Zinc in PDB 7u8z: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor, PDB code: 7u8z was solved by P.R.Watson, A.D.Cragin, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.48 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.34, 95.13, 98.139, 90, 98.73, 90
R / Rfree (%)	17.2 / 21.5

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor also contains other interesting chemical elements:

Fluorine	(F)	5 atoms
Potassium	(K)	8 atoms

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor (pdb code 7u8z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor, PDB code: 7u8z:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid 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 (CD2) Complexed with Fluorinated Peptoid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:9.2 occ:1.00 OD1 A:ASP612 2.0 5.8 1.0 OD2 A:ASP705 2.1 5.0 1.0 O23 A:M0I902 2.1 9.1 1.0 ND1 A:HIS614 2.1 8.1 1.0 O24 A:M0I902 2.4 13.2 1.0 N22 A:M0I902 2.7 22.4 1.0 CG A:ASP612 2.7 9.1 1.0 OD2 A:ASP612 2.8 10.8 1.0 C21 A:M0I902 2.8 13.4 1.0 CE1 A:HIS614 3.0 8.5 1.0 CG A:ASP705 3.1 10.8 1.0 CG A:HIS614 3.2 12.8 1.0 OD1 A:ASP705 3.6 11.5 1.0 CB A:HIS614 3.7 6.9 1.0 N A:HIS614 3.9 6.9 1.0 NE2 A:HIS614 4.2 9.1 1.0 CB A:ASP612 4.2 5.7 1.0 NE2 A:HIS573 4.2 6.2 1.0 C20 A:M0I902 4.2 7.4 1.0 CG1 A:VAL613 4.3 6.3 1.0 CD2 A:HIS614 4.3 7.5 1.0 CA A:GLY743 4.3 8.7 1.0 CB A:ASP705 4.4 6.6 1.0 N A:VAL613 4.4 7.6 1.0 CA A:HIS614 4.4 5.0 1.0 NE2 A:HIS574 4.5 10.3 1.0 OH A:TYR745 4.5 13.2 1.0 CE1 A:HIS573 4.6 6.3 1.0 CE2 A:TYR745 4.7 10.2 1.0 N A:GLY743 4.8 10.0 1.0 C25 A:M0I902 4.8 9.5 1.0 C A:VAL613 4.9 6.5 1.0 C A:ASP612 4.9 5.9 1.0 CA A:ASP612 4.9 3.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid 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 (CD2) Complexed with Fluorinated Peptoid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn805 b:12.1 occ:1.00 OD2 B:ASP705 2.0 9.6 1.0 OD1 B:ASP612 2.1 5.2 1.0 ND1 B:HIS614 2.2 6.1 1.0 O23 B:M0I801 2.2 8.5 0.7 O23 B:M0I801 2.3 10.2 0.2 O24 B:M0I801 2.3 12.1 0.7 O24 B:M0I801 2.4 12.0 0.2 OD2 B:ASP612 2.7 9.2 1.0 N22 B:M0I801 2.7 19.0 0.7 CG B:ASP612 2.7 6.2 1.0 N22 B:M0I801 2.8 16.0 0.2 C21 B:M0I801 2.8 12.1 0.7 C21 B:M0I801 2.8 12.0 0.2 CE1 B:HIS614 3.0 8.8 1.0 CG B:ASP705 3.1 9.4 1.0 CG B:HIS614 3.3 11.0 1.0 OD1 B:ASP705 3.6 8.0 1.0 CB B:HIS614 3.7 9.7 1.0 N B:HIS614 4.0 6.7 1.0 C20 B:M0I801 4.2 9.5 0.7 C20 B:M0I801 4.2 9.6 0.2 NE2 B:HIS614 4.2 8.4 1.0 NE2 B:HIS573 4.2 6.9 1.0 CB B:ASP612 4.2 3.8 1.0 CG1 B:VAL613 4.3 6.1 1.0 CD2 B:HIS614 4.3 8.1 1.0 CB B:ASP705 4.3 5.8 1.0 N B:VAL613 4.4 7.0 1.0 CA B:GLY743 4.4 9.1 1.0 CA B:HIS614 4.5 7.6 1.0 OH B:TYR745 4.6 13.3 1.0 CE1 B:HIS573 4.6 10.3 1.0 NE2 B:HIS574 4.7 11.1 1.0 C25 B:M0I801 4.7 11.0 0.7 C19 B:M0I801 4.7 10.8 0.2 CE2 B:TYR745 4.8 7.8 1.0 N B:GLY743 4.8 6.8 1.0 C B:VAL613 4.9 7.0 1.0 C B:ASP612 4.9 7.2 1.0 CA B:ASP612 5.0 4.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn803 b:10.9 occ:1.00 O23 C:M0I801 1.8 35.1 1.0 OD1 C:ASP612 2.1 11.4 1.0 OD2 C:ASP705 2.1 11.8 1.0 ND1 C:HIS614 2.2 13.3 1.0 O C:HOH908 2.2 11.2 1.0 N22 C:M0I801 2.4 7.5 1.0 CG C:ASP612 2.7 7.8 1.0 OD2 C:ASP612 2.7 8.1 1.0 CE1 C:HIS614 3.0 12.5 1.0 CG C:ASP705 3.1 13.8 1.0 CG C:HIS614 3.2 7.3 1.0 C21 C:M0I801 3.3 16.2 1.0 OD1 C:ASP705 3.5 11.4 1.0 CB C:HIS614 3.6 6.9 1.0 O24 C:M0I801 3.7 21.2 1.0 N C:HIS614 3.9 9.3 1.0 NE2 C:HIS614 4.2 7.5 1.0 CB C:ASP612 4.2 12.6 1.0 NE2 C:HIS573 4.2 9.9 1.0 CD2 C:HIS614 4.3 12.8 1.0 CA C:GLY743 4.3 6.9 1.0 N C:VAL613 4.3 8.9 1.0 CG1 C:VAL613 4.3 12.6 1.0 CA C:HIS614 4.4 6.9 1.0 CB C:ASP705 4.4 10.6 1.0 OH C:TYR745 4.4 12.3 1.0 C20 C:M0I801 4.5 11.6 1.0 NE2 C:HIS574 4.5 7.4 1.0 CE1 C:HIS573 4.6 10.2 1.0 N C:GLY743 4.7 10.5 1.0 CE2 C:TYR745 4.7 9.5 1.0 C C:VAL613 4.9 9.9 1.0 C25 C:M0I801 4.9 13.7 1.0 C C:ASP612 4.9 6.5 1.0 CA C:ASP612 5.0 9.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Fluorinated Peptoid Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn806 b:12.1 occ:1.00 O23 D:M0I801 1.8 33.6 1.0 OD2 D:ASP705 2.0 9.9 1.0 O D:HOH902 2.1 9.8 1.0 OD1 D:ASP612 2.1 10.8 1.0 ND1 D:HIS614 2.2 10.0 1.0 N22 D:M0I801 2.4 9.3 1.0 OD2 D:ASP612 2.6 12.6 1.0 CG D:ASP612 2.7 9.1 1.0 CE1 D:HIS614 3.1 17.6 1.0 CG D:ASP705 3.1 15.2 1.0 C21 D:M0I801 3.1 18.4 1.0 CG D:HIS614 3.2 8.5 1.0 O24 D:M0I801 3.4 31.6 1.0 OD1 D:ASP705 3.5 9.8 1.0 CB D:HIS614 3.5 9.4 1.0 N D:HIS614 3.9 8.5 1.0 CB D:ASP612 4.2 8.8 1.0 CG1 D:VAL613 4.2 7.6 1.0 NE2 D:HIS573 4.2 10.9 1.0 NE2 D:HIS614 4.2 13.3 1.0 CD2 D:HIS614 4.3 12.9 1.0 CA D:GLY743 4.3 13.8 1.0 CA D:HIS614 4.4 11.5 1.0 C20 D:M0I801 4.4 7.0 1.0 CB D:ASP705 4.4 7.2 1.0 N D:VAL613 4.4 8.8 1.0 OH D:TYR745 4.6 14.1 1.0 NE2 D:HIS574 4.6 10.1 1.0 CE1 D:HIS573 4.6 17.4 1.0 N D:GLY743 4.7 12.9 1.0 CE2 D:TYR745 4.8 9.3 1.0 C D:VAL613 4.9 9.0 1.0 C25 D:M0I801 4.9 7.1 1.0 C D:ASP612 4.9 5.8 1.0 CA D:ASP612 4.9 10.3 1.0

N.Ressing, J.Schliehe-Diecks, P.R.Watson, M.Sonnichsen, A.D.Cragin, A.Scholer, J.Yang, L.Schaker-Hubner, A.Borkhardt, D.W.Christianson, S.Bhatia, F.K.Hansen. Development of Fluorinated Peptoid-Based Histone Deacetylase (Hdac) Inhibitors For Therapy-Resistant Acute Leukemia. J.Med.Chem. V. 65 15457 2022.
ISSN: ISSN 0022-2623
PubMed: 36351184
DOI: 10.1021/ACS.JMEDCHEM.2C01418