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Zinc in PDB 5ef7: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob, PDB code: 5ef7 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) 50.55 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.672, 56.637, 74.784, 106.45, 90.11, 97.09
R / Rfree (%) 18.1 / 22.1

Other elements in 5ef7:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob also contains other interesting chemical elements:

Potassium (K) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob (pdb code 5ef7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob, PDB code: 5ef7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5ef7

Go back to Zinc Binding Sites List in 5ef7
Zinc binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob


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 in Complex with Hpob within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:15.4
occ:0.65
O2 A:5OJ804 1.9 46.6 1.0
OD2 A:ASP705 2.0 15.0 1.0
OD1 A:ASP612 2.1 11.3 1.0
O A:HOH921 2.1 24.1 1.0
ND1 A:HIS614 2.2 12.6 1.0
N1 A:5OJ804 2.4 45.9 1.0
CG A:ASP612 2.7 17.4 1.0
OD2 A:ASP612 2.8 16.0 1.0
CE1 A:HIS614 3.1 13.5 1.0
CG A:ASP705 3.1 17.0 1.0
CG A:HIS614 3.2 11.3 1.0
C1 A:5OJ804 3.3 43.9 1.0
O1 A:5OJ804 3.6 44.7 1.0
OD1 A:ASP705 3.6 18.7 1.0
CB A:HIS614 3.6 7.9 1.0
N A:HIS614 3.8 8.2 1.0
NE2 A:HIS573 4.1 14.8 1.0
NE2 A:HIS614 4.2 12.9 1.0
CB A:ASP612 4.2 13.5 1.0
CG1 A:VAL613 4.3 13.4 1.0
CD2 A:HIS614 4.3 13.4 1.0
N A:VAL613 4.3 12.2 1.0
CA A:HIS614 4.4 7.8 1.0
CB A:ASP705 4.4 12.0 1.0
C2 A:5OJ804 4.4 37.0 1.0
OH A:TYR745 4.4 21.0 1.0
NE2 A:HIS574 4.4 14.9 1.0
CE1 A:HIS573 4.5 17.6 1.0
CA A:GLY743 4.5 15.9 1.0
C A:VAL613 4.8 13.7 1.0
CE2 A:TYR745 4.8 18.0 1.0
C A:ASP612 4.9 15.2 1.0
N A:GLY743 4.9 14.3 1.0
C17 A:5OJ804 4.9 35.3 1.0
CA A:ASP612 5.0 16.0 1.0
CA A:VAL613 5.0 7.4 1.0

Zinc binding site 2 out of 2 in 5ef7

Go back to Zinc Binding Sites List in 5ef7
Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Hpob within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:17.5
occ:0.71
O2 B:5OJ804 2.0 48.0 1.0
O B:HOH905 2.0 29.0 1.0
OD2 B:ASP705 2.0 15.1 1.0
OD1 B:ASP612 2.1 14.8 1.0
ND1 B:HIS614 2.2 6.8 1.0
N1 B:5OJ804 2.5 47.4 1.0
CG B:ASP612 2.8 18.4 1.0
OD2 B:ASP612 2.8 18.9 1.0
CG B:ASP705 3.1 19.1 1.0
CE1 B:HIS614 3.1 7.7 1.0
CG B:HIS614 3.2 7.5 1.0
C1 B:5OJ804 3.3 45.9 1.0
OD1 B:ASP705 3.5 16.2 1.0
CB B:HIS614 3.5 6.8 1.0
O1 B:5OJ804 3.5 47.1 1.0
N B:HIS614 3.9 9.8 1.0
NE2 B:HIS573 4.1 12.3 1.0
NE2 B:HIS614 4.3 5.3 1.0
CB B:ASP612 4.3 13.6 1.0
CD2 B:HIS614 4.3 5.3 1.0
CA B:HIS614 4.3 14.0 1.0
CG1 B:VAL613 4.3 10.7 1.0
N B:VAL613 4.4 12.6 1.0
CB B:ASP705 4.4 17.0 1.0
CA B:GLY743 4.4 17.8 1.0
C2 B:5OJ804 4.4 40.2 1.0
CE1 B:HIS573 4.4 14.2 1.0
NE2 B:HIS574 4.5 16.1 1.0
OH B:TYR745 4.7 18.8 1.0
N B:GLY743 4.8 18.2 1.0
C B:VAL613 4.9 11.3 1.0
CE2 B:TYR745 4.9 22.2 1.0
C B:ASP612 4.9 13.7 1.0
C17 B:5OJ804 4.9 38.4 1.0
CA B:ASP612 5.0 13.1 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 15:14:04 2024

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