Atomistry » Potassium » PDB 6pcd-6qm2 » 6pzr
Atomistry »
  Potassium »
    PDB 6pcd-6qm2 »
      6pzr »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy