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Potassium in PDB 6pzr: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat

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

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Resminostat, PDB code: 6pzr 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) 68.94 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.883, 97.364, 97.642, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 6pzr:

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

Iodine (I) 7 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 Resminostat (pdb code 6pzr). 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 Resminostat, PDB code: 6pzr:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6pzr

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


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 Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:20.8
occ:1.00
 O A:LEU634 2.6 13.5 1.0
OD1 A:ASP610 2.6 19.1 1.0
O A:ASP612 2.6 20.9 1.0
O A:HIS614 2.7 17.8 1.0
OG A:SER633 2.8 14.4 1.0
O A:ASP610 3.0 16.7 1.0
CG A:ASP610 3.2 18.5 1.0
C A:ASP612 3.6 21.4 1.0
C A:ASP610 3.7 18.1 1.0
C A:HIS614 3.7 19.5 1.0
C A:LEU634 3.7 19.1 1.0
OD2 A:ASP610 3.8 18.1 1.0
N A:ASP612 3.9 15.6 1.0
CB A:HIS635 3.9 17.7 1.0
CB A:ASP610 3.9 19.5 1.0
N A:LEU634 4.1 19.3 1.0
CA A:ASP612 4.1 18.6 1.0
CB A:SER633 4.1 20.6 1.0
CB A:ASP612 4.2 15.9 1.0
C A:TRP611 4.2 17.7 1.0
CA A:HIS615 4.2 18.7 1.0
N A:TRP611 4.3 16.4 1.0
N A:HIS615 4.3 18.3 1.0
CA A:ASP610 4.4 13.2 1.0
CA A:TRP611 4.4 19.6 1.0
N A:HIS614 4.5 16.4 1.0
N A:GLY616 4.5 21.5 1.0
CA A:HIS635 4.5 24.2 1.0
ND1 A:HIS635 4.5 18.7 1.0
CA A:SER633 4.5 19.3 1.0
N A:HIS635 4.5 22.7 1.0
CA A:LEU634 4.6 17.9 1.0
C A:VAL613 4.6 23.8 1.0
C A:HIS615 4.7 19.4 1.0
C A:SER633 4.7 19.6 1.0
N A:VAL613 4.7 16.9 1.0
CA A:HIS614 4.7 16.7 1.0
CG A:HIS635 4.7 19.5 1.0
OH A:TYR631 4.8 20.8 1.0
CE1 A:HIS573 4.8 20.5 1.0
O A:HOH906 4.9 22.0 1.0
O A:TRP611 4.9 19.3 1.0
ND1 A:HIS573 4.9 15.6 1.0
O A:VAL613 5.0 18.1 1.0

Potassium binding site 2 out of 4 in 6pzr

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


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 Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:19.4
occ:1.00
 O A:HOH940 2.7 16.3 1.0
O A:PHE623 2.7 20.4 1.0
O A:VAL629 2.8 21.4 1.0
O A:TYR662 2.9 15.1 1.0
O A:ASP626 3.0 18.7 1.0
O A:HOH931 3.2 21.2 1.0
C A:PHE623 3.7 21.5 1.0
C A:TYR662 3.7 19.4 1.0
CB A:TYR662 3.8 20.1 1.0
CB A:PHE623 3.8 17.6 1.0
C A:VAL629 4.0 19.4 1.0
C A:ASP626 4.1 21.9 1.0
CA A:TYR662 4.3 18.8 1.0
N A:TYR631 4.4 15.2 1.0
CA A:PHE623 4.4 17.4 1.0
N A:ASN663 4.4 20.6 1.0
N A:GLU624 4.5 20.3 1.0
CA A:GLU624 4.6 20.3 1.0
N A:ASP626 4.6 22.6 1.0
CB A:ASP626 4.7 21.1 1.0
CA A:LEU630 4.7 15.8 1.0
CA A:ASP626 4.7 27.0 1.0
CB A:TYR631 4.7 15.6 1.0
CB A:ASN663 4.7 14.4 1.0
CA A:ASN663 4.8 17.3 1.0
C A:GLU624 4.8 23.8 1.0
O A:GLU624 4.8 19.2 1.0
N A:LEU630 4.8 16.7 1.0
OD1 A:ASN663 4.9 16.5 1.0
C A:LEU630 5.0 17.1 1.0

Potassium binding site 3 out of 4 in 6pzr

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


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 Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:18.8
occ:1.00
 O B:ASP612 2.6 16.8 1.0
O B:HIS614 2.7 14.2 1.0
O B:LEU634 2.8 13.8 1.0
OD2 B:ASP610 2.9 19.1 1.0
O B:ASP610 3.0 16.2 1.0
OG B:SER633 3.0 17.5 1.0
CG B:ASP610 3.3 17.6 1.0
C B:ASP610 3.6 16.2 1.0
C B:ASP612 3.6 18.7 1.0
C B:HIS614 3.7 14.1 1.0
C B:LEU634 3.8 22.2 1.0
CB B:ASP610 3.8 18.6 1.0
OD1 B:ASP610 3.8 14.9 1.0
N B:ASP612 3.9 15.5 1.0
N B:LEU634 3.9 22.2 1.0
CB B:HIS635 4.0 18.6 1.0
CA B:ASP612 4.1 13.3 1.0
CB B:SER633 4.1 16.7 1.0
CA B:HIS615 4.2 16.0 1.0
N B:TRP611 4.2 17.4 1.0
CB B:ASP612 4.2 11.9 1.0
C B:TRP611 4.2 16.0 1.0
N B:HIS615 4.3 17.6 1.0
CA B:ASP610 4.3 14.6 1.0
CA B:TRP611 4.4 17.8 1.0
O B:HOH909 4.4 17.0 1.0
N B:GLY616 4.4 18.5 1.0
N B:HIS614 4.4 17.3 1.0
CA B:SER633 4.5 17.4 1.0
CA B:HIS635 4.5 22.8 1.0
ND1 B:HIS635 4.5 20.3 1.0
CA B:LEU634 4.6 17.9 1.0
N B:HIS635 4.6 23.9 1.0
C B:SER633 4.6 19.7 1.0
C B:VAL613 4.7 18.1 1.0
CA B:HIS614 4.7 17.0 1.0
C B:HIS615 4.7 18.0 1.0
CG B:HIS635 4.7 21.1 1.0
N B:VAL613 4.7 17.5 1.0
OH B:TYR631 4.9 19.7 1.0
CE1 B:HIS573 4.9 13.6 1.0
O B:TRP611 4.9 16.7 1.0

Potassium binding site 4 out of 4 in 6pzr

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


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 Resminostat within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:15.5
occ:1.00
 O B:TYR662 2.6 17.9 1.0
O B:VAL629 2.7 20.8 1.0
O B:PHE623 2.7 24.5 1.0
O B:HOH950 2.7 18.7 1.0
O B:ASP626 3.1 21.3 1.0
O B:HOH914 3.5 18.7 1.0
C B:TYR662 3.6 19.8 1.0
CB B:TYR662 3.7 21.1 1.0
C B:PHE623 3.7 19.8 1.0
CB B:PHE623 3.9 22.1 1.0
C B:VAL629 3.9 16.2 1.0
C B:ASP626 4.2 22.4 1.0
CA B:TYR662 4.3 21.2 1.0
N B:TYR631 4.3 19.6 1.0
N B:ASN663 4.4 22.1 1.0
CA B:PHE623 4.4 17.5 1.0
N B:GLU624 4.6 16.0 1.0
CA B:GLU624 4.6 19.2 1.0
CA B:LEU630 4.6 14.2 1.0
N B:ASP626 4.6 20.5 1.0
CB B:ASN663 4.7 16.9 1.0
CB B:TYR631 4.7 15.7 1.0
CA B:ASN663 4.7 19.5 1.0
N B:LEU630 4.7 16.1 1.0
CB B:ASP626 4.8 12.6 1.0
C B:GLU624 4.8 20.8 1.0
CA B:ASP626 4.8 20.6 1.0
O B:GLU624 4.8 20.9 1.0
C B:LEU630 4.9 14.7 1.0
CA B:VAL629 4.9 14.8 1.0
OD1 B:ASN663 5.0 17.0 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 17:14:44 2024

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