Zinc in PDB 1zz0: Crystal Structure of A Hdac-Like Protein with Acetate Bound

The structure of Crystal Structure of A Hdac-Like Protein with Acetate Bound, PDB code: 1zz0 was solved by T.K.Nielsen, C.Hildmann, A.Dickmanns, A.Schwienhorst, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.86 / 1.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.586, 127.886, 251.681, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 18.6

The structure of Crystal Structure of A Hdac-Like Protein with Acetate Bound also contains other interesting chemical elements:

Potassium

(K)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of A Hdac-Like Protein with Acetate Bound (pdb code 1zz0). 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 A Hdac-Like Protein with Acetate Bound, PDB code: 1zz0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Hdac-Like Protein with Acetate Bound


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 A Hdac-Like Protein with Acetate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1451 b:13.4 occ:0.40 OD2 A:ASP268 2.0 10.8 1.0 O A:ACT1452 2.1 15.3 1.0 OD1 A:ASP180 2.1 10.9 1.0 ND1 A:HIS182 2.2 13.4 1.0 OXT A:ACT1452 2.2 17.1 1.0 OD2 A:ASP180 2.4 12.8 1.0 C A:ACT1452 2.5 16.6 1.0 CG A:ASP180 2.6 10.7 1.0 CE1 A:HIS182 3.0 11.9 1.0 CG A:ASP268 3.1 10.4 1.0 CG A:HIS182 3.3 10.6 1.0 OD1 A:ASP268 3.4 10.8 1.0 CB A:HIS182 3.7 9.6 1.0 NE2 A:HIS142 3.9 14.7 1.0 CH3 A:ACT1452 4.0 17.1 1.0 N A:HIS182 4.0 9.0 1.0 CB A:ASP180 4.1 9.0 1.0 CA A:GLY310 4.1 11.4 1.0 NE2 A:HIS182 4.2 12.0 1.0 CB A:ASP268 4.3 10.6 1.0 N A:VAL181 4.3 9.4 1.0 CD2 A:HIS182 4.3 12.2 1.0 CE1 A:HIS142 4.4 13.4 1.0 CE2 A:TYR312 4.4 11.7 1.0 CG1 A:VAL181 4.4 10.3 1.0 N A:GLY310 4.4 10.9 1.0 CA A:HIS182 4.5 9.1 1.0 OH A:TYR312 4.5 14.0 1.0 NE2 A:HIS143 4.6 13.2 1.0 C A:ASP180 4.8 9.3 1.0 CA A:ASP180 4.8 9.5 1.0 C A:GLY310 4.9 12.7 1.0 CZ A:TYR312 4.9 15.5 1.0 N A:GLY311 5.0 13.3 1.0 C A:VAL181 5.0 9.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Hdac-Like Protein with Acetate Bound


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 A Hdac-Like Protein with Acetate Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1551 b:13.8 occ:0.40 OD2 B:ASP268 1.9 12.1 1.0 OD1 B:ASP180 2.0 11.1 1.0 OXT B:ACT1552 2.1 13.9 1.0 O B:ACT1552 2.1 13.1 1.0 ND1 B:HIS182 2.2 11.2 1.0 OD2 B:ASP180 2.4 13.6 1.0 C B:ACT1552 2.5 14.8 1.0 CG B:ASP180 2.5 10.9 1.0 CG B:ASP268 3.0 10.6 1.0 CE1 B:HIS182 3.0 12.1 1.0 CG B:HIS182 3.3 10.8 1.0 OD1 B:ASP268 3.4 10.0 1.0 CB B:HIS182 3.7 9.7 1.0 CH3 B:ACT1552 4.0 15.1 1.0 N B:HIS182 4.0 9.7 1.0 NE2 B:HIS142 4.0 13.9 1.0 CB B:ASP180 4.0 9.8 1.0 CA B:GLY310 4.1 11.9 1.0 NE2 B:HIS182 4.2 11.2 1.0 CB B:ASP268 4.3 10.3 1.0 CE2 B:TYR312 4.3 10.3 1.0 CD2 B:HIS182 4.3 10.7 1.0 N B:VAL181 4.4 9.4 1.0 CG1 B:VAL181 4.4 10.5 1.0 N B:GLY310 4.4 10.7 1.0 CE1 B:HIS142 4.4 14.9 1.0 CA B:HIS182 4.5 9.5 1.0 OH B:TYR312 4.5 14.3 1.0 NE2 B:HIS143 4.7 14.7 1.0 CA B:ASP180 4.8 10.5 1.0 C B:ASP180 4.8 10.5 1.0 C B:GLY310 4.8 12.1 1.0 CZ B:TYR312 4.9 11.9 1.0 N B:GLY311 4.9 11.7 1.0 C B:VAL181 5.0 9.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Hdac-Like Protein with Acetate Bound


