Atomistry » Potassium » PDB 5vt3-5x23 » 5wgl
Atomistry »
  Potassium »
    PDB 5vt3-5x23 »
      5wgl »

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: Mon Aug 12 14:55:32 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy