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

Potassium in PDB 5wgm: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083, PDB code: 5wgm 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) 49.95 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.813, 174.304, 149.064, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 18.5

Other elements in 5wgm:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083 also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Zinc (Zn) 3 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 Acy-1083 (pdb code 5wgm). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083, PDB code: 5wgm:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 5wgm

Go back to Potassium Binding Sites List in 5wgm
Potassium binding site 1 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:10.2
occ:1.00
O A:ASP612 2.6 8.8 1.0
O A:LEU634 2.6 9.0 1.0
O A:HIS614 2.7 10.0 1.0
OG A:SER633 2.7 10.4 1.0
OD1 A:ASP610 2.8 8.2 1.0
O A:ASP610 2.9 7.9 1.0
CG A:ASP610 3.3 12.8 1.0
C A:ASP610 3.5 8.4 1.0
C A:ASP612 3.6 7.3 1.0
C A:LEU634 3.7 8.8 1.0
C A:HIS614 3.7 10.3 1.0
N A:ASP612 3.8 8.3 1.0
CB A:ASP610 3.8 9.6 1.0
OD2 A:ASP610 3.9 10.7 1.0
N A:LEU634 3.9 7.4 1.0
CB A:SER633 3.9 8.5 1.0
CB A:HIS635 3.9 8.3 1.0
CA A:ASP612 4.1 8.1 1.0
N A:TRP611 4.2 6.1 1.0
CB A:ASP612 4.2 8.8 1.0
C A:TRP611 4.2 6.6 1.0
CA A:ASP610 4.3 6.7 1.0
CA A:HIS615 4.3 8.5 1.0
CA A:SER633 4.3 8.4 1.0
CA A:TRP611 4.3 6.6 1.0
ND1 A:HIS635 4.3 10.2 1.0
N A:HIS615 4.3 9.4 1.0
N A:HIS614 4.4 8.2 1.0
CA A:HIS635 4.4 7.5 1.0
C A:SER633 4.5 9.7 1.0
CA A:LEU634 4.5 7.6 1.0
O A:HOH956 4.5 10.5 1.0
N A:GLY616 4.5 10.7 1.0
N A:HIS635 4.5 8.9 1.0
CG A:HIS635 4.6 10.6 1.0
C A:VAL613 4.7 8.4 1.0
CA A:HIS614 4.7 10.9 1.0
OH A:TYR631 4.7 11.3 1.0
N A:VAL613 4.7 7.2 1.0
C A:HIS615 4.8 9.5 1.0
CE1 A:HIS573 4.8 8.8 1.0
O A:TRP611 4.9 6.7 1.0
ND1 A:HIS573 4.9 10.9 1.0

Potassium binding site 2 out of 6 in 5wgm

Go back to Potassium Binding Sites List in 5wgm
Potassium binding site 2 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:22.5
occ:1.00
O A:PHE623 2.6 13.2 1.0
O A:HOH934 2.6 16.9 1.0
O A:VAL629 2.6 15.4 1.0
O A:ASP626 2.8 18.7 1.0
O A:TYR662 3.0 13.2 1.0
O A:HOH1021 3.3 17.1 1.0
CB A:TYR662 3.5 14.8 1.0
C A:PHE623 3.5 13.2 1.0
C A:TYR662 3.7 13.8 1.0
CB A:PHE623 3.7 13.4 1.0
C A:VAL629 3.9 13.5 1.0
C A:ASP626 4.0 19.6 1.0
CA A:TYR662 4.2 15.2 1.0
CA A:PHE623 4.2 14.3 1.0
N A:ASP626 4.3 16.5 1.0
N A:GLU624 4.5 16.4 0.6
N A:GLU624 4.5 16.4 0.4
N A:TYR631 4.5 10.8 1.0
N A:ASN663 4.5 15.8 1.0
CA A:GLU624 4.5 16.6 0.6
CA A:ASP626 4.5 16.5 1.0
CA A:LEU630 4.6 9.9 1.0
CA A:GLU624 4.6 16.6 0.4
O A:GLU624 4.6 17.1 0.6
C A:GLU624 4.6 17.6 0.6
CB A:ASP626 4.6 17.1 1.0
C A:GLU624 4.7 17.7 0.4
N A:LEU630 4.7 8.6 1.0
O A:GLU624 4.7 17.1 0.4
O A:GLY659 4.8 18.2 1.0
CA A:VAL629 4.8 12.3 1.0
CG A:TYR662 4.9 14.7 1.0
CB A:ASN663 4.9 13.1 1.0
CA A:ASN663 4.9 13.5 1.0
CB A:TYR631 4.9 8.7 1.0
C A:LEU630 5.0 10.0 1.0
CG A:PHE623 5.0 12.7 1.0
CB A:VAL629 5.0 13.6 1.0

