Zinc in PDB 1tkh: Streptomyces Griseus Aminopeptidase Complexed with D- Phenylalanine

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

Resolution Low / High (Å)	50.00 / 1.25
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.465, 60.465, 143.637, 90.00, 90.00, 90.00
R / Rfree (%)	11.4 / 15.6

The structure of Streptomyces Griseus Aminopeptidase Complexed with D- Phenylalanine also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Streptomyces Griseus Aminopeptidase Complexed with D- Phenylalanine (pdb code 1tkh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Streptomyces Griseus Aminopeptidase Complexed with D- Phenylalanine, PDB code: 1tkh:
Jump to Zinc binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Streptomyces Griseus Aminopeptidase Complexed with D- Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:6.8 occ:1.00 OXT A:DPN913 1.9 12.5 0.7 NE2 A:HIS85 2.0 4.9 1.0 OD1 A:ASP97 2.0 5.8 1.0 OD1 A:ASP160 2.0 6.6 1.0 OD2 A:ASP160 2.7 6.9 1.0 CG A:ASP160 2.7 5.9 1.0 C A:DPN913 2.8 11.5 0.7 CE1 A:HIS85 3.0 5.7 1.0 CG A:ASP97 3.0 5.7 1.0 CD2 A:HIS85 3.0 5.3 1.0 CA A:DPN913 3.4 15.9 0.7 OD2 A:ASP97 3.5 6.4 1.0 ZN A:ZN902 3.6 8.2 1.0 O A:DPN913 3.8 15.6 0.7 CB A:DPN913 3.9 19.7 0.7 CB A:ASN98 4.0 5.3 1.0 OE2 A:GLU132 4.0 7.9 1.0 OE1 A:GLU131 4.1 8.0 1.0 ND1 A:HIS85 4.1 5.6 1.0 CB A:ASP160 4.1 5.5 1.0 CG A:HIS85 4.2 5.0 1.0 CG A:MET161 4.2 5.9 1.0 CB A:ASP97 4.3 5.3 1.0 CD A:GLU131 4.4 7.7 1.0 SD A:MET161 4.5 6.3 1.0 OE2 A:GLU131 4.6 11.8 1.0 CA A:ASP97 4.6 4.8 1.0 CG A:ASN98 4.6 4.6 1.0 CA A:ASP160 4.7 4.9 1.0 C A:ASP97 4.7 4.4 1.0 N A:DPN913 4.8 26.1 0.7 C A:ASP160 4.8 5.3 1.0 CD1 A:DPN913 4.9 19.7 0.7 CD A:GLU132 4.9 7.0 1.0 CG A:DPN913 4.9 19.7 0.7 N A:ASN98 4.9 4.5 1.0 CA A:ASN98 4.9 5.4 1.0

Zinc binding site 2 out of 2 in the Streptomyces Griseus Aminopeptidase Complexed with D- Phenylalanine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Streptomyces Griseus Aminopeptidase Complexed with D- Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:8.2 occ:1.00 OD2 A:ASP97 2.0 6.4 1.0 OE2 A:GLU132 2.0 7.9 1.0 NE2 A:HIS247 2.0 7.6 1.0 O A:DPN913 2.0 15.6 0.7 OXT A:DPN913 2.3 12.5 0.7 C A:DPN913 2.5 11.5 0.7 CD A:GLU132 2.7 7.0 1.0 OE1 A:GLU132 2.7 8.5 1.0 CG A:ASP97 3.0 5.7 1.0 CD2 A:HIS247 3.0 5.7 1.0 CE1 A:HIS247 3.1 9.2 1.0 OD1 A:ASP97 3.4 5.8 1.0 ZN A:ZN901 3.6 6.8 1.0 O A:HOH1017 4.0 7.8 1.0 CE1 A:TYR246 4.0 11.4 1.0 CA A:DPN913 4.0 15.9 0.7 CG A:GLU132 4.2 6.7 1.0 ND1 A:HIS247 4.2 8.7 1.0 CG A:HIS247 4.2 6.4 1.0 O A:HOH1444 4.2 44.0 1.0 OH A:TYR246 4.2 19.6 1.0 OE1 A:GLU131 4.3 8.0 1.0 CB A:ASP97 4.3 5.3 1.0 CZ A:TYR246 4.5 14.9 1.0 CE1 A:HIS85 4.5 5.7 1.0 NE2 A:HIS85 4.5 4.9 1.0 CG1 A:VAL89 4.7 6.8 1.0 CB A:DPN913 4.7 19.7 0.7 N A:DPN913 4.7 26.1 0.7 CD1 A:TYR246 4.9 8.9 1.0

V.Reiland, R.Gilboa, A.Spungin-Bialik, D.Schomburg, Y.Shoham, S.Blumberg, G.Shoham. Interactions of D Amino Acids with Streptomyces Griseus Aminopeptidase To Be Published.