Zinc in PDB 6uo5: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant Complexed with Ar-42

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant Complexed with Ar-42, PDB code: 6uo5 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) 60.99 / 1.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.569, 60.546, 121.972, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.7

Other elements in 6uo5:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant Complexed with Ar-42 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 1 (CD1) Y363F Mutant Complexed with Ar-42 (pdb code 6uo5). 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 1 (CD1) Y363F Mutant Complexed with Ar-42, PDB code: 6uo5:

Zinc binding site 1 out of 1 in 6uo5

Go back to Zinc Binding Sites List in 6uo5
Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 1 (CD1) Y363F Mutant Complexed with Ar-42


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 1 (CD1) Y363F Mutant Complexed with Ar-42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:11.9
occ:0.88
H231 A:QCP501 1.8 52.0 1.0
H221 A:QCP501 1.9 25.9 1.0
O23 A:QCP501 2.0 43.4 1.0
OD1 A:ASP230 2.0 12.4 1.0
O A:HOH613 2.0 18.8 1.0
N22 A:QCP501 2.1 21.6 1.0
ND1 A:HIS232 2.1 11.8 1.0
OD2 A:ASP323 2.1 16.9 1.0
CG A:ASP230 2.7 12.8 1.0
OD2 A:ASP230 2.8 13.6 1.0
CE1 A:HIS232 3.0 13.5 1.0
CG A:ASP323 3.1 14.0 1.0
CG A:HIS232 3.2 11.1 1.0
C02 A:QCP501 3.2 30.6 1.0
OD1 A:ASP323 3.5 14.4 1.0
CB A:HIS232 3.6 11.9 1.0
N A:HIS232 3.8 11.6 1.0
O01 A:QCP501 3.9 33.7 1.0
C03 A:QCP501 4.1 20.0 1.0
O A:HOH759 4.1 25.0 1.0
NE2 A:HIS232 4.1 15.1 1.0
CA A:GLY361 4.2 13.6 1.0
CB A:ASP230 4.2 12.1 1.0
CD2 A:HIS232 4.2 13.9 1.0
NE2 A:HIS192 4.2 13.8 1.0
CG1 A:VAL231 4.3 14.7 1.0
N A:VAL231 4.3 11.6 1.0
CA A:HIS232 4.3 10.6 1.0
H041 A:QCP501 4.4 21.8 1.0
CB A:ASP323 4.4 13.6 1.0
N A:GLY361 4.6 13.1 1.0
C04 A:QCP501 4.6 18.2 1.0
NE2 A:HIS193 4.6 12.1 1.0
CE1 A:HIS192 4.6 13.1 1.0
C A:VAL231 4.8 13.3 1.0
C A:ASP230 4.9 11.7 1.0
CA A:ASP230 4.9 10.7 1.0
CA A:VAL231 5.0 13.4 1.0
C A:GLY361 5.0 13.5 1.0
C21 A:QCP501 5.0 16.8 1.0
N A:GLY362 5.0 15.0 1.0

Reference:

J.D.Osko, D.W.Christianson. Structural Basis of Catalysis and Inhibition of HDAC6 CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31755702
DOI: 10.1021/ACS.BIOCHEM.9B00934
Page generated: Wed Dec 16 12:59:25 2020

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