Zinc in PDB 1zz3: Crystal Structure of A Hdac-Like Protein with Cypx Bound

The structure of Crystal Structure of A Hdac-Like Protein with Cypx Bound, PDB code: 1zz3 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)	44.77 / 1.76
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.098, 94.486, 122.632, 90.00, 104.27, 90.00
R / Rfree (%)	15.6 / 19.1

The structure of Crystal Structure of A Hdac-Like Protein with Cypx 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 Cypx Bound (pdb code 1zz3). 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 Cypx Bound, PDB code: 1zz3:
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 Cypx 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 Cypx Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1451 b:22.4 occ:0.50 OD2 A:ASP268 2.0 11.6 1.0 OAB A:3YP1452 2.0 25.3 1.0 OD1 A:ASP180 2.1 12.9 1.0 OAA A:3YP1452 2.2 15.7 1.0 ND1 A:HIS182 2.3 14.0 1.0 OD2 A:ASP180 2.3 13.7 1.0 CG A:ASP180 2.5 13.7 1.0 NAI A:3YP1452 2.7 14.4 1.0 CAJ A:3YP1452 2.8 2.0 1.0 CG A:ASP268 3.0 12.7 1.0 CE1 A:HIS182 3.1 15.1 1.0 CG A:HIS182 3.3 12.9 1.0 OD1 A:ASP268 3.4 12.3 1.0 CB A:HIS182 3.7 11.8 1.0 NE2 A:HIS142 4.0 16.6 1.0 N A:HIS182 4.0 11.5 1.0 CB A:ASP180 4.1 12.8 1.0 CA A:GLY310 4.1 12.8 1.0 CAE A:3YP1452 4.2 22.9 1.0 CB A:ASP268 4.3 11.6 1.0 CE2 A:TYR312 4.3 12.6 1.0 CG1 A:VAL181 4.3 11.9 1.0 NE2 A:HIS182 4.3 13.3 1.0 CAH A:3YP1452 4.4 28.2 1.0 N A:GLY310 4.4 12.7 1.0 N A:VAL181 4.4 10.8 1.0 CE1 A:HIS142 4.4 15.3 1.0 CD2 A:HIS182 4.4 13.6 1.0 OH A:TYR312 4.4 15.0 1.0 CA A:HIS182 4.5 12.5 1.0 C A:ASP180 4.8 12.2 1.0 NE2 A:HIS143 4.8 15.1 1.0 CA A:ASP180 4.8 12.9 1.0 C A:GLY310 4.8 12.7 1.0 N A:GLY311 4.9 12.2 1.0 CZ A:TYR312 4.9 11.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Hdac-Like Protein with Cypx 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 Cypx Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1551 b:19.2 occ:0.50 OD2 B:ASP268 2.0 9.5 1.0 OAB B:3YP1552 2.0 17.0 1.0 OD1 B:ASP180 2.1 10.0 1.0 OAA B:3YP1552 2.1 18.4 1.0 ND1 B:HIS182 2.2 12.9 1.0 OD2 B:ASP180 2.4 13.5 1.0 CG B:ASP180 2.5 10.2 1.0 NAI B:3YP1552 2.8 2.0 1.0 CAJ B:3YP1552 2.8 2.0 1.0 CG B:ASP268 3.1 11.5 1.0 CE1 B:HIS182 3.1 15.1 1.0 CG B:HIS182 3.3 10.1 1.0 OD1 B:ASP268 3.5 11.1 1.0 CB B:HIS182 3.6 9.7 1.0 NE2 B:HIS142 3.9 12.6 1.0 N B:HIS182 4.0 10.9 1.0 CB B:ASP180 4.0 10.4 1.0 CA B:GLY310 4.1 10.7 1.0 CAE B:3YP1552 4.2 24.9 1.0 NE2 B:HIS182 4.3 12.3 1.0 CE1 B:HIS142 4.3 9.6 1.0 CB B:ASP268 4.3 10.5 1.0 CE1 B:TYR312 4.4 11.8 1.0 CD2 B:HIS182 4.4 13.4 1.0 CG1 B:VAL181 4.4 8.1 1.0 N B:VAL181 4.4 9.3 1.0 CAG B:3YP1552 4.4 41.3 1.0 OH B:TYR312 4.4 15.4 1.0 N B:GLY310 4.4 10.0 1.0 CA B:HIS182 4.5 10.3 1.0 NE2 B:HIS143 4.6 17.0 1.0 C B:ASP180 4.7 10.2 1.0 CA B:ASP180 4.8 10.2 1.0 C B:GLY310 4.8 11.8 1.0 CAH B:3YP1552 4.9 31.9 1.0 N B:GLY311 4.9 12.1 1.0 CZ B:TYR312 4.9 12.8 1.0 C B:VAL181 5.0 9.