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

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate, PDB code: 6csr 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) 48.20 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.890, 91.980, 96.400, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.9

Other elements in 6csr:

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

Potassium binding site 1 out of 4 in 6csr

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


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

b:7.9
occ:1.00
 O A:ASP612 2.6 5.8 1.0
O A:HIS614 2.7 7.1 1.0
O A:LEU634 2.7 8.1 1.0
OD1 A:ASP610 2.8 4.3 1.0
OG A:SER633 2.8 5.6 1.0
O A:ASP610 2.8 7.5 1.0
CG A:ASP610 3.2 4.6 1.0
C A:ASP610 3.5 6.7 1.0
C A:HIS614 3.6 5.6 1.0
C A:ASP612 3.6 5.1 1.0
C A:LEU634 3.7 6.7 1.0
CB A:ASP610 3.8 5.1 1.0
OD2 A:ASP610 3.9 4.9 1.0
N A:ASP612 3.9 5.5 1.0
CB A:SER633 4.0 5.4 1.0
N A:LEU634 4.0 5.6 1.0
CB A:HIS635 4.0 6.0 1.0
CA A:ASP612 4.2 5.0 1.0
CA A:HIS615 4.2 5.5 1.0
N A:TRP611 4.2 6.8 1.0
C A:TRP611 4.3 6.1 1.0
CB A:ASP612 4.3 5.7 1.0
N A:HIS615 4.3 4.9 1.0
CA A:ASP610 4.3 5.5 1.0
CA A:SER633 4.3 6.7 1.0
ND1 A:HIS635 4.3 6.7 1.0
CA A:TRP611 4.4 6.5 1.0
N A:HIS614 4.4 4.4 1.0
N A:GLY616 4.4 6.4 1.0
C A:SER633 4.5 7.6 1.0
CA A:HIS635 4.5 6.8 1.0
CA A:LEU634 4.5 5.6 1.0
N A:HIS635 4.6 6.1 1.0
O A:HOH967 4.6 8.0 1.0
OH A:TYR631 4.6 4.5 1.0
C A:VAL613 4.6 5.6 1.0
CA A:HIS614 4.7 5.4 1.0
CG A:HIS635 4.7 5.8 1.0
C A:HIS615 4.7 6.7 1.0
N A:VAL613 4.7 5.1 1.0
CE1 A:HIS573 4.8 6.4 1.0
ND1 A:HIS573 4.9 5.2 1.0
O A:TRP611 5.0 6.0 1.0

Potassium binding site 2 out of 4 in 6csr

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


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

b:11.2
occ:1.00
 O A:VAL629 2.7 8.7 1.0
O A:PHE623 2.7 7.5 1.0
O A:HOH971 2.7 6.1 1.0
O A:TYR662 2.8 6.9 1.0
O A:ASP626 2.8 11.1 1.0
O A:HOH1084 3.0 8.9 1.0
C A:PHE623 3.6 7.1 1.0
C A:TYR662 3.6 7.3 1.0
CB A:TYR662 3.7 8.1 1.0
CB A:PHE623 3.7 7.0 1.0
C A:VAL629 3.9 7.9 1.0
C A:ASP626 4.0 10.5 1.0
CA A:TYR662 4.3 8.5 1.0
CA A:PHE623 4.3 7.3 1.0
N A:TYR631 4.3 6.1 1.0
N A:ASP626 4.4 10.6 1.0
N A:ASN663 4.4 7.7 1.0
N A:GLU624 4.5 7.5 1.0
CA A:LEU630 4.5 7.7 1.0
CA A:GLU624 4.6 8.5 1.0
CA A:ASP626 4.6 10.9 1.0
CB A:ASP626 4.6 11.6 1.0
N A:LEU630 4.7 7.0 1.0
C A:GLU624 4.7 8.2 1.0
O A:GLU624 4.8 8.2 1.0
CB A:TYR631 4.8 6.4 1.0
CA A:ASN663 4.8 7.5 1.0
CB A:ASN663 4.8 7.1 1.0
O A:GLY659 4.8 11.6 1.0
C A:LEU630 4.9 8.2 1.0
CA A:VAL629 4.9 7.8 1.0
CG A:TYR662 5.0 9.8 1.0
CG A:PHE623 5.0 6.2 1.0

Potassium binding site 3 out of 4 in 6csr

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


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

b:7.8
occ:1.00
 O B:ASP612 2.6 5.9 1.0
O B:LEU634 2.7 6.7 1.0
O B:HIS614 2.7 7.4 1.0
OD1 B:ASP610 2.8 6.4 1.0
OG B:SER633 2.8 6.8 1.0
O B:ASP610 2.8 5.7 1.0
CG B:ASP610 3.3 5.8 1.0
C B:ASP610 3.5 4.8 1.0
C B:ASP612 3.7 5.2 1.0
C B:HIS614 3.7 6.6 1.0
C B:LEU634 3.7 6.2 1.0
CB B:ASP610 3.8 5.9 1.0
N B:ASP612 3.9 4.5 1.0
OD2 B:ASP610 3.9 7.3 1.0
CB B:HIS635 3.9 6.7 1.0
N B:LEU634 4.0 7.0 1.0
CB B:SER633 4.0 6.9 1.0
N B:TRP611 4.2 2.9 1.0
CA B:ASP612 4.2 3.9 1.0
C B:TRP611 4.2 4.5 1.0
CA B:HIS615 4.2 5.1 1.0
CA B:ASP610 4.3 5.4 1.0
CB B:ASP612 4.3 3.3 1.0
N B:HIS615 4.3 5.7 1.0
CA B:TRP611 4.3 4.1 1.0
CA B:SER633 4.3 6.4 1.0
ND1 B:HIS635 4.4 6.5 1.0
N B:GLY616 4.4 6.1 1.0
N B:HIS614 4.4 6.0 1.0
CA B:HIS635 4.4 6.8 1.0
C B:SER633 4.5 7.5 1.0
CA B:LEU634 4.5 6.0 1.0
N B:HIS635 4.5 5.8 1.0
O B:HOH933 4.6 4.7 1.0
CG B:HIS635 4.6 6.5 1.0
C B:VAL613 4.6 6.4 1.0
C B:HIS615 4.7 6.1 1.0
CA B:HIS614 4.7 6.0 1.0
OH B:TYR631 4.7 6.0 1.0
N B:VAL613 4.8 4.6 1.0
CE1 B:HIS573 4.8 5.7 1.0
ND1 B:HIS573 4.9 5.1 1.0
O B:TRP611 4.9 5.2 1.0

Potassium binding site 4 out of 4 in 6csr

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


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

b:10.1
occ:1.00
 O B:VAL629 2.7 9.6 1.0
O B:PHE623 2.7 6.9 1.0
O B:HOH948 2.8 13.2 1.0
O B:TYR662 2.9 8.0 1.0
O B:ASP626 2.9 11.6 1.0
O B:HOH1067 2.9 7.1 1.0
C B:TYR662 3.6 8.9 1.0
C B:PHE623 3.6 7.2 1.0
CB B:TYR662 3.7 10.5 1.0
CB B:PHE623 3.7 6.7 1.0
C B:VAL629 3.9 7.7 1.0
C B:ASP626 4.0 10.7 1.0
CA B:TYR662 4.3 10.0 1.0
CA B:PHE623 4.3 6.7 1.0
N B:TYR631 4.3 6.5 1.0
N B:ASN663 4.4 8.3 1.0
N B:ASP626 4.5 11.3 1.0
N B:GLU624 4.5 7.5 1.0
CA B:LEU630 4.6 7.9 1.0
CA B:GLU624 4.6 9.0 1.0
CB B:ASP626 4.6 11.8 1.0
CA B:ASP626 4.6 11.4 1.0
N B:LEU630 4.7 8.1 1.0
CB B:TYR631 4.7 5.2 1.0
C B:GLU624 4.7 8.9 1.0
O B:GLU624 4.8 9.0 1.0
CA B:ASN663 4.8 8.7 1.0
CB B:ASN663 4.8 9.1 1.0
C B:LEU630 4.8 7.2 1.0
O B:GLY659 4.9 10.9 1.0
CA B:VAL629 4.9 6.6 1.0
CG B:PHE623 5.0 5.7 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 15:39:39 2024

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