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

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexylhydroxamate, PDB code: 6csq 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) 66.61 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.622, 91.961, 96.600, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.3

Other elements in 6csq:

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

Potassium binding site 1 out of 4 in 6csq

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


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

b:5.6
occ:1.00
 O A:PHE623 2.7 4.9 1.0
O A:VAL629 2.7 5.0 1.0
O A:TYR662 2.7 6.4 1.0
O A:HOH901 2.8 5.5 1.0
O A:ASP626 2.9 11.2 1.0
O A:HOH971 3.0 6.5 1.0
C A:TYR662 3.6 10.2 1.0
C A:PHE623 3.6 8.1 1.0
CB A:TYR662 3.6 10.8 1.0
CB A:PHE623 3.8 4.8 1.0
C A:VAL629 3.9 8.3 1.0
C A:ASP626 4.0 13.4 1.0
CA A:TYR662 4.2 10.7 1.0
N A:TYR631 4.3 4.2 1.0
CA A:PHE623 4.4 6.5 1.0
N A:ASN663 4.4 8.1 1.0
N A:ASP626 4.5 8.9 1.0
N A:GLU624 4.5 7.5 1.0
CA A:GLU624 4.5 7.3 1.0
CA A:LEU630 4.6 5.0 1.0
CA A:ASP626 4.6 9.9 1.0
O A:GLY659 4.6 9.8 1.0
C A:GLU624 4.7 8.6 1.0
O A:GLU624 4.7 12.1 1.0
CB A:ASP626 4.7 8.5 0.9
N A:LEU630 4.7 9.2 1.0
CB A:ASN663 4.7 7.0 1.0
CA A:ASN663 4.7 5.8 1.0
CB A:TYR631 4.8 4.3 1.0
C A:LEU630 4.9 6.5 1.0
CG A:TYR662 5.0 13.0 1.0
CA A:VAL629 5.0 6.7 1.0

Potassium binding site 2 out of 4 in 6csq

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


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

b:8.1
occ:1.00
 O A:ASP612 2.6 5.0 1.0
O A:LEU634 2.7 4.8 1.0
OG A:SER633 2.7 4.3 1.0
O A:HIS614 2.8 5.2 1.0
O A:ASP610 2.8 2.9 1.0
OD1 A:ASP610 2.9 3.3 1.0
CG A:ASP610 3.4 6.1 1.0
C A:ASP610 3.6 2.6 1.0
C A:LEU634 3.7 8.8 1.0
C A:HIS614 3.7 6.2 1.0
C A:ASP612 3.7 4.2 1.0
CB A:ASP610 3.8 3.9 1.0
CB A:HIS635 3.9 7.8 1.0
N A:LEU634 3.9 6.7 1.0
CB A:SER633 3.9 4.5 1.0
N A:ASP612 4.0 4.0 1.0
OD2 A:ASP610 4.1 3.8 1.0
CA A:HIS615 4.1 5.1 1.0
CA A:ASP612 4.3 3.7 1.0
N A:HIS615 4.3 8.2 1.0
CA A:SER633 4.3 5.7 1.0
CA A:ASP610 4.3 4.5 1.0
N A:TRP611 4.3 2.6 1.0
N A:GLY616 4.4 4.4 1.0
C A:TRP611 4.4 4.2 1.0
CA A:HIS635 4.4 5.5 1.0
CB A:ASP612 4.4 3.8 1.0
C A:SER633 4.4 7.6 1.0
ND1 A:HIS635 4.4 5.1 1.0
N A:HIS635 4.4 4.3 1.0
N A:HIS614 4.5 4.7 1.0
CA A:TRP611 4.5 3.1 1.0
CA A:LEU634 4.5 8.6 1.0
C A:HIS615 4.6 7.3 1.0
CG A:HIS635 4.6 5.4 1.0
O A:HOH930 4.6 3.0 1.0
C A:VAL613 4.6 5.4 1.0
OH A:TYR631 4.7 4.4 1.0
CA A:HIS614 4.7 6.1 1.0
N A:VAL613 4.8 5.0 1.0
ND1 A:HIS573 5.0 3.9 1.0
CE1 A:HIS573 5.0 4.3 1.0

