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Potassium in PDB 5efk: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (Y745F Mutant) in Complex with Alpha Tubulin K40 Tripeptide Substrate

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (Y745F Mutant) in Complex with Alpha Tubulin K40 Tripeptide Substrate

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (Y745F Mutant) in Complex with Alpha Tubulin K40 Tripeptide Substrate:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (Y745F Mutant) in Complex with Alpha Tubulin K40 Tripeptide Substrate, PDB code: 5efk 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) 45.32 / 1.82
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.277, 94.667, 51.622, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.3

Other elements in 5efk:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (Y745F Mutant) in Complex with Alpha Tubulin K40 Tripeptide Substrate also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (Y745F Mutant) in Complex with Alpha Tubulin K40 Tripeptide Substrate (pdb code 5efk). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (Y745F Mutant) in Complex with Alpha Tubulin K40 Tripeptide Substrate, PDB code: 5efk:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 5efk

Go back to Potassium Binding Sites List in 5efk
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (Y745F Mutant) in Complex with Alpha Tubulin K40 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 (Y745F Mutant) in Complex with Alpha Tubulin K40 Tripeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2002

b:11.6
occ:1.00
 O B:ASP612 2.6 7.3 1.0
O B:HIS614 2.6 8.7 1.0
OG B:SER633 2.7 9.8 1.0
O B:LEU634 2.7 10.2 1.0
OD1 B:ASP610 2.7 9.8 1.0
O B:ASP610 2.8 7.8 1.0
CG B:ASP610 3.3 8.0 1.0
C B:ASP610 3.5 12.0 1.0
C B:ASP612 3.6 10.5 1.0
C B:HIS614 3.7 10.4 1.0
C B:LEU634 3.7 9.5 1.0
CB B:ASP610 3.8 7.7 1.0
CB B:SER633 3.9 10.6 1.0
CB B:HIS635 3.9 9.2 1.0
N B:LEU634 3.9 10.8 1.0
OD2 B:ASP610 3.9 11.4 1.0
N B:ASP612 3.9 8.0 1.0
CA B:ASP612 4.2 8.7 1.0
N B:TRP611 4.2 7.8 1.0
C B:TRP611 4.3 7.5 1.0
CA B:HIS615 4.3 10.1 1.0
CA B:ASP610 4.3 7.0 1.0
CB B:ASP612 4.3 6.2 1.0
CA B:SER633 4.3 9.5 1.0
ND1 B:HIS635 4.3 10.6 1.0
CA B:TRP611 4.4 6.2 1.0
N B:HIS615 4.4 8.2 1.0
N B:HIS614 4.4 8.6 1.0
N B:GLY616 4.4 9.4 1.0
C B:SER633 4.5 12.8 1.0
CA B:HIS635 4.5 7.6 1.0
N B:HIS635 4.5 11.2 1.0
CA B:LEU634 4.5 8.7 1.0
CG B:HIS635 4.6 12.5 1.0
O B:HOH2127 4.6 10.1 1.0
CE1 B:HIS573 4.6 9.5 1.0
OH B:TYR631 4.6 8.6 1.0
C B:VAL613 4.7 10.3 1.0
CA B:HIS614 4.7 10.2 1.0
C B:HIS615 4.7 8.4 1.0
N B:VAL613 4.7 9.5 1.0
ND1 B:HIS573 4.9 9.6 1.0
O B:TRP611 5.0 9.0 1.0

Potassium binding site 2 out of 2 in 5efk

Go back to Potassium Binding Sites List in 5efk
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (Y745F Mutant) in Complex with Alpha Tubulin K40 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 (Y745F Mutant) in Complex with Alpha Tubulin K40 Tripeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K2003

b:13.5
occ:1.00
 O B:HOH2117 2.7 12.1 1.0
O B:PHE623 2.7 12.7 1.0
O B:VAL629 2.7 12.2 1.0
O B:TYR662 2.9 10.4 1.0
O B:HOH2213 2.9 11.2 1.0
O B:ASP626 2.9 14.0 1.0
C B:TYR662 3.6 8.3 1.0
C B:PHE623 3.6 10.6 1.0
CB B:TYR662 3.6 11.8 1.0
CB B:PHE623 3.7 10.3 1.0
C B:VAL629 3.9 8.9 1.0
C B:ASP626 4.1 11.7 1.0
CA B:TYR662 4.3 7.6 1.0
N B:TYR631 4.3 8.0 1.0
CA B:PHE623 4.3 10.8 1.0
N B:ASN663 4.4 11.5 1.0
N B:ASP626 4.5 16.2 1.0
N B:GLU624 4.5 8.0 1.0
CA B:GLU624 4.5 9.6 1.0
CA B:LEU630 4.6 10.8 1.0
CA B:ASP626 4.6 13.7 1.0
C B:GLU624 4.7 11.8 1.0
CB B:ASP626 4.7 19.3 1.0
O B:GLU624 4.7 12.8 1.0
CB B:TYR631 4.7 10.9 1.0
O B:GLY659 4.7 15.7 1.0
N B:LEU630 4.7 9.5 1.0
CA B:ASN663 4.8 12.7 1.0
CB B:ASN663 4.8 12.4 1.0
C B:LEU630 4.9 8.4 1.0
CA B:VAL629 4.9 7.3 1.0
CG B:TYR662 4.9 13.5 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 13:27:59 2024

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