Zinc in PDB 3vh9: Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol

All present enzymatic activity of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol:
3.4.11.10;

The structure of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol, PDB code: 3vh9 was solved by S.Saijo, K.Hanaya, M.Suetsugu, K.Kobayashi, I.Yamato, S.Aoki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.62 / 1.29
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	108.463, 108.463, 90.737, 90.00, 90.00, 120.00
R / Rfree (%)	13.1 / 15.3

The structure of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol also contains other interesting chemical elements:

Chlorine	(Cl)	9 atoms
Sodium	(Na)	9 atoms

The binding sites of Zinc atom in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol (pdb code 3vh9). 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 Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol, PDB code: 3vh9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol


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 Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:7.0 occ:1.00 OD2 A:ASP117 2.0 6.2 1.0 OE2 A:GLU152 2.0 8.5 1.0 NE2 A:HIS256 2.1 6.9 1.0 NAH A:HQY303 2.1 9.6 1.0 OAA A:HQY303 2.2 7.8 1.0 OE1 A:GLU152 2.7 8.7 1.0 CD A:GLU152 2.7 8.1 1.0 CG A:ASP117 2.9 5.4 1.0 CAM A:HQY303 3.0 9.0 1.0 CAJ A:HQY303 3.0 8.0 1.0 CD2 A:HIS256 3.1 6.5 1.0 CE1 A:HIS256 3.1 8.0 1.0 CAE A:HQY303 3.1 10.5 1.0 OD1 A:ASP117 3.3 5.9 1.0 ZN A:ZN302 3.4 6.2 1.0 O A:HOH451 3.7 12.0 1.0 NA A:NA310 3.9 15.9 1.0 O A:HOH422 4.1 8.3 1.0 CG A:GLU152 4.2 8.2 1.0 ND1 A:HIS256 4.2 9.1 1.0 CG A:HIS256 4.2 7.5 1.0 CAL A:HQY303 4.3 10.6 1.0 CB A:ASP117 4.3 5.4 1.0 CAK A:HQY303 4.3 10.3 1.0 CAD A:HQY303 4.4 11.4 1.0 OE1 A:GLU151 4.6 7.7 1.0 NE2 A:HIS97 4.6 5.8 1.0 CD1 A:ILE255 4.6 11.3 1.0 CE1 A:HIS97 4.7 6.2 1.0 CAF A:HQY303 4.9 11.9 1.0 O A:HOH535 5.0 17.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol


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 Aeromonas Proteolytica Aminopeptidase Complexed with 8-Quinolinol within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:6.2 occ:1.00 OAA A:HQY303 1.9 7.8 1.0 OD1 A:ASP117 2.0 5.9 1.0 NE2 A:HIS97 2.0 5.8 1.0 OD1 A:ASP179 2.1 7.2 1.0 OD2 A:ASP179 2.3 7.8 1.0 CG A:ASP179 2.6 6.9 1.0 CAJ A:HQY303 2.9 8.0 1.0 CE1 A:HIS97 3.0 6.2 1.0 CG A:ASP117 3.0 5.4 1.0 CD2 A:HIS97 3.0 5.7 1.0 OE2 A:GLU152 3.3 8.5 1.0 CAK A:HQY303 3.4 10.3 1.0 ZN A:ZN301 3.4 7.0 1.0 OD2 A:ASP117 3.5 6.2 1.0 OE1 A:GLU151 3.9 7.7 1.0 CB A:ASP118 4.1 5.5 1.0 CB A:ASP179 4.1 6.9 1.0 ND1 A:HIS97 4.1 5.9 1.0 O A:HOH451 4.2 12.0 1.0 CD A:GLU152 4.2 8.1 1.0 CAM A:HQY303 4.2 9.0 1.0 CG A:HIS97 4.2 5.6 1.0 CB A:ASP117 4.3 5.4 1.0 CD A:GLU151 4.4 8.2 1.0 NAH A:HQY303 4.5 9.6 1.0 CA A:ASP117 4.5 5.6 1.0 OE2 A:GLU151 4.6 10.7 1.0 OE1 A:GLU152 4.6 8.7 1.0 CG A:ASP118 4.7 5.6 1.0 C A:ASP117 4.7 5.9 1.0 CAG A:HQY303 4.7 11.2 1.0 OG A:SER228 4.8 7.8 1.0 CG A:MET180 4.8 7.1 1.0 CA A:ASP179 4.8 6.1 1.0 N A:ASP118 4.8 5.6 1.0 CA A:ASP118 4.9 5.1 1.0 OD2 A:ASP118 4.9 5.5 1.0 SD A:MET180 4.9 8.7 1.0

K.Hanaya, M.Suetsugu, S.Saijo, I.Yamato, S.Aoki. Potent Inhibition of Dinuclear Zinc(II) Peptidase, An Aminopeptidase From Aeromonas Proteolytica, By 8-Quinolinol Derivatives: Inhibitor Design Based on Zn(2+) Fluorophores, Kinetic, and X-Ray Crystallographic Study. J.Biol.Inorg.Chem. V. 17 517 2012.
ISSN: ISSN 0949-8257
PubMed: 22311113
DOI: 10.1007/S00775-012-0873-4