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Potassium in PDB 6uo4: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant Complexed with Trichostatin A

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant Complexed with Trichostatin A, PDB code: 6uo4 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) 62.20 / 1.27
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.892, 124.407, 55.630, 90.00, 114.46, 90.00
R / Rfree (%) 18.2 / 19.6

Other elements in 6uo4:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant 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) Y363F Mutant Complexed with Trichostatin A (pdb code 6uo4). 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) Y363F Mutant Complexed with Trichostatin A, PDB code: 6uo4:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6uo4

Go back to Potassium Binding Sites List in 6uo4
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant 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) Y363F Mutant Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:10.5
occ:1.00
 O A:ASP230 2.5 11.0 1.0
OG A:SER251 2.7 9.7 1.0
O A:HIS232 2.7 10.8 1.0
OD1 A:ASP228 2.7 10.3 1.0
O A:VAL252 2.8 9.9 1.0
O A:ASP228 2.8 9.2 1.0
CG A:ASP228 3.2 9.6 1.0
C A:ASP228 3.5 10.6 1.0
C A:ASP230 3.6 9.4 1.0
C A:HIS232 3.6 12.1 1.0
C A:VAL252 3.7 9.5 1.0
CB A:ASP228 3.8 9.8 1.0
N A:ASP230 3.9 9.6 1.0
CB A:SER251 3.9 10.5 1.0
OD2 A:ASP228 3.9 9.8 1.0
N A:VAL252 3.9 10.5 1.0
CB A:HIS253 4.0 11.6 1.0
CA A:ASP230 4.1 10.9 1.0
CA A:SER251 4.2 9.0 1.0
N A:TRP229 4.2 9.9 1.0
C A:TRP229 4.2 10.3 1.0
CB A:ASP230 4.2 8.7 1.0
CA A:ASP228 4.3 9.1 1.0
CA A:HIS233 4.3 10.7 1.0
ND1 A:HIS253 4.3 11.2 1.0
N A:HIS233 4.3 11.2 1.0
C A:SER251 4.4 10.8 1.0
CA A:TRP229 4.4 10.0 1.0
N A:HIS232 4.4 10.2 1.0
CA A:HIS253 4.5 11.7 1.0
N A:HIS253 4.5 11.1 1.0
CA A:VAL252 4.5 10.1 1.0
N A:GLY234 4.6 10.7 1.0
CG A:HIS253 4.6 9.8 1.0
C A:VAL231 4.6 11.0 1.0
CA A:HIS232 4.7 12.1 1.0
O A:HOH635 4.7 12.4 1.0
N A:VAL231 4.7 11.2 1.0
OH A:TYR249 4.8 10.4 1.0
C A:HIS233 4.8 11.1 1.0
CE1 A:HIS192 4.9 9.8 1.0
O A:TRP229 4.9 11.4 1.0

Potassium binding site 2 out of 4 in 6uo4

Go back to Potassium Binding Sites List in 6uo4
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant 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) Y363F Mutant Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:14.7
occ:0.78
 O A:HOH682 2.5 15.3 1.0
O A:VAL247 2.5 17.5 1.0
O A:PHE241 2.6 12.9 1.0
O A:ASP244 2.9 14.3 1.0
O A:TYR280 3.0 10.5 1.0
O A:HOH697 3.2 17.2 1.0
C A:PHE241 3.5 11.3 1.0
CB A:PHE241 3.6 12.7 1.0
CB A:TYR280 3.7 12.1 1.0
C A:TYR280 3.7 10.8 1.0
C A:VAL247 3.8 13.7 1.0
C A:ASP244 4.0 13.7 1.0
CA A:PHE241 4.2 11.2 1.0
CA A:TYR280 4.3 12.6 1.0
N A:ASP244 4.4 13.6 1.0
N A:TYR249 4.5 10.9 1.0
N A:ASN281 4.5 11.3 1.0
N A:GLU242 4.5 11.8 1.0
CA A:LEU248 4.5 11.1 1.0
N A:LEU248 4.6 10.1 1.0
CA A:ASP244 4.6 14.0 1.0
CB A:ASP244 4.7 14.1 1.0
CA A:GLU242 4.7 13.3 1.0
C A:GLU242 4.7 14.2 1.0
O A:GLU242 4.7 14.1 1.0
CA A:VAL247 4.8 11.9 1.0
CG A:PHE241 4.8 10.8 1.0
O A:GLY277 4.8 14.2 1.0
CA A:ASN281 4.9 10.5 1.0
N A:VAL247 4.9 11.6 1.0
CB A:VAL247 4.9 13.1 1.0
CB A:ASN281 4.9 12.1 1.0
N A:PRO245 5.0 15.2 1.0
C A:LEU248 5.0 10.5 1.0
CG A:TYR280 5.0 12.1 1.0

Potassium binding site 3 out of 4 in 6uo4

Go back to Potassium Binding Sites List in 6uo4
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant 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) Y363F Mutant Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:9.3
occ:1.00
 O B:ASP230 2.6 9.6 1.0
OD1 B:ASP228 2.7 9.0 1.0
OG B:SER251 2.7 9.8 1.0
O B:HIS232 2.7 10.2 1.0
O B:VAL252 2.8 9.4 1.0
O B:ASP228 2.8 8.5 1.0
CG B:ASP228 3.2 9.2 1.0
C B:ASP228 3.5 9.7 1.0
C B:ASP230 3.6 8.3 1.0
C B:HIS232 3.7 10.2 1.0
C B:VAL252 3.7 9.9 1.0
CB B:ASP228 3.8 9.3 1.0
N B:ASP230 3.8 8.1 1.0
N B:VAL252 3.9 9.4 1.0
OD2 B:ASP228 3.9 9.6 1.0
CB B:SER251 3.9 8.7 1.0
CB B:HIS253 3.9 10.1 1.0
CA B:ASP230 4.1 9.0 1.0
CA B:SER251 4.2 9.7 1.0
C B:TRP229 4.2 9.1 1.0
N B:TRP229 4.2 9.0 1.0
CB B:ASP230 4.2 10.2 1.0
CA B:ASP228 4.3 8.3 1.0
ND1 B:HIS253 4.3 9.9 1.0
CA B:HIS233 4.3 8.9 1.0
N B:HIS233 4.3 9.7 1.0
C B:SER251 4.4 9.9 1.0
CA B:TRP229 4.4 9.7 1.0
N B:HIS232 4.4 9.4 1.0
CA B:HIS253 4.4 11.0 1.0
CA B:VAL252 4.5 10.0 1.0
N B:HIS253 4.5 10.1 1.0
N B:GLY234 4.6 8.9 1.0
CG B:HIS253 4.6 8.9 1.0
C B:VAL231 4.6 9.2 1.0
CA B:HIS232 4.7 10.3 1.0
N B:VAL231 4.7 9.8 1.0
O B:HOH632 4.7 10.8 1.0
OH B:TYR249 4.8 9.6 1.0
C B:HIS233 4.9 9.3 1.0
CE1 B:HIS192 4.9 10.2 1.0
O B:TRP229 4.9 10.0 1.0

Potassium binding site 4 out of 4 in 6uo4

Go back to Potassium Binding Sites List in 6uo4
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant 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) Y363F Mutant Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:17.1
occ:0.89
 O B:HOH681 2.5 15.6 1.0
O B:VAL247 2.5 14.7 1.0
O B:PHE241 2.6 12.5 1.0
O B:ASP244 2.8 13.1 1.0
O B:TYR280 3.0 10.3 1.0
O B:HOH649 3.4 16.6 1.0
C B:PHE241 3.6 12.3 1.0
CB B:PHE241 3.6 13.1 1.0
CB B:TYR280 3.7 10.7 1.0
C B:TYR280 3.7 10.9 1.0
C B:VAL247 3.7 12.7 1.0
C B:ASP244 3.9 14.3 1.0
CA B:PHE241 4.2 12.5 1.0
CA B:TYR280 4.3 10.9 1.0
N B:ASP244 4.4 13.8 1.0
CA B:LEU248 4.5 10.7 1.0
N B:TYR249 4.5 10.9 1.0
N B:ASN281 4.5 10.4 1.0
N B:GLU242 4.5 12.6 1.0
CA B:ASP244 4.5 14.2 1.0
N B:LEU248 4.6 10.8 1.0
CB B:ASP244 4.6 14.7 1.0
O B:GLU242 4.6 13.8 1.0
C B:GLU242 4.7 12.9 1.0
CA B:GLU242 4.7 13.5 1.0
CA B:VAL247 4.8 11.4 1.0
O B:GLY277 4.8 13.4 1.0
N B:VAL247 4.9 11.5 1.0
CG B:PHE241 4.9 10.8 1.0
CA B:ASN281 4.9 10.8 1.0
CB B:ASN281 4.9 10.2 1.0
CB B:VAL247 4.9 12.9 1.0
CG B:TYR280 4.9 9.3 1.0
N B:PRO245 5.0 14.2 1.0
C B:LEU248 5.0 9.1 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 17:50:54 2024

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