Zinc in PDB 6pzs: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JR005

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JR005

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JR005:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JR005, PDB code: 6pzs was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.39 / 1.79
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.650, 83.670, 94.779, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 6pzs:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JR005 also contains other interesting chemical elements:

Potassium (K) 2 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JR005 (pdb code 6pzs). 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 Complexed with JR005, PDB code: 6pzs:

Zinc binding site 1 out of 1 in 6pzs

Go back to Zinc Binding Sites List in 6pzs
Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with JR005


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 Complexed with JR005 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:10.3
occ:1.00
 OD2 A:ASP705 2.0 10.2 1.0
OD1 A:ASP612 2.0 6.1 1.0
O14 A:P7J804 2.0 37.3 1.0
ND1 A:HIS614 2.1 10.2 1.0
O A:HOH905 2.1 13.8 1.0
N13 A:P7J804 2.4 19.3 1.0
CG A:ASP612 2.7 8.2 1.0
OD2 A:ASP612 2.8 8.6 1.0
CE1 A:HIS614 2.9 10.1 1.0
CG A:ASP705 3.0 10.7 1.0
CG A:HIS614 3.2 10.6 1.0
OD1 A:ASP705 3.3 9.6 1.0
C11 A:P7J804 3.4 24.0 1.0
CB A:HIS614 3.6 7.2 1.0
O12 A:P7J804 3.8 32.3 1.0
N A:HIS614 3.9 9.5 1.0
NE2 A:HIS614 4.1 13.2 1.0
NE2 A:HIS573 4.1 7.7 1.0
CG1 A:VAL613 4.2 7.0 1.0
CB A:ASP612 4.2 7.6 1.0
CD2 A:HIS614 4.2 11.2 1.0
CB A:ASP705 4.3 9.8 1.0
CA A:GLY743 4.3 10.0 1.0
CA A:HIS614 4.4 7.9 1.0
OH A:TYR745 4.4 15.7 1.0
N A:VAL613 4.4 5.6 1.0
CE1 A:HIS573 4.5 7.9 1.0
C08 A:P7J804 4.5 20.1 1.0
NE2 A:HIS574 4.6 10.2 1.0
CE2 A:TYR745 4.6 13.7 1.0
N A:GLY743 4.7 9.3 1.0
C07 A:P7J804 4.8 22.8 1.0
C A:ASP612 4.9 7.9 1.0
C A:VAL613 4.9 8.9 1.0
CA A:ASP612 4.9 7.9 1.0

Reference:

J.D.Osko, N.J.Porter, P.A.Narayana Reddy, Y.C.Xiao, J.Rokka, M.Jung, J.M.Hooker, J.M.Salvino, D.W.Christianson. Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. J.Med.Chem. V. 63 295 2020.
ISSN: ISSN 0022-2623
PubMed: 31793776
DOI: 10.1021/ACS.JMEDCHEM.9B01540
Page generated: Wed Dec 16 12:33:06 2020

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