Zinc in PDB 3c10: Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa)

The structure of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa), PDB code: 3c10 was solved by J.Min, A.Schuetz, P.Loppnau, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, 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)	35.42 / 2.00
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	81.827, 81.827, 148.970, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 26.3

The structure of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa) 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 in Complex with Trichostatin A (Tsa) (pdb code 3c10). 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 in Complex with Trichostatin A (Tsa), PDB code: 3c10:
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 in Complex with Trichostatin A (Tsa)


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 in Complex with Trichostatin A (Tsa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:29.4 occ:1.00 OD1 A:ASP707 1.9 23.2 1.0 ND1 A:HIS709 2.0 23.0 1.0 OD2 A:ASP801 2.0 29.2 1.0 O1 A:TSN301 2.1 34.7 1.0 O2 A:TSN301 2.6 54.3 1.0 CG A:ASP707 2.7 24.4 1.0 OD2 A:ASP707 2.8 24.5 1.0 N1 A:TSN301 2.8 48.9 1.0 CE1 A:HIS709 2.8 26.8 1.0 C13 A:TSN301 2.9 50.8 1.0 CG A:ASP801 3.0 29.9 1.0 CG A:HIS709 3.1 24.1 1.0 OD1 A:ASP801 3.4 25.2 1.0 CB A:HIS709 3.6 19.9 1.0 N A:HIS709 3.9 21.4 1.0 NE2 A:HIS709 4.0 25.3 1.0 NE2 A:HIS669 4.1 23.5 1.0 C12 A:TSN301 4.1 51.2 1.0 CB A:ASP707 4.1 23.2 1.0 CD2 A:HIS709 4.2 24.8 1.0 CA A:GLY841 4.2 25.6 1.0 CB A:ASP801 4.3 31.4 1.0 CA A:HIS709 4.4 21.6 1.0 CG1 A:VAL708 4.4 22.2 1.0 N A:VAL708 4.5 22.7 1.0 C11 A:TSN301 4.6 52.5 1.0 NE2 A:HIS670 4.6 22.9 1.0 CE1 A:HIS669 4.6 20.8 1.0 N A:GLY841 4.7 24.7 1.0 O A:HOH469 4.7 53.1 1.0 O A:HOH260 4.7 39.8 1.0 CA A:ASP707 4.9 23.0 1.0 C A:ASP707 4.9 22.8 1.0 C A:VAL708 4.9 23.2 1.0 C A:GLY841 4.9 26.9 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa)


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 in Complex with Trichostatin A (Tsa) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:39.9 occ:1.00 NE2 A:HIS541 2.0 29.7 1.0 SG A:CYS618 2.1 40.0 1.0 SG A:CYS535 2.4 37.9 1.0 SG A:CYS533 2.4 35.1 1.0 CE1 A:HIS541 2.9 32.8 1.0 CB A:CYS535 3.0 40.9 1.0 CD2 A:HIS541 3.1 31.2 1.0 CB A:CYS618 3.1 43.0 1.0 CB A:CYS533 3.2 32.9 1.0 ND1 A:HIS541 4.0 34.1 1.0 O A:HOH278 4.1 44.3 1.0 CG A:HIS541 4.1 36.3 1.0 CA A:CYS535 4.2 41.4 1.0 N A:CYS535 4.2 39.9 1.0 NE A:ARG540 4.3 59.1 1.0 CA A:CYS618 4.5 41.9 1.0 CA A:CYS533 4.6 34.1 1.0 CD A:ARG540 4.8 55.1 1.0 N A:GLY620 4.8 37.1 1.0 CG A:ARG540 4.8 49.8 1.0 CA A:GLY620 4.9 36.2 1.0 C A:CYS618 4.9 41.0 1.0 C A:CYS535 5.0 43.4 1.0 O A:CYS618 5.0 40.9 1.0 C A:CYS533 5.0 35.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa)


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 in Complex with Trichostatin A (Tsa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:34.4 occ:1.00 OD2 B:ASP801 2.0 29.1 1.0 O1 B:TSN301 2.0 43.2 1.0 ND1 B:HIS709 2.0 28.2 1.0 OD1 B:ASP707 2.1 26.1 1.0 N1 B:TSN301 2.7 49.0 1.0 O2 B:TSN301 2.7 43.7 1.0 CG B:ASP707 2.7 24.7 1.0 CE1 B:HIS709 2.8 28.7 1.0 OD2 B:ASP707 2.8 29.6 1.0 C13 B:TSN301 2.9 48.0 1.0 CG B:ASP801 3.0 32.0 1.0 CG B:HIS709 3.2 26.9 1.0 OD1 B:ASP801 3.4 29.6 1.0 CB B:HIS709 3.8 26.6 1.0 N B:HIS709 3.9 26.0 1.0 NE2 B:HIS709 4.0 29.9 1.0 C12 B:TSN301 4.1 49.1 1.0 CA B:GLY841 4.1 29.7 1.0 CB B:ASP707 4.2 25.3 1.0 CD2 B:HIS709 4.2 27.5 1.0 NE2 B:HIS669 4.3 27.6 1.0 CB B:ASP801 4.3 29.7 1.0 N B:VAL708 4.4 28.2 1.0 CA B:HIS709 4.4 26.7 1.0 CG1 B:VAL708 4.4 26.1 1.0 N B:GLY841 4.5 27.6 1.0 NE2 B:HIS670 4.6 29.5 1.0 O B:HOH953 4.6 39.1 1.0 C11 B:TSN301 4.6 53.2 1.0 CE1 B:HIS669 4.8 25.0 1.0 C B:ASP707 4.8 27.1 1.0 C B:GLY841 4.8 31.0 1.0 O B:HOH1038 4.8 56.4 1.0 CA B:ASP707 4.9 25.1 1.0 N B:GLY842 4.9 33.6 1.0 C B:VAL708 4.9 27.0 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa)


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 in Complex with Trichostatin A (Tsa) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:42.1 occ:1.00 NE2 B:HIS541 2.1 41.5 1.0 SG B:CYS533 2.3 37.7 1.0 SG B:CYS535 2.3 46.8 1.0 SG B:CYS618 2.4 48.0 1.0 CB B:CYS535 2.9 47.8 1.0 CE1 B:HIS541 2.9 37.0 1.0 CD2 B:HIS541 3.1 37.6 1.0 CB B:CYS533 3.2 37.1 1.0 CB B:CYS618 3.6 48.7 1.0 CA B:CYS535 4.0 47.3 1.0 ND1 B:HIS541 4.1 39.4 1.0 N B:CYS535 4.1 46.3 1.0 CG B:HIS541 4.1 39.4 1.0 NE B:ARG540 4.2 54.5 1.0 CA B:CYS533 4.6 37.6 1.0 CD1 B:LEU616 4.6 51.9 1.0 N B:GLY620 4.8 42.9 1.0 C B:CYS535 4.8 47.9 1.0 NH2 B:ARG540 4.8 57.2 1.0 CA B:GLY620 4.9 41.1 1.0 C B:CYS533 4.9 39.3 1.0 CD B:ARG540 4.9 54.2 1.0 CA B:CYS618 5.0 48.1 1.0 O B:HOH991 5.0 43.1 1.0 CZ B:ARG540 5.0 57.5 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa)


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 in Complex with Trichostatin A (Tsa) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:36.0 occ:1.00 OD2 C:ASP801 1.9 30.6 1.0 O1 C:TSN301 2.0 45.3 1.0 OD1 C:ASP707 2.1 35.6 1.0 ND1 C:HIS709 2.1 34.9 1.0 O2 C:TSN301 2.7 45.4 1.0 CG C:ASP707 2.8 32.9 1.0 N1 C:TSN301 2.8 51.0 1.0 OD2 C:ASP707 2.8 33.0 1.0 C13 C:TSN301 2.9 50.7 1.0 CE1 C:HIS709 3.0 35.8 1.0 CG C:ASP801 3.1 33.2 1.0 CG C:HIS709 3.1 31.0 1.0 CB C:HIS709 3.5 30.0 1.0 OD1 C:ASP801 3.6 29.8 1.0 N C:HIS709 3.9 30.4 1.0 NE2 C:HIS669 4.1 28.2 1.0 NE2 C:HIS709 4.1 35.8 1.0 CD2 C:HIS709 4.2 32.0 1.0 C12 C:TSN301 4.2 51.1 1.0 CB C:ASP707 4.2 30.8 1.0 CA C:GLY841 4.3 34.0 1.0 CB C:ASP801 4.3 33.1 1.0 CA C:HIS709 4.3 30.7 1.0 CG1 C:VAL708 4.5 28.3 1.0 N C:VAL708 4.5 30.9 1.0 CE1 C:HIS669 4.5 26.5 1.0 O C:HOH991 4.6 49.3 1.0 NE2 C:HIS670 4.6 31.0 1.0 N C:GLY841 4.7 33.4 1.0 C11 C:TSN301 4.8 54.7 1.0 C C:VAL708 4.9 31.1 1.0 CA C:ASP707 4.9 31.0 1.0 C C:ASP707 4.9 30.8 1.0 N C:GLY842 5.0 37.1 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa)


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 in Complex with Trichostatin A (Tsa) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:47.3 occ:1.00 NE2 C:HIS541 2.1 43.9 1.0 SG C:CYS618 2.1 51.1 1.0 SG C:CYS535 2.3 45.3 1.0 SG C:CYS533 2.5 40.5 1.0 CE1 C:HIS541 3.0 43.2 1.0 CD2 C:HIS541 3.1 44.2 1.0 CB C:CYS533 3.1 42.1 1.0 CB C:CYS618 3.2 53.9 1.0 CB C:CYS535 3.3 46.2 1.0 N C:CYS535 4.1 45.2 1.0 ND1 C:HIS541 4.1 43.8 1.0 CG C:HIS541 4.2 45.2 1.0 CA C:CYS535 4.2 45.6 1.0 NE C:ARG540 4.5 63.5 1.0 CA C:CYS533 4.5 42.5 1.0 CA C:CYS618 4.6 53.7 1.0 CD C:ARG540 4.8 60.2 1.0 N C:GLY620 4.8 52.2 1.0 C C:CYS533 4.8 42.5 1.0 CG C:ARG540 4.9 55.1 1.0 CA C:GLY620 4.9 51.3 1.0 CD1 C:LEU616 4.9 51.5 1.0 N C:SER534 5.0 43.5 1.0 C C:CYS618 5.0 53.6 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