Zinc in PDB 1poj: Isoaspartyl Dipeptidase with Bound Inhibitor

The structure of Isoaspartyl Dipeptidase with Bound Inhibitor, PDB code: 1poj 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)	26.00 / 3.30
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	119.137, 119.137, 138.152, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 28.6

The binding sites of Zinc atom in the Isoaspartyl Dipeptidase with Bound Inhibitor (pdb code 1poj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Isoaspartyl Dipeptidase with Bound Inhibitor, PDB code: 1poj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Isoaspartyl Dipeptidase with Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Isoaspartyl Dipeptidase with Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:52.0 occ:0.70 O1P A:AE1401 2.2 42.4 1.0 OQ1 A:KCX162 2.2 51.4 1.0 OD1 A:ASP285 2.4 38.5 1.0 NE2 A:HIS70 2.5 35.6 1.0 OQ2 A:KCX162 2.6 52.4 1.0 NE2 A:HIS68 2.7 31.6 1.0 CX A:KCX162 2.7 49.5 1.0 CE1 A:HIS70 3.2 35.9 1.0 CD2 A:HIS68 3.3 31.9 1.0 CG A:ASP285 3.4 37.6 1.0 P A:AE1401 3.5 46.4 1.0 CE1 A:HIS68 3.6 31.3 1.0 CD2 A:HIS70 3.6 35.3 1.0 ZN A:ZN602 3.7 50.1 0.7 NE2 A:HIS230 3.8 42.0 1.0 C2 A:AE1401 3.8 43.0 1.0 NZ A:KCX162 3.9 47.1 1.0 OD2 A:ASP285 3.9 38.7 1.0 O2P A:AE1401 3.9 43.4 1.0 CE1 A:HIS230 4.1 41.5 1.0 CD2 A:LEU103 4.2 33.8 1.0 C1 A:AE1401 4.3 43.3 1.0 ND1 A:HIS70 4.4 35.8 1.0 CG A:HIS68 4.4 32.2 1.0 ND1 A:HIS68 4.5 31.6 1.0 CB A:ASP285 4.5 35.6 1.0 CG A:HIS70 4.6 34.6 1.0 C8 A:AE1401 4.7 45.6 1.0 CA A:ASP285 4.9 34.4 1.0 CE A:KCX162 4.9 42.2 1.0 CG A:LEU103 5.0 34.2 1.0

Zinc binding site 2 out of 4 in the Isoaspartyl Dipeptidase with Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Isoaspartyl Dipeptidase with Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:50.1 occ:0.70 ND1 A:HIS201 1.9 41.3 1.0 O2P A:AE1401 2.0 43.4 1.0 OQ2 A:KCX162 2.5 52.4 1.0 NE2 A:HIS230 2.5 42.0 1.0 CE1 A:HIS201 2.8 42.5 1.0 CG A:HIS201 2.9 40.7 1.0 CD2 A:HIS230 2.9 40.7 1.0 CX A:KCX162 3.0 49.5 1.0 OQ1 A:KCX162 3.2 51.4 1.0 OH A:TYR137 3.2 46.9 1.0 P A:AE1401 3.3 46.4 1.0 CB A:HIS201 3.3 38.1 1.0 O1P A:AE1401 3.4 42.4 1.0 CE1 A:HIS230 3.7 41.5 1.0 ZN A:ZN601 3.7 52.0 0.7 CE2 A:TYR137 3.8 44.7 1.0 NE2 A:HIS201 3.8 42.3 1.0 CZ A:TYR137 3.8 45.1 1.0 CD2 A:HIS201 3.9 41.4 1.0 NZ A:KCX162 4.0 47.1 1.0 CA A:HIS201 4.1 36.0 1.0 CG A:HIS230 4.2 39.5 1.0 C8 A:AE1401 4.4 45.6 1.0 NE2 A:HIS68 4.5 31.6 1.0 ND1 A:HIS230 4.5 40.7 1.0 CE A:KCX162 4.6 42.2 1.0 C1 A:AE1401 4.6 43.3 1.0 C6 A:AE1401 4.7 48.1 1.0 C7 A:AE1401 4.7 49.9 1.0 C2 A:AE1401 4.9 43.0 1.0 O4 A:AE1401 5.0 51.2 1.0 CD2 A:TYR137 5.0 42.1 1.0 CG2 A:THR229 5.0 32.8 1.0 CE1 A:TYR137 5.0 44.3 1.0 C A:HIS201 5.0 36.6 1.0

Zinc binding site 3 out of 4 in the Isoaspartyl Dipeptidase with Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Isoaspartyl Dipeptidase with Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:46.0 occ:0.70 O1P B:AE1402 2.2 38.6 1.0 OQ1 B:KCX162 2.2 45.6 1.0 OD1 B:ASP285 2.4 37.3 1.0 NE2 B:HIS70 2.5 31.8 1.0 OQ2 B:KCX162 2.6 46.0 1.0 NE2 B:HIS68 2.7 31.9 1.0 CX B:KCX162 2.7 44.8 1.0 CE1 B:HIS70 3.2 31.6 1.0 CD2 B:HIS68 3.3 32.1 1.0 CG B:ASP285 3.4 36.8 1.0 P B:AE1402 3.5 40.1 1.0 CE1 B:HIS68 3.6 32.0 1.0 CD2 B:HIS70 3.6 31.9 1.0 ZN B:ZN604 3.7 41.4 0.7 NE2 B:HIS230 3.8 44.4 1.0 C2 B:AE1402 3.8 36.0 1.0 NZ B:KCX162 3.9 43.1 1.0 OD2 B:ASP285 3.9 37.1 1.0 O2P B:AE1402 3.9 38.3 1.0 CE1 B:HIS230 4.1 43.4 1.0 CD2 B:LEU103 4.2 25.2 1.0 C1 B:AE1402 4.3 37.6 1.0 ND1 B:HIS70 4.4 32.5 1.0 CG B:HIS68 4.4 32.0 1.0 ND1 B:HIS68 4.5 32.1 1.0 CB B:ASP285 4.5 35.2 1.0 CG B:HIS70 4.6 33.1 1.0 C8 B:AE1402 4.7 42.4 1.0 CA B:ASP285 4.9 34.8 1.0 CE B:KCX162 4.9 39.8 1.0 CG B:LEU103 5.0 27.1 1.0

Zinc binding site 4 out of 4 in the Isoaspartyl Dipeptidase with Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Isoaspartyl Dipeptidase with Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:41.4 occ:0.70 ND1 B:HIS201 1.9 35.0 1.0 O2P B:AE1402 2.0 38.3 1.0 OQ2 B:KCX162 2.5 46.0 1.0 NE2 B:HIS230 2.5 44.4 1.0 CE1 B:HIS201 2.8 34.9 1.0 CG B:HIS201 2.9 35.1 1.0 CD2 B:HIS230 2.9 43.0 1.0 CX B:KCX162 3.0 44.8 1.0 OQ1 B:KCX162 3.2 45.6 1.0 OH B:TYR137 3.2 39.3 1.0 P B:AE1402 3.3 40.1 1.0 CB B:HIS201 3.3 34.8 1.0 O1P B:AE1402 3.4 38.6 1.0 CE1 B:HIS230 3.7 43.4 1.0 ZN B:ZN603 3.7 46.0 0.7 CE2 B:TYR137 3.8 37.1 1.0 NE2 B:HIS201 3.8 34.4 1.0 CZ B:TYR137 3.8 37.2 1.0 CD2 B:HIS201 3.9 34.5 1.0 NZ B:KCX162 4.0 43.1 1.0 CA B:HIS201 4.1 35.0 1.0 CG B:HIS230 4.2 41.3 1.0 C8 B:AE1402 4.4 42.4 1.0 NE2 B:HIS68 4.5 31.9 1.0 ND1 B:HIS230 4.5 42.2 1.0 CE B:KCX162 4.6 39.8 1.0 C1 B:AE1402 4.6 37.6 1.0 C6 B:AE1402 4.7 45.2 1.0 C7 B:AE1402 4.7 46.2 1.0 C2 B:AE1402 4.9 36.0 1.0 O4 B:AE1402 5.0 46.6 1.0 CD2 B:TYR137 5.0 35.3 1.0 CG2 B:THR229 5.0 35.7 1.0 CE1 B:TYR137 5.0 36.9 1.0 C B:HIS201 5.0 35.6 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