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Potassium in PDB 6pzu: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Ap-1-62-A

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Ap-1-62-A, PDB code: 6pzu 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) 42.39 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.626, 84.273, 87.355, 90.00, 98.04, 90.00
R / Rfree (%) n/a / n/a

Other elements in 6pzu:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Ap-1-62-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 2 Complexed with Ap-1-62-A (pdb code 6pzu). 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 Ap-1-62-A, PDB code: 6pzu:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6pzu

Go back to Potassium Binding Sites List in 6pzu
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Ap-1-62-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 2 Complexed with Ap-1-62-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:7.2
occ:1.00
 O A:ASP612 2.6 8.1 1.0
O A:LEU634 2.7 8.8 1.0
OG A:SER633 2.7 7.5 1.0
O A:HIS614 2.7 8.0 1.0
OD1 A:ASP610 2.7 7.3 1.0
O A:ASP610 2.8 4.2 1.0
CG A:ASP610 3.3 9.4 1.0
C A:ASP610 3.5 5.9 1.0
C A:ASP612 3.6 7.2 1.0
C A:HIS614 3.6 5.3 1.0
C A:LEU634 3.7 5.0 1.0
CB A:ASP610 3.8 7.5 1.0
N A:ASP612 3.9 6.3 1.0
CB A:SER633 3.9 5.1 1.0
N A:LEU634 3.9 6.0 1.0
CB A:HIS635 3.9 4.8 1.0
OD2 A:ASP610 4.0 8.2 1.0
CA A:ASP612 4.1 5.0 1.0
C A:TRP611 4.2 7.9 1.0
N A:TRP611 4.2 4.0 1.0
CB A:ASP612 4.2 6.9 1.0
CA A:SER633 4.2 7.6 1.0
CA A:ASP610 4.3 7.1 1.0
ND1 A:HIS635 4.3 5.2 1.0
CA A:HIS615 4.3 4.1 1.0
N A:HIS615 4.3 4.7 1.0
CA A:TRP611 4.3 7.1 1.0
C A:SER633 4.4 7.2 1.0
N A:HIS614 4.4 4.5 1.0
O A:HOH980 4.4 8.8 1.0
CA A:LEU634 4.5 9.1 1.0
CA A:HIS635 4.5 6.7 1.0
N A:GLY616 4.5 3.9 1.0
N A:HIS635 4.5 4.9 1.0
CG A:HIS635 4.6 6.2 1.0
CA A:HIS614 4.6 3.9 1.0
C A:VAL613 4.7 5.8 1.0
OH A:TYR631 4.7 6.9 1.0
C A:HIS615 4.7 4.8 1.0
N A:VAL613 4.7 4.7 1.0
CE1 A:HIS573 4.8 8.8 1.0
O A:TRP611 4.9 5.6 1.0
ND1 A:HIS573 4.9 9.0 1.0

Potassium binding site 2 out of 4 in 6pzu

Go back to Potassium Binding Sites List in 6pzu
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Ap-1-62-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 2 Complexed with Ap-1-62-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:12.5
occ:1.00
 O A:PHE623 2.6 8.2 1.0
O A:HOH966 2.7 10.3 1.0
O A:VAL629 2.7 7.2 1.0
O A:TYR662 2.9 6.7 1.0
O A:ASP626 2.9 12.1 1.0
O A:HOH1066 3.0 7.8 1.0
CB A:TYR662 3.6 10.9 1.0
C A:TYR662 3.6 9.2 1.0
C A:PHE623 3.6 7.7 1.0
CB A:PHE623 3.7 6.5 1.0
C A:VAL629 3.9 8.2 1.0
C A:ASP626 4.0 10.7 1.0
CA A:TYR662 4.2 8.0 1.0
CA A:PHE623 4.3 5.8 1.0
N A:ASN663 4.4 8.1 1.0
N A:TYR631 4.4 6.2 1.0
N A:ASP626 4.4 10.3 1.0
N A:GLU624 4.5 8.1 1.0
CA A:GLU624 4.6 9.9 1.0
CA A:ASP626 4.6 10.9 1.0
CB A:ASP626 4.6 11.6 1.0
CA A:LEU630 4.7 5.2 1.0
C A:GLU624 4.7 10.4 1.0
O A:GLU624 4.7 10.3 1.0
N A:LEU630 4.8 7.7 1.0
CB A:TYR631 4.8 5.2 1.0
CA A:ASN663 4.8 6.6 1.0
CB A:ASN663 4.8 7.2 1.0
O A:GLY659 4.8 9.3 1.0
CG A:TYR662 4.9 9.4 1.0
CG A:PHE623 4.9 6.2 1.0
CA A:VAL629 4.9 6.0 1.0
C A:LEU630 5.0 8.0 1.0

