Zinc in PDB 1pok: Crystal Structure of Isoaspartyl Dipeptidase

The structure of Crystal Structure of Isoaspartyl Dipeptidase, PDB code: 1pok was solved by D.Jozic, J.T.Kaiser, R.Huber, W.Bode, K.Maskos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.70
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.475, 117.475, 137.955, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 26.6

The binding sites of Zinc atom in the Crystal Structure of Isoaspartyl Dipeptidase (pdb code 1pok). 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 Isoaspartyl Dipeptidase, PDB code: 1pok:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase


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 Isoaspartyl Dipeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:77.3 occ:0.70 OQ2 B:KCX162 2.0 60.5 1.0 OD1 B:ASP285 2.2 41.5 1.0 NE2 B:HIS70 2.6 30.8 1.0 ZN B:ZN604 2.7 66.8 1.0 NE2 B:HIS68 3.0 33.1 1.0 CX B:KCX162 3.1 59.5 1.0 CG B:ASP285 3.1 40.9 1.0 O B:ASN401 3.1 68.7 1.0 CE1 B:HIS70 3.1 29.9 1.0 OQ1 B:KCX162 3.4 60.8 1.0 OD2 B:ASP285 3.4 40.9 1.0 CD2 B:HIS68 3.5 32.1 1.0 O1 B:SO4391 3.6 13.2 0.4 CD2 B:HIS70 3.9 29.8 1.0 CE1 B:HIS230 4.1 52.8 1.0 C B:ASN401 4.1 69.0 1.0 NE2 B:HIS230 4.2 52.5 1.0 CE1 B:HIS68 4.2 33.3 1.0 NZ B:KCX162 4.3 56.0 1.0 CB B:ASP285 4.4 38.2 1.0 ND1 B:HIS70 4.4 29.0 1.0 OXT B:ASN401 4.6 70.8 1.0 OH B:TYR137 4.6 47.6 1.0 S B:SO4391 4.8 15.8 0.4 O4 B:SO4391 4.8 14.1 0.4 CG B:HIS70 4.8 28.6 1.0 CG B:HIS68 4.8 31.6 1.0 CA B:ASP285 5.0 38.3 1.0 ND1 B:HIS201 5.0 45.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase


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 Isoaspartyl Dipeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:66.8 occ:1.00 OQ1 B:KCX162 2.2 60.8 1.0 ND1 B:HIS201 2.3 45.5 1.0 ZN B:ZN603 2.7 77.3 0.7 CX B:KCX162 2.9 59.5 1.0 OQ2 B:KCX162 2.9 60.5 1.0 O B:ASN401 3.0 68.7 1.0 CE1 B:HIS201 3.1 45.8 1.0 CE1 B:HIS230 3.2 52.8 1.0 OH B:TYR137 3.3 47.6 1.0 CG B:HIS201 3.3 43.2 1.0 NE2 B:HIS230 3.4 52.5 1.0 CB B:HIS201 3.8 40.1 1.0 NE2 B:HIS68 3.8 33.1 1.0 CE2 B:TYR137 3.8 46.7 1.0 ND1 B:HIS230 3.9 52.1 1.0 CZ B:TYR137 4.0 47.6 1.0 C B:ASN401 4.0 69.0 1.0 NZ B:KCX162 4.1 56.0 1.0 NE2 B:HIS201 4.2 44.9 1.0 N B:ASN401 4.2 67.1 1.0 CD2 B:HIS230 4.3 50.5 1.0 CD2 B:HIS201 4.3 44.2 1.0 OD1 B:ASP285 4.4 41.5 1.0 CA B:ASN401 4.5 68.0 1.0 CE1 B:HIS68 4.5 33.3 1.0 CG B:HIS230 4.5 49.2 1.0 O1 B:SO4391 4.6 13.2 0.4 CA B:HIS201 4.6 37.5 1.0 OD2 B:ASP285 4.6 40.9 1.0 CG B:ASP285 4.8 40.9 1.0 CE B:KCX162 4.8 50.8 1.0 CD2 B:HIS68 4.9 32.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase


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 Isoaspartyl Dipeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:42.6 occ:0.70 OQ2 A:KCX162 2.1 46.0 1.0 NE2 A:HIS70 2.4 25.3 1.0 OD1 A:ASP285 2.6 34.1 1.0 NE2 A:HIS68 2.7 22.9 1.0 ZN A:ZN602 3.0 42.9 0.7 CX A:KCX162 3.1 43.7 1.0 CG A:ASP285 3.2 36.0 1.0 OD2 A:ASP285 3.3 34.5 1.0 CE1 A:HIS70 3.3 26.1 1.0 CD2 A:HIS68 3.4 25.5 1.0 OQ1 A:KCX162 3.4 41.5 1.0 CD2 A:HIS70 3.4 24.9 1.0 CE1 A:HIS68 3.6 23.6 1.0 O3 A:SO4391 3.8 20.5 0.4 O A:ASN400 4.0 62.7 1.0 CE1 A:HIS230 4.2 41.0 1.0 NE2 A:HIS230 4.2 39.5 1.0 NZ A:KCX162 4.2 41.2 1.0 CD2 A:LEU103 4.4 22.3 1.0 CG A:HIS68 4.5 25.9 1.0 ND1 A:HIS70 4.5 25.9 1.0 CB A:ASP285 4.5 36.2 1.0 ND1 A:HIS68 4.5 25.1 1.0 CG A:HIS70 4.6 24.8 1.0 CA A:ASP285 4.7 37.8 1.0 S A:SO4391 4.8 21.7 0.4 O2 A:SO4391 4.9 19.6 0.4 ND1 A:HIS201 5.0 30.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase


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 Isoaspartyl Dipeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:42.9 occ:0.70 OQ1 A:KCX162 2.0 41.5 1.0 ND1 A:HIS201 2.0 30.2 1.0 CE1 A:HIS230 2.4 41.0 1.0 CE1 A:HIS201 2.5 30.1 1.0 CX A:KCX162 2.8 43.7 1.0 OQ2 A:KCX162 2.8 46.0 1.0 ZN A:ZN601 3.0 42.6 0.7 O A:ASN400 3.2 62.7 1.0 CG A:HIS201 3.3 30.9 1.0 OH A:TYR137 3.3 43.4 1.0 ND1 A:HIS230 3.3 40.4 1.0 NE2 A:HIS230 3.3 39.5 1.0 NE2 A:HIS201 3.7 32.0 1.0 NE2 A:HIS68 3.9 22.9 1.0 OD2 A:ASP285 3.9 34.5 1.0 CE1 A:HIS68 4.0 23.6 1.0 CB A:HIS201 4.0 30.3 1.0 NZ A:KCX162 4.0 41.2 1.0 CD2 A:HIS201 4.1 30.2 1.0 CZ A:TYR137 4.1 41.3 1.0 CE2 A:TYR137 4.1 40.7 1.0 C A:ASN400 4.2 62.1 1.0 N A:ASN400 4.3 60.7 1.0 CG A:HIS230 4.5 39.2 1.0 CD2 A:HIS230 4.5 40.0 1.0 CG A:ASP285 4.7 36.0 1.0 OD1 A:ASP285 4.7 34.1 1.0 CE A:KCX162 4.8 37.0 1.0 CA A:HIS201 4.9 30.4 1.0 CA A:ASN400 4.9 60.4 1.0

D.Jozic, J.T.Kaiser, R.Huber, W.Bode, K.Maskos. X-Ray Structure of Isoaspartyl Dipeptidase From E.Coli: A Dinuclear Zinc Peptidase Evolved From Amidohydrolases. J.Mol.Biol. V. 332 243 2003.
ISSN: ISSN 0022-2836
PubMed: 12946361
DOI: 10.1016/S0022-2836(03)00845-3