Zinc in PDB 1onw: Crystal Structure of Isoaspartyl Dipeptidase From E. Coli

The structure of Crystal Structure of Isoaspartyl Dipeptidase From E. Coli, PDB code: 1onw 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 / 1.65
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	116.700, 116.700, 138.500, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Isoaspartyl Dipeptidase From E. Coli also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Isoaspartyl Dipeptidase From E. Coli (pdb code 1onw). 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 E. Coli, PDB code: 1onw:
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 E. Coli


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 E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn800 b:29.4 occ:1.00 OQ2 A:KCX162 2.1 19.2 1.0 NE2 A:HIS70 2.1 17.6 1.0 O A:HOH841 2.1 34.8 1.0 NE2 A:HIS68 2.2 12.3 1.0 OD1 A:ASP285 2.4 20.0 1.0 CE1 A:HIS70 2.8 17.7 1.0 CX A:KCX162 3.0 36.1 1.0 CD2 A:HIS68 3.0 15.1 1.0 CG A:ASP285 3.1 23.5 1.0 CE1 A:HIS68 3.2 13.6 1.0 CD2 A:HIS70 3.3 16.7 1.0 OQ1 A:KCX162 3.4 25.4 1.0 ZN A:ZN801 3.4 31.4 1.0 OD2 A:ASP285 3.4 31.4 1.0 O A:HOH1017 3.6 29.6 1.0 CD1 A:LEU103 4.0 24.4 1.0 ND1 A:HIS70 4.1 14.4 1.0 NZ A:KCX162 4.1 13.7 1.0 CG A:HIS68 4.2 14.9 1.0 CG A:HIS70 4.3 12.9 1.0 ND1 A:HIS68 4.3 18.5 1.0 O A:HOH1133 4.3 53.0 1.0 NE2 A:HIS230 4.4 21.1 1.0 CB A:ASP285 4.4 16.6 1.0 CE1 A:HIS230 4.5 24.8 1.0 CA A:ASP285 4.8 16.2 1.0 O A:HOH821 4.9 21.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase From E. Coli


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 E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:31.4 occ:1.00 ND1 A:HIS201 2.1 22.2 1.0 NE2 A:HIS230 2.1 21.1 1.0 OQ1 A:KCX162 2.1 25.4 1.0 O A:HOH841 2.2 34.8 1.0 CX A:KCX162 2.9 36.1 1.0 CE1 A:HIS201 3.0 17.9 1.0 CD2 A:HIS230 3.0 25.0 1.0 CG A:HIS201 3.1 18.1 1.0 CE1 A:HIS230 3.1 24.8 1.0 OQ2 A:KCX162 3.2 19.2 1.0 ZN A:ZN800 3.4 29.4 1.0 OH A:TYR137 3.4 38.8 1.0 CB A:HIS201 3.5 18.2 1.0 O A:HOH1133 3.5 53.0 1.0 O A:HOH1017 3.8 29.6 1.0 CE1 A:HIS68 3.9 13.6 1.0 CE1 A:TYR137 4.0 19.2 1.0 NE2 A:HIS68 4.0 12.3 1.0 CZ A:TYR137 4.1 27.6 1.0 NE2 A:HIS201 4.1 22.6 1.0 CG A:HIS230 4.1 27.6 1.0 ND1 A:HIS230 4.2 21.5 1.0 CD2 A:HIS201 4.2 25.0 1.0 O A:HOH890 4.3 43.4 1.0 NZ A:KCX162 4.3 13.7 1.0 OD2 A:ASP285 4.3 31.4 1.0 CA A:HIS201 4.3 15.3 1.0 CE A:KCX162 4.6 19.9 1.0 O A:HOH981 4.8 50.2 1.0 O A:HOH1018 4.8 45.0 1.0 CG A:ASP285 4.9 23.5 1.0 OD1 A:ASP285 4.9 20.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase From E. Coli


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 E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn802 b:25.1 occ:1.00 O B:HOH864 1.9 26.1 1.0 OQ2 B:KCX162 2.1 16.1 1.0 NE2 B:HIS68 2.1 13.8 1.0 NE2 B:HIS70 2.2 12.8 1.0 OD1 B:ASP285 2.2 17.4 1.0 CX B:KCX162 2.9 29.2 1.0 CE1 B:HIS70 3.0 14.7 1.0 CG B:ASP285 3.0 23.4 1.0 CD2 B:HIS68 3.1 23.3 1.0 CE1 B:HIS68 3.1 14.8 1.0 OQ1 B:KCX162 3.2 25.2 1.0 CD2 B:HIS70 3.3 12.4 1.0 O B:HOH844 3.3 28.1 1.0 OD2 B:ASP285 3.4 25.9 1.0 ZN B:ZN803 3.4 28.5 1.0 O B:HOH1002 3.9 35.4 1.0 CD1 B:LEU103 4.0 13.4 1.0 NZ B:KCX162 4.1 15.8 1.0 ND1 B:HIS70 4.2 13.7 1.0 ND1 B:HIS68 4.3 14.2 1.0 CG B:HIS68 4.3 16.3 1.0 CG B:HIS70 4.3 10.7 1.0 CE1 B:HIS230 4.3 17.2 1.0 CB B:ASP285 4.4 14.0 1.0 NE2 B:HIS230 4.5 17.8 1.0 CA B:ASP285 4.7 19.4 1.0 O B:HOH827 4.8 21.8 1.0 O B:HOH1054 4.9 47.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Isoaspartyl Dipeptidase From E. Coli


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 E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn803 b:28.5 occ:1.00 ND1 B:HIS201 2.0 16.4 1.0 OQ1 B:KCX162 2.1 25.2 1.0 O B:HOH864 2.1 26.1 1.0 NE2 B:HIS230 2.1 17.8 1.0 CX B:KCX162 2.9 29.2 1.0 CE1 B:HIS230 3.0 17.2 1.0 CE1 B:HIS201 3.0 18.7 1.0 CG B:HIS201 3.1 20.0 1.0 CD2 B:HIS230 3.1 15.7 1.0 OQ2 B:KCX162 3.3 16.1 1.0 CB B:HIS201 3.4 15.9 1.0 ZN B:ZN802 3.4 25.1 1.0 O B:HOH844 3.4 28.1 1.0 OH B:TYR137 3.4 32.2 1.0 CE1 B:HIS68 4.0 14.8 1.0 CE1 B:TYR137 4.0 13.4 1.0 ND1 B:HIS230 4.1 19.8 1.0 NE2 B:HIS68 4.1 13.8 1.0 CZ B:TYR137 4.1 23.9 1.0 NE2 B:HIS201 4.2 17.5 1.0 CG B:HIS230 4.2 19.5 1.0 CD2 B:HIS201 4.2 13.4 1.0 OD2 B:ASP285 4.2 25.9 1.0 CA B:HIS201 4.2 14.2 1.0 NZ B:KCX162 4.2 15.8 1.0 O B:HOH1015 4.5 37.3 1.0 CE B:KCX162 4.6 18.9 1.0 OD1 B:ASP285 4.8 17.4 1.0 CG B:ASP285 4.8 23.4 1.0 CG2 B:THR229 4.9 13.3 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