Zinc in PDB 3c0y: Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7

The structure of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7, PDB code: 3c0y was solved by J.R.Min, A.Schuetz, A.Allali-Hassani, P.Loppnau, N.P.Kwiatkowski, R.Mazitschek, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, M.Vedadi, A.Bochkarev, A.N.Plotnikov, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.44 / 2.10
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	81.750, 81.750, 148.895, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 26.4

The structure of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 also contains other interesting chemical elements:

Potassium

(K)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 (pdb code 3c0y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7, PDB code: 3c0y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7


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 Catalytic Domain of Human Histone Deacetylase HDAC7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:35.0 occ:1.00 OD1 A:ASP707 1.9 31.1 1.0 OD2 A:ASP801 2.0 35.5 1.0 ND1 A:HIS709 2.1 29.9 1.0 O A:HOH289 2.4 30.5 1.0 CG A:ASP707 2.6 28.4 1.0 OD2 A:ASP707 2.8 28.3 1.0 CG A:ASP801 3.0 37.1 1.0 CE1 A:HIS709 3.1 31.0 1.0 CG A:HIS709 3.2 31.5 1.0 OD1 A:ASP801 3.3 32.7 1.0 CB A:HIS709 3.5 28.6 1.0 N A:HIS709 3.9 28.4 1.0 CB A:ASP707 4.1 26.6 1.0 NE2 A:HIS669 4.2 26.7 1.0 NE2 A:HIS709 4.2 31.9 1.0 CA A:GLY841 4.2 30.4 1.0 CD2 A:HIS709 4.3 31.7 1.0 CB A:ASP801 4.4 35.4 1.0 N A:VAL708 4.4 26.9 1.0 CA A:HIS709 4.4 28.2 1.0 NE2 A:HIS670 4.4 24.9 1.0 CG1 A:VAL708 4.5 24.2 1.0 O A:HOH156 4.6 49.0 1.0 N A:GLY841 4.6 29.9 1.0 CE1 A:HIS669 4.7 23.9 1.0 C A:ASP707 4.8 27.2 1.0 CA A:ASP707 4.8 26.8 1.0 C A:VAL708 4.9 27.8 1.0 O A:HOH290 4.9 65.0 1.0 C A:GLY841 5.0 31.5 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7


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 Catalytic Domain of Human Histone Deacetylase HDAC7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:47.0 occ:1.00 NE2 A:HIS541 2.0 36.6 1.0 SG A:CYS618 2.2 47.6 1.0 SG A:CYS535 2.3 45.7 1.0 SG A:CYS533 2.5 39.7 1.0 CB A:CYS535 2.9 49.9 1.0 CE1 A:HIS541 2.9 39.1 1.0 CD2 A:HIS541 3.1 40.0 1.0 CB A:CYS533 3.2 42.2 1.0 CB A:CYS618 3.3 51.2 1.0 ND1 A:HIS541 4.1 41.1 1.0 CA A:CYS535 4.1 50.5 1.0 N A:CYS535 4.1 50.3 1.0 CG A:HIS541 4.2 43.2 1.0 CA A:CYS533 4.6 43.2 1.0 CA A:CYS618 4.7 50.5 1.0 CG A:ARG540 4.8 57.7 1.0 NE A:ARG540 4.8 64.3 1.0 C A:CYS535 4.9 52.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7


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 Catalytic Domain of Human Histone Deacetylase HDAC7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:38.7 occ:1.00 OD1 B:ASP707 2.1 30.2 1.0 ND1 B:HIS709 2.1 35.3 1.0 OD2 B:ASP801 2.1 38.8 1.0 O B:HOH352 2.4 31.5 1.0 O B:HOH142 2.6 37.6 1.0 CE1 B:HIS709 2.9 34.7 1.0 CG B:ASP707 2.9 29.8 1.0 OD2 B:ASP707 3.0 32.0 1.0 CG B:ASP801 3.1 38.9 1.0 CG B:HIS709 3.2 35.6 1.0 OD1 B:ASP801 3.4 34.2 1.0 CB B:HIS709 3.7 32.3 1.0 N B:HIS709 4.0 31.8 1.0 NE2 B:HIS709 4.1 35.3 1.0 NE2 B:HIS669 4.2 34.1 1.0 CD2 B:HIS709 4.3 32.7 1.0 CB B:ASP707 4.3 31.1 1.0 CA B:GLY841 4.3 34.3 1.0 CB B:ASP801 4.4 36.6 1.0 NE2 B:HIS670 4.4 31.1 1.0 O B:HOH157 4.4 50.3 1.0 N B:VAL708 4.4 33.1 1.0 CA B:HIS709 4.5 31.5 1.0 CG1 B:VAL708 4.5 30.5 1.0 N B:GLY841 4.7 31.4 1.0 CE1 B:HIS669 4.7 31.4 1.0 C B:ASP707 4.8 32.6 1.0 CA B:ASP707 4.9 31.2 1.0 C B:VAL708 4.9 31.4 1.0 C B:GLY841 5.0 35.4 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7


