Potassium in PDB 8eqi: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0, PDB code: 8eqi was solved by P.R.Watson, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.89 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.45, 92.03, 153.2, 90, 90, 90
R / Rfree (%) 23.6 / 27.2

Other elements in 8eqi:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0 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 Cyclopeptide DES4.2.0 (pdb code 8eqi). 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 Cyclopeptide DES4.2.0, PDB code: 8eqi:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8eqi

Go back to Potassium Binding Sites List in 8eqi
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0


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 Cyclopeptide DES4.2.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:10.8
occ:1.00
 O A:ASP612 2.5 7.7 1.0
O A:HIS614 2.7 6.8 1.0
OD1 A:ASP610 2.7 10.5 1.0
OG A:SER633 2.8 11.8 1.0
O A:LEU634 2.8 11.6 1.0
O A:ASP610 2.8 11.2 1.0
CG A:ASP610 3.2 8.9 1.0
C A:ASP610 3.5 10.1 1.0
C A:ASP612 3.6 7.8 1.0
C A:LEU634 3.7 15.7 1.0
C A:HIS614 3.7 10.9 1.0
N A:ASP612 3.8 6.4 1.0
CB A:ASP610 3.8 9.7 1.0
OD2 A:ASP610 3.8 9.2 1.0
CB A:SER633 3.9 12.1 1.0
N A:LEU634 3.9 13.0 1.0
CB A:HIS635 4.0 11.4 1.0
CA A:ASP612 4.1 7.6 1.0
C A:TRP611 4.2 10.2 1.0
N A:TRP611 4.2 8.7 1.0
CB A:ASP612 4.2 6.8 1.0
CA A:HIS615 4.3 11.5 1.0
CA A:ASP610 4.3 10.2 1.0
CA A:SER633 4.3 12.1 1.0
CA A:TRP611 4.3 11.4 1.0
ND1 A:HIS635 4.3 11.3 1.0
O A:HOH901 4.3 9.9 1.0
N A:HIS615 4.4 8.4 1.0
N A:GLY616 4.4 11.8 1.0
C A:SER633 4.5 11.1 1.0
N A:HIS614 4.5 9.2 1.0
CA A:HIS635 4.5 9.0 1.0
CA A:LEU634 4.5 12.6 1.0
N A:HIS635 4.5 11.8 1.0
CG A:HIS635 4.6 12.3 1.0
C A:VAL613 4.7 9.2 1.0
N A:VAL613 4.7 10.5 1.0
CA A:HIS614 4.8 8.5 1.0
C A:HIS615 4.8 10.5 1.0
OH A:TYR631 4.8 10.4 1.0
O A:TRP611 4.9 9.1 1.0
ND1 A:HIS573 4.9 7.8 1.0
CE1 A:HIS573 5.0 6.8 1.0

Potassium binding site 2 out of 4 in 8eqi

Go back to Potassium Binding Sites List in 8eqi
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0


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 Cyclopeptide DES4.2.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:16.7
occ:1.00
 O A:PHE623 2.5 12.1 1.0
O A:HOH996 2.7 12.4 1.0
O A:VAL629 2.8 13.6 1.0
O A:ASP626 2.9 14.9 1.0
O A:TYR662 3.0 14.8 1.0
O A:HOH983 3.0 13.5 1.0
C A:PHE623 3.6 11.6 1.0
C A:TYR662 3.6 13.9 1.0
CB A:TYR662 3.7 9.6 1.0
CB A:PHE623 3.7 11.8 1.0
C A:VAL629 4.0 8.0 1.0
C A:ASP626 4.0 16.5 1.0
CA A:PHE623 4.3 14.7 1.0
N A:TYR631 4.3 13.0 1.0
CA A:TYR662 4.3 19.1 1.0
N A:ASN663 4.4 16.1 1.0
CB A:ASP626 4.5 12.4 1.0
N A:ASP626 4.5 19.0 1.0
N A:GLU624 4.5 11.5 1.0
CA A:ASP626 4.5 16.0 1.0
CA A:LEU630 4.6 16.9 1.0
CB A:ASN663 4.6 13.9 1.0
CA A:GLU624 4.6 13.4 1.0
CB A:TYR631 4.6 10.1 1.0
CA A:ASN663 4.6 13.5 1.0
O A:GLU624 4.7 20.3 1.0
N A:LEU630 4.7 12.6 1.0
C A:GLU624 4.8 16.5 1.0
C A:LEU630 4.9 12.1 1.0
O A:GLY659 5.0 16.9 1.0

Potassium binding site 3 out of 4 in 8eqi

Go back to Potassium Binding Sites List in 8eqi
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0


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 Cyclopeptide DES4.2.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:11.8
occ:1.00
 O B:ASP612 2.5 10.3 1.0
O B:ASP610 2.8 11.6 1.0
OD1 B:ASP610 2.8 11.1 1.0
O B:HIS614 2.8 8.2 1.0
O B:LEU634 2.8 11.2 1.0
OG B:SER633 2.9 11.7 1.0
CG B:ASP610 3.2 8.4 1.0
C B:ASP610 3.5 11.5 1.0
C B:ASP612 3.5 9.7 1.0
C B:HIS614 3.7 10.9 1.0
CB B:ASP610 3.8 9.6 1.0
C B:LEU634 3.8 16.3 1.0
N B:ASP612 3.8 8.1 1.0
OD2 B:ASP610 3.9 11.0 1.0
CB B:HIS635 3.9 14.1 1.0
CB B:SER633 4.0 14.2 1.0
N B:LEU634 4.0 13.8 1.0
CA B:ASP612 4.0 8.5 1.0
CB B:ASP612 4.1 9.3 1.0
C B:TRP611 4.1 10.3 1.0
N B:TRP611 4.2 10.4 1.0
CA B:HIS615 4.2 13.6 1.0
CA B:ASP610 4.2 7.7 1.0
CA B:TRP611 4.3 10.5 1.0
ND1 B:HIS635 4.3 13.3 1.0
CA B:SER633 4.3 11.7 1.0
N B:HIS615 4.3 9.5 1.0
N B:GLY616 4.4 12.5 1.0
N B:HIS614 4.4 9.5 1.0
O B:HOH908 4.4 12.3 1.0
C B:SER633 4.5 14.2 1.0
CA B:HIS635 4.5 11.0 1.0
CA B:LEU634 4.5 12.7 1.0
N B:HIS635 4.6 13.1 1.0
CG B:HIS635 4.6 13.8 1.0
C B:VAL613 4.7 10.4 1.0
N B:VAL613 4.7 11.0 1.0
CA B:HIS614 4.7 9.7 1.0
C B:HIS615 4.7 11.2 1.0
OH B:TYR631 4.7 11.9 1.0
O B:TRP611 4.9 10.3 1.0
CE1 B:HIS573 4.9 8.9 1.0
ND1 B:HIS573 4.9 8.0 1.0

Potassium binding site 4 out of 4 in 8eqi

Go back to Potassium Binding Sites List in 8eqi
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0


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 Cyclopeptide DES4.2.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:16.3
occ:1.00
 O B:PHE623 2.6 15.1 1.0
O B:VAL629 2.7 13.9 1.0
O B:HOH934 2.8 13.6 1.0
O B:TYR662 2.8 16.2 1.0
O B:ASP626 2.9 18.5 1.0
O B:HOH926 3.2 12.9 1.0
C B:TYR662 3.6 19.1 1.0
C B:PHE623 3.6 12.6 1.0
CB B:TYR662 3.7 9.9 1.0
CB B:PHE623 3.7 8.6 1.0
C B:VAL629 3.9 11.7 1.0
C B:ASP626 4.0 19.0 1.0
CA B:TYR662 4.2 14.8 1.0
N B:TYR631 4.2 13.7 1.0
CA B:PHE623 4.3 14.7 1.0
N B:ASN663 4.4 15.6 1.0
N B:ASP626 4.5 13.2 1.0
CA B:LEU630 4.5 17.4 1.0
N B:GLU624 4.5 11.4 1.0
CB B:ASP626 4.5 16.3 1.0
CA B:ASP626 4.6 14.7 1.0
CA B:GLU624 4.6 15.1 1.0
CB B:TYR631 4.6 12.0 1.0
N B:LEU630 4.6 13.9 1.0
CB B:ASN663 4.7 16.7 1.0
CA B:ASN663 4.7 14.0 1.0
O B:GLU624 4.7 18.3 1.0
C B:GLU624 4.7 16.0 1.0
C B:LEU630 4.8 13.8 1.0
CA B:VAL629 5.0 12.1 1.0
O B:GLY659 5.0 18.3 1.0
CG B:PHE623 5.0 11.2 1.0

Reference:

P.R.Watson, S.Gupta, P.Hosseinzadeh, B.P.Brown, D.Baker, D.W.Christianson. Macrocyclic Octapeptide Binding and Inferences on Protein Substrate Binding to Histone Deacetylase 6. Acs Chem.Biol. 2023.
ISSN: ESSN 1554-8937
PubMed: 37027789
DOI: 10.1021/ACSCHEMBIO.3C00113
Page generated: Tue Apr 25 21:42:12 2023

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