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Potassium in PDB 6uob: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Resminostat

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Resminostat, PDB code: 6uob 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) 56.45 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.270, 102.620, 112.900, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 20.8

Other elements in 6uob:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Resminostat 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) K330L Mutant Complexed with Resminostat (pdb code 6uob). 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) K330L Mutant Complexed with Resminostat, PDB code: 6uob:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6uob

Go back to Potassium Binding Sites List in 6uob
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Resminostat


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) K330L Mutant Complexed with Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:11.2
occ:1.00
 O A:ASP230 2.6 11.3 1.0
O A:HIS232 2.7 11.0 1.0
OD1 A:ASP228 2.7 11.8 1.0
O A:VAL252 2.8 10.0 1.0
OG A:SER251 2.8 11.4 1.0
O A:ASP228 2.8 10.5 1.0
CG A:ASP228 3.2 14.4 1.0
C A:ASP228 3.5 11.9 1.0
C A:ASP230 3.6 9.7 1.0
C A:HIS232 3.7 10.5 1.0
C A:VAL252 3.7 10.6 1.0
OD2 A:ASP228 3.8 12.5 1.0
N A:ASP230 3.8 10.4 1.0
CB A:ASP228 3.8 9.3 1.0
N A:VAL252 3.9 9.7 1.0
CB A:HIS253 3.9 9.3 1.0
CB A:SER251 3.9 8.4 1.0
CA A:ASP230 4.1 10.8 1.0
N A:TRP229 4.2 10.8 1.0
C A:TRP229 4.2 11.1 1.0
CA A:SER251 4.2 9.2 1.0
CB A:ASP230 4.2 11.4 1.0
CA A:ASP228 4.3 9.8 1.0
ND1 A:HIS253 4.3 11.6 1.0
CA A:TRP229 4.3 10.1 1.0
CA A:HIS233 4.4 12.0 1.0
N A:HIS233 4.4 10.4 1.0
C A:SER251 4.4 10.4 1.0
N A:HIS232 4.5 9.7 1.0
CA A:HIS253 4.5 8.4 1.0
CA A:VAL252 4.5 10.2 1.0
N A:HIS253 4.5 10.7 1.0
N A:GLY234 4.6 11.0 1.0
CG A:HIS253 4.6 10.1 1.0
O A:HOH656 4.6 12.4 1.0
N A:VAL231 4.7 10.6 1.0
C A:VAL231 4.7 12.1 1.0
CA A:HIS232 4.7 12.1 1.0
OH A:TYR249 4.8 11.9 1.0
CE1 A:HIS192 4.9 14.2 1.0
C A:HIS233 4.9 8.8 1.0
O A:TRP229 4.9 12.5 1.0

Potassium binding site 2 out of 4 in 6uob

Go back to Potassium Binding Sites List in 6uob
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Resminostat


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) K330L Mutant Complexed with Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K504

b:16.0
occ:1.00
 O A:PHE241 2.7 13.0 1.0
O A:VAL247 2.7 12.6 1.0
O A:HOH665 2.7 13.1 1.0
O A:TYR280 2.9 11.6 1.0
O A:ASP244 2.9 13.8 1.0
O A:HOH661 3.0 11.9 1.0
C A:PHE241 3.6 11.0 1.0
C A:TYR280 3.6 11.1 1.0
CB A:PHE241 3.7 10.1 1.0
CB A:TYR280 3.8 8.7 1.0
C A:VAL247 3.9 11.0 1.0
C A:ASP244 4.0 13.1 1.0
CA A:PHE241 4.3 9.8 1.0
CA A:TYR280 4.3 10.3 1.0
N A:TYR249 4.4 10.7 1.0
N A:ASP244 4.4 14.9 1.0
N A:ASN281 4.4 10.1 1.0
N A:GLU242 4.5 13.5 1.0
CA A:LEU248 4.6 9.9 1.0
O A:GLU242 4.6 14.2 1.0
CA A:ASP244 4.6 12.4 1.0
CA A:GLU242 4.7 14.8 1.0
C A:GLU242 4.7 13.9 1.0
N A:LEU248 4.7 11.3 1.0
CB A:ASP244 4.7 13.2 1.0
CB A:ASN281 4.7 10.0 1.0
CA A:ASN281 4.8 10.0 1.0
CB A:TYR249 4.9 10.2 1.0
CA A:VAL247 4.9 11.9 1.0
O A:GLY277 4.9 11.0 1.0
C A:LEU248 5.0 12.0 1.0
OD1 A:ASN281 5.0 11.5 1.0
CG A:PHE241 5.0 11.5 1.0