Potassium binding site 3 out of 4 in 6csq

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


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

b:7.2
occ:1.00
 O B:PHE623 2.6 7.0 1.0
O B:VAL629 2.7 7.3 1.0
O B:TYR662 2.8 6.3 1.0
O B:HOH918 2.9 5.1 1.0
O B:ASP626 2.9 11.2 1.0
O B:HOH1042 3.1 5.7 1.0
C B:PHE623 3.6 4.6 1.0
C B:TYR662 3.6 10.6 1.0
CB B:TYR662 3.7 7.5 1.0
CB B:PHE623 3.7 5.6 1.0
C B:VAL629 3.9 11.9 1.0
C B:ASP626 4.0 9.7 1.0
CA B:TYR662 4.3 8.2 1.0
CA B:PHE623 4.3 6.3 1.0
N B:TYR631 4.4 3.0 1.0
N B:ASP626 4.5 9.7 1.0
N B:ASN663 4.5 9.5 1.0
N B:GLU624 4.5 5.7 1.0
CA B:GLU624 4.6 7.7 1.0
CA B:LEU630 4.6 10.4 1.0
CA B:ASP626 4.6 11.4 1.0
CB B:ASP626 4.6 10.1 0.8
N B:LEU630 4.7 7.8 1.0
O B:GLY659 4.7 9.0 1.0
C B:GLU624 4.7 7.5 1.0
O B:GLU624 4.7 8.8 1.0
CB B:ASN663 4.8 5.0 1.0
CB B:TYR631 4.8 7.0 1.0
CA B:ASN663 4.8 5.5 1.0
CA B:VAL629 4.9 9.4 1.0
C B:LEU630 4.9 10.7 1.0
CG B:PHE623 5.0 5.7 1.0
CG B:TYR662 5.0 11.1 1.0

Potassium binding site 4 out of 4 in 6csq

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


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

b:8.1
occ:1.00
 O B:ASP612 2.6 6.5 1.0
O B:LEU634 2.7 5.6 1.0
O B:ASP610 2.8 7.8 1.0
OG B:SER633 2.8 5.1 1.0
O B:HIS614 2.8 7.3 1.0
OD1 B:ASP610 2.8 5.3 1.0
CG B:ASP610 3.2 5.8 1.0
C B:ASP610 3.5 6.2 1.0
C B:ASP612 3.7 5.2 1.0
C B:LEU634 3.7 7.5 1.0
C B:HIS614 3.7 7.3 1.0
CB B:ASP610 3.7 4.7 1.0
OD2 B:ASP610 3.9 6.3 1.0
N B:LEU634 3.9 6.3 1.0
N B:ASP612 3.9 4.0 1.0
CB B:SER633 4.0 6.1 1.0
CB B:HIS635 4.0 6.7 1.0
CA B:HIS615 4.1 4.9 1.0
CA B:ASP612 4.2 5.6 1.0
CA B:ASP610 4.2 5.3 1.0
N B:TRP611 4.3 5.6 1.0
N B:HIS615 4.3 5.9 1.0
CA B:SER633 4.3 5.1 1.0
ND1 B:HIS635 4.3 7.2 1.0
C B:TRP611 4.3 6.7 1.0
CB B:ASP612 4.4 4.4 1.0
N B:GLY616 4.4 5.4 1.0
CA B:TRP611 4.4 3.3 1.0
C B:SER633 4.5 8.4 1.0
N B:HIS614 4.5 4.8 1.0
CA B:LEU634 4.5 6.5 1.0
CA B:HIS635 4.5 7.1 1.0
O B:HOH974 4.5 5.8 1.0
N B:HIS635 4.5 4.2 1.0
OH B:TYR631 4.6 3.2 1.0
CG B:HIS635 4.6 6.2 1.0
C B:HIS615 4.7 5.4 1.0
C B:VAL613 4.7 6.8 1.0
CA B:HIS614 4.7 6.8 1.0
N B:VAL613 4.8 6.2 1.0
ND1 B:HIS573 5.0 6.8 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 15:39:23 2024

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