Zinc in PDB 1zz1: Crystal Structure of A Hdac-Like Protein with Saha Bound

The structure of Crystal Structure of A Hdac-Like Protein with Saha Bound, PDB code: 1zz1 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)	38.38 / 1.57
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.606, 94.716, 123.924, 90.00, 104.75, 90.00
R / Rfree (%)	17.2 / 20.1

The structure of Crystal Structure of A Hdac-Like Protein with Saha 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 Saha Bound (pdb code 1zz1). 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 Saha Bound, PDB code: 1zz1:
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 Saha 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 Saha Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2451 b:21.4 occ:0.50 O1 A:SHH2452 1.9 6.9 0.5 OD1 A:ASP180 2.0 13.8 1.0 OD2 A:ASP268 2.1 12.8 1.0 O2 A:SHH2452 2.2 7.8 0.5 ND1 A:HIS182 2.2 14.9 1.0 OD2 A:ASP180 2.2 15.2 1.0 CG A:ASP180 2.4 14.0 1.0 C1 A:SHH2452 2.7 7.9 0.5 N1 A:SHH2452 2.7 7.0 0.5 CE1 A:HIS182 3.1 14.2 1.0 CG A:ASP268 3.1 12.8 1.0 CG A:HIS182 3.3 13.8 1.0 OD1 A:ASP268 3.5 13.1 1.0 CB A:HIS182 3.7 13.7 1.0 NE2 A:HIS142 3.9 15.4 1.0 CB A:ASP180 4.0 13.7 1.0 N A:HIS182 4.0 13.1 1.0 CA A:GLY310 4.1 11.9 1.0 C2 A:SHH2452 4.1 8.7 0.5 NE2 A:HIS182 4.3 13.6 1.0 CE1 A:HIS142 4.3 13.3 1.0 N A:VAL181 4.3 12.4 1.0 CD2 A:HIS182 4.4 13.5 1.0 N A:GLY310 4.4 11.9 1.0 CE2 A:TYR312 4.4 12.6 1.0 OH A:TYR312 4.4 14.5 1.0 CB A:ASP268 4.4 12.0 1.0 CA A:HIS182 4.4 12.8 1.0 CG1 A:VAL181 4.5 13.4 1.0 C3 A:SHH2452 4.5 13.3 0.5 C A:ASP180 4.7 13.0 1.0 CA A:ASP180 4.7 13.0 1.0 NE2 A:HIS143 4.8 21.2 1.0 C A:GLY310 4.9 11.6 1.0 CZ A:TYR312 4.9 13.3 1.0 C A:VAL181 4.9 12.2 1.0 N A:GLY311 5.0 11.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Hdac-Like Protein with Saha 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 Saha Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2551 b:15.0 occ:0.50 OD2 B:ASP268 2.0 8.6 1.0 O1 B:SHH2552 2.0 2.4 0.5 OD1 B:ASP180 2.0 8.2 1.0 O2 B:SHH2552 2.1 6.5 0.5 ND1 B:HIS182 2.2 9.7 1.0 OD2 B:ASP180 2.3 9.7 1.0 CG B:ASP180 2.5 8.8 1.0 C1 B:SHH2552 2.6 8.7 0.5 N1 B:SHH2552 2.7 2.0 0.5 CG B:ASP268 3.0 9.2 1.0 CE1 B:HIS182 3.2 10.8 1.0 CG B:HIS182 3.2 7.3 1.0 OD1 B:ASP268 3.5 9.4 1.0 CB B:HIS182 3.5 8.8 1.0 NE2 B:HIS142 3.9 10.5 1.0 C2 B:SHH2552 4.0 10.7 0.5 N B:HIS182 4.0 8.5 1.0 CB B:ASP180 4.0 8.3 1.0 CA B:GLY310 4.2 8.6 1.0 NE2 B:HIS182 4.3 9.2 1.0 CE1 B:TYR312 4.3 8.9 1.0 CB B:ASP268 4.3 8.6 1.0 CD2 B:HIS182 4.4 9.3 1.0 CE1 B:HIS142 4.4 10.3 1.0 OH B:TYR312 4.4 11.1 1.0 CA B:HIS182 4.4 8.4 1.0 N B:VAL181 4.4 8.1 1.0 N B:GLY310 4.5 7.8 1.0 CG1 B:VAL181 4.5 8.2 1.0 C3 B:SHH2552 4.6 16.4 0.5 NE2 B:HIS143 4.7 13.2 1.0 CA B:ASP180 4.8 8.5 1.0 C B:ASP180 4.8 8.7 1.0 C B:GLY310 4.9 9.1 1.0 CZ B:TYR312 4.9 11.9 1.0 N B:GLY311 4.9 7.8 1.0 C B:VAL181 5.0 8.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Hdac-Like Protein with Saha 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 Saha Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2651 b:14.4 occ:0.50 OD2 C:ASP268 2.0 8.3 1.0 O1 C:SHH2652 2.0 2.0 0.5 O2 C:SHH2652 2.1 5.3 0.5 OD1 C:ASP180 2.1 8.4 1.0 ND1 C:HIS182 2.2 10.3 1.0 OD2 C:ASP180 2.4 9.0 1.0 CG C:ASP180 2.6 8.5 1.0 C1 C:SHH2652 2.7 8.0 0.5 N1 C:SHH2652 2.7 4.0 0.5 CG C:ASP268 3.0 8.7 1.0 CE1 C:HIS182 3.0 9.1 1.0 CG C:HIS182 3.2 8.5 1.0 OD1 C:ASP268 3.5 8.1 1.0 CB C:HIS182 3.6 8.3 1.0 N C:HIS182 4.0 7.4 1.0 NE2 C:HIS142 4.0 10.7 1.0 CB C:ASP180 4.1 8.5 1.0 C2 C:SHH2652 4.1 7.3 0.5 CA C:GLY310 4.1 7.5 1.0 NE2 C:HIS182 4.2 10.4 1.0 CB C:ASP268 4.3 8.6 1.0 CD2 C:HIS182 4.3 9.2 1.0 CE2 C:TYR312 4.3 8.8 1.0 OH C:TYR312 4.4 12.6 1.0 CE1 C:HIS142 4.4 8.6 1.0 N C:VAL181 4.4 7.3 1.0 N C:GLY310 4.4 6.3 1.0 CG1 C:VAL181 4.4 7.7 1.0 CA C:HIS182 4.5 8.2 1.0 C3 C:SHH2652 4.6 9.5 0.5 CA C:ASP180 4.8 7.7 1.0 C C:ASP180 4.8 7.5 1.0 C C:GLY310 4.8 7.9 1.0 CZ C:TYR312 4.9 10.3 1.0 N C:GLY311 4.9 8.0 1.0 NE2 C:HIS143 4.9 13.5 1.0 C C:VAL181 5.0 8.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Hdac-Like Protein with Saha 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 Saha Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2751 b:17.2 occ:0.50 O1 D:SHH2752 2.0 5.7 0.5 OD2 D:ASP268 2.0 13.0 1.0 OD1 D:ASP180 2.0 10.1 1.0 O2 D:SHH2752 2.1 7.8 0.5 ND1 D:HIS182 2.2 11.6 1.0 OD2 D:ASP180 2.4 11.3 1.0 CG D:ASP180 2.5 11.2 1.0 C1 D:SHH2752 2.7 7.1 0.5 N1 D:SHH2752 2.7 6.4 0.5 CE1 D:HIS182 3.1 13.6 1.0 CG D:ASP268 3.1 10.6 1.0 CG D:HIS182 3.3 11.9 1.0 OD1 D:ASP268 3.5 10.0 1.0 CB D:HIS182 3.6 12.2 1.0 NE2 D:HIS142 3.9 12.4 1.0 CB D:ASP180 4.0 10.3 1.0 N D:HIS182 4.0 11.5 1.0 C2 D:SHH2752 4.1 11.2 0.5 CA D:GLY310 4.2 9.9 1.0 NE2 D:HIS182 4.3 13.1 1.0 CE1 D:HIS142 4.3 9.3 1.0 CE1 D:TYR312 4.4 12.8 1.0 CD2 D:HIS182 4.4 13.2 1.0 CB D:ASP268 4.4 11.0 1.0 OH D:TYR312 4.4 17.1 1.0 N D:GLY310 4.4 10.0 1.0 N D:VAL181 4.5 10.5 1.0 CA D:HIS182 4.5 11.8 1.0 CG1 D:VAL181 4.6 12.3 1.0 C3 D:SHH2752 4.6 13.5 0.5 CA D:ASP180 4.8 10.5 1.0 C D:ASP180 4.8 10.9 1.0 NE2 D:HIS143 4.8 15.1 1.0 C D:GLY310 4.9 10.7 1.0 CZ D:TYR312 4.9 11.1 1.0 N D:GLY311 5.0 10.4 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