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Potassium in PDB 6pzo: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153, PDB code: 6pzo 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) 66.88 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.810, 92.580, 96.730, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 6pzo:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153 also contains other interesting chemical elements:

Fluorine (F) 6 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 2 Complexed with Yx-153 (pdb code 6pzo). 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 2 Complexed with Yx-153, PDB code: 6pzo:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6pzo

Go back to Potassium Binding Sites List in 6pzo
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153


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 2 Complexed with Yx-153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:6.2
occ:1.00
 O A:ASP612 2.6 6.3 1.0
O A:HIS614 2.7 7.0 1.0
O A:LEU634 2.7 7.1 1.0
OD1 A:ASP610 2.7 6.0 1.0
OG A:SER633 2.8 7.9 1.0
O A:ASP610 2.8 5.9 1.0
CG A:ASP610 3.2 6.9 1.0
C A:ASP610 3.5 6.0 1.0
C A:ASP612 3.6 5.9 1.0
C A:HIS614 3.7 5.9 1.0
C A:LEU634 3.7 8.9 1.0
N A:ASP612 3.8 7.2 1.0
CB A:ASP610 3.8 8.6 1.0
OD2 A:ASP610 3.9 6.2 1.0
CB A:SER633 3.9 5.2 1.0
N A:LEU634 4.0 8.0 1.0
CB A:HIS635 4.0 6.8 1.0
CA A:ASP612 4.1 4.4 1.0
CB A:ASP612 4.2 6.3 1.0
C A:TRP611 4.2 6.7 1.0
N A:TRP611 4.2 5.9 1.0
CA A:HIS615 4.3 7.4 1.0
CA A:ASP610 4.3 5.6 1.0
CA A:SER633 4.3 5.0 1.0
N A:HIS615 4.3 6.2 1.0
CA A:TRP611 4.4 6.9 1.0
N A:GLY616 4.4 6.8 1.0
N A:HIS614 4.4 5.3 1.0
ND1 A:HIS635 4.4 8.4 1.0
CA A:HIS635 4.5 6.0 1.0
C A:SER633 4.5 9.7 1.0
CA A:LEU634 4.5 7.2 1.0
N A:HIS635 4.6 6.5 1.0
O A:HOH920 4.6 9.2 1.0
CA A:HIS614 4.7 7.9 1.0
C A:VAL613 4.7 6.1 1.0
OH A:TYR631 4.7 6.8 1.0
CG A:HIS635 4.7 7.1 1.0
C A:HIS615 4.7 6.0 1.0
N A:VAL613 4.7 5.8 1.0
CE1 A:HIS573 4.8 8.2 1.0
ND1 A:HIS573 4.9 6.0 1.0
O A:TRP611 4.9 6.4 1.0

Potassium binding site 2 out of 4 in 6pzo

Go back to Potassium Binding Sites List in 6pzo
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153


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 2 Complexed with Yx-153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:8.4
occ:1.00
 O A:PHE623 2.7 8.5 1.0
O A:VAL629 2.7 10.0 1.0
O A:HOH950 2.7 10.1 1.0
O A:TYR662 2.9 9.1 1.0
O A:ASP626 2.9 13.9 1.0
O A:HOH983 3.1 9.4 1.0
C A:PHE623 3.6 8.9 1.0
C A:TYR662 3.6 8.8 1.0
CB A:PHE623 3.7 6.9 1.0
CB A:TYR662 3.7 9.4 1.0
C A:VAL629 4.0 8.6 1.0
C A:ASP626 4.0 12.6 1.0
CA A:TYR662 4.3 8.2 1.0
CA A:PHE623 4.3 6.9 1.0
N A:TYR631 4.3 8.8 1.0
N A:ASP626 4.4 11.2 1.0
N A:ASN663 4.4 8.9 1.0
N A:GLU624 4.5 5.5 1.0
CA A:GLU624 4.6 8.8 1.0
CB A:ASP626 4.6 11.8 1.0
CA A:ASP626 4.6 12.0 1.0
CA A:LEU630 4.6 8.1 1.0
C A:GLU624 4.7 9.2 1.0
CB A:TYR631 4.7 5.5 1.0
O A:GLU624 4.7 7.8 1.0
N A:LEU630 4.7 7.2 1.0
CA A:ASN663 4.8 7.8 1.0
CB A:ASN663 4.8 6.5 1.0
C A:LEU630 4.9 10.8 1.0
O A:GLY659 4.9 13.8 1.0
CG A:PHE623 5.0 5.6 1.0
CA A:VAL629 5.0 9.5 1.0

Potassium binding site 3 out of 4 in 6pzo

Go back to Potassium Binding Sites List in 6pzo
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153


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 2 Complexed with Yx-153 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:6.0
occ:1.00
 O B:ASP612 2.6 6.8 1.0
O B:HIS614 2.7 6.0 1.0
O B:LEU634 2.7 5.2 1.0
OG B:SER633 2.8 6.7 1.0
O B:ASP610 2.8 6.6 1.0
OD1 B:ASP610 2.8 6.3 1.0
CG B:ASP610 3.3 5.5 1.0
C B:ASP610 3.5 7.1 1.0
C B:ASP612 3.6 7.4 1.0
C B:HIS614 3.7 6.4 1.0
C B:LEU634 3.8 6.7 1.0
CB B:ASP610 3.8 5.6 1.0
N B:ASP612 3.9 4.9 1.0
OD2 B:ASP610 3.9 6.3 1.0
CB B:SER633 4.0 6.5 1.0
N B:LEU634 4.0 5.0 1.0
CB B:HIS635 4.0 7.2 1.0
CA B:ASP612 4.1 5.0 1.0
CB B:ASP612 4.2 5.8 1.0
N B:TRP611 4.2 5.2 1.0
C B:TRP611 4.2 5.4 1.0
CA B:HIS615 4.3 9.3 1.0
CA B:ASP610 4.3 5.4 1.0
N B:HIS615 4.3 5.0 1.0
CA B:TRP611 4.3 6.5 1.0
CA B:SER633 4.3 6.7 1.0
ND1 B:HIS635 4.4 7.6 1.0
N B:GLY616 4.4 4.6 1.0
N B:HIS614 4.4 4.5 1.0
C B:SER633 4.5 6.8 1.0
CA B:HIS635 4.5 6.4 1.0
CA B:LEU634 4.6 6.9 1.0
O B:HOH935 4.6 7.7 1.0
N B:HIS635 4.6 7.4 1.0
OH B:TYR631 4.6 5.0 1.0
CG B:HIS635 4.7 6.5 1.0
CA B:HIS614 4.7 7.9 1.0
C B:VAL613 4.7 6.1 1.0
C B:HIS615 4.7 6.0 1.0
N B:VAL613 4.7 6.5 1.0
CE1 B:HIS573 4.8 7.2 1.0
ND1 B:HIS573 4.9 8.0 1.0
O B:TRP611 5.0 4.4 1.0

Potassium binding site 4 out of 4 in 6pzo

Go back to Potassium Binding Sites List in 6pzo
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153


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 2 Complexed with Yx-153 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:8.7
occ:1.00
 O B:VAL629 2.7 10.8 1.0
O B:PHE623 2.7 10.5 1.0
O B:HOH956 2.7 7.9 1.0
O B:ASP626 2.8 13.5 1.0
O B:TYR662 2.8 6.9 1.0
O B:HOH1038 3.0 7.0 1.0
C B:TYR662 3.6 8.3 1.0
C B:PHE623 3.6 8.2 1.0
CB B:TYR662 3.6 10.7 1.0
CB B:PHE623 3.7 6.5 1.0
C B:VAL629 3.9 9.8 1.0
C B:ASP626 4.0 10.8 1.0
CA B:TYR662 4.2 11.3 1.0
CA B:PHE623 4.3 9.8 1.0
N B:TYR631 4.3 6.1 1.0
N B:ASP626 4.4 10.2 1.0
N B:ASN663 4.4 11.2 1.0
N B:GLU624 4.5 10.2 1.0
CA B:LEU630 4.5 9.1 1.0
CA B:ASP626 4.6 9.6 1.0
CB B:ASP626 4.6 11.8 1.0
CA B:GLU624 4.6 10.0 1.0
N B:LEU630 4.7 7.0 1.0
C B:GLU624 4.7 10.8 1.0
O B:GLU624 4.7 10.4 1.0
CA B:ASN663 4.8 8.5 1.0
CB B:TYR631 4.8 7.7 1.0
CB B:ASN663 4.8 7.6 1.0
O B:GLY659 4.9 13.7 1.0
C B:LEU630 4.9 9.5 1.0
CA B:VAL629 5.0 9.5 1.0
CG B:TYR662 5.0 12.6 1.0

Reference:

J.D.Osko, N.J.Porter, P.A.Narayana Reddy, Y.C.Xiao, J.Rokka, M.Jung, J.M.Hooker, J.M.Salvino, D.W.Christianson. Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. J.Med.Chem. V. 63 295 2020.
ISSN: ISSN 0022-2623
PubMed: 31793776
DOI: 10.1021/ACS.JMEDCHEM.9B01540
Page generated: Sat Aug 9 11:51:54 2025

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