Zinc in PDB 1tkf: Streptomyces Griseus Aminopeptidase Complexed with D- Tryptophan

The structure of Streptomyces Griseus Aminopeptidase Complexed with D- Tryptophan, PDB code: 1tkf 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 / 1.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.606, 60.606, 144.186, 90.00, 90.00, 90.00
R / Rfree (%)	12.7 / 16.6

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

Calcium

(Ca)

1 atom

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

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


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- Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:6.8 occ:1.00 O A:DTR913 1.8 19.4 1.0 OD1 A:ASP97 2.0 6.2 1.0 NE2 A:HIS85 2.0 5.5 1.0 OD1 A:ASP160 2.0 6.9 1.0 OD2 A:ASP160 2.6 7.0 1.0 CG A:ASP160 2.6 6.3 1.0 CE1 A:HIS85 3.0 5.5 1.0 C A:DTR913 3.0 12.0 1.0 CG A:ASP97 3.0 5.6 1.0 CD2 A:HIS85 3.0 5.1 1.0 OD2 A:ASP97 3.5 6.6 1.0 OXT A:DTR913 3.7 13.1 1.0 ZN A:ZN902 3.7 7.8 1.0 CB A:ASN98 4.0 5.3 1.0 OE2 A:GLU132 4.0 8.9 1.0 CA A:DTR913 4.1 11.7 1.0 ND1 A:HIS85 4.1 5.8 1.0 CB A:ASP160 4.1 6.8 1.0 OE1 A:GLU131 4.1 10.2 1.0 CG A:HIS85 4.2 5.4 1.0 CG A:MET161 4.2 7.0 1.0 CB A:ASP97 4.3 5.7 1.0 CD A:GLU131 4.4 10.3 1.0 CB A:DTR913 4.5 12.5 1.0 CG A:ASN98 4.5 5.0 1.0 CA A:ASP97 4.5 5.8 1.0 OE2 A:GLU131 4.6 13.9 1.0 SD A:MET161 4.6 7.0 1.0 C A:ASP97 4.7 5.2 1.0 CA A:ASP160 4.8 6.1 1.0 CA A:ASN98 4.9 5.7 1.0 C A:ASP160 4.9 6.2 1.0 CD A:GLU132 4.9 7.7 1.0 N A:ASN98 4.9 5.5 1.0 ND2 A:ASN98 5.0 5.8 1.0 N A:MET161 5.0 5.7 1.0

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


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- Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:7.8 occ:1.00 OE2 A:GLU132 1.9 8.9 1.0 OXT A:DTR913 2.0 13.1 1.0 OD2 A:ASP97 2.0 6.6 1.0 NE2 A:HIS247 2.0 8.7 1.0 CD A:GLU132 2.7 7.7 1.0 OE1 A:GLU132 2.7 9.7 1.0 C A:DTR913 2.8 12.0 1.0 CD2 A:HIS247 3.0 6.1 1.0 CG A:ASP97 3.0 5.6 1.0 CE1 A:HIS247 3.0 11.3 1.0 O A:DTR913 3.0 19.4 1.0 OD1 A:ASP97 3.4 6.2 1.0 ZN A:ZN901 3.7 6.8 1.0 CE1 A:TYR246 3.9 9.6 1.0 O A:HOH1012 4.0 9.5 1.0 O A:HOH1321 4.0 33.0 1.0 ND1 A:HIS247 4.1 11.3 1.0 CG A:HIS247 4.1 7.0 1.0 CG A:GLU132 4.2 8.4 1.0 CA A:DTR913 4.2 11.7 1.0 OH A:TYR246 4.3 16.7 1.0 OE1 A:GLU131 4.3 10.2 1.0 CB A:ASP97 4.3 5.7 1.0 CZ A:TYR246 4.5 12.7 1.0 N A:DTR913 4.5 17.0 1.0 CE1 A:HIS85 4.6 5.5 1.0 NE2 A:HIS85 4.6 5.5 1.0 CG1 A:VAL89 4.7 8.7 1.0 CD1 A:TYR246 4.8 8.6 1.0 O A:HOH1236 4.8 18.6 1.0 CB A:DTR913 4.9 12.5 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.