Zinc in PDB 1f2p: Crystal Structure of the Streptomyces Griseus Aminopeptidase Complexed with L-Phenylalanine

The structure of Crystal Structure of the Streptomyces Griseus Aminopeptidase Complexed with L-Phenylalanine, PDB code: 1f2p was solved by R.Gilboa, A.Spungin-Bialik, G.Wohlfahrt, D.Schomburg, S.Blumberg, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 1.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.180, 62.180, 146.980, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.5

The structure of Crystal Structure of the Streptomyces Griseus Aminopeptidase Complexed with L-Phenylalanine also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Streptomyces Griseus Aminopeptidase Complexed with L-Phenylalanine (pdb code 1f2p). 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 Streptomyces Griseus Aminopeptidase Complexed with L-Phenylalanine, PDB code: 1f2p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Streptomyces Griseus Aminopeptidase Complexed with L-Phenylalanine


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 Streptomyces Griseus Aminopeptidase Complexed with L-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:27.9 occ:1.00 NE2 A:HIS85 2.1 7.4 1.0 OD1 A:ASP160 2.2 5.7 1.0 OD1 A:ASP97 2.2 7.1 1.0 O A:PHE903 2.4 15.1 1.0 CG A:ASP160 2.8 4.6 1.0 OD2 A:ASP160 2.9 5.6 1.0 C A:PHE903 2.9 16.9 1.0 CE1 A:HIS85 3.0 5.9 1.0 CD2 A:HIS85 3.1 6.3 1.0 CG A:ASP97 3.3 8.1 1.0 CA A:PHE903 3.6 17.1 1.0 OXT A:PHE903 3.6 15.1 1.0 N A:PHE903 3.6 16.4 1.0 CB A:PHE903 3.7 19.4 1.0 ZN A:ZN902 3.7 10.7 1.0 OD2 A:ASP97 3.7 8.0 1.0 OE1 A:GLU131 4.0 9.2 1.0 CB A:ASN98 4.1 5.1 1.0 ND1 A:HIS85 4.2 5.0 1.0 CG A:HIS85 4.3 5.6 1.0 CB A:ASP160 4.3 6.0 1.0 OE2 A:GLU132 4.3 9.7 1.0 CG A:MET161 4.3 6.2 1.0 CB A:ASP97 4.4 6.1 1.0 CD A:GLU131 4.5 8.6 1.0 SD A:MET161 4.6 7.6 1.0 OE2 A:GLU131 4.6 10.0 1.0 CG A:PHE903 4.6 20.9 1.0 CD2 A:PHE903 4.6 21.3 1.0 CA A:ASP97 4.7 4.8 1.0 CG A:ASN98 4.8 5.7 1.0 CA A:ASP160 4.9 6.2 1.0 C A:ASP97 4.9 5.8 1.0 C A:ASP160 5.0 7.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Streptomyces Griseus Aminopeptidase Complexed with L-Phenylalanine


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 Streptomyces Griseus Aminopeptidase Complexed with L-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:10.7 occ:1.00 OXT A:PHE903 2.1 15.1 1.0 OD2 A:ASP97 2.1 8.0 1.0 OE2 A:GLU132 2.1 9.7 1.0 NE2 A:HIS247 2.2 8.1 1.0 O A:PHE903 2.6 15.1 1.0 C A:PHE903 2.7 16.9 1.0 OE1 A:GLU132 2.8 7.7 1.0 CD A:GLU132 2.8 8.8 1.0 CG A:ASP97 3.0 8.1 1.0 CD2 A:HIS247 3.0 7.6 1.0 CE1 A:HIS247 3.2 10.0 1.0 OD1 A:ASP97 3.2 7.1 1.0 ZN A:ZN901 3.7 27.9 1.0 CE1 A:TYR246 4.0 10.6 1.0 O A:HOH303 4.0 8.9 1.0 CA A:PHE903 4.1 17.1 1.0 OH A:TYR246 4.1 10.9 1.0 CG A:HIS247 4.2 7.8 1.0 ND1 A:HIS247 4.3 8.6 1.0 CG A:GLU132 4.3 7.6 1.0 CB A:ASP97 4.4 6.1 1.0 CZ A:TYR246 4.4 11.4 1.0 OE1 A:GLU131 4.5 9.2 1.0 CB A:PHE903 4.6 19.4 1.0 CE1 A:HIS85 4.7 5.9 1.0 NE2 A:HIS85 4.8 7.4 1.0 CG1 A:VAL89 4.8 7.8 1.0 CD1 A:TYR246 4.9 9.5 1.0

R.Gilboa, A.Spungin-Bialik, G.Wohlfahrt, D.Schomburg, S.Blumberg, G.Shoham. Interactions of Streptomyces Griseus Aminopeptidase with Amino Acid Reaction Products and Their Implications Toward A Catalytic Mechanism. Proteins V. 44 490 2001.
ISSN: ISSN 0887-3585
PubMed: 11484227
DOI: 10.1002/PROT.1115