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 Catalytic Domain of Human Histone Deacetylase HDAC7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:50.0 occ:1.00 NE2 B:HIS541 2.2 44.8 1.0 SG B:CYS535 2.3 53.2 1.0 SG B:CYS533 2.3 44.0 1.0 SG B:CYS618 2.4 50.7 1.0 CB B:CYS535 2.9 54.5 1.0 CD2 B:HIS541 3.1 42.3 1.0 CE1 B:HIS541 3.2 45.1 1.0 CB B:CYS533 3.2 43.7 1.0 CB B:CYS618 3.5 50.4 1.0 CA B:CYS535 4.1 54.0 1.0 NE B:ARG540 4.1 62.8 1.0 N B:CYS535 4.1 53.2 1.0 CG B:HIS541 4.3 45.2 1.0 ND1 B:HIS541 4.3 47.3 1.0 CA B:CYS533 4.6 45.0 1.0 CD B:ARG540 4.7 61.4 1.0 CD1 B:LEU616 4.8 52.7 1.0 C B:CYS535 4.8 54.6 1.0 N B:GLY620 4.8 46.8 1.0 NH2 B:ARG540 4.9 64.8 1.0 C B:CYS533 4.9 47.2 1.0 CA B:CYS618 4.9 50.6 1.0 CZ B:ARG540 4.9 66.3 1.0 CA B:GLY620 4.9 45.5 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn405 b:43.8 occ:1.00 OD2 C:ASP801 1.9 39.0 1.0 O C:HOH291 1.9 40.8 1.0 OD1 C:ASP707 2.1 44.5 1.0 ND1 C:HIS709 2.1 42.6 1.0 CG C:ASP707 2.8 41.7 1.0 OD2 C:ASP707 2.9 39.9 1.0 CG C:ASP801 3.0 41.8 1.0 CE1 C:HIS709 3.0 42.3 1.0 CG C:HIS709 3.1 40.5 1.0 OD1 C:ASP801 3.4 42.7 1.0 CB C:HIS709 3.5 37.0 1.0 N C:HIS709 3.9 37.0 1.0 NE2 C:HIS709 4.1 43.1 1.0 CD2 C:HIS709 4.2 41.3 1.0 NE2 C:HIS669 4.2 35.5 1.0 CB C:ASP707 4.3 37.7 1.0 CB C:ASP801 4.3 41.0 1.0 CA C:HIS709 4.3 36.9 1.0 CA C:GLY841 4.4 43.0 1.0 N C:VAL708 4.5 37.4 1.0 CG1 C:VAL708 4.5 39.6 1.0 NE2 C:HIS670 4.6 43.0 1.0 CE1 C:HIS669 4.6 36.6 1.0 N C:GLY841 4.8 43.8 1.0 C C:VAL708 4.8 37.2 1.0 C C:ASP707 4.9 37.5 1.0 CA C:ASP707 4.9 37.8 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn406 b:54.6 occ:1.00 SG C:CYS535 2.2 49.1 1.0 SG C:CYS618 2.2 54.3 1.0 NE2 C:HIS541 2.2 55.1 1.0 SG C:CYS533 2.4 52.5 1.0 CD2 C:HIS541 3.1 55.2 1.0 CB C:CYS618 3.2 58.9 1.0 CB C:CYS535 3.2 53.4 1.0 CB C:CYS533 3.2 52.2 1.0 CE1 C:HIS541 3.3 55.7 1.0 N C:CYS535 4.1 54.3 1.0 CA C:CYS535 4.2 53.4 1.0 CG C:HIS541 4.2 56.9 1.0 ND1 C:HIS541 4.3 56.7 1.0 NE C:ARG540 4.6 77.2 1.0 CA C:CYS533 4.6 52.0 1.0 CA C:CYS618 4.6 59.0 1.0 CA C:GLY620 4.7 57.6 1.0 N C:GLY620 4.7 58.4 1.0 CD1 C:LEU616 4.8 56.6 1.0 CD C:ARG540 4.8 73.2 1.0 CG C:ARG540 4.9 67.0 1.0 C C:CYS533 4.9 51.2 1.0 C C:CYS618 4.9 59.0 1.0 O C:CYS618 5.0 59.5 1.0 C C:CYS535 5.0 54.7 1.0

A.Schuetz, J.Min, A.Allali-Hassani, M.Schapira, M.Shuen, P.Loppnau, R.Mazitschek, N.P.Kwiatkowski, T.A.Lewis, R.L.Maglathin, T.H.Mclean, A.Bochkarev, A.N.Plotnikov, M.Vedadi, C.H.Arrowsmith. Human HDAC7 Harbors A Class Iia Histone Deacetylase-Specific Zinc Binding Motif and Cryptic Deacetylase Activity. J.Biol.Chem. V. 283 11355 2008.
ISSN: ISSN 0021-9258
PubMed: 18285338
DOI: 10.1074/JBC.M707362200