Zinc in PDB 1y0y: Crystal Structure of Tetrahedral Aminopeptidase From P. Horikoshii in Complex with Amastatin

The structure of Crystal Structure of Tetrahedral Aminopeptidase From P. Horikoshii in Complex with Amastatin, PDB code: 1y0y was solved by M.Groll, L.Borissenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.91 / 1.60
Space group	P 2 3
Cell size a, b, c (Å), α, β, γ (°)	111.560, 111.560, 111.560, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 22.2

The binding sites of Zinc atom in the Crystal Structure of Tetrahedral Aminopeptidase From P. Horikoshii in Complex with Amastatin (pdb code 1y0y). 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 Tetrahedral Aminopeptidase From P. Horikoshii in Complex with Amastatin, PDB code: 1y0y:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Tetrahedral Aminopeptidase From P. Horikoshii in Complex with Amastatin


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 Tetrahedral Aminopeptidase From P. Horikoshii in Complex with Amastatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:31.1 occ:1.00 O1 B:L2O1 2.0 34.2 1.0 OD1 A:ASP182 2.1 24.7 1.0 N B:L2O1 2.2 39.2 1.0 NE2 A:HIS68 2.3 23.8 1.0 OD1 A:ASP235 2.3 26.8 1.0 OD2 A:ASP235 2.4 27.0 1.0 CG A:ASP235 2.7 27.1 1.0 C6 B:L2O1 2.8 38.2 1.0 C1 B:L2O1 2.9 39.2 1.0 CG A:ASP182 3.2 24.9 1.0 CD2 A:HIS68 3.2 19.3 1.0 CE1 A:HIS68 3.3 21.3 1.0 OD2 A:ASP182 3.6 23.7 1.0 ZN A:ZN1002 3.6 29.2 1.0 OE1 A:GLU212 3.8 25.9 1.0 OE2 A:GLU213 4.0 23.3 1.0 CB A:ASP183 4.1 22.5 1.0 CG A:ASP183 4.1 25.2 1.0 CD A:GLU212 4.2 27.5 1.0 OE2 A:GLU212 4.2 28.2 1.0 CB A:ASP235 4.2 24.6 1.0 C B:L2O1 4.2 39.0 1.0 CG2 A:VAL236 4.3 20.8 1.0 C2 B:L2O1 4.3 41.1 1.0 ND1 A:HIS68 4.4 23.6 1.0 CG A:HIS68 4.4 19.5 1.0 C A:ASP182 4.4 27.1 1.0 OD1 A:ASP183 4.4 25.4 1.0 OD2 A:ASP183 4.4 26.8 1.0 CB A:ASP182 4.5 22.7 1.0 O A:ASP182 4.5 29.5 1.0 N A:ASP183 4.6 30.7 1.0 N A:VAL236 4.7 22.0 1.0 CA A:ASP182 4.7 24.6 1.0 O B:L2O1 4.7 36.6 1.0 O A:HOH1142 4.7 30.1 1.0 CD A:GLU213 4.7 22.2 1.0 CA A:ASP183 4.9 25.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Tetrahedral Aminopeptidase From P. Horikoshii in Complex with Amastatin


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 Tetrahedral Aminopeptidase From P. Horikoshii in Complex with Amastatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:29.2 occ:1.00 O1 B:L2O1 2.1 34.2 1.0 OD2 A:ASP182 2.1 23.7 1.0 NE2 A:HIS323 2.2 23.8 1.0 OE2 A:GLU213 2.2 23.3 1.0 O B:L2O1 2.4 36.6 1.0 OE1 A:GLU213 2.4 22.5 1.0 CD A:GLU213 2.6 22.2 1.0 C6 B:L2O1 2.9 38.2 1.0 CG A:ASP182 2.9 24.9 1.0 C B:L2O1 2.9 39.0 1.0 CE1 A:HIS323 3.1 27.0 1.0 CD2 A:HIS323 3.2 24.5 1.0 OD1 A:ASP182 3.2 24.7 1.0 C1 B:L2O1 3.4 39.2 1.0 ZN A:ZN1001 3.6 31.1 1.0 O B:ASP4 3.9 46.9 0.0 N B:L2O1 4.1 39.2 1.0 CG A:GLU213 4.1 20.2 1.0 N B:VAL2 4.1 40.7 1.0 CB A:ASP182 4.2 22.7 1.0 OE1 A:GLU212 4.2 25.9 1.0 ND1 A:HIS323 4.2 25.6 1.0 O A:HOH1123 4.3 23.4 1.0 CG A:HIS323 4.3 22.8 1.0 NE2 A:HIS68 4.5 23.8 1.0 O A:HOH1122 4.5 21.7 1.0 CE1 A:HIS68 4.6 21.3 1.0 C2 B:L2O1 4.7 41.1 1.0 CG2 A:ILE72 4.9 19.8 1.0 C B:ASP4 4.9 47.3 1.0 CA B:VAL2 5.0 43.5 1.0 CG2 A:ILE322 5.0 22.4 1.0

L.Borissenko, M.Groll. Crystal Structure of Tet Protease Reveals Complementary Protein Degradation Pathways in Prokaryotes J.Mol.Biol. V. 346 1207 2005.
ISSN: ISSN 0022-2836
PubMed: 15713475
DOI: 10.1016/J.JMB.2004.12.056