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Potassium in PDB 6wyq: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with 4-Iodo-Saha

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with 4-Iodo-Saha, PDB code: 6wyq 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) 39.14 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.050, 123.790, 55.100, 90.00, 113.52, 90.00
R / Rfree (%) 17.6 / 22.3

Other elements in 6wyq:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) K330L Mutant Complexed with 4-Iodo-Saha also contains other interesting chemical elements:

Iodine (I) 2 atoms
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 4-Iodo-Saha (pdb code 6wyq). 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 4-Iodo-Saha, PDB code: 6wyq:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6wyq

Go back to Potassium Binding Sites List in 6wyq
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 4-Iodo-Saha


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

b:7.6
occ:1.00
 O A:ASP230 2.6 6.9 1.0
O A:HIS232 2.8 6.8 1.0
O A:VAL252 2.8 5.9 1.0
O A:ASP228 2.8 5.3 1.0
OG A:SER251 2.8 7.3 1.0
OD1 A:ASP228 2.9 4.4 1.0
CG A:ASP228 3.3 6.0 1.0
C A:ASP228 3.5 5.6 1.0
C A:ASP230 3.6 8.6 1.0
C A:VAL252 3.6 7.0 1.0
C A:HIS232 3.7 7.5 1.0
N A:VAL252 3.8 6.1 1.0
N A:ASP230 3.8 6.1 1.0
CB A:HIS253 3.9 7.4 1.0
CB A:SER251 3.9 5.8 1.0
CB A:ASP228 3.9 4.7 1.0
OD2 A:ASP228 4.0 5.2 1.0
CA A:ASP230 4.1 6.0 1.0
CA A:SER251 4.2 5.0 1.0
C A:TRP229 4.2 7.3 1.0
N A:TRP229 4.2 5.6 1.0
C A:SER251 4.3 6.5 1.0
ND1 A:HIS253 4.3 5.9 1.0
CA A:ASP228 4.3 5.2 1.0
CA A:HIS233 4.3 7.6 1.0
CB A:ASP230 4.3 6.0 1.0
CA A:HIS253 4.4 6.5 1.0
CA A:TRP229 4.4 6.1 1.0
N A:HIS233 4.4 5.3 1.0
CA A:VAL252 4.4 7.6 1.0
N A:HIS253 4.4 6.1 1.0
N A:HIS232 4.5 7.3 1.0
CG A:HIS253 4.6 8.9 1.0
N A:GLY234 4.6 6.9 1.0
N A:VAL231 4.7 7.6 1.0
C A:VAL231 4.7 6.6 1.0
O A:HOH639 4.7 7.9 1.0
CA A:HIS232 4.8 7.1 1.0
OH A:TYR249 4.8 7.1 1.0
C A:HIS233 4.9 6.5 1.0
CE1 A:HIS192 4.9 8.7 1.0
O A:TRP229 5.0 8.1 1.0
CA A:VAL231 5.0 7.6 1.0

Potassium binding site 2 out of 4 in 6wyq

Go back to Potassium Binding Sites List in 6wyq
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 4-Iodo-Saha


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

b:11.1
occ:1.00
 O A:VAL247 2.6 9.3 1.0
O A:PHE241 2.6 10.2 1.0
O A:HOH629 2.6 9.9 1.0
O A:ASP244 2.9 11.9 1.0
O A:TYR280 2.9 7.9 1.0
O A:HOH674 2.9 9.8 1.0
C A:PHE241 3.6 10.3 1.0
C A:TYR280 3.7 9.2 1.0
CB A:PHE241 3.7 8.9 1.0
CB A:TYR280 3.8 8.9 1.0
C A:VAL247 3.8 9.9 1.0
C A:ASP244 4.0 10.9 1.0
CA A:PHE241 4.3 10.4 1.0
CA A:TYR280 4.4 9.3 1.0
N A:TYR249 4.4 8.4 1.0
N A:ASP244 4.4 10.0 1.0
CA A:LEU248 4.5 9.5 1.0
N A:ASN281 4.5 7.9 1.0
N A:GLU242 4.6 9.7 1.0
N A:LEU248 4.6 9.5 1.0
CA A:ASP244 4.6 11.0 1.0
CB A:ASP244 4.7 11.3 1.0
O A:GLU242 4.7 10.4 1.0
CA A:GLU242 4.7 8.4 1.0
C A:GLU242 4.7 10.2 1.0
CB A:ASN281 4.8 5.0 1.0
CA A:VAL247 4.8 9.7 1.0
CA A:ASN281 4.9 7.3 1.0
C A:LEU248 4.9 7.4 1.0
CB A:VAL247 4.9 10.0 1.0
O A:GLY277 4.9 10.1 1.0
CB A:TYR249 4.9 7.0 1.0
N A:VAL247 4.9 8.6 1.0
CG A:PHE241 5.0 10.8 1.0