Potassium binding site 3 out of 4 in 6uob

Go back to Potassium Binding Sites List in 6uob
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Resminostat


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) K330L Mutant Complexed with Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:11.9
occ:1.00
 O B:ASP230 2.6 10.2 1.0
O B:HIS232 2.7 12.1 1.0
OG B:SER251 2.8 12.3 1.0
OD1 B:ASP228 2.8 12.8 1.0
O B:VAL252 2.8 11.4 1.0
O B:ASP228 2.9 10.9 1.0
CG B:ASP228 3.2 12.5 1.0
C B:ASP228 3.5 11.4 1.0
C B:ASP230 3.6 11.1 1.0
C B:HIS232 3.7 11.7 1.0
C B:VAL252 3.8 9.6 1.0
OD2 B:ASP228 3.8 14.1 1.0
N B:ASP230 3.8 10.3 1.0
CB B:ASP228 3.9 8.7 1.0
N B:VAL252 3.9 11.5 1.0
CB B:SER251 4.0 10.4 1.0
CB B:HIS253 4.0 11.9 1.0
CA B:ASP230 4.1 11.0 1.0
C B:TRP229 4.2 11.2 1.0
N B:TRP229 4.2 11.3 1.0
CA B:SER251 4.2 10.8 1.0
ND1 B:HIS253 4.3 12.9 1.0
CA B:ASP228 4.3 12.8 1.0
CB B:ASP230 4.3 9.1 1.0
CA B:HIS233 4.4 12.5 1.0
CA B:TRP229 4.4 11.0 1.0
C B:SER251 4.4 12.4 1.0
N B:HIS233 4.4 11.7 1.0
N B:HIS232 4.5 11.3 1.0
CA B:HIS253 4.5 9.9 1.0
CA B:VAL252 4.5 10.8 1.0
N B:GLY234 4.6 15.5 1.0
N B:HIS253 4.6 11.2 1.0
CG B:HIS253 4.6 13.0 1.0
O B:HOH643 4.6 12.1 1.0
N B:VAL231 4.7 11.0 1.0
C B:VAL231 4.7 10.3 1.0
CA B:HIS232 4.8 9.8 1.0
OH B:TYR249 4.8 13.1 1.0
C B:HIS233 4.9 12.7 1.0
O B:TRP229 4.9 11.4 1.0
CE1 B:HIS192 4.9 16.4 1.0

Potassium binding site 4 out of 4 in 6uob

Go back to Potassium Binding Sites List in 6uob
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Resminostat


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) K330L Mutant Complexed with Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:18.5
occ:0.80
 O B:VAL247 2.7 16.8 1.0
O B:PHE241 2.7 17.8 1.0
O B:TYR280 2.9 18.1 1.0
O B:HOH623 2.9 18.1 1.0
O B:ASP244 2.9 24.6 1.0
O B:HOH669 3.0 18.5 1.0
CB B:PHE241 3.6 16.1 1.0
C B:PHE241 3.7 17.5 1.0
C B:TYR280 3.7 14.4 1.0
CB B:TYR280 3.8 17.9 1.0
C B:VAL247 3.9 13.6 1.0
C B:ASP244 4.1 25.2 1.0
CA B:PHE241 4.3 16.6 1.0
CA B:TYR280 4.4 16.1 1.0
N B:TYR249 4.4 14.3 1.0
N B:ASN281 4.5 14.2 1.0
N B:ASP244 4.5 21.3 1.0
CA B:LEU248 4.6 13.2 1.0
N B:GLU242 4.6 20.9 1.0
CA B:ASP244 4.7 20.4 1.0
O B:GLU242 4.7 23.8 1.0
N B:LEU248 4.7 14.7 1.0
CB B:ASP244 4.7 23.8 1.0
CB B:ASN281 4.8 14.1 1.0
C B:GLU242 4.8 22.9 1.0
CA B:ASN281 4.8 13.5 1.0
CA B:GLU242 4.8 18.3 1.0
CG B:PHE241 4.9 17.0 1.0
CB B:TYR249 4.9 13.2 1.0
CA B:VAL247 4.9 18.2 1.0
C B:LEU248 5.0 12.8 1.0
O B:GLY277 5.0 22.6 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 17:51:41 2024

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