Zinc in PDB 1xjo: Structure of Aminopeptidase

The structure of Structure of Aminopeptidase, PDB code: 1xjo was solved by H.M.Greenblatt, D.Barra, S.Blumberg, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.75
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.810, 61.810, 146.300, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / n/a

The structure of Structure of Aminopeptidase also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

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

Zinc binding site 1 out of 2 in the Structure of Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:11.3 occ:1.00 OD1 A:ASP160 2.0 9.8 1.0 NE2 A:HIS85 2.0 8.6 1.0 OD1 A:ASP97 2.1 9.0 1.0 O3 A:PO4903 2.2 19.4 0.5 O4 A:PO4903 2.3 13.2 0.5 OD2 A:ASP160 2.6 12.5 1.0 CG A:ASP160 2.7 12.7 1.0 P A:PO4903 2.9 20.0 0.5 CE1 A:HIS85 3.0 10.1 1.0 CD2 A:HIS85 3.0 9.4 1.0 CG A:ASP97 3.1 13.3 1.0 OD2 A:ASP97 3.5 11.0 1.0 ZN A:ZN902 3.6 13.8 1.0 O1 A:PO4903 3.8 20.6 0.5 CB A:ASN98 3.9 5.9 1.0 O2 A:PO4903 4.1 14.7 0.5 OE1 A:GLU131 4.1 14.0 1.0 CB A:ASP160 4.1 10.4 1.0 OE2 A:GLU132 4.1 15.1 1.0 ND1 A:HIS85 4.2 9.8 1.0 CG A:HIS85 4.2 9.4 1.0 O A:HOH557 4.2 62.5 1.0 CG A:MHO161 4.2 9.4 1.0 CB A:ASP97 4.3 8.8 1.0 CD A:GLU131 4.4 17.3 1.0 OE2 A:GLU131 4.4 21.0 1.0 SD A:MHO161 4.5 12.8 1.0 CA A:ASP97 4.5 6.1 1.0 CG A:ASN98 4.6 8.1 1.0 OD1 A:MHO161 4.6 7.9 0.5 C A:ASP97 4.8 11.4 1.0 CA A:ASP160 4.8 10.8 1.0 C A:ASP160 4.9 14.5 1.0 CD A:GLU132 4.9 13.4 1.0 CA A:ASN98 4.9 7.7 1.0 OD1 A:ASN98 5.0 12.3 1.0 N A:ASN98 5.0 10.5 1.0

Zinc binding site 2 out of 2 in the Structure of Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:13.8 occ:1.00 OE2 A:GLU132 1.9 15.1 1.0 NE2 A:HIS247 2.0 14.3 1.0 O4 A:PO4903 2.0 13.2 0.5 OD2 A:ASP97 2.0 11.0 1.0 CD A:GLU132 2.6 13.4 1.0 OE1 A:GLU132 2.7 13.7 1.0 O2 A:PO4903 2.8 14.7 0.5 P A:PO4903 2.9 20.0 0.5 CG A:ASP97 3.0 13.3 1.0 CE1 A:HIS247 3.0 19.6 1.0 CD2 A:HIS247 3.0 12.4 1.0 OD1 A:ASP97 3.5 9.0 1.0 O3 A:PO4903 3.6 19.4 0.5 ZN A:ZN901 3.6 11.3 1.0 O A:HOH578 3.8 52.3 1.0 O A:HOH303 3.9 10.5 1.0 CG A:GLU132 4.1 12.9 1.0 O1 A:PO4903 4.1 20.6 0.5 CE1 A:TYR246 4.1 11.8 1.0 ND1 A:HIS247 4.1 17.9 1.0 CG A:HIS247 4.2 16.4 1.0 OE1 A:GLU131 4.2 14.0 1.0 OH A:TYR246 4.3 24.4 1.0 CB A:ASP97 4.3 8.8 1.0 CE1 A:HIS85 4.4 10.1 1.0 NE2 A:HIS85 4.5 8.6 1.0 CZ A:TYR246 4.6 24.7 1.0 CG1 A:VAL89 4.7 14.9 1.0

H.M.Greenblatt, O.Almog, B.Maras, A.Spungin-Bialik, D.Barra, S.Blumberg, G.Shoham. Streptomyces Griseus Aminopeptidase: X-Ray Crystallographic Structure at 1.75 A Resolution. J.Mol.Biol. V. 265 620 1997.
ISSN: ISSN 0022-2836
PubMed: 9048953
DOI: 10.1006/JMBI.1996.0729