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

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy