Zinc in PDB 1ybq: Crystal Structure of Escherichia Coli Isoaspartyl Dipeptidase Mutant D285N Complexed with Beta-Aspartylhistidine

The structure of Crystal Structure of Escherichia Coli Isoaspartyl Dipeptidase Mutant D285N Complexed with Beta-Aspartylhistidine, PDB code: 1ybq was solved by R.Marti-Arbona, V.Fresquet, J.B.Thoden, M.L.Davis, 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 / 2.00
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	119.300, 119.300, 138.300, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Zinc atom in the Crystal Structure of Escherichia Coli Isoaspartyl Dipeptidase Mutant D285N Complexed with Beta-Aspartylhistidine (pdb code 1ybq). 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 Escherichia Coli Isoaspartyl Dipeptidase Mutant D285N Complexed with Beta-Aspartylhistidine, PDB code: 1ybq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Escherichia Coli Isoaspartyl Dipeptidase Mutant D285N Complexed with Beta-Aspartylhistidine


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 Escherichia Coli Isoaspartyl Dipeptidase Mutant D285N Complexed with Beta-Aspartylhistidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn391 b:28.0 occ:0.25 O A:HOH508 1.7 42.3 1.0 NE2 A:HIS70 2.2 20.2 1.0 OD1 A:ASN285 2.3 26.5 1.0 NE2 A:HIS68 2.6 25.9 1.0 CE1 A:HIS70 3.0 19.6 1.0 CD2 A:HIS68 3.1 26.8 1.0 CD2 A:HIS70 3.3 24.2 1.0 CG A:ASN285 3.5 58.1 1.0 C2 A:BDH393 3.5 29.6 1.0 ZN A:ZN392 3.5 32.2 0.2 O3 A:BDH393 3.6 39.9 1.0 C3 A:BDH393 3.8 75.4 1.0 CE1 A:HIS68 3.8 29.2 1.0 NZ A:LYS162 4.0 37.0 1.0 CD1 A:LEU103 4.1 22.1 1.0 NE2 A:HIS230 4.1 48.5 1.0 ND1 A:HIS70 4.2 20.6 1.0 ND2 A:ASN285 4.2 42.6 1.0 CE1 A:HIS230 4.3 45.6 1.0 CG A:HIS70 4.4 23.5 1.0 CG A:HIS68 4.4 24.6 1.0 CB A:ASN285 4.5 32.9 1.0 ND1 A:HIS68 4.8 32.4 1.0 CA A:ASN285 4.8 23.8 1.0 N2 A:BDH393 4.8 43.7 1.0 C1 A:BDH393 4.9 29.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Escherichia Coli Isoaspartyl Dipeptidase Mutant D285N Complexed with Beta-Aspartylhistidine


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 Escherichia Coli Isoaspartyl Dipeptidase Mutant D285N Complexed with Beta-Aspartylhistidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn392 b:32.2 occ:0.25 NE2 A:HIS230 2.2 48.5 1.0 ND1 A:HIS201 2.3 28.1 1.0 O3 A:BDH393 2.5 39.9 1.0 O A:HOH508 2.7 42.3 1.0 CD2 A:HIS230 2.9 46.9 1.0 CG A:HIS201 3.2 28.6 1.0 CE1 A:HIS230 3.3 45.6 1.0 CE1 A:HIS201 3.4 30.4 1.0 CB A:HIS201 3.4 24.4 1.0 OH A:TYR137 3.5 39.6 1.0 ZN A:ZN391 3.5 28.0 0.2 C3 A:BDH393 3.7 75.4 1.0 NZ A:LYS162 3.8 37.0 1.0 CE1 A:TYR137 4.0 26.5 1.0 NE2 A:HIS68 4.0 25.9 1.0 CG A:HIS230 4.1 34.3 1.0 CZ A:TYR137 4.2 29.5 1.0 ND1 A:HIS230 4.3 39.2 1.0 CE1 A:HIS68 4.3 29.2 1.0 CA A:HIS201 4.4 27.9 1.0 CD2 A:HIS201 4.4 37.1 1.0 NE2 A:HIS201 4.5 35.9 1.0 C2 A:BDH393 4.5 29.6 1.0 CE A:LYS162 4.6 34.6 1.0 N2 A:BDH393 4.6 43.7 1.0 C5 A:BDH393 4.7 45.4 1.0 C7 A:BDH393 4.8 90.0 1.0 O5 A:BDH393 4.8 43.5 1.0 OD1 A:ASN285 4.9 26.5 1.0 CG2 A:THR229 5.0 24.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Escherichia Coli Isoaspartyl Dipeptidase Mutant D285N Complexed with Beta-Aspartylhistidine


