Zinc in PDB 2aqv: Crystal Structure of E. Coli Isoaspartyl Dipeptidase Mutant Y137F

The structure of Crystal Structure of E. Coli Isoaspartyl Dipeptidase Mutant Y137F, PDB code: 2aqv was solved by R.Marti-Arbona, J.B.Thoden, H.M.Holden, F.M.Raushel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.95
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	119.100, 119.100, 138.600, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Zinc atom in the Crystal Structure of E. Coli Isoaspartyl Dipeptidase Mutant Y137F (pdb code 2aqv). 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 E. Coli Isoaspartyl Dipeptidase Mutant Y137F, PDB code: 2aqv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of E. Coli Isoaspartyl Dipeptidase Mutant Y137F


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 E. Coli Isoaspartyl Dipeptidase Mutant Y137F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:36.9 occ:1.00 OQ2 A:KCX162 2.2 22.6 1.0 NE2 A:HIS68 2.2 18.8 1.0 NE2 A:HIS70 2.2 17.8 1.0 OD1 A:ASP285 2.3 20.1 1.0 O A:HOH910 2.6 58.3 1.0 CE1 A:HIS70 3.0 12.1 1.0 CG A:ASP285 3.0 29.9 1.0 CD2 A:HIS68 3.1 18.5 1.0 CX A:KCX162 3.1 15.4 1.0 CE1 A:HIS68 3.3 17.3 1.0 ZN A:ZN802 3.3 36.7 1.0 OD2 A:ASP285 3.3 35.1 1.0 OQ1 A:KCX162 3.4 30.1 1.0 CD2 A:HIS70 3.4 21.8 1.0 CD1 A:LEU103 4.1 19.0 1.0 ND1 A:HIS70 4.2 18.3 1.0 CG A:HIS68 4.3 15.0 1.0 NZ A:KCX162 4.3 20.6 1.0 CB A:ASP285 4.4 18.5 1.0 NE2 A:HIS230 4.4 38.4 1.0 ND1 A:HIS68 4.4 15.7 1.0 CE1 A:HIS230 4.4 30.0 1.0 CG A:HIS70 4.4 19.7 1.0 CA A:ASP285 4.7 16.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of E. Coli Isoaspartyl Dipeptidase Mutant Y137F


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 E. Coli Isoaspartyl Dipeptidase Mutant Y137F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:36.7 occ:1.00 NE2 A:HIS230 2.1 38.4 1.0 ND1 A:HIS201 2.2 17.7 1.0 OQ1 A:KCX162 2.4 30.1 1.0 O A:HOH910 2.6 58.3 1.0 CD2 A:HIS230 3.0 35.9 1.0 CE1 A:HIS230 3.1 30.0 1.0 CX A:KCX162 3.1 15.4 1.0 CG A:HIS201 3.2 13.8 1.0 CE1 A:HIS201 3.2 19.0 1.0 OQ2 A:KCX162 3.3 22.6 1.0 ZN A:ZN801 3.3 36.9 1.0 CB A:HIS201 3.5 15.4 1.0 NE2 A:HIS68 3.9 18.8 1.0 CE1 A:HIS68 4.0 17.3 1.0 CG A:HIS230 4.1 28.8 1.0 CZ A:PHE137 4.1 24.3 1.0 CE1 A:PHE137 4.1 19.7 1.0 ND1 A:HIS230 4.1 30.3 1.0 OD2 A:ASP285 4.1 35.1 1.0 CA A:HIS201 4.3 22.1 1.0 NE2 A:HIS201 4.3 23.7 1.0 CD2 A:HIS201 4.4 22.2 1.0 NZ A:KCX162 4.4 20.6 1.0 CE A:KCX162 4.7 20.9 1.0 CG A:ASP285 4.7 29.9 1.0 OD1 A:ASP285 4.8 20.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of E. Coli Isoaspartyl Dipeptidase Mutant Y137F


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 E. Coli Isoaspartyl Dipeptidase Mutant Y137F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn803 b:33.8 occ:1.00 O B:HOH981 2.2 33.9 1.0 OQ2 B:KCX162 2.2 15.6 1.0 OD1 B:ASP285 2.2 16.4 1.0 NE2 B:HIS70 2.2 22.4 1.0 NE2 B:HIS68 2.3 19.1 1.0 CE1 B:HIS70 2.9 19.6 1.0 CX B:KCX162 3.0 24.8 1.0 CD2 B:HIS68 3.1 16.6 1.0 CG B:ASP285 3.1 26.9 1.0 O B:HOH982 3.2 43.8 1.0 OQ1 B:KCX162 3.3 30.6 1.0 ZN B:ZN804 3.3 34.8 1.0 CE1 B:HIS68 3.3 18.3 1.0 CD2 B:HIS70 3.4 19.0 1.0 OD2 B:ASP285 3.4 25.6 1.0 CD1 B:LEU103 4.0 24.3 1.0 ND1 B:HIS70 4.2 19.2 1.0 NZ B:KCX162 4.2 27.3 1.0 CG B:HIS68 4.3 15.6 1.0 CB B:ASP285 4.4 15.2 1.0 CG B:HIS70 4.4 15.1 1.0 ND1 B:HIS68 4.4 16.3 1.0 NE2 B:HIS230 4.5 28.9 1.0 CE1 B:HIS230 4.5 23.4 1.0 CA B:ASP285 4.7 19.6 1.0 O B:HOH846 5.0 21.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of E. Coli Isoaspartyl Dipeptidase Mutant Y137F


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 E. Coli Isoaspartyl Dipeptidase Mutant Y137F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn804 b:34.8 occ:1.00 O B:HOH981 2.0 33.9 1.0 OQ1 B:KCX162 2.1 30.6 1.0 ND1 B:HIS201 2.1 16.4 1.0 NE2 B:HIS230 2.2 28.9 1.0 CX B:KCX162 2.9 24.8 1.0 CD2 B:HIS230 3.1 17.8 1.0 CG B:HIS201 3.1 18.4 1.0 CE1 B:HIS201 3.1 19.2 1.0 OQ2 B:KCX162 3.1 15.6 1.0 CE1 B:HIS230 3.2 23.4 1.0 CB B:HIS201 3.3 17.0 1.0 ZN B:ZN803 3.3 33.8 1.0 O B:HOH982 3.5 43.8 1.0 CZ B:PHE137 3.8 24.4 1.0 CE1 B:HIS68 3.9 18.3 1.0 NE2 B:HIS68 3.9 19.1 1.0 CE1 B:PHE137 4.1 28.0 1.0 OD2 B:ASP285 4.2 25.6 1.0 CA B:HIS201 4.2 19.1 1.0 CG B:HIS230 4.2 22.5 1.0 NE2 B:HIS201 4.2 21.0 1.0 NZ B:KCX162 4.2 27.3 1.0 CD2 B:HIS201 4.3 19.5 1.0 ND1 B:HIS230 4.3 25.5 1.0 CE B:KCX162 4.6 29.8 1.0 OD1 B:ASP285 4.7 16.4 1.0 CG B:ASP285 4.8 26.9 1.0 CG2 B:THR229 4.9 13.2 1.0 CE2 B:PHE137 5.0 18.5 1.0

R.Marti-Arbona, J.B.Thoden, H.M.Holden, F.M.Raushel. Functional Significance of Glu-77 and Tyr-137 Within the Active Site of Isoaspartyl Dipeptidase. Bioorg.Chem. V. 33 448 2005.
ISSN: ISSN 0045-2068
PubMed: 16289685
DOI: 10.1016/J.BIOORG.2005.10.002