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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: Mon Aug 12 23:36:41 2024

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