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Zinc 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:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc was 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:

Zinc binding site 1 out of 1 in 5efk

Go back to Zinc Binding Sites List in 5efk
Zinc binding site 1 out of 1 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 Zinc with other atoms in the Zn 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:Zn2001

b:13.2
occ:1.00
 OD1 B:ASP612 2.1 9.2 1.0
OD2 B:ASP705 2.1 8.6 1.0
ND1 B:HIS614 2.2 11.5 1.0
O B:HOH2114 2.2 10.6 1.0
OH A:ALY4 2.2 12.5 1.0
OD2 B:ASP612 2.7 8.3 1.0
CG B:ASP612 2.7 6.9 1.0
CE1 B:HIS614 3.0 15.0 1.0
CH A:ALY4 3.1 12.0 1.0
CG B:ASP705 3.1 9.6 1.0
CG B:HIS614 3.2 11.9 1.0
OD1 B:ASP705 3.5 9.3 1.0
CB B:HIS614 3.6 11.2 1.0
NZ A:ALY4 3.9 10.4 1.0
CH3 A:ALY4 3.9 13.8 1.0
N B:HIS614 3.9 8.6 1.0
CE A:ALY4 4.0 9.3 1.0
NE2 B:HIS573 4.1 10.7 1.0
NE2 B:HIS614 4.2 12.1 1.0
CB B:ASP612 4.2 6.2 1.0
CA B:GLY743 4.2 12.7 1.0
CD2 B:HIS614 4.3 11.1 1.0
CG1 B:VAL613 4.3 9.9 1.0
CA B:HIS614 4.4 10.2 1.0
CB B:ASP705 4.4 9.0 1.0
N B:VAL613 4.5 9.5 1.0
NE2 B:HIS574 4.5 8.6 1.0
N B:GLY743 4.6 11.1 1.0
CE1 B:HIS573 4.7 9.5 1.0
CE2 B:PHE745 4.7 7.4 1.0
C B:ASP612 4.9 10.5 1.0
C B:VAL613 4.9 10.3 1.0
CA B:ASP612 4.9 8.7 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: Sun Oct 27 15:16:04 2024

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