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 A Hdac-Like Protein with Acetate Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1651 b:15.4 occ:0.40 OD2 C:ASP268 2.0 14.8 1.0 OD1 C:ASP180 2.1 12.8 1.0 OXT C:ACT1652 2.1 15.8 1.0 ND1 C:HIS182 2.2 13.2 1.0 O C:ACT1652 2.2 16.1 1.0 OD2 C:ASP180 2.5 13.8 1.0 C C:ACT1652 2.5 16.4 1.0 CG C:ASP180 2.6 12.6 1.0 CE1 C:HIS182 3.0 15.5 1.0 CG C:ASP268 3.0 14.3 1.0 CG C:HIS182 3.2 12.1 1.0 OD1 C:ASP268 3.5 13.3 1.0 CB C:HIS182 3.6 11.7 1.0 N C:HIS182 4.0 11.2 1.0 NE2 C:HIS142 4.0 14.9 1.0 CH3 C:ACT1652 4.0 16.0 1.0 CB C:ASP180 4.1 11.8 1.0 CA C:GLY310 4.1 13.4 1.0 NE2 C:HIS182 4.2 13.3 1.0 CB C:ASP268 4.3 12.6 1.0 CD2 C:HIS182 4.3 12.2 1.0 CE2 C:TYR312 4.3 15.4 1.0 N C:VAL181 4.4 10.3 1.0 CE1 C:HIS142 4.4 14.3 1.0 CG1 C:VAL181 4.4 12.6 1.0 N C:GLY310 4.4 12.6 1.0 CA C:HIS182 4.5 11.6 1.0 OH C:TYR312 4.5 15.3 1.0 NE2 C:HIS143 4.7 13.9 1.0 C C:ASP180 4.8 11.1 1.0 CA C:ASP180 4.8 10.9 1.0 C C:GLY310 4.9 13.8 1.0 C C:VAL181 4.9 10.6 1.0 CZ C:TYR312 5.0 13.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Hdac-Like Protein with Acetate Bound


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 A Hdac-Like Protein with Acetate Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1751 b:15.6 occ:0.40 OD2 D:ASP268 2.0 13.1 1.0 OD1 D:ASP180 2.1 12.0 1.0 O D:ACT1752 2.1 16.9 1.0 ND1 D:HIS182 2.2 14.4 1.0 OXT D:ACT1752 2.2 18.1 1.0 OD2 D:ASP180 2.4 15.6 1.0 CG D:ASP180 2.6 12.3 1.0 C D:ACT1752 2.6 19.1 1.0 CG D:ASP268 3.0 13.9 1.0 CE1 D:HIS182 3.0 14.0 1.0 CG D:HIS182 3.3 13.5 1.0 OD1 D:ASP268 3.4 13.5 1.0 CB D:HIS182 3.7 12.6 1.0 NE2 D:HIS142 4.0 15.2 1.0 N D:HIS182 4.0 11.0 1.0 CB D:ASP180 4.1 11.3 1.0 CH3 D:ACT1752 4.1 18.0 1.0 CA D:GLY310 4.1 13.2 1.0 NE2 D:HIS182 4.2 14.6 1.0 CB D:ASP268 4.2 11.5 1.0 CD2 D:HIS182 4.3 13.6 1.0 CE2 D:TYR312 4.3 15.0 1.0 CG1 D:VAL181 4.3 12.8 1.0 N D:VAL181 4.4 10.8 1.0 CE1 D:HIS142 4.4 15.0 1.0 N D:GLY310 4.4 12.2 1.0 OH D:TYR312 4.5 17.4 1.0 CA D:HIS182 4.5 12.0 1.0 NE2 D:HIS143 4.7 15.4 1.0 C D:ASP180 4.7 10.7 1.0 CA D:ASP180 4.8 10.7 1.0 C D:GLY310 4.9 13.3 1.0 CZ D:TYR312 4.9 16.0 1.0 C D:VAL181 4.9 11.7 1.0 N D:GLY311 5.0 14.6 1.0

T.K.Nielsen, C.Hildmann, A.Dickmanns, A.Schwienhorst, R.Ficner. Crystal Structure of A Bacterial Class 2 Histone Deacetylase Homologue J.Mol.Biol. V. 354 107 2005.
ISSN: ISSN 0022-2836
PubMed: 16242151
DOI: 10.1016/J.JMB.2005.09.065