Atomistry » Potassium » PDB 6css-6doi » 6cw8
Atomistry »
  Potassium »
    PDB 6css-6doi »
      6cw8 »

Potassium in PDB 6cw8: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Rts-V5

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Rts-V5, PDB code: 6cw8 was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.72 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 48.310, 128.430, 260.490, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 18.8

Other elements in 6cw8:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Rts-V5 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 Complexed with Rts-V5 (pdb code 6cw8). 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 Complexed with Rts-V5, PDB code: 6cw8:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6cw8

Go back to Potassium Binding Sites List in 6cw8
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Rts-V5


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 Complexed with Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:4.6
occ:1.00
 O A:ASP612 2.6 4.8 1.0
O A:LEU634 2.7 1.7 1.0
O A:HIS614 2.7 4.0 1.0
OD1 A:ASP610 2.7 4.2 1.0
O A:ASP610 2.8 1.6 1.0
OG A:SER633 2.8 5.3 1.0
CG A:ASP610 3.2 2.9 1.0
C A:ASP610 3.5 1.9 1.0
C A:ASP612 3.6 3.2 1.0
C A:HIS614 3.7 3.6 1.0
C A:LEU634 3.7 2.2 1.0
CB A:ASP610 3.8 3.2 1.0
N A:ASP612 3.8 5.1 1.0
OD2 A:ASP610 3.9 10.0 1.0
CB A:SER633 3.9 5.9 1.0
CB A:HIS635 4.0 3.3 1.0
N A:LEU634 4.0 1.8 1.0
CA A:ASP612 4.1 2.1 1.0
N A:TRP611 4.2 0.8 1.0
C A:TRP611 4.2 3.7 1.0
CB A:ASP612 4.2 3.4 1.0
CA A:ASP610 4.3 2.6 1.0
CA A:TRP611 4.3 3.7 1.0
CA A:HIS615 4.3 2.4 1.0
CA A:SER633 4.3 4.6 1.0
N A:HIS614 4.4 4.6 1.0
N A:HIS615 4.4 4.2 1.0
ND1 A:HIS635 4.5 3.5 1.0
CA A:HIS635 4.5 7.3 1.0
N A:GLY616 4.5 4.1 1.0
C A:SER633 4.5 6.6 1.0
O A:HOH941 4.5 5.6 1.0
N A:HIS635 4.5 2.6 1.0
CA A:LEU634 4.5 2.4 1.0
C A:VAL613 4.7 2.6 1.0
N A:VAL613 4.7 2.0 1.0
CG A:HIS635 4.7 5.2 1.0
CA A:HIS614 4.7 2.7 1.0
CE1 A:HIS573 4.7 6.2 1.0
C A:HIS615 4.8 4.8 1.0
OH A:TYR631 4.8 4.3 1.0
ND1 A:HIS573 4.9 7.0 1.0
O A:TRP611 4.9 3.8 1.0

Potassium binding site 2 out of 4 in 6cw8

Go back to Potassium Binding Sites List in 6cw8
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Rts-V5


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 Complexed with Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:5.9
occ:1.00
 O A:VAL629 2.7 5.5 1.0
O A:PHE623 2.7 4.9 1.0
O A:HOH975 2.7 2.4 1.0
O A:TYR662 2.7 5.2 1.0
O A:ASP626 2.9 7.0 1.0
O A:HOH994 3.0 4.5 1.0
C A:TYR662 3.6 5.6 1.0
CB A:TYR662 3.6 3.7 1.0
C A:PHE623 3.6 8.1 1.0
CB A:PHE623 3.7 4.3 1.0
C A:VAL629 3.9 4.7 1.0
C A:ASP626 4.1 9.0 1.0
CA A:TYR662 4.2 4.2 1.0
N A:TYR631 4.3 2.1 1.0
CA A:PHE623 4.3 3.0 1.0
N A:ASN663 4.4 2.8 1.0
N A:ASP626 4.4 8.0 1.0
CA A:LEU630 4.5 3.8 1.0
N A:GLU624 4.5 2.6 1.0
CA A:GLU624 4.6 3.6 1.0
CA A:ASP626 4.6 7.8 1.0
CB A:ASP626 4.6 7.1 1.0
O A:GLU624 4.7 7.0 1.0
N A:LEU630 4.7 3.8 1.0
C A:GLU624 4.7 5.6 1.0
CB A:TYR631 4.7 4.1 1.0
CA A:ASN663 4.8 3.3 1.0
C A:LEU630 4.8 3.8 1.0
CB A:ASN663 4.9 3.5 1.0
O A:GLY659 4.9 5.0 1.0
CA A:VAL629 4.9 4.2 1.0
CG A:TYR662 4.9 6.2 1.0
CG A:PHE623 5.0 4.8 1.0

Potassium binding site 3 out of 4 in 6cw8

Go back to Potassium Binding Sites List in 6cw8
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Rts-V5


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 Complexed with Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:6.3
occ:1.00
 O B:ASP612 2.6 7.6 1.0
O B:HIS614 2.7 3.8 1.0
O B:LEU634 2.8 3.7 1.0
OD1 B:ASP610 2.8 5.0 1.0
OG B:SER633 2.8 6.8 1.0
O B:ASP610 2.8 4.5 1.0
CG B:ASP610 3.3 7.0 1.0
C B:ASP610 3.5 9.2 1.0
C B:ASP612 3.6 4.3 1.0
C B:HIS614 3.7 6.6 1.0
C B:LEU634 3.8 6.6 1.0
N B:ASP612 3.8 9.4 1.0
CB B:ASP610 3.8 10.3 1.0
CB B:SER633 3.9 2.7 1.0
OD2 B:ASP610 4.0 10.2 1.0
N B:LEU634 4.0 6.8 1.0
CB B:HIS635 4.0 5.5 1.0
CA B:ASP612 4.1 6.9 1.0
N B:TRP611 4.1 6.6 1.0
CB B:ASP612 4.2 6.8 1.0
C B:TRP611 4.2 6.0 1.0
CA B:ASP610 4.2 7.3 1.0
CA B:SER633 4.3 2.9 1.0
CA B:TRP611 4.3 5.6 1.0
CA B:HIS615 4.3 5.1 1.0
N B:HIS615 4.4 5.4 1.0
ND1 B:HIS635 4.4 6.5 1.0
N B:HIS614 4.4 4.8 1.0
N B:GLY616 4.5 5.1 1.0
C B:SER633 4.5 5.2 1.0
CA B:HIS635 4.5 5.1 1.0
CA B:LEU634 4.5 5.3 1.0
N B:HIS635 4.6 4.7 1.0
O B:HOH917 4.6 13.8 1.0
CG B:HIS635 4.7 6.7 1.0
C B:VAL613 4.7 4.5 1.0
N B:VAL613 4.7 3.8 1.0
OH B:TYR631 4.7 9.0 1.0
CA B:HIS614 4.7 6.0 1.0
C B:HIS615 4.8 5.2 1.0
CE1 B:HIS573 4.8 13.6 1.0
ND1 B:HIS573 4.9 9.8 1.0
O B:TRP611 5.0 5.5 1.0

Potassium binding site 4 out of 4 in 6cw8

Go back to Potassium Binding Sites List in 6cw8
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Rts-V5


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 Complexed with Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:10.5
occ:1.00
 O B:VAL629 2.6 9.0 1.0
O B:PHE623 2.7 7.7 1.0
O B:HOH996 2.7 8.2 1.0
O B:TYR662 2.8 8.2 1.0
O B:ASP626 2.9 12.2 1.0
O B:HOH1028 3.0 6.5 1.0
C B:TYR662 3.6 9.9 1.0
C B:PHE623 3.6 9.5 1.0
CB B:TYR662 3.6 7.8 1.0
CB B:PHE623 3.8 7.5 1.0
C B:VAL629 3.9 9.6 1.0
C B:ASP626 4.0 15.4 1.0
CA B:TYR662 4.2 7.5 1.0
N B:TYR631 4.3 5.0 1.0
CA B:PHE623 4.3 4.8 1.0
N B:ASN663 4.4 9.1 1.0
N B:ASP626 4.5 11.2 1.0
N B:GLU624 4.5 6.6 1.0
CA B:GLU624 4.5 7.4 1.0
CA B:LEU630 4.5 8.1 1.0
CA B:ASP626 4.6 11.6 1.0
O B:GLU624 4.6 12.6 1.0
CB B:ASP626 4.6 15.3 1.0
C B:GLU624 4.6 10.3 1.0
N B:LEU630 4.7 9.7 1.0
CA B:ASN663 4.8 5.5 1.0
CB B:ASN663 4.8 5.3 1.0
CB B:TYR631 4.8 5.4 1.0
C B:LEU630 4.9 7.1 1.0
O B:GLY659 4.9 11.0 1.0
CA B:VAL629 4.9 8.0 1.0
CG B:TYR662 4.9 8.2 1.0

Reference:

S.Bhatia, V.Krieger, M.Groll, J.D.Osko, H.Ahlert, A.Borkhardt, T.Kurz, D.W.Christianson, J.Hauer, F.K.Hansen. Discovery of the First-in-Class Dual Histone Deacetylase-Proteasome Inhibitor. J. Med. Chem. V. 61 10299 2018.
ISSN: ISSN 1520-4804
PubMed: 30365892
DOI: 10.1021/ACS.JMEDCHEM.8B01487
Page generated: Mon Aug 12 15:42:36 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