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Potassium in PDB 5wgl: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ricolinostat (Acy-1215)

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ricolinostat (Acy-1215), PDB code: 5wgl 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) 49.30 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.189, 88.002, 119.025, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 20.9

Other elements in 5wgl:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ricolinostat (Acy-1215) 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 Ricolinostat (Acy-1215) (pdb code 5wgl). 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 Ricolinostat (Acy-1215), PDB code: 5wgl:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5wgl

Go back to Potassium Binding Sites List in 5wgl
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ricolinostat (Acy-1215)


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 Ricolinostat (Acy-1215) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:7.1
occ:1.00
 O A:ASP612 2.6 6.0 1.0
OG A:SER633 2.8 6.6 1.0
OD1 A:ASP610 2.8 6.0 1.0
O A:LEU634 2.8 5.5 1.0
O A:HIS614 2.8 6.8 1.0
O A:ASP610 2.9 6.0 1.0
CG A:ASP610 3.3 7.0 1.0
C A:ASP610 3.6 5.0 1.0
C A:ASP612 3.7 5.2 1.0
C A:HIS614 3.8 6.7 1.0
C A:LEU634 3.8 5.9 1.0
CB A:ASP610 3.9 4.9 1.0
CB A:SER633 4.0 5.7 1.0
N A:LEU634 4.0 5.0 1.0
N A:ASP612 4.0 5.3 1.0
OD2 A:ASP610 4.1 7.4 1.0
CB A:HIS635 4.1 6.9 1.0
CA A:ASP612 4.3 4.3 1.0
N A:TRP611 4.3 4.1 1.0
CA A:ASP610 4.4 6.0 1.0
C A:TRP611 4.4 5.0 1.0
CB A:ASP612 4.4 4.8 1.0
CA A:HIS615 4.4 3.6 1.0
CA A:SER633 4.4 5.0 1.0
ND1 A:HIS635 4.4 5.8 1.0
N A:HIS615 4.5 3.9 1.0
CA A:TRP611 4.5 7.8 1.0
N A:HIS614 4.5 6.1 1.0
CA A:LEU634 4.6 6.8 1.0
C A:SER633 4.6 7.0 1.0
O A:HOH963 4.6 6.7 1.0
CA A:HIS635 4.7 6.8 1.0
N A:HIS635 4.7 4.7 1.0
N A:GLY616 4.7 7.0 1.0
CG A:HIS635 4.8 5.7 1.0
C A:VAL613 4.8 7.3 1.0
N A:VAL613 4.8 5.1 1.0
CA A:HIS614 4.8 4.6 1.0
CE1 A:HIS573 4.9 5.2 1.0
C A:HIS615 4.9 6.0 1.0
OH A:TYR631 4.9 7.2 1.0

Potassium binding site 2 out of 4 in 5wgl

Go back to Potassium Binding Sites List in 5wgl
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ricolinostat (Acy-1215)


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 Ricolinostat (Acy-1215) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:9.4
occ:1.00
 O A:HOH990 2.8 10.2 1.0
O A:VAL629 2.8 9.9 1.0
O A:PHE623 2.8 9.0 1.0
O A:ASP626 3.0 11.6 1.0
O A:TYR662 3.0 8.9 1.0
O A:HOH1016 3.1 8.9 1.0
C A:PHE623 3.8 10.5 1.0
C A:TYR662 3.8 10.1 1.0
CB A:TYR662 3.8 10.9 1.0
CB A:PHE623 3.9 10.2 1.0
C A:VAL629 4.0 8.7 1.0
C A:ASP626 4.2 12.5 1.0
CA A:TYR662 4.4 11.1 1.0
CA A:PHE623 4.5 10.7 1.0
N A:TYR631 4.5 6.5 1.0
N A:ASP626 4.6 10.6 1.0
N A:ASN663 4.6 8.3 1.0
CA A:LEU630 4.7 8.0 1.0
N A:GLU624 4.7 8.4 1.0
CB A:ASP626 4.7 10.5 1.0
CA A:GLU624 4.7 10.5 1.0
CA A:ASP626 4.8 9.2 1.0
N A:LEU630 4.8 9.5 1.0
O A:GLU624 4.8 9.5 1.0
C A:GLU624 4.8 9.7 1.0
CB A:ASN663 5.0 11.2 1.0
CB A:TYR631 5.0 6.4 1.0
CA A:ASN663 5.0 7.8 1.0

Potassium binding site 3 out of 4 in 5wgl

Go back to Potassium Binding Sites List in 5wgl
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ricolinostat (Acy-1215)


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 Ricolinostat (Acy-1215) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:8.8
occ:1.00
 O B:ASP612 2.6 7.3 1.0
O B:LEU634 2.7 8.0 1.0
OG B:SER633 2.8 8.9 1.0
O B:HIS614 2.8 8.5 1.0
OD1 B:ASP610 2.8 7.9 1.0
O B:ASP610 2.9 8.2 1.0
CG B:ASP610 3.4 9.6 1.0
C B:ASP610 3.6 7.2 1.0
C B:ASP612 3.7 7.2 1.0
C B:LEU634 3.7 7.9 1.0
C B:HIS614 3.8 6.9 1.0
CB B:ASP610 4.0 7.9 1.0
N B:LEU634 4.0 6.1 1.0
CB B:SER633 4.0 7.8 1.0
N B:ASP612 4.0 6.0 1.0
CB B:HIS635 4.1 7.2 1.0
OD2 B:ASP610 4.1 9.8 1.0
CA B:ASP612 4.2 5.9 1.0
C B:TRP611 4.3 6.4 1.0
N B:TRP611 4.4 5.7 1.0
CB B:ASP612 4.4 6.2 1.0
CA B:ASP610 4.4 6.5 1.0
CA B:HIS615 4.4 5.1 1.0
CA B:SER633 4.4 6.0 1.0
ND1 B:HIS635 4.4 8.8 1.0
N B:HIS614 4.5 7.6 1.0
CA B:TRP611 4.5 5.1 1.0
N B:HIS615 4.5 5.7 1.0
CA B:LEU634 4.5 8.5 1.0
O B:HOH971 4.6 7.5 1.0
C B:SER633 4.6 8.4 1.0
N B:HIS635 4.6 5.5 1.0
CA B:HIS635 4.6 8.1 1.0
CG B:HIS635 4.7 8.2 1.0
C B:VAL613 4.8 4.9 1.0
N B:VAL613 4.8 5.3 1.0
N B:GLY616 4.8 7.1 1.0
CA B:HIS614 4.8 5.7 1.0
C B:HIS615 5.0 8.6 1.0
CE1 B:HIS573 5.0 7.4 1.0

Potassium binding site 4 out of 4 in 5wgl

Go back to Potassium Binding Sites List in 5wgl
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Ricolinostat (Acy-1215)


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 Ricolinostat (Acy-1215) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:11.8
occ:1.00
 O B:HOH982 2.8 12.6 1.0
O B:PHE623 2.8 12.1 1.0
O B:VAL629 2.8 16.6 1.0
O B:TYR662 3.0 11.1 1.0
O B:ASP626 3.1 14.7 1.0
O B:HOH995 3.1 10.2 1.0
CB B:TYR662 3.7 14.8 1.0
C B:TYR662 3.8 12.2 1.0
C B:PHE623 3.8 12.5 1.0
CB B:PHE623 3.9 13.6 1.0
C B:VAL629 4.1 12.2 1.0
C B:ASP626 4.2 18.5 1.0
CA B:TYR662 4.4 12.4 1.0
CA B:PHE623 4.5 10.3 1.0
N B:ASP626 4.5 14.6 1.0
N B:ASN663 4.6 11.0 1.0
N B:TYR631 4.6 8.7 1.0
CA B:LEU630 4.7 10.3 1.0
N B:GLU624 4.7 11.2 1.0
CA B:GLU624 4.7 13.2 1.0
CB B:ASP626 4.7 16.9 0.5
CA B:ASP626 4.7 14.1 0.5
CA B:ASP626 4.8 14.1 0.5
CB B:ASP626 4.8 16.9 0.5
C B:GLU624 4.8 14.7 1.0
O B:GLU624 4.8 11.2 1.0
N B:LEU630 4.8 10.0 1.0
CA B:ASN663 5.0 10.3 1.0

Reference:

N.J.Porter, A.Mahendran, R.Breslow, D.W.Christianson. Unusual Zinc-Binding Mode of HDAC6-Selective Hydroxamate Inhibitors. Proc. Natl. Acad. Sci. V. 114 13459 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29203661
DOI: 10.1073/PNAS.1718823114
Page generated: Sat Aug 9 10:04:03 2025

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