Zinc in PDB 1tkj: Streptomyces Griseus Aminopeptidase Complexed with D- Methionine

The structure of Streptomyces Griseus Aminopeptidase Complexed with D- Methionine, PDB code: 1tkj 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)	20.00 / 1.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.962, 60.962, 144.705, 90.00, 90.00, 90.00
R / Rfree (%)	11.5 / 14.7

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

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Streptomyces Griseus Aminopeptidase Complexed with D- Methionine (pdb code 1tkj). 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- Methionine, PDB code: 1tkj:
Jump to Zinc binding site number: 1; 2;

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


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- Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:8.0 occ:1.00 OD1 A:ASP97 2.0 7.2 1.0 OD1 A:ASP160 2.0 8.0 1.0 N A:MED913 2.0 14.7 0.5 NE2 A:HIS85 2.0 6.3 1.0 O A:MED913 2.1 12.8 0.5 CG A:ASP160 2.7 7.3 1.0 OD2 A:ASP160 2.7 9.1 1.0 CG A:ASP97 3.0 6.6 1.0 CE1 A:HIS85 3.0 6.5 1.0 CD2 A:HIS85 3.0 6.5 1.0 C A:MED913 3.1 13.5 0.5 CA A:MED913 3.2 17.5 0.5 OD2 A:ASP97 3.4 8.0 1.0 ZN A:ZN902 3.6 9.4 1.0 N A:MED913 3.6 15.4 0.5 CB A:ASN98 4.0 7.0 1.0 OE1 A:GLU131 4.0 9.7 1.0 OE2 A:GLU132 4.0 9.2 1.0 ND1 A:HIS85 4.1 6.7 1.0 CB A:ASP160 4.1 7.5 1.0 CG A:HIS85 4.2 6.7 1.0 CG A:MET161 4.2 7.8 1.0 OXT A:MED913 4.2 18.4 0.5 CB A:MED913 4.3 16.0 0.5 CA A:MED913 4.3 14.9 0.5 CB A:ASP97 4.3 7.3 1.0 CD A:GLU131 4.4 9.3 1.0 SD A:MET161 4.5 7.8 1.0 OE2 A:GLU131 4.5 11.9 1.0 CA A:ASP97 4.6 6.7 1.0 CG A:ASN98 4.6 5.8 1.0 CA A:ASP160 4.7 7.4 1.0 C A:ASP97 4.8 6.5 1.0 C A:ASP160 4.8 7.1 1.0 N A:ASN98 4.9 6.0 1.0 CA A:ASN98 4.9 6.3 1.0 CD A:GLU132 4.9 8.1 1.0

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


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- Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:9.4 occ:1.00 NE2 A:HIS247 2.0 9.2 1.0 OD2 A:ASP97 2.0 8.0 1.0 OE2 A:GLU132 2.0 9.2 1.0 C A:MED913 2.1 13.5 0.5 OXT A:MED913 2.1 18.4 0.5 O A:MED913 2.2 12.8 0.5 OE1 A:GLU132 2.7 10.3 1.0 CD A:GLU132 2.7 8.1 1.0 CD2 A:HIS247 3.0 7.4 1.0 CG A:ASP97 3.0 6.6 1.0 CE1 A:HIS247 3.0 12.7 1.0 CA A:MED913 3.3 17.5 0.5 OD1 A:ASP97 3.4 7.2 1.0 N A:MED913 3.5 14.7 0.5 ZN A:ZN901 3.6 8.0 1.0 O A:HOH1003 3.9 8.6 1.0 CE1 A:TYR246 4.0 11.4 1.0 ND1 A:HIS247 4.1 12.7 1.0 CG A:GLU132 4.1 8.7 1.0 CG A:HIS247 4.1 8.6 1.0 O A:MED913 4.2 20.4 0.5 OE1 A:GLU131 4.2 9.7 1.0 OH A:TYR246 4.3 18.0 1.0 CB A:ASP97 4.3 7.3 1.0 CE1 A:HIS85 4.5 6.5 1.0 NE2 A:HIS85 4.5 6.3 1.0 CZ A:TYR246 4.5 14.2 1.0 CB A:MED913 4.6 16.0 0.5 CG1 A:VAL89 4.8 8.9 1.0 N A:MED913 4.8 15.4 0.5 CD1 A:TYR246 4.9 9.8 1.0 C A:MED913 5.0 15.9 0.5

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.