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Potassium in PDB 6wyo: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) H82F F202Y Double Mutant Complexed with Trichostatin A

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) H82F F202Y Double Mutant Complexed with Trichostatin A, PDB code: 6wyo 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) 50.09 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.087, 123.993, 55.012, 90.00, 114.42, 90.00
R / Rfree (%) 17.1 / 23.2

Other elements in 6wyo:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) H82F F202Y Double 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) H82F F202Y Double Mutant Complexed with Trichostatin A (pdb code 6wyo). 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) H82F F202Y Double Mutant Complexed with Trichostatin A, PDB code: 6wyo:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6wyo

Go back to Potassium Binding Sites List in 6wyo
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) H82F F202Y Double 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) H82F F202Y Double Mutant Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:20.4
occ:1.00
 O A:ASP230 2.6 19.9 1.0
OD1 A:ASP228 2.7 16.6 1.0
O A:HIS232 2.7 22.7 1.0
OG A:SER251 2.9 18.4 1.0
O A:ASP228 2.9 19.0 1.0
O A:VAL252 2.9 23.0 1.0
CG A:ASP228 3.1 21.1 1.0
C A:ASP228 3.5 20.5 1.0
C A:ASP230 3.7 19.3 1.0
CB A:ASP228 3.7 17.8 1.0
C A:HIS232 3.7 25.1 1.0
OD2 A:ASP228 3.8 20.0 1.0
C A:VAL252 3.8 20.9 1.0
N A:ASP230 3.9 18.1 1.0
N A:VAL252 3.9 22.3 1.0
CB A:SER251 3.9 22.5 1.0
CB A:HIS253 4.0 20.3 1.0
N A:TRP229 4.1 19.2 1.0
CA A:ASP230 4.2 20.8 1.0
CA A:ASP228 4.2 17.9 1.0
CA A:SER251 4.2 19.5 1.0
C A:TRP229 4.3 21.3 1.0
CA A:HIS233 4.3 21.8 1.0
ND1 A:HIS253 4.3 19.9 1.0
CA A:TRP229 4.3 17.8 1.0
CB A:ASP230 4.3 19.8 1.0
N A:HIS233 4.4 21.6 1.0
C A:SER251 4.4 23.2 1.0
N A:HIS232 4.5 17.6 1.0
N A:GLY234 4.5 20.5 1.0
CA A:HIS253 4.6 20.8 1.0
CA A:VAL252 4.6 21.0 1.0
N A:HIS253 4.6 19.3 1.0
CG A:HIS253 4.6 20.4 1.0
CA A:HIS232 4.8 19.3 1.0
C A:VAL231 4.8 20.6 1.0
OH A:TYR249 4.8 24.6 1.0
N A:VAL231 4.8 19.5 1.0
O A:HOH606 4.8 19.7 1.0
C A:HIS233 4.8 22.3 1.0

Potassium binding site 2 out of 4 in 6wyo

Go back to Potassium Binding Sites List in 6wyo
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) H82F F202Y Double 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) H82F F202Y Double Mutant Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:24.2
occ:1.00
 O A:VAL247 2.6 25.9 1.0
O A:PHE241 2.7 24.0 1.0
O A:HOH630 2.8 22.4 1.0
O A:TYR280 2.9 21.4 1.0
O A:HOH625 3.0 25.0 1.0
O A:ASP244 3.1 29.6 1.0
C A:TYR280 3.6 25.9 1.0
C A:PHE241 3.7 25.5 1.0
CB A:PHE241 3.7 23.3 1.0
CB A:TYR280 3.7 26.0 1.0
C A:VAL247 3.9 22.9 1.0
C A:ASP244 4.1 33.3 1.0
CA A:TYR280 4.3 24.5 1.0
CA A:PHE241 4.3 24.6 1.0
N A:TYR249 4.4 20.5 1.0
N A:ASN281 4.4 26.8 1.0
CA A:LEU248 4.5 21.7 1.0
N A:ASP244 4.5 28.0 1.0
N A:GLU242 4.6 21.4 1.0
N A:LEU248 4.6 19.3 1.0
CA A:ASP244 4.7 29.4 1.0
CA A:GLU242 4.8 29.0 1.0
CA A:ASN281 4.8 24.6 1.0
CB A:ASP244 4.8 31.3 1.0
CB A:ASN281 4.8 21.9 1.0
C A:GLU242 4.9 25.5 1.0
C A:LEU248 4.9 22.9 1.0
CB A:TYR249 4.9 21.6 1.0
CA A:VAL247 4.9 23.6 1.0
O A:GLY277 4.9 33.2 1.0
CG A:PHE241 4.9 23.3 1.0
O A:GLU242 5.0 23.9 1.0
OD1 A:ASN281 5.0 23.7 1.0