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Hdac-Like Protein with Cypx 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 Cypx Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1651 b:19.8 occ:0.50 OD2 C:ASP268 2.0 9.1 1.0 OD1 C:ASP180 2.1 11.1 1.0 OAA C:3YP1652 2.1 21.0 1.0 OAB C:3YP1652 2.1 16.0 1.0 ND1 C:HIS182 2.2 11.0 1.0 OD2 C:ASP180 2.4 11.8 1.0 CG C:ASP180 2.5 9.9 1.0 CAJ C:3YP1652 2.8 17.9 1.0 NAI C:3YP1652 2.8 2.0 1.0 CG C:ASP268 3.0 11.3 1.0 CE1 C:HIS182 3.1 11.7 1.0 CG C:HIS182 3.2 11.6 1.0 OD1 C:ASP268 3.4 12.2 1.0 CB C:HIS182 3.6 11.3 1.0 N C:HIS182 4.0 10.8 1.0 NE2 C:HIS142 4.0 14.3 1.0 CB C:ASP180 4.0 11.9 1.0 CA C:GLY310 4.2 10.1 1.0 CAE C:3YP1652 4.2 32.1 1.0 NE2 C:HIS182 4.2 10.0 1.0 CB C:ASP268 4.3 10.4 1.0 N C:VAL181 4.3 10.3 1.0 CD2 C:HIS182 4.3 10.9 1.0 CG1 C:VAL181 4.3 10.4 1.0 CE1 C:HIS142 4.3 11.8 1.0 CE2 C:TYR312 4.4 13.2 1.0 CA C:HIS182 4.4 11.2 1.0 N C:GLY310 4.4 9.3 1.0 CAH C:3YP1652 4.6 38.2 1.0 OH C:TYR312 4.6 13.9 1.0 C C:ASP180 4.7 10.9 1.0 CA C:ASP180 4.7 11.3 1.0 NE2 C:HIS143 4.8 13.1 1.0 C C:GLY310 4.8 11.6 1.0 N C:GLY311 4.9 11.6 1.0 CAK C:3YP1652 4.9 42.5 1.0 C C:VAL181 4.9 9.9 1.0 CZ C:TYR312 5.0 14.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Hdac-Like Protein with Cypx 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 Cypx Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1751 b:20.9 occ:0.50 OAB D:3YP1752 1.7 27.3 1.0 OD2 D:ASP268 2.0 14.0 1.0 OD1 D:ASP180 2.1 10.4 1.0 OAA D:3YP1752 2.1 18.5 1.0 ND1 D:HIS182 2.3 16.8 1.0 OD2 D:ASP180 2.3 12.1 1.0 CG D:ASP180 2.5 13.0 1.0 NAI D:3YP1752 2.5 18.3 1.0 CAJ D:3YP1752 2.7 2.0 1.0 CG D:ASP268 3.0 13.8 1.0 CE1 D:HIS182 3.1 15.9 1.0 CG D:HIS182 3.4 13.2 1.0 OD1 D:ASP268 3.4 12.8 1.0 CB D:HIS182 3.8 12.6 1.0 CA D:GLY310 4.0 12.9 1.0 NE2 D:HIS142 4.0 15.1 1.0 CB D:ASP180 4.0 11.2 1.0 CAE D:3YP1752 4.1 21.4 1.0 N D:HIS182 4.2 12.6 1.0 CE1 D:TYR312 4.3 14.8 1.0 CB D:ASP268 4.3 12.8 1.0 NE2 D:HIS182 4.3 16.2 1.0 N D:GLY310 4.3 12.1 1.0 CE1 D:HIS142 4.3 14.0 1.0 N D:VAL181 4.4 10.7 1.0 CD2 D:HIS182 4.4 15.5 1.0 OH D:TYR312 4.4 13.5 1.0 CG1 D:VAL181 4.4 13.9 1.0 CA D:HIS182 4.6 13.0 1.0 C D:GLY310 4.7 13.0 1.0 CAG D:3YP1752 4.7 36.6 1.0 C D:ASP180 4.8 11.8 1.0 NE2 D:HIS143 4.8 14.4 1.0 N D:GLY311 4.8 13.5 1.0 CA D:ASP180 4.8 11.7 1.0 CAH D:3YP1752 4.8 28.0 1.0 CZ D:TYR312 4.8 13.5 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