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Potassium in PDB 5efn: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate, PDB code: 5efn was solved by Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.34 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.997, 83.908, 86.903, 90.00, 98.12, 90.00
R / Rfree (%) 16.2 / 19.4

Other elements in 5efn:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate 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 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate (pdb code 5efn). 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 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate, PDB code: 5efn:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5efn

Go back to Potassium Binding Sites List in 5efn
Potassium binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate


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 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K802

b:9.2
occ:1.00
 O B:ASP612 2.6 5.9 1.0
O B:HIS614 2.7 5.5 1.0
OD1 B:ASP610 2.7 6.1 1.0
OG B:SER633 2.7 7.0 1.0
O B:LEU634 2.7 8.5 1.0
O B:ASP610 2.8 6.2 1.0
CG B:ASP610 3.2 8.8 1.0
C B:ASP610 3.5 5.3 1.0
C B:ASP612 3.6 6.7 1.0
C B:HIS614 3.7 6.6 1.0
C B:LEU634 3.7 5.5 1.0
CB B:ASP610 3.8 6.9 1.0
N B:ASP612 3.9 6.6 1.0
CB B:SER633 3.9 6.5 1.0
N B:LEU634 3.9 5.5 1.0
CB B:HIS635 3.9 5.4 1.0
OD2 B:ASP610 3.9 10.5 1.0
CA B:ASP612 4.1 5.2 1.0
N B:TRP611 4.2 4.7 1.0
C B:TRP611 4.2 5.8 1.0
CB B:ASP612 4.3 6.3 1.0
CA B:HIS615 4.3 5.8 1.0
CA B:ASP610 4.3 6.3 1.0
CA B:SER633 4.3 6.5 1.0
CA B:TRP611 4.3 5.6 1.0
N B:HIS615 4.4 6.1 1.0
ND1 B:HIS635 4.4 7.0 1.0
N B:GLY616 4.4 7.2 1.0
N B:HIS614 4.4 7.7 1.0
C B:SER633 4.4 7.9 1.0
CA B:HIS635 4.5 6.2 1.0
CA B:LEU634 4.5 5.8 1.0
N B:HIS635 4.5 7.5 1.0
O B:HOH925 4.6 7.8 1.0
CG B:HIS635 4.6 5.7 1.0
C B:HIS615 4.6 8.2 1.0
CA B:HIS614 4.7 8.7 1.0
C B:VAL613 4.7 7.5 1.0
N B:VAL613 4.7 4.9 1.0
CE1 B:HIS573 4.7 6.9 1.0
OH B:TYR631 4.7 5.0 1.0
ND1 B:HIS573 4.8 6.3 1.0
O B:TRP611 5.0 8.8 1.0

Potassium binding site 2 out of 4 in 5efn

Go back to Potassium Binding Sites List in 5efn
Potassium binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate


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 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K803

b:9.2
occ:1.00
 O B:PHE623 2.7 7.6 1.0
O B:VAL629 2.7 10.6 1.0
O B:HOH998 2.7 11.2 1.0
O B:TYR662 2.8 7.2 1.0
O B:ASP626 2.9 9.8 1.0
O B:HOH1025 3.0 8.7 1.0
C B:TYR662 3.5 6.9 1.0
CB B:TYR662 3.6 9.2 1.0
C B:PHE623 3.6 9.7 1.0
CB B:PHE623 3.7 8.1 1.0
C B:VAL629 3.9 8.1 1.0
C B:ASP626 4.0 11.7 1.0
CA B:TYR662 4.2 7.8 1.0
N B:TYR631 4.3 6.2 1.0
CA B:PHE623 4.3 8.8 1.0
N B:ASN663 4.4 8.5 1.0
N B:ASP626 4.5 10.0 1.0
N B:GLU624 4.5 9.3 1.0
CA B:LEU630 4.6 7.8 1.0
CA B:ASP626 4.6 11.8 1.0
CA B:GLU624 4.6 10.4 1.0
CB B:ASP626 4.6 11.2 1.0
CB B:TYR631 4.7 5.7 1.0
C B:GLU624 4.7 10.7 1.0
N B:LEU630 4.7 8.3 1.0
CA B:ASN663 4.8 7.4 1.0
O B:GLU624 4.8 12.3 1.0
CB B:ASN663 4.8 7.7 1.0
CG B:TYR662 4.9 10.6 1.0
C B:LEU630 4.9 7.3 1.0
O B:GLY659 4.9 9.2 1.0
CA B:VAL629 4.9 7.5 1.0
CG B:PHE623 4.9 7.1 1.0

Potassium binding site 3 out of 4 in 5efn

Go back to Potassium Binding Sites List in 5efn
Potassium binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate


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 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K802

b:10.6
occ:1.00
 O A:ASP612 2.6 12.1 1.0
O A:LEU634 2.7 11.2 1.0
OD1 A:ASP610 2.7 9.7 1.0
OG A:SER633 2.7 11.2 1.0
O A:HIS614 2.8 7.8 1.0
O A:ASP610 2.9 8.6 1.0
CG A:ASP610 3.2 10.4 1.0
C A:ASP610 3.5 8.5 1.0
C A:ASP612 3.6 9.4 1.0
C A:LEU634 3.6 10.0 1.0
C A:HIS614 3.7 8.9 1.0
N A:ASP612 3.8 7.6 1.0
CB A:ASP610 3.9 7.8 1.0
N A:LEU634 3.9 9.6 1.0
OD2 A:ASP610 3.9 11.2 1.0
CB A:SER633 4.0 10.0 1.0
CB A:HIS635 4.0 8.9 1.0
CA A:ASP612 4.1 7.7 1.0
N A:TRP611 4.2 7.7 1.0
C A:TRP611 4.2 8.7 1.0
CB A:ASP612 4.2 6.9 1.0
CA A:HIS615 4.3 10.8 1.0
ND1 A:HIS635 4.3 10.0 1.0
CA A:TRP611 4.3 8.1 1.0
CA A:SER633 4.3 10.2 1.0
CA A:ASP610 4.3 7.7 1.0
N A:HIS615 4.4 10.2 1.0
C A:SER633 4.4 10.7 1.0
CA A:LEU634 4.5 10.4 1.0
N A:HIS635 4.5 11.3 1.0
CA A:HIS635 4.5 8.9 1.0
N A:GLY616 4.5 10.0 1.0
N A:HIS614 4.5 8.6 1.0
O A:HOH934 4.6 10.6 1.0
CG A:HIS635 4.6 9.6 1.0
C A:HIS615 4.7 10.3 1.0
N A:VAL613 4.7 7.5 1.0
OH A:TYR631 4.7 9.8 1.0
C A:VAL613 4.7 9.4 1.0
CA A:HIS614 4.8 9.6 1.0
CE1 A:HIS573 4.8 6.7 1.0
ND1 A:HIS573 4.9 8.4 1.0
O A:TRP611 5.0 10.2 1.0

Potassium binding site 4 out of 4 in 5efn

Go back to Potassium Binding Sites List in 5efn
Potassium binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate


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 (H574A) in Complex with Histone H4 LYS6 Tripeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K803

b:12.8
occ:1.00
 O A:PHE623 2.7 14.6 1.0
O A:VAL629 2.7 11.6 1.0
O A:HOH999 2.7 10.7 1.0
O A:TYR662 2.8 11.2 1.0
O A:ASP626 2.9 15.1 1.0
O A:HOH1053 3.0 10.4 1.0
C A:TYR662 3.6 12.8 1.0
CB A:TYR662 3.6 12.9 1.0
C A:PHE623 3.6 12.0 1.0
CB A:PHE623 3.8 10.4 1.0
C A:VAL629 3.9 11.4 1.0
C A:ASP626 4.0 16.3 1.0
CA A:TYR662 4.2 12.8 1.0
N A:TYR631 4.3 10.3 1.0
CA A:PHE623 4.3 11.2 1.0
N A:ASN663 4.4 12.0 1.0
N A:ASP626 4.4 18.6 1.0
N A:GLU624 4.5 13.3 1.0
CB A:ASP626 4.5 21.7 1.0
CA A:LEU630 4.6 10.4 1.0
CA A:ASP626 4.6 18.9 1.0
CA A:GLU624 4.6 15.5 1.0
N A:LEU630 4.7 12.1 1.0
C A:GLU624 4.7 14.2 1.0
CB A:TYR631 4.7 9.4 1.0
O A:GLU624 4.7 14.8 1.0
CA A:ASN663 4.8 14.1 1.0
CB A:ASN663 4.8 11.3 1.0
O A:GLY659 4.8 14.4 1.0
C A:LEU630 4.9 9.7 1.0
CA A:VAL629 4.9 12.5 1.0
CG A:TYR662 4.9 14.2 1.0

Reference:

Y.Hai, D.W.Christianson. Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134
Page generated: Mon Aug 12 13:28:55 2024

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