Potassium binding site 3 out of 6 in 5wgm

Go back to Potassium Binding Sites List in 5wgm
Potassium binding site 3 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:10.6
occ:1.00
O B:ASP612 2.6 7.8 1.0
O B:HIS614 2.7 11.0 1.0
OD1 B:ASP610 2.7 9.9 1.0
O B:LEU634 2.7 9.6 1.0
OG B:SER633 2.8 9.2 1.0
O B:ASP610 2.9 7.2 1.0
CG B:ASP610 3.2 11.4 1.0
C B:ASP610 3.5 9.9 1.0
C B:ASP612 3.6 9.3 1.0
C B:HIS614 3.6 9.8 1.0
C B:LEU634 3.8 9.0 1.0
N B:ASP612 3.9 9.8 1.0
CB B:ASP610 3.9 9.9 1.0
OD2 B:ASP610 3.9 12.1 1.0
N B:LEU634 4.0 10.0 1.0
CB B:SER633 4.0 9.2 1.0
CB B:HIS635 4.0 9.1 1.0
CA B:ASP612 4.1 8.9 1.0
N B:TRP611 4.2 7.1 1.0
C B:TRP611 4.2 8.2 1.0
CB B:ASP612 4.2 7.8 1.0
CA B:HIS615 4.3 10.5 1.0
CA B:ASP610 4.3 10.3 1.0
N B:HIS615 4.3 9.3 1.0
CA B:TRP611 4.3 10.5 1.0
CA B:SER633 4.3 9.1 1.0
ND1 B:HIS635 4.4 11.0 1.0
N B:HIS614 4.4 8.1 1.0
N B:GLY616 4.4 9.6 1.0
O B:HOH960 4.5 12.0 1.0
CA B:HIS635 4.5 7.5 1.0
C B:SER633 4.5 12.5 1.0
CA B:LEU634 4.5 10.8 1.0
N B:HIS635 4.6 8.1 1.0
CG B:HIS635 4.6 9.6 1.0
CA B:HIS614 4.7 10.1 1.0
C B:VAL613 4.7 9.1 1.0
OH B:TYR631 4.7 12.0 1.0
C B:HIS615 4.7 10.6 1.0
CE1 B:HIS573 4.7 9.7 1.0
N B:VAL613 4.8 7.5 1.0
ND1 B:HIS573 4.9 10.2 1.0
O B:TRP611 4.9 8.2 1.0

Potassium binding site 4 out of 6 in 5wgm

Go back to Potassium Binding Sites List in 5wgm
Potassium binding site 4 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:21.9
occ:1.00
O B:VAL629 2.6 16.0 1.0
O B:HOH984 2.6 17.3 1.0
O B:PHE623 2.6 15.4 1.0
O B:ASP626 2.8 18.6 1.0
O B:TYR662 3.0 13.1 1.0
O B:HOH959 3.3 14.1 1.0
CB B:TYR662 3.5 16.1 1.0
C B:PHE623 3.6 14.1 1.0
C B:TYR662 3.7 15.3 1.0
CB B:PHE623 3.7 14.2 1.0
C B:VAL629 3.8 15.0 1.0
C B:ASP626 4.0 20.3 1.0
CA B:TYR662 4.2 16.4 1.0
CA B:PHE623 4.3 12.9 1.0
N B:ASP626 4.4 17.1 1.0
N B:TYR631 4.5 10.3 1.0
N B:ASN663 4.5 16.3 1.0
CA B:LEU630 4.5 7.9 1.0
CA B:ASP626 4.6 16.3 1.0
CB B:ASP626 4.6 17.5 1.0
N B:GLU624 4.6 12.9 1.0
N B:LEU630 4.6 10.1 1.0
CA B:GLU624 4.6 14.5 1.0
O B:GLU624 4.7 17.6 1.0
C B:GLU624 4.7 13.7 1.0
CG B:TYR662 4.8 17.1 1.0
O B:GLY659 4.8 18.1 1.0
CA B:VAL629 4.8 13.7 1.0
CA B:ASN663 4.9 16.5 1.0
CB B:TYR631 4.9 9.7 1.0
C B:LEU630 4.9 13.1 1.0
CB B:ASN663 4.9 16.3 1.0
CG B:PHE623 5.0 13.5 1.0
N B:VAL629 5.0 12.4 1.0
CB B:VAL629 5.0 14.9 1.0