Potassium binding site 3 out of 4 in 6pzu

Go back to Potassium Binding Sites List in 6pzu
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Ap-1-62-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 2 Complexed with Ap-1-62-A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:10.7
occ:1.00
 O B:ASP612 2.6 9.0 1.0
O B:LEU634 2.6 8.9 1.0
O B:HIS614 2.7 9.8 1.0
OG B:SER633 2.7 8.8 1.0
O B:ASP610 2.8 6.8 1.0
OD1 B:ASP610 2.8 11.0 1.0
CG B:ASP610 3.3 12.2 1.0
C B:ASP610 3.4 10.9 1.0
C B:ASP612 3.6 7.8 1.0
C B:LEU634 3.6 11.4 1.0
C B:HIS614 3.7 11.0 1.0
CB B:ASP610 3.8 9.6 1.0
N B:ASP612 3.8 10.3 1.0
CB B:SER633 3.9 10.2 1.0
CB B:HIS635 3.9 6.2 1.0
N B:LEU634 3.9 9.4 1.0
OD2 B:ASP610 3.9 9.0 1.0
CA B:ASP612 4.1 6.0 1.0
N B:TRP611 4.1 7.0 1.0
C B:TRP611 4.2 6.9 1.0
CA B:ASP610 4.2 7.6 1.0
CA B:TRP611 4.3 5.3 1.0
CB B:ASP612 4.3 7.4 1.0
CA B:SER633 4.3 10.5 1.0
ND1 B:HIS635 4.3 10.0 1.0
CA B:HIS615 4.3 7.5 1.0
O B:HOH941 4.3 10.8 1.0
N B:HIS615 4.4 7.2 1.0
N B:HIS614 4.4 9.8 1.0
CA B:HIS635 4.4 7.8 1.0
C B:SER633 4.4 12.8 1.0
CA B:LEU634 4.5 9.8 1.0
N B:HIS635 4.5 8.2 1.0
N B:GLY616 4.5 4.7 1.0
CG B:HIS635 4.6 12.0 1.0
C B:VAL613 4.6 8.4 1.0
OH B:TYR631 4.7 7.5 1.0
N B:VAL613 4.7 7.7 1.0
CA B:HIS614 4.7 5.3 1.0
C B:HIS615 4.8 4.8 1.0
CE1 B:HIS573 4.8 9.0 1.0
O B:TRP611 4.9 7.5 1.0
ND1 B:HIS573 4.9 9.4 1.0

Potassium binding site 4 out of 4 in 6pzu

Go back to Potassium Binding Sites List in 6pzu
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Ap-1-62-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 2 Complexed with Ap-1-62-A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:16.9
occ:1.00
 O B:VAL629 2.7 11.1 1.0
O B:HOH982 2.7 13.0 1.0
O B:PHE623 2.7 13.4 1.0
O B:ASP626 2.9 17.7 1.0
O B:TYR662 2.9 9.7 1.0
O B:HOH1051 3.1 14.9 1.0
CB B:TYR662 3.6 14.3 1.0
C B:TYR662 3.6 15.3 1.0
C B:PHE623 3.6 8.5 1.0
CB B:PHE623 3.7 11.7 1.0
C B:VAL629 3.9 7.8 1.0
C B:ASP626 4.1 16.6 1.0
CA B:TYR662 4.2 12.6 1.0
N B:TYR631 4.3 12.1 1.0
CA B:PHE623 4.3 12.3 1.0
N B:ASN663 4.4 12.8 1.0
N B:ASP626 4.5 16.4 1.0
N B:GLU624 4.6 13.3 1.0
CA B:LEU630 4.6 6.8 1.0
CA B:GLU624 4.6 13.7 1.0
CB B:ASP626 4.6 15.0 1.0
CA B:ASP626 4.6 13.4 1.0
N B:LEU630 4.7 8.9 1.0
O B:GLU624 4.7 15.9 1.0
C B:GLU624 4.7 16.7 1.0
CB B:TYR631 4.8 9.1 1.0
CA B:ASN663 4.8 10.4 1.0
C B:LEU630 4.9 10.8 1.0
CG B:TYR662 4.9 14.7 1.0
O B:GLY659 4.9 11.8 1.0
CB B:ASN663 4.9 11.4 1.0
CA B:VAL629 4.9 9.6 1.0
CB B:VAL629 5.0 9.0 1.0
CG B:PHE623 5.0 10.5 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: Mon Aug 12 17:15:45 2024

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