Potassium binding site 3 out of 4 in 6wyo

Go back to Potassium Binding Sites List in 6wyo
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) H82F F202Y Double 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) H82F F202Y Double Mutant Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:19.8
occ:1.00
 O B:ASP230 2.6 19.4 1.0
O B:VAL252 2.8 20.4 1.0
OG B:SER251 2.8 22.0 1.0
O B:ASP228 2.8 15.8 1.0
O B:HIS232 2.8 17.8 1.0
OD1 B:ASP228 2.9 24.1 1.0
CG B:ASP228 3.3 23.2 1.0
C B:ASP228 3.5 20.0 1.0
C B:ASP230 3.6 19.2 1.0
C B:VAL252 3.7 21.1 1.0
C B:HIS232 3.8 20.4 1.0
N B:ASP230 3.8 23.0 1.0
CB B:HIS253 3.8 14.1 1.0
CB B:ASP228 3.9 17.5 1.0
OD2 B:ASP228 3.9 21.9 1.0
N B:VAL252 3.9 19.9 1.0
CB B:SER251 4.0 16.5 1.0
CA B:ASP230 4.1 18.5 1.0
C B:TRP229 4.2 21.7 1.0
CA B:SER251 4.2 16.0 1.0
N B:TRP229 4.2 20.5 1.0
ND1 B:HIS253 4.3 19.0 1.0
CA B:ASP228 4.3 17.6 1.0
CB B:ASP230 4.3 20.0 1.0
CA B:HIS233 4.3 15.4 1.0
C B:SER251 4.4 19.1 1.0
CA B:TRP229 4.4 20.7 1.0
N B:HIS233 4.4 19.2 1.0
CA B:HIS253 4.4 18.9 1.0
N B:HIS253 4.5 18.6 1.0
CA B:VAL252 4.5 16.8 1.0
N B:HIS232 4.5 16.6 1.0
CG B:HIS253 4.6 17.4 1.0
N B:GLY234 4.6 19.2 1.0
C B:VAL231 4.7 20.4 1.0
N B:VAL231 4.7 22.5 1.0
O B:HOH614 4.7 19.3 1.0
CA B:HIS232 4.8 17.7 1.0
OH B:TYR249 4.8 20.1 1.0
C B:HIS233 4.9 22.5 1.0
O B:TRP229 4.9 20.7 1.0
CE1 B:HIS192 5.0 20.5 1.0

Potassium binding site 4 out of 4 in 6wyo

Go back to Potassium Binding Sites List in 6wyo
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) H82F F202Y Double 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) H82F F202Y Double Mutant Complexed with Trichostatin A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:27.2
occ:1.00
 O B:PHE241 2.6 27.6 1.0
O B:VAL247 2.7 25.1 1.0
O B:HOH617 2.7 23.8 1.0
O B:TYR280 2.9 16.8 1.0
O B:ASP244 2.9 25.2 1.0
O B:HOH641 3.0 19.8 1.0
C B:PHE241 3.6 22.4 1.0
C B:TYR280 3.6 22.4 1.0
CB B:TYR280 3.7 25.7 1.0
CB B:PHE241 3.8 22.3 1.0
C B:VAL247 3.9 26.2 1.0
C B:ASP244 4.0 30.7 1.0
CA B:TYR280 4.3 24.2 1.0
CA B:PHE241 4.3 24.7 1.0
N B:TYR249 4.4 21.9 1.0
N B:ASN281 4.4 22.6 1.0
N B:ASP244 4.5 30.2 1.0
CA B:LEU248 4.5 21.2 1.0
N B:GLU242 4.5 24.4 1.0
CA B:ASP244 4.7 28.3 1.0
CA B:GLU242 4.7 31.2 1.0
N B:LEU248 4.7 26.1 1.0
CB B:ASN281 4.7 18.5 1.0
CB B:ASP244 4.7 30.2 1.0
CA B:ASN281 4.7 19.0 1.0
C B:GLU242 4.7 27.3 1.0
O B:GLU242 4.8 25.7 1.0
O B:GLY277 4.8 31.7 1.0
C B:LEU248 4.9 22.2 1.0
CB B:TYR249 4.9 17.3 1.0
CA B:VAL247 5.0 24.6 1.0

Reference:

J.D.Osko, D.W.Christianson. Binding of Inhibitors to Active-Site Mutants of CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6. Acta Crystallogr.,Sect.F V. 76 428 2020.
ISSN: ESSN 2053-230X
PubMed: 32880591
DOI: 10.1107/S2053230X20010250
Page generated: Mon Aug 12 18:18:51 2024

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