Potassium binding site 3 out of 4 in 6wyq

Go back to Potassium Binding Sites List in 6wyq
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 4-Iodo-Saha


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

b:7.2
occ:1.00
 O B:ASP230 2.6 6.8 1.0
OD1 B:ASP228 2.7 6.0 1.0
OG B:SER251 2.7 7.1 1.0
O B:HIS232 2.8 8.4 1.0
O B:ASP228 2.8 5.7 1.0
O B:VAL252 2.9 6.0 1.0
CG B:ASP228 3.2 8.5 1.0
C B:ASP228 3.5 6.4 1.0
C B:ASP230 3.7 6.5 1.0
CB B:ASP228 3.7 7.4 1.0
C B:VAL252 3.7 6.3 1.0
C B:HIS232 3.7 7.7 1.0
N B:VAL252 3.8 6.8 1.0
CB B:SER251 3.8 5.9 1.0
OD2 B:ASP228 3.9 10.3 1.0
N B:ASP230 3.9 7.2 1.0
CB B:HIS253 4.0 6.9 1.0
CA B:SER251 4.2 7.0 1.0
CA B:ASP228 4.2 5.5 1.0
CA B:ASP230 4.2 7.4 1.0
N B:TRP229 4.2 5.1 1.0
CA B:HIS233 4.3 7.1 1.0
C B:TRP229 4.3 9.1 1.0
CB B:ASP230 4.3 6.6 1.0
C B:SER251 4.3 7.3 1.0
ND1 B:HIS253 4.3 6.1 1.0
N B:HIS233 4.4 6.0 1.0
CA B:TRP229 4.4 5.9 1.0
CA B:HIS253 4.5 7.2 1.0
CA B:VAL252 4.5 5.5 1.0
N B:HIS253 4.5 8.2 1.0
N B:GLY234 4.5 9.2 1.0
N B:HIS232 4.5 7.9 1.0
CG B:HIS253 4.6 6.8 1.0
OH B:TYR249 4.7 7.4 1.0
C B:VAL231 4.8 8.7 1.0
N B:VAL231 4.8 6.6 1.0
CA B:HIS232 4.8 9.7 1.0
O B:HOH632 4.8 8.6 1.0
C B:HIS233 4.8 7.4 1.0
CE1 B:HIS192 4.9 9.1 1.0

Potassium binding site 4 out of 4 in 6wyq

Go back to Potassium Binding Sites List in 6wyq
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 4-Iodo-Saha


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

b:12.6
occ:1.00
 O B:PHE241 2.6 8.4 1.0
O B:HOH668 2.7 10.3 1.0
O B:VAL247 2.7 9.5 1.0
O B:TYR280 2.9 10.3 1.0
O B:HOH679 2.9 7.4 1.0
O B:ASP244 3.0 13.9 1.0
C B:PHE241 3.6 9.6 1.0
CB B:PHE241 3.6 10.6 1.0
C B:TYR280 3.6 11.8 1.0
CB B:TYR280 3.8 11.2 1.0
C B:VAL247 4.0 10.3 1.0
C B:ASP244 4.1 12.4 1.0
CA B:PHE241 4.2 8.7 1.0
CA B:TYR280 4.3 11.7 1.0
N B:ASN281 4.4 10.1 1.0
N B:TYR249 4.4 7.7 1.0
N B:ASP244 4.5 14.4 1.0
N B:GLU242 4.5 11.1 1.0
O B:GLU242 4.6 15.8 1.0
CA B:LEU248 4.6 11.4 1.0
CA B:GLU242 4.7 7.2 1.0
CA B:ASP244 4.7 13.2 1.0
C B:GLU242 4.7 13.5 1.0
CB B:ASN281 4.8 7.8 1.0
N B:LEU248 4.8 9.4 1.0
CA B:ASN281 4.8 8.9 1.0
CB B:ASP244 4.8 14.3 1.0
CB B:TYR249 4.9 8.5 1.0
CG B:PHE241 4.9 8.6 1.0
O B:GLY277 4.9 12.5 1.0
CA B:VAL247 4.9 9.1 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 18:19:06 2024

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