4.5 15.9 1.0
N A:GLU242 4.6 17.8 1.0
O A:GLU242 4.6 20.3 1.0
CA A:ASP244 4.7 21.8 1.0
N A:LEU248 4.7 17.7 1.0
CB A:ASN281 4.7 17.0 1.0
CA A:GLU242 4.7 18.8 1.0
C A:GLU242 4.7 22.5 1.0
CB A:ASP244 4.7 18.1 1.0
CA A:ASN281 4.7 14.1 1.0
CA A:VAL247 4.9 19.4 1.0
C A:LEU248 4.9 15.4 1.0
CB A:TYR249 4.9 15.6 1.0
OD1 A:ASN281 4.9 15.8 1.0
CG A:PHE241 4.9 16.0 1.0
O A:GLY277 5.0 18.9 1.0

Potassium binding site 2 out of 4 in 6uo2

Go back to Potassium Binding Sites List in 6uo2
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed 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 1 (CD1) Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:18.2
occ:1.00
 O A:ASP230 2.6 17.8 1.0
OG A:SER251 2.7 16.6 1.0
OD1 A:ASP228 2.8 15.7 1.0
O A:HIS232 2.8 17.3 1.0
O A:VAL252 2.9 15.8 1.0
O A:ASP228 2.9 14.8 1.0
CG A:ASP228 3.2 16.1 1.0
C A:ASP228 3.5 15.9 1.0
C A:ASP230 3.6 15.8 1.0
C A:HIS232 3.7 17.1 1.0
C A:VAL252 3.8 16.1 1.0
CB A:ASP228 3.8 14.0 1.0
N A:ASP230 3.8 13.9 1.0
CB A:HIS253 3.9 14.7 1.0
OD2 A:ASP228 3.9 16.6 1.0
N A:VAL252 3.9 17.2 1.0
CB A:SER251 3.9 15.0 1.0
CA A:ASP230 4.1 12.4 1.0
C A:TRP229 4.2 17.2 1.0
N A:TRP229 4.2 14.5 1.0
CA A:SER251 4.2 15.4 1.0
ND1 A:HIS253 4.3 16.0 1.0
CB A:ASP230 4.3 14.4 1.0
CA A:ASP228 4.3 13.5 1.0
CA A:HIS233 4.3 14.5 1.0
CA A:TRP229 4.3 14.2 1.0
C A:SER251 4.4 18.3 1.0
N A:HIS233 4.4 16.6 1.0
N A:HIS232 4.5 15.1 1.0
CA A:HIS253 4.5 14.8 1.0
CA A:VAL252 4.5 16.7 1.0
N A:GLY234 4.5 14.4 1.0
N A:HIS253 4.5 15.7 1.0
CG A:HIS253 4.5 15.3 1.0
C A:VAL231 4.7 18.2 1.0
N A:VAL231 4.7 15.2 1.0
CA A:HIS232 4.7 15.8 1.0
O A:HOH617 4.8 20.7 1.0
OH A:TYR249 4.8 14.8 1.0
C A:HIS233 4.9 17.6 1.0
O A:TRP229 4.9 15.8 1.0
CE1 A:HIS192 4.9 15.1 1.0

Potassium binding site 3 out of 4 in 6uo2

Go back to Potassium Binding Sites List in 6uo2
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed 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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:26.1
occ:1.00
 O B:HOH636 2.7 18.5 1.0
O B:VAL247 2.7 21.3 1.0
O B:PHE241 2.7 19.7 1.0
O B:TYR280 2.9 15.3 1.0
O B:HOH653 3.0 17.2 1.0
O B:ASP244 3.0 19.2 1.0
C B:PHE241 3.6 16.6 1.0
CB B:PHE241 3.6 17.0 1.0
C B:TYR280 3.7 16.7 1.0
CB B:TYR280 3.8 18.6 1.0
C B:VAL247 3.9 17.0 1.0
C B:ASP244 4.1 18.4 1.0
CA B:PHE241 4.3 16.9 1.0
CA B:TYR280 4.4 17.6 1.0
N B:ASN281 4.4 18.0 1.0
N B:TYR249 4.4 13.2 1.0
N B:ASP244 4.5 22.0 1.0
N B:GLU242 4.6 17.8 1.0
CA B:LEU248 4.6 16.4 1.0
CA B:GLU242 4.7 15.8 1.0
O B:GLU242 4.7 22.5 1.0
N B:LEU248 4.7 15.1 1.0
CB B:ASN281 4.7 15.0 1.0
CA B:ASN281 4.7 17.5 1.0
C B:GLU242 4.7 21.0 1.0
CA B:ASP244 4.8 20.9 1.0
CB B:TYR249 4.8 12.3 1.0
CG B:PHE241 4.8 18.5 1.0
CB B:ASP244 4.9 20.4 1.0
CA B:VAL247 4.9 14.2 1.0
O B:GLY277 5.0 21.9 1.0
C B:LEU248 5.0 15.2 1.0
OD1 B:ASN281 5.0 19.1 1.0

Potassium binding site 4 out of 4 in 6uo2

Go back to Potassium Binding Sites List in 6uo2
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed 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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:18.7
occ:1.00
 O B:ASP230 2.6 16.5 1.0
O B:HIS232 2.7 17.9 1.0
OD1 B:ASP228 2.8 14.9 1.0
OG B:SER251 2.8 14.6 1.0
O B:VAL252 2.8 16.2 1.0
O B:ASP228 2.8 15.6 1.0
CG B:ASP228 3.3 14.6 1.0
C B:ASP228 3.5 15.3 1.0
C B:ASP230 3.6 14.9 1.0
C B:VAL252 3.7 15.0 1.0
C B:HIS232 3.7 20.3 1.0
N B:ASP230 3.8 16.0 1.0
CB B:ASP228 3.8 13.9 1.0
N B:VAL252 3.9 16.8 1.0
OD2 B:ASP228 3.9 15.1 1.0
CB B:HIS253 3.9 14.2 1.0
CB B:SER251 4.0 16.0 1.0
CA B:ASP230 4.1 14.6 1.0
N B:TRP229 4.2 13.8 1.0
C B:TRP229 4.2 17.4 1.0
CB B:ASP230 4.2 13.9 1.0
CA B:SER251 4.2 12.8 1.0
CA B:ASP228 4.3 16.4 1.0
ND1 B:HIS253 4.3 17.2 1.0
CA B:HIS233 4.3 15.9 1.0
CA B:TRP229 4.3 14.2 1.0
C B:SER251 4.4 18.8 1.0
N B:HIS233 4.4 16.3 1.0
N B:HIS232 4.5 15.9 1.0
CA B:HIS253 4.5 14.6 1.0
CA B:VAL252 4.5 16.4 1.0
N B:GLY234 4.5 17.2 1.0
N B:HIS253 4.5 15.1 1.0
CG B:HIS253 4.6 18.4 1.0
C B:VAL231 4.7 19.8 1.0
N B:VAL231 4.7 17.3 1.0
O B:HOH615 4.7 20.4 1.0
CA B:HIS232 4.7 18.1 1.0
OH B:TYR249 4.8 15.2 1.0
C B:HIS233 4.9 21.7 1.0
CE1 B:HIS192 4.9 14.8 1.0
O B:TRP229 4.9 16.2 1.0

Reference:

J.D.Osko, D.W.Christianson. Structural Basis of Catalysis and Inhibition of HDAC6 CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31755702
DOI: 10.1021/ACS.BIOCHEM.9B00934
Page generated: Mon Aug 12 17:50:29 2024

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