Zinc in PDB 2dea: Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7

All present enzymatic activity of Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7:
3.4.11.10;

The structure of Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7, PDB code: 2dea was solved by G.A.Petsko, D.Ringe, W.Desmarais, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.24
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.605, 109.605, 90.816, 90.00, 90.00, 120.00
R / Rfree (%)	15.3 / 16.3

The structure of Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7 (pdb code 2dea). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7, PDB code: 2dea:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7


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 the Aminopeptidase of Aeromonas Proteolytica at pH 4.7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:13.4 occ:1.00 NE2 A:HIS256 2.0 14.2 1.0 OD2 A:ASP117 2.0 12.0 1.0 O A:HOH644 2.0 22.8 1.0 OE2 A:GLU152 2.1 11.4 1.0 O A:HOH640 2.2 16.5 1.0 OE1 A:GLU152 2.6 12.7 1.0 CD A:GLU152 2.7 11.1 1.0 CE1 A:HIS256 2.9 24.4 1.0 CG A:ASP117 2.9 9.0 1.0 CD2 A:HIS256 3.0 12.1 1.0 OD1 A:ASP117 3.2 10.1 1.0 O A:HOH797 3.3 37.1 1.0 ZN A:ZN402 3.5 11.3 1.0 O A:HOH691 3.9 29.7 1.0 ND1 A:HIS256 4.0 22.1 1.0 O A:HOH516 4.1 10.3 1.0 CG A:HIS256 4.1 12.1 1.0 CG A:GLU152 4.2 12.3 1.0 CB A:ASP117 4.3 9.4 1.0 O A:HOH845 4.3 55.6 1.0 OE1 A:GLU151 4.4 10.1 1.0 O A:HOH639 4.5 30.7 1.0 CD1 A:ILE255 4.5 12.8 1.0 NE2 A:HIS97 4.6 8.7 1.0 CE1 A:HIS97 4.6 8.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Aminopeptidase of Aeromonas Proteolytica at pH 4.7


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 the Aminopeptidase of Aeromonas Proteolytica at pH 4.7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:11.3 occ:1.00 O A:HOH640 1.9 16.5 1.0 OD1 A:ASP117 2.0 10.1 1.0 NE2 A:HIS97 2.0 8.7 1.0 OD1 A:ASP179 2.1 10.9 1.0 OD2 A:ASP179 2.2 10.9 1.0 O A:HOH797 2.3 37.1 1.0 CG A:ASP179 2.5 10.0 1.0 CG A:ASP117 3.0 9.0 1.0 CE1 A:HIS97 3.0 8.6 1.0 CD2 A:HIS97 3.1 8.2 1.0 OD2 A:ASP117 3.4 12.0 1.0 ZN A:ZN401 3.5 13.4 1.0 OE2 A:GLU152 3.8 11.4 1.0 OE1 A:GLU151 3.9 10.1 1.0 O A:HOH644 3.9 22.8 1.0 CB A:ASP179 4.0 10.4 1.0 CB A:ASP118 4.2 8.6 1.0 ND1 A:HIS97 4.2 8.6 1.0 CB A:ASP117 4.2 9.4 1.0 CD A:GLU151 4.2 10.5 1.0 CG A:HIS97 4.2 8.5 1.0 OE2 A:GLU151 4.4 13.8 1.0 CA A:ASP117 4.5 8.3 1.0 CD A:GLU152 4.6 11.1 1.0 O A:HOH691 4.6 29.7 1.0 C A:ASP117 4.7 7.6 1.0 CG A:ASP118 4.7 7.6 1.0 OG A:SER228 4.7 10.3 1.0 CA A:ASP179 4.8 9.1 1.0 CG A:MET180 4.8 10.3 1.0 OE1 A:GLU152 4.9 12.7 1.0 SD A:MET180 4.9 11.1 1.0 N A:ASP118 4.9 7.9 1.0 CA A:ASP118 4.9 7.8 1.0 OD2 A:ASP118 4.9 8.6 1.0

W.Desmarais, D.L.Bienvenue, K.P.Bzymek, G.A.Petsko, D.Ringe, R.C.Holz. The High-Resolution Structures of the Neutral and the Low pH Crystals of Aminopeptidase From Aeromonas Proteolytica. J.Biol.Inorg.Chem. V. 11 398 2006.
ISSN: ISSN 0949-8257
PubMed: 16596389
DOI: 10.1007/S00775-006-0093-X