Atomistry » Potassium » PDB 6css-6doi » 6css
Atomistry »
  Potassium »
    PDB 6css-6doi »
      6css »

Potassium in PDB 6css: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclopentenylhydroxamate

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclopentenylhydroxamate, PDB code: 6css was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.32 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.791, 92.021, 96.640, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.3

Other elements in 6css:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclopentenylhydroxamate 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 in Complex with Cyclopentenylhydroxamate (pdb code 6css). 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 in Complex with Cyclopentenylhydroxamate, PDB code: 6css:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6css

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


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 in Complex with Cyclopentenylhydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:3.4
occ:1.00
 O A:ASP612 2.6 3.1 1.0
O A:LEU634 2.7 4.8 1.0
O A:HIS614 2.7 2.7 1.0
OD1 A:ASP610 2.8 2.9 1.0
OG A:SER633 2.8 3.0 1.0
O A:ASP610 2.8 1.9 1.0
CG A:ASP610 3.3 3.2 1.0
C A:ASP610 3.5 3.2 1.0
C A:ASP612 3.6 3.5 1.0
C A:HIS614 3.7 3.7 1.0
C A:LEU634 3.7 3.2 1.0
CB A:ASP610 3.8 2.3 1.0
N A:ASP612 3.8 1.4 1.0
OD2 A:ASP610 3.9 5.3 1.0
N A:LEU634 4.0 2.2 1.0
CB A:SER633 4.0 3.7 1.0
CB A:HIS635 4.0 1.9 1.0
CA A:ASP612 4.1 1.2 1.0
N A:TRP611 4.2 2.1 1.0
C A:TRP611 4.2 2.3 1.0
CB A:ASP612 4.2 2.4 1.0
CA A:ASP610 4.3 1.7 1.0
CA A:HIS615 4.3 2.5 1.0
CA A:TRP611 4.3 3.1 1.0
CA A:SER633 4.4 2.6 1.0
ND1 A:HIS635 4.4 3.6 1.0
N A:HIS615 4.4 2.5 1.0
N A:GLY616 4.4 3.6 1.0
N A:HIS614 4.5 3.8 1.0
CA A:HIS635 4.5 1.8 1.0
C A:SER633 4.5 4.9 1.0
CA A:LEU634 4.5 2.5 1.0
O A:HOH929 4.6 3.5 1.0
N A:HIS635 4.6 2.4 1.0
CG A:HIS635 4.7 2.7 1.0
OH A:TYR631 4.7 4.7 1.0
C A:VAL613 4.7 4.6 1.0
C A:HIS615 4.7 3.4 1.0
CA A:HIS614 4.7 3.3 1.0
N A:VAL613 4.7 3.2 1.0
CE1 A:HIS573 4.8 3.9 1.0
ND1 A:HIS573 4.9 3.7 1.0
O A:TRP611 4.9 3.1 1.0

Potassium binding site 2 out of 4 in 6css

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


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 in Complex with Cyclopentenylhydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:8.3
occ:1.00
 O A:PHE623 2.7 5.8 1.0
O A:VAL629 2.7 5.3 1.0
O A:HOH943 2.8 5.8 1.0
O A:TYR662 2.8 4.3 1.0
O A:ASP626 2.9 8.3 1.0
O A:HOH960 3.1 6.0 1.0
C A:TYR662 3.6 5.7 1.0
C A:PHE623 3.6 4.1 1.0
CB A:TYR662 3.7 5.6 1.0
CB A:PHE623 3.7 3.9 1.0
C A:VAL629 3.9 5.2 1.0
C A:ASP626 4.1 8.3 1.0
CA A:TYR662 4.3 4.7 1.0
N A:TYR631 4.3 3.4 1.0
CA A:PHE623 4.3 5.0 1.0
N A:ASN663 4.4 4.5 1.0
N A:ASP626 4.5 7.9 1.0
N A:GLU624 4.5 4.2 1.0
CA A:LEU630 4.6 3.0 1.0
CA A:GLU624 4.6 5.8 1.0
CA A:ASP626 4.6 9.1 1.0
CB A:ASP626 4.6 9.8 1.0
N A:LEU630 4.7 3.3 1.0
C A:GLU624 4.7 6.5 1.0
O A:GLU624 4.7 6.0 1.0
CB A:TYR631 4.8 2.5 1.0
CA A:ASN663 4.8 3.1 1.0
CB A:ASN663 4.8 4.6 1.0
C A:LEU630 4.9 5.3 1.0
O A:GLY659 4.9 6.9 1.0
CA A:VAL629 5.0 2.6 1.0
CG A:PHE623 5.0 2.8 1.0

