Potassium in PDB 6wyp: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Saha-Bpyne

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Saha-Bpyne, PDB code: 6wyp 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) 54.25 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 66.029, 95.170, 119.710, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.3

Other elements in 6wyp:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with Saha-Bpyne also contains other interesting chemical elements:

Zinc (Zn) 1 atom

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 Saha-Bpyne (pdb code 6wyp). 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 1 (CD1) K330L Mutant Complexed with Saha-Bpyne, PDB code: 6wyp:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6wyp

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


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 Saha-Bpyne within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:33.6
occ:1.00
O A:ASP230 2.7 34.1 1.0
O A:VAL252 2.7 33.3 1.0
O A:ASP228 2.8 30.1 1.0
OD1 A:ASP228 2.8 31.9 1.0
OG A:SER251 2.9 35.5 1.0
O A:HIS232 3.0 32.0 1.0
CG A:ASP228 3.3 33.9 1.0
C A:ASP228 3.5 27.6 1.0
C A:ASP230 3.6 33.4 1.0
C A:VAL252 3.6 38.3 1.0
CB A:ASP228 3.7 29.8 1.0
CB A:HIS253 3.8 33.5 1.0
N A:ASP230 3.8 28.2 1.0
C A:HIS232 3.8 38.4 1.0
N A:VAL252 3.9 34.7 1.0
OD2 A:ASP228 4.0 37.6 1.0
CB A:SER251 4.0 36.9 1.0
CA A:ASP230 4.1 28.8 1.0
CA A:SER251 4.2 31.6 1.0
CA A:ASP228 4.2 32.0 1.0
CB A:ASP230 4.2 26.7 1.0
C A:TRP229 4.2 33.9 1.0
N A:TRP229 4.3 29.8 1.0
ND1 A:HIS253 4.3 39.0 1.0
CA A:HIS253 4.3 35.3 1.0
CA A:HIS233 4.3 39.0 1.0
C A:SER251 4.3 33.7 1.0
N A:HIS253 4.4 31.1 1.0
CA A:TRP229 4.4 25.1 1.0
N A:HIS233 4.4 36.4 1.0
CA A:VAL252 4.4 33.7 1.0
N A:HIS232 4.5 29.4 1.0
CG A:HIS253 4.5 37.6 1.0
O A:HOH619 4.5 28.8 1.0
N A:GLY234 4.6 29.8 1.0
N A:VAL231 4.7 34.5 1.0
C A:VAL231 4.7 30.7 1.0
CA A:HIS232 4.8 34.9 1.0
OH A:TYR249 4.8 33.0 1.0
C A:HIS233 4.9 37.7 1.0
O A:TRP229 5.0 31.6 1.0

Potassium binding site 2 out of 2 in 6wyp

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


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 Saha-Bpyne within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:55.7
occ:1.00
O A:PHE241 2.7 62.1 1.0
O A:TYR280 2.7 43.7 1.0
O A:VAL247 2.8 44.9 1.0
O A:ASP244 2.8 54.5 1.0
O A:HOH607 3.1 52.5 1.0
O A:HOH602 3.1 35.2 1.0
C A:TYR280 3.5 52.1 1.0
CB A:TYR280 3.6 50.8 1.0
C A:PHE241 3.8 55.3 1.0
CB A:PHE241 3.9 50.3 1.0
C A:VAL247 4.0 44.0 1.0
C A:ASP244 4.0 58.8 1.0
CA A:TYR280 4.2 51.7 1.0
N A:ASN281 4.4 52.6 1.0
N A:TYR249 4.4 35.9 1.0
CA A:PHE241 4.5 51.5 1.0
N A:ASP244 4.5 58.2 1.0
CA A:LEU248 4.6 43.1 1.0
CA A:ASP244 4.7 53.6 1.0
CB A:ASN281 4.7 43.8 1.0
N A:LEU248 4.7 42.1 1.0
CA A:ASN281 4.7 42.2 1.0
CB A:ASP244 4.8 45.8 1.0
O A:GLU242 4.8 54.4 1.0
C A:GLU242 4.9 57.3 1.0
N A:GLU242 4.9 49.3 1.0
CG A:TYR280 4.9 61.5 1.0
O A:GLY277 4.9 60.9 1.0
CB A:TYR249 4.9 39.6 1.0
N A:PRO245 5.0 61.6 1.0
C A:LEU248 5.0 39.9 1.0
CA A:VAL247 5.0 45.4 1.0
CA A:GLU242 5.0 52.4 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 Dec 14 02:23:44 2020

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