Zinc in PDB 6mr5: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor, PDB code: 6mr5 was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.76 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 159.010, 46.460, 96.400, 90.00, 119.19, 90.00
R / Rfree (%) 19 / 22.6

Other elements in 6mr5:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor also contains other interesting chemical elements:

Potassium (K) 4 atoms
Chlorine (Cl) 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 A Mercaptoacetamide-Based Inhibitor (pdb code 6mr5). 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 A Mercaptoacetamide-Based Inhibitor, PDB code: 6mr5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6mr5

Go back to Zinc Binding Sites List in 6mr5
Zinc binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


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 A Mercaptoacetamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:20.9
occ:1.00
OD2 A:ASP705 1.9 14.5 1.0
OD1 A:ASP612 2.1 19.7 1.0
ND1 A:HIS614 2.2 23.2 1.0
S04 A:W45804 2.3 22.6 1.0
CG A:ASP612 2.7 18.9 1.0
OD2 A:ASP612 2.8 19.9 1.0
CG A:ASP705 3.0 23.6 1.0
CE1 A:HIS614 3.0 25.8 1.0
CG A:HIS614 3.2 22.9 1.0
O01 A:W45804 3.3 23.6 1.0
C02 A:W45804 3.4 21.7 1.0
OD1 A:ASP705 3.5 21.6 1.0
C03 A:W45804 3.5 21.5 1.0
CB A:HIS614 3.6 20.3 1.0
N A:HIS614 3.9 25.6 1.0
N05 A:W45804 4.1 23.7 1.0
NE2 A:HIS573 4.1 16.5 1.0
CA A:GLY743 4.2 18.3 1.0
NE2 A:HIS614 4.2 24.4 1.0
CB A:ASP612 4.2 18.3 1.0
CB A:ASP705 4.2 17.2 1.0
CG1 A:VAL613 4.3 18.7 1.0
CD2 A:HIS614 4.3 24.2 1.0
N A:VAL613 4.3 19.4 1.0
CA A:HIS614 4.4 23.1 1.0
CE1 A:HIS573 4.4 19.8 1.0
OH A:TYR745 4.5 19.2 1.0
N A:GLY743 4.6 18.5 1.0
CE2 A:TYR745 4.7 18.7 1.0
C06 A:W45804 4.8 25.4 1.0
C A:VAL613 4.8 21.8 1.0
C A:ASP612 4.9 18.6 1.0
NE2 A:HIS574 4.9 20.7 1.0
CA A:ASP612 4.9 18.6 1.0
CA A:VAL613 5.0 21.7 1.0

Zinc binding site 2 out of 2 in 6mr5

Go back to Zinc Binding Sites List in 6mr5
Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with A Mercaptoacetamide-Based Inhibitor


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 A Mercaptoacetamide-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:18.1
occ:1.00
OD2 B:ASP705 1.9 15.0 1.0
OD1 B:ASP612 2.0 19.2 1.0
ND1 B:HIS614 2.1 16.9 1.0
S04 B:W45804 2.3 29.2 1.0
CG B:ASP612 2.7 15.8 1.0
OD2 B:ASP612 2.7 15.0 1.0
CG B:ASP705 3.0 17.9 1.0
CE1 B:HIS614 3.0 19.3 1.0
CG B:HIS614 3.2 18.9 1.0
OD1 B:ASP705 3.4 16.7 1.0
O01 B:W45804 3.4 26.8 1.0
C02 B:W45804 3.5 31.4 1.0
C03 B:W45804 3.6 23.2 1.0
CB B:HIS614 3.6 16.9 1.0
N B:HIS614 3.8 16.4 1.0
NE2 B:HIS614 4.2 17.5 1.0
N05 B:W45804 4.2 25.8 1.0
CB B:ASP612 4.2 14.4 1.0
CG1 B:VAL613 4.2 16.4 1.0
NE2 B:HIS573 4.2 15.3 1.0
CD2 B:HIS614 4.3 16.7 1.0
CB B:ASP705 4.3 12.8 1.0
N B:VAL613 4.3 15.2 1.0
CA B:GLY743 4.3 19.8 1.0
CA B:HIS614 4.3 19.0 1.0
OH B:TYR745 4.5 20.4 1.0
CE1 B:HIS573 4.6 17.8 1.0
CE2 B:TYR745 4.7 17.2 1.0
N B:GLY743 4.7 15.0 1.0
NE2 B:HIS574 4.8 20.3 1.0
C B:VAL613 4.8 16.6 1.0
C06 B:W45804 4.8 28.2 1.0
C B:ASP612 4.8 15.1 1.0
CA B:ASP612 4.9 14.0 1.0
CA B:VAL613 4.9 15.5 1.0

Reference:

N.J.Porter, S.Shen, C.Barinka, A.P.Kozikowski, D.W.Christianson. Molecular Basis For the Selective Inhibition of Histone Deacetylase 6 By A Mercaptoacetamide Inhibitor. Acs Med Chem Lett V. 9 1301 2018.
ISSN: ISSN 1948-5875
PubMed: 30613344
DOI: 10.1021/ACSMEDCHEMLETT.8B00487
Page generated: Wed Dec 16 12:20:27 2020

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