Zinc in PDB 1onx: Crystal Structure of Isoaspartyl Dipeptidase From Escherichia Coli Complexed with Aspartate

The structure of Crystal Structure of Isoaspartyl Dipeptidase From Escherichia Coli Complexed with Aspartate, PDB code: 1onx was solved by J.B.Thoden, R.Marti-Arbona, F.M.Raushel, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.10
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	119.100, 119.100, 138.100, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Zinc atom in the Crystal Structure of Isoaspartyl Dipeptidase From Escherichia Coli Complexed with Aspartate (pdb code 1onx). 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 From Escherichia Coli Complexed with Aspartate, PDB code: 1onx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase From Escherichia Coli Complexed with Aspartate


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 From Escherichia Coli Complexed with Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:51.6 occ:1.00 OD1 A:ASP285 2.1 33.2 1.0 OQ1 A:KCX162 2.2 35.1 1.0 NE2 A:HIS70 2.3 17.3 1.0 NE2 A:HIS68 2.4 22.6 1.0 OD1 A:ASP450 2.8 87.1 1.0 CG A:ASP285 3.0 47.3 1.0 CG A:ASP450 3.0 36.8 1.0 OD2 A:ASP450 3.0 70.8 1.0 CE1 A:HIS70 3.0 14.7 1.0 CD2 A:HIS68 3.2 25.6 1.0 CX A:KCX162 3.2 42.2 1.0 OD2 A:ASP285 3.4 42.9 1.0 CD2 A:HIS70 3.4 18.9 1.0 CE1 A:HIS68 3.5 26.8 1.0 OQ2 A:KCX162 3.7 71.5 1.0 ZN A:ZN402 3.8 52.4 1.0 CB A:ASP450 4.0 40.9 1.0 CD1 A:LEU103 4.1 26.9 1.0 CB A:ASP285 4.2 31.7 1.0 ND1 A:HIS70 4.2 19.9 1.0 CE1 A:HIS230 4.3 43.1 1.0 CA A:ASP450 4.3 34.3 1.0 CG A:HIS70 4.4 16.1 1.0 NE2 A:HIS230 4.4 54.1 1.0 NZ A:KCX162 4.4 50.8 1.0 CG A:HIS68 4.5 23.4 1.0 ND1 A:HIS68 4.6 21.4 1.0 CA A:ASP285 4.7 29.4 1.0 C A:ASP450 5.0 40.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase From Escherichia Coli Complexed with Aspartate


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 From Escherichia Coli Complexed with Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:52.4 occ:1.00 ND1 A:HIS201 1.9 36.2 1.0 NE2 A:HIS230 2.2 54.1 1.0 OD2 A:ASP450 2.2 70.8 1.0 CE1 A:HIS201 2.8 29.0 1.0 OQ2 A:KCX162 2.8 71.5 1.0 CG A:ASP450 2.9 36.8 1.0 CE1 A:HIS230 3.0 43.1 1.0 CG A:HIS201 3.0 22.5 1.0 CD2 A:HIS230 3.1 50.5 1.0 OD1 A:ASP450 3.2 87.1 1.0 OQ1 A:KCX162 3.2 35.1 1.0 CX A:KCX162 3.3 42.2 1.0 CB A:HIS201 3.5 21.5 1.0 OH A:TYR137 3.5 28.9 1.0 ZN A:ZN401 3.8 51.6 1.0 NE2 A:HIS201 3.9 33.6 1.0 ND1 A:HIS230 4.0 34.9 1.0 CG A:HIS230 4.0 39.0 1.0 CD2 A:HIS201 4.1 37.0 1.0 CE1 A:TYR137 4.1 22.7 1.0 CZ A:TYR137 4.2 25.2 1.0 CB A:ASP450 4.2 40.9 1.0 O A:HOH495 4.3 55.6 1.0 NZ A:KCX162 4.4 50.8 1.0 CA A:HIS201 4.4 31.9 1.0 NE2 A:HIS68 4.4 22.6 1.0 CE1 A:HIS68 4.5 26.8 1.0 OD2 A:ASP285 4.7 42.9 1.0 CE A:KCX162 5.0 53.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase From Escherichia Coli Complexed with Aspartate


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 From Escherichia Coli Complexed with Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:46.5 occ:1.00 OD1 B:ASP285 2.2 28.9 1.0 OQ1 B:KCX162 2.2 27.7 1.0 NE2 B:HIS70 2.3 27.8 1.0 NE2 B:HIS68 2.4 21.4 1.0 OD2 B:ASP550 2.9 51.8 1.0 CE1 B:HIS70 3.0 21.1 1.0 CD2 B:HIS68 3.1 19.6 1.0 CG B:ASP285 3.1 27.6 1.0 CG B:ASP550 3.2 47.3 1.0 CX B:KCX162 3.2 37.2 1.0 CD2 B:HIS70 3.4 30.5 1.0 OD1 B:ASP550 3.4 38.4 1.0 OD2 B:ASP285 3.5 31.8 1.0 OQ2 B:KCX162 3.6 45.7 1.0 CE1 B:HIS68 3.6 25.7 1.0 ZN B:ZN502 3.7 45.2 1.0 CB B:ASP550 4.0 40.6 1.0 ND1 B:HIS70 4.2 19.2 1.0 CD1 B:LEU103 4.3 24.4 1.0 NZ B:KCX162 4.3 52.9 1.0 CE1 B:HIS230 4.3 33.5 1.0 CG B:HIS68 4.3 22.9 1.0 CB B:ASP285 4.4 14.6 1.0 CG B:HIS70 4.4 22.3 1.0 CA B:ASP550 4.4 0.0 1.0 NE2 B:HIS230 4.4 31.1 1.0 ND1 B:HIS68 4.6 26.6 1.0 CA B:ASP285 4.7 26.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase From Escherichia Coli Complexed with Aspartate


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 From Escherichia Coli Complexed with Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:45.2 occ:1.00 ND1 B:HIS201 1.9 23.4 1.0 OD1 B:ASP550 2.0 38.4 1.0 NE2 B:HIS230 2.1 31.1 1.0 OQ2 B:KCX162 2.2 45.7 1.0 CE1 B:HIS201 2.9 23.0 1.0 CX B:KCX162 2.9 37.2 1.0 CG B:HIS201 3.0 25.1 1.0 CD2 B:HIS230 3.0 34.9 1.0 CG B:ASP550 3.0 47.3 1.0 OQ1 B:KCX162 3.1 27.7 1.0 CE1 B:HIS230 3.2 33.5 1.0 CB B:HIS201 3.3 23.9 1.0 OH B:TYR137 3.5 24.5 1.0 OD2 B:ASP550 3.6 51.8 1.0 ZN B:ZN501 3.7 46.5 1.0 NE2 B:HIS201 4.0 24.8 1.0 CE1 B:TYR137 4.1 29.2 1.0 CD2 B:HIS201 4.1 25.4 1.0 CA B:HIS201 4.2 24.2 1.0 CG B:HIS230 4.2 40.7 1.0 CZ B:TYR137 4.2 40.1 1.0 ND1 B:HIS230 4.2 35.5 1.0 CB B:ASP550 4.3 40.6 1.0 NZ B:KCX162 4.3 52.9 1.0 NE2 B:HIS68 4.3 21.4 1.0 O B:HOH494 4.4 40.8 1.0 CE1 B:HIS68 4.5 25.7 1.0 OD2 B:ASP285 4.7 31.8 1.0 CE B:KCX162 4.7 41.4 1.0 C B:HIS201 4.9 30.9 1.0

J.B.Thoden, R.Marti-Arbona, F.M.Raushel, H.M.Holden. High Resolution X-Ray Structure of Isoaspartyl Dipeptidase From Escherichia Coli Biochemistry V. 42 4874 2003.
ISSN: ISSN 0006-2960
PubMed: 12718528
DOI: 10.1021/BI034233P