Potassium binding site 3 out of 4 in 6css

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


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 in Complex with Cyclopentenylhydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:4.8
occ:1.00
 O B:ASP612 2.6 3.2 1.0
O B:LEU634 2.7 4.2 1.0
O B:HIS614 2.7 3.0 1.0
OD1 B:ASP610 2.8 2.6 1.0
O B:ASP610 2.8 3.0 1.0
OG B:SER633 2.8 3.9 1.0
CG B:ASP610 3.3 4.1 1.0
C B:ASP610 3.5 2.9 1.0
C B:ASP612 3.6 2.6 1.0
C B:HIS614 3.7 4.0 1.0
C B:LEU634 3.7 5.0 1.0
CB B:ASP610 3.8 2.5 1.0
N B:ASP612 3.8 3.1 1.0
OD2 B:ASP610 3.9 6.0 1.0
CB B:SER633 4.0 4.4 1.0
N B:LEU634 4.0 3.1 1.0
CB B:HIS635 4.0 4.2 1.0
CA B:ASP612 4.1 2.2 1.0
CB B:ASP612 4.2 3.2 1.0
N B:TRP611 4.2 3.4 1.0
C B:TRP611 4.2 2.9 1.0
CA B:ASP610 4.3 2.0 1.0
CA B:HIS615 4.3 2.5 1.0
CA B:SER633 4.3 3.9 1.0
CA B:TRP611 4.3 3.6 1.0
N B:HIS615 4.4 1.9 1.0
ND1 B:HIS635 4.4 4.1 1.0
N B:HIS614 4.4 2.5 1.0
N B:GLY616 4.5 3.7 1.0
CA B:HIS635 4.5 3.7 1.0
C B:SER633 4.5 6.1 1.0
CA B:LEU634 4.5 3.6 1.0
O B:HOH921 4.5 5.8 1.0
N B:HIS635 4.6 4.4 1.0
OH B:TYR631 4.7 3.7 1.0
CG B:HIS635 4.7 2.5 1.0
C B:VAL613 4.7 4.4 1.0
CA B:HIS614 4.7 5.2 1.0
N B:VAL613 4.7 2.8 1.0
C B:HIS615 4.7 2.7 1.0
CE1 B:HIS573 4.9 5.5 1.0
ND1 B:HIS573 4.9 3.6 1.0
O B:TRP611 5.0 3.4 1.0

Potassium binding site 4 out of 4 in 6css

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


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 in Complex with Cyclopentenylhydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:8.8
occ:1.00
 O B:PHE623 2.7 4.3 1.0
O B:VAL629 2.7 7.8 1.0
O B:HOH957 2.7 4.3 1.0
O B:TYR662 2.9 6.3 1.0
O B:ASP626 2.9 11.1 1.0
O B:HOH1009 3.0 6.6 1.0
C B:TYR662 3.6 8.7 1.0
C B:PHE623 3.6 4.0 1.0
CB B:TYR662 3.7 6.2 1.0
CB B:PHE623 3.8 4.4 1.0
C B:VAL629 3.9 5.1 1.0
C B:ASP626 4.1 9.7 1.0
CA B:TYR662 4.3 5.8 1.0
N B:TYR631 4.3 2.5 1.0
CA B:PHE623 4.3 4.7 1.0
N B:ASN663 4.4 5.8 1.0
N B:ASP626 4.5 8.6 1.0
CA B:LEU630 4.5 4.1 1.0
N B:GLU624 4.5 5.9 1.0
CA B:GLU624 4.6 6.7 1.0
CB B:ASP626 4.6 9.7 1.0
CA B:ASP626 4.6 7.3 1.0
N B:LEU630 4.7 4.3 1.0
C B:GLU624 4.7 8.6 1.0
CA B:ASN663 4.7 4.4 1.0
CB B:TYR631 4.8 4.6 1.0
CB B:ASN663 4.8 6.7 1.0
O B:GLU624 4.8 6.4 1.0
C B:LEU630 4.9 6.6 1.0
O B:GLY659 4.9 9.0 1.0
CA B:VAL629 5.0 4.1 1.0
CG B:TYR662 5.0 8.1 1.0

Reference:

N.J.Porter, F.F.Wagner, D.W.Christianson. Entropy As A Driver of Selectivity For Inhibitor Binding to Histone Deacetylase 6. Biochemistry V. 57 3916 2018.
ISSN: ISSN 1520-4995
PubMed: 29775292
DOI: 10.1021/ACS.BIOCHEM.8B00367
Page generated: Mon Aug 12 15:42:36 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