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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 Dec 14 00:29:44 2020

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