Zinc in PDB 6v79: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2376

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2376, PDB code: 6v79 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) 74.34 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.252, 108.135, 74.345, 90.00, 90.01, 90.00
R / Rfree (%) 19.5 / 23.4

Other elements in 6v79:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2376 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 (CD2) Complexed with NF2376 (pdb code 6v79). 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 (CD2) Complexed with NF2376, PDB code: 6v79:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6v79

Go back to Zinc Binding Sites List in 6v79
Zinc binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2376


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 (CD2) Complexed with NF2376 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:31.5
occ:1.00
OD2 A:ASP705 2.0 26.4 1.0
OD1 A:ASP612 2.1 16.9 1.0
O04 A:QQD804 2.1 40.8 1.0
O A:HOH915 2.1 28.9 1.0
ND1 A:HIS614 2.1 22.4 1.0
N03 A:QQD804 2.6 32.1 1.0
CG A:ASP612 2.7 20.4 1.0
OD2 A:ASP612 2.7 20.5 1.0
CE1 A:HIS614 3.0 22.1 1.0
CG A:ASP705 3.1 28.1 1.0
CG A:HIS614 3.2 22.7 1.0
OD1 A:ASP705 3.4 23.2 1.0
C02 A:QQD804 3.5 30.8 1.0
CB A:HIS614 3.5 19.9 1.0
O01 A:QQD804 3.7 37.8 1.0
N A:HIS614 3.9 17.9 1.0
NE2 A:HIS573 4.0 19.0 1.0
NE2 A:HIS614 4.2 24.8 1.0
CB A:ASP612 4.2 17.5 1.0
CG1 A:VAL613 4.2 20.8 1.0
CD2 A:HIS614 4.3 19.9 1.0
CA A:GLY743 4.3 22.8 1.0
CA A:HIS614 4.3 18.4 1.0
CB A:ASP705 4.4 17.5 1.0
N A:VAL613 4.4 20.1 1.0
CE1 A:HIS573 4.4 22.8 1.0
NE2 A:HIS574 4.6 21.4 1.0
OH A:TYR745 4.6 32.6 1.0
C05 A:QQD804 4.6 31.1 1.0
N A:GLY743 4.7 19.4 1.0
CE2 A:TYR745 4.7 25.3 1.0
C A:VAL613 4.9 17.6 1.0
C A:ASP612 4.9 21.6 1.0
CA A:ASP612 4.9 19.9 1.0

Zinc binding site 2 out of 2 in 6v79

Go back to Zinc Binding Sites List in 6v79
Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with NF2376


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 (CD2) Complexed with NF2376 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:29.2
occ:1.00
OD2 B:ASP705 2.0 23.3 1.0
OD1 B:ASP612 2.1 19.5 1.0
O B:HOH909 2.1 30.0 1.0
O04 B:QQD804 2.1 39.5 1.0
ND1 B:HIS614 2.1 25.2 1.0
N03 B:QQD804 2.6 32.9 1.0
OD2 B:ASP612 2.7 20.6 1.0
CG B:ASP612 2.7 23.4 1.0
CE1 B:HIS614 3.1 24.3 1.0
CG B:HIS614 3.2 24.1 1.0
CG B:ASP705 3.2 25.2 1.0
CB B:HIS614 3.5 21.2 1.0
C02 B:QQD804 3.6 32.4 1.0
OD1 B:ASP705 3.7 23.1 1.0
N B:HIS614 3.9 19.3 1.0
O01 B:QQD804 3.9 42.9 1.0
NE2 B:HIS573 4.1 19.4 1.0
CG1 B:VAL613 4.1 19.3 1.0
CB B:ASP612 4.2 16.6 1.0
NE2 B:HIS614 4.2 30.2 1.0
CD2 B:HIS614 4.3 24.0 1.0
CA B:HIS614 4.3 20.7 1.0
N B:VAL613 4.3 20.9 1.0
CE1 B:HIS573 4.4 26.2 1.0
CA B:GLY743 4.4 23.6 1.0
CB B:ASP705 4.4 16.1 1.0
OH B:TYR745 4.5 27.3 1.0
NE2 B:HIS574 4.5 23.9 1.0
CE2 B:TYR745 4.7 21.5 1.0
C05 B:QQD804 4.7 36.9 1.0
C B:VAL613 4.8 22.6 1.0
N B:GLY743 4.8 24.6 1.0
C B:ASP612 4.8 21.4 1.0
CA B:ASP612 4.9 19.3 1.0
CA B:VAL613 5.0 21.4 1.0

Reference:

J.D.Osko, D.W.Christianson. Harnessing An Epigenetic Approach to Idiopathic Pulmonary Fibrosis: Design, Synthesis, Structural Analysis, and Biological Evaluation of Selective HDAC6 Inhibitors To Be Published.
Page generated: Wed Dec 16 13:01:04 2020

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