Zinc in PDB 3mru: Crystal Structure of Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus

All present enzymatic activity of Crystal Structure of Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus:
3.4.13.3;

The structure of Crystal Structure of Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus, PDB code: 3mru was solved by C.-Y.Chang, Y.-C.Hsieh, T.-K.Wu, C.-J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.57 / 3.00
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	80.407, 80.407, 303.095, 90.00, 90.00, 120.00
R / Rfree (%)	23.1 / 27.3

The binding sites of Zinc atom in the Crystal Structure of Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus (pdb code 3mru). 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 Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus, PDB code: 3mru:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus


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 Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn491 b:0.8 occ:1.00 OD2 A:ASP119 2.5 92.3 1.0 NE2 A:HIS461 2.6 87.0 1.0 ZN A:ZN492 2.8 0.4 1.0 CE1 A:HIS461 3.0 86.2 1.0 OE2 A:GLU149 3.4 92.9 1.0 CG A:ASP119 3.6 94.8 1.0 CD2 A:HIS461 3.8 86.6 1.0 OD1 A:ASP119 4.0 92.8 1.0 CD A:GLU149 4.1 93.9 1.0 ND1 A:HIS461 4.2 85.9 1.0 CG2 A:VAL84 4.4 62.1 1.0 NE2 A:HIS80 4.4 55.9 1.0 OE1 A:GLU149 4.5 95.1 1.0 OE1 A:GLU150 4.5 0.9 1.0 CG A:HIS461 4.6 85.4 1.0 CE1 A:HIS80 4.8 56.3 1.0 CB A:ASP119 4.9 96.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus


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 Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn492 b:0.4 occ:1.00 OD2 A:ASP173 2.4 73.5 1.0 OD1 A:ASP119 2.5 92.8 1.0 NE2 A:HIS80 2.8 55.9 1.0 ZN A:ZN491 2.8 0.8 1.0 OD2 A:ASP119 2.9 92.3 1.0 CG A:ASP119 3.0 94.8 1.0 OD1 A:ASP173 3.1 75.4 1.0 CG A:ASP173 3.1 77.1 1.0 CD2 A:HIS80 3.5 55.9 1.0 CD A:GLU149 3.6 93.9 1.0 OE1 A:GLU149 3.7 95.1 1.0 ND2 A:ASN120 3.8 78.0 1.0 CE1 A:HIS80 3.8 56.3 1.0 OE2 A:GLU149 3.8 92.9 1.0 CG A:GLU149 4.1 93.9 1.0 CB A:ASP119 4.3 96.5 1.0 CB A:GLU149 4.5 94.3 1.0 O A:ASP173 4.5 75.8 1.0 CB A:ASP173 4.6 78.7 1.0 O A:ASP119 4.7 80.5 1.0 CG A:HIS80 4.7 56.9 1.0 ND1 A:HIS80 4.8 56.3 1.0 C A:ASP119 4.9 81.1 1.0 CG A:ASN120 4.9 74.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus


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 Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn491 b:0.1 occ:1.00 OD2 B:ASP119 2.5 73.7 1.0 NE2 B:HIS461 2.6 98.6 1.0 ZN B:ZN492 2.8 33.8 1.0 OE2 B:GLU149 3.0 92.5 1.0 CE1 B:HIS461 3.1 97.2 1.0 CG B:ASP119 3.6 76.2 1.0 CD2 B:HIS461 3.8 97.4 1.0 OD1 B:ASP119 3.9 74.3 1.0 CD B:GLU149 4.0 92.8 1.0 ND1 B:HIS461 4.3 96.0 1.0 NE2 B:HIS80 4.4 41.5 1.0 OE1 B:GLU149 4.5 94.5 1.0 CG B:HIS461 4.7 95.2 1.0 OD2 B:ASP173 4.8 50.3 1.0 CB B:ASP119 4.9 77.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus


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 Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn492 b:33.8 occ:1.00 OD2 B:ASP173 2.2 50.3 1.0 OD1 B:ASP119 2.2 74.3 1.0 NE2 B:HIS80 2.7 41.5 1.0 ZN B:ZN491 2.8 0.1 1.0 CG B:ASP119 2.8 76.2 1.0 OD2 B:ASP119 2.8 73.7 1.0 CG B:ASP173 3.1 53.2 1.0 CD2 B:HIS80 3.1 41.1 1.0 OE2 B:GLU149 3.2 92.5 1.0 OD1 B:ASP173 3.2 53.3 1.0 ND2 B:ASN120 3.4 96.0 1.0 CD B:GLU149 3.5 92.8 1.0 CE1 B:HIS80 3.9 42.1 1.0 CG B:GLU149 4.0 91.3 1.0 OE1 B:GLU149 4.1 94.5 1.0 CB B:ASP119 4.2 77.9 1.0 O B:ASP119 4.3 74.5 1.0 O B:ASP173 4.4 78.9 1.0 CG B:HIS80 4.4 42.2 1.0 CB B:ASP173 4.5 54.5 1.0 CB B:GLU149 4.6 91.4 1.0 C B:ASP119 4.6 75.1 1.0 CG B:ASN120 4.6 92.8 1.0 ND1 B:HIS80 4.8 41.4 1.0 OD1 B:ASN120 4.9 93.3 1.0 CA B:ASP173 5.0 78.0 1.0 CA B:ASP119 5.0 74.5 1.0

C.-Y.Chang, Y.-C.Hsieh, T.-Y.Wang, Y.-C.Chen, Y.-K.Wang, T.-W.Chiang, Y.-J.Chen, C.-H.Chang, C.-J.Chen, T.-K.Wu. Crystal Structure and Mutational Analysis of Aminoacylhistidine Dipeptidase From Vibrio Alginolyticus Reveal A New Architecture of M20 Metallopeptidases J.Biol.Chem. V. 285 39500 2010.
ISSN: ISSN 0021-9258
PubMed: 20819954
DOI: 10.1074/JBC.M110.139683