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 Escherichia Coli Isoaspartyl Dipeptidase Mutant D285N Complexed with Beta-Aspartylhistidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn391 b:21.9 occ:0.25 OQ1 B:KCX162 1.7 41.3 0.2 NE2 B:HIS70 2.3 21.0 1.0 OD1 B:ASN285 2.3 33.5 1.0 NE2 B:HIS68 2.6 31.0 1.0 CX B:KCX162 2.8 30.2 0.2 C2 B:BDH393 3.0 27.2 1.0 CE1 B:HIS70 3.1 23.2 1.0 CD2 B:HIS68 3.3 27.4 1.0 OQ2 B:KCX162 3.4 37.4 0.2 CD2 B:HIS70 3.4 25.2 1.0 O3 B:BDH393 3.4 49.8 1.0 C3 B:BDH393 3.4 69.2 1.0 ZN B:ZN392 3.5 29.9 0.2 CG B:ASN285 3.5 49.6 1.0 CE1 B:HIS68 3.8 32.6 1.0 NZ B:KCX162 3.9 38.0 1.0 CD1 B:LEU103 4.0 27.1 1.0 ND2 B:ASN285 4.2 39.1 1.0 NE2 B:HIS230 4.2 43.7 1.0 ND1 B:HIS70 4.3 22.4 1.0 CE1 B:HIS230 4.4 41.4 1.0 N2 B:BDH393 4.4 40.3 1.0 CG B:HIS70 4.5 20.7 1.0 C1 B:BDH393 4.5 47.6 1.0 CG B:HIS68 4.6 29.7 1.0 CB B:ASN285 4.7 21.3 1.0 ND1 B:HIS68 4.8 33.6 1.0 C4 B:BDH393 4.9 77.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Escherichia Coli Isoaspartyl Dipeptidase Mutant D285N Complexed with Beta-Aspartylhistidine


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 Escherichia Coli Isoaspartyl Dipeptidase Mutant D285N Complexed with Beta-Aspartylhistidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn392 b:29.9 occ:0.25 OQ2 B:KCX162 1.7 37.4 0.2 ND1 B:HIS201 2.1 34.4 1.0 NE2 B:HIS230 2.2 43.7 1.0 O3 B:BDH393 2.3 49.8 1.0 CX B:KCX162 2.5 30.2 0.2 OQ1 B:KCX162 2.9 41.3 0.2 CD2 B:HIS230 2.9 35.0 1.0 CG B:HIS201 3.0 38.0 1.0 CB B:HIS201 3.1 27.4 1.0 CE1 B:HIS201 3.2 33.5 1.0 CE1 B:HIS230 3.4 41.4 1.0 C3 B:BDH393 3.4 69.2 1.0 ZN B:ZN391 3.5 21.9 0.2 OH B:TYR137 3.6 35.3 1.0 NZ B:KCX162 3.9 38.0 1.0 NE2 B:HIS68 3.9 31.0 1.0 CE1 B:TYR137 4.1 23.9 1.0 CA B:HIS201 4.1 26.3 1.0 CE1 B:HIS68 4.1 32.6 1.0 CE B:KCX162 4.1 34.0 1.0 CG B:HIS230 4.2 27.4 1.0 CZ B:TYR137 4.2 42.0 1.0 CD2 B:HIS201 4.2 39.1 1.0 C2 B:BDH393 4.2 27.2 1.0 NE2 B:HIS201 4.3 36.0 1.0 N2 B:BDH393 4.4 40.3 1.0 ND1 B:HIS230 4.4 32.4 1.0 C5 B:BDH393 4.6 77.8 1.0 CG2 B:THR229 4.8 14.3 1.0 OD1 B:ASN285 4.8 33.5 1.0

R.Marti-Arbona, V.Fresquet, J.B.Thoden, M.L.Davis, H.M.Holden, F.M.Raushel. Mechanism of the Reaction Catalyzed By Isoaspartyl Dipeptidase From Escherichia Coli. Biochemistry V. 44 7115 2005.
ISSN: ISSN 0006-2960
PubMed: 15882050
DOI: 10.1021/BI050008R