Potassium binding site 5 out of 6 in 5wgm

Go back to Potassium Binding Sites List in 5wgm
Potassium binding site 5 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K802

b:10.5
occ:1.00
O C:ASP612 2.6 8.4 1.0
O C:LEU634 2.7 9.3 1.0
O C:HIS614 2.7 9.2 1.0
OD1 C:ASP610 2.8 10.1 1.0
OG C:SER633 2.8 10.2 1.0
O C:ASP610 2.8 8.6 1.0
CG C:ASP610 3.3 12.7 1.0
C C:ASP610 3.5 9.4 1.0
C C:ASP612 3.6 7.5 1.0
C C:HIS614 3.7 9.9 1.0
C C:LEU634 3.7 11.2 1.0
N C:ASP612 3.8 8.6 1.0
CB C:ASP610 3.9 10.0 1.0
CB C:SER633 3.9 10.7 1.0
OD2 C:ASP610 3.9 11.9 1.0
N C:LEU634 3.9 9.6 1.0
CB C:HIS635 4.0 9.5 1.0
CA C:ASP612 4.1 7.6 1.0
C C:TRP611 4.2 9.5 1.0
N C:TRP611 4.2 7.8 1.0
CB C:ASP612 4.2 11.9 1.0
CA C:ASP610 4.3 8.4 1.0
CA C:HIS615 4.3 11.6 1.0
CA C:TRP611 4.3 6.8 1.0
CA C:SER633 4.3 9.1 1.0
N C:HIS615 4.4 9.7 1.0
ND1 C:HIS635 4.4 12.4 1.0
N C:HIS614 4.4 8.1 1.0
N C:GLY616 4.5 11.3 1.0
CA C:HIS635 4.5 8.0 1.0
C C:SER633 4.5 10.3 1.0
CA C:LEU634 4.5 8.7 1.0
O C:HOH933 4.6 10.5 1.0
N C:HIS635 4.6 9.9 1.0
OH C:TYR631 4.7 10.1 1.0
CG C:HIS635 4.7 11.3 1.0
C C:VAL613 4.7 9.8 1.0
CA C:HIS614 4.7 10.2 1.0
N C:VAL613 4.7 9.3 1.0
C C:HIS615 4.7 11.4 1.0
CE1 C:HIS573 4.8 11.4 1.0
O C:TRP611 4.9 8.4 1.0
ND1 C:HIS573 4.9 12.0 1.0

Potassium binding site 6 out of 6 in 5wgm

Go back to Potassium Binding Sites List in 5wgm
Potassium binding site 6 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K803

b:23.8
occ:1.00
O C:HOH992 2.6 19.0 1.0
O C:VAL629 2.6 15.5 1.0
O C:PHE623 2.6 14.5 1.0
O C:ASP626 2.9 21.8 1.0
O C:TYR662 2.9 13.3 1.0
O C:HOH1012 3.4 16.2 1.0
CB C:TYR662 3.6 15.0 1.0
C C:PHE623 3.6 13.8 1.0
C C:TYR662 3.7 12.5 1.0
CB C:PHE623 3.7 13.3 1.0
C C:VAL629 3.8 14.6 1.0
C C:ASP626 4.0 21.7 1.0
CA C:TYR662 4.3 16.8 1.0
CA C:PHE623 4.3 14.8 1.0
N C:ASP626 4.4 21.4 1.0
N C:TYR631 4.5 12.1 1.0
N C:ASN663 4.5 14.5 1.0
N C:GLU624 4.5 16.1 0.3
N C:GLU624 4.5 16.1 0.7
CA C:LEU630 4.5 12.7 1.0
CA C:GLU624 4.6 16.6 0.3
CA C:GLU624 4.6 16.6 0.7
CA C:ASP626 4.6 21.7 1.0
O C:GLU624 4.6 19.2 0.7
N C:LEU630 4.6 12.5 1.0
CB C:ASP626 4.7 18.9 1.0
C C:GLU624 4.7 16.9 0.7
C C:GLU624 4.7 17.0 0.3
O C:GLU624 4.7 19.2 0.3
CA C:VAL629 4.8 14.3 1.0
O C:GLY659 4.8 19.3 1.0
CG C:TYR662 4.8 18.8 1.0
CA C:ASN663 4.9 13.9 1.0
CB C:TYR631 4.9 9.2 1.0
CB C:VAL629 4.9 14.4 1.0
C C:LEU630 4.9 12.4 1.0
CB C:ASN663 4.9 14.2 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 Dec 14 00:11:32 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy