Zinc in PDB 3s2l: Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Leu-D-Glu

The structure of Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Leu-D-Glu, PDB code: 3s2l was solved by A.A.Fedorov, E.V.Fedorov, J.Cummings, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.56 / 1.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.871, 96.871, 104.760, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 18.2

The binding sites of Zinc atom in the Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Leu-D-Glu (pdb code 3s2l). 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 Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Leu-D-Glu, PDB code: 3s2l:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Leu-D-Glu


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 Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Leu-D-Glu within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:11.8 occ:1.00 OD2 A:ASP22 2.0 11.5 1.0 O31 A:LDE401 2.1 13.5 1.0 OE1 A:GLU123 2.1 11.5 1.0 NE2 A:HIS20 2.1 10.8 1.0 N1 A:LDE401 2.2 12.3 1.0 CG A:ASP22 2.8 11.7 1.0 OD1 A:ASP22 2.9 12.2 1.0 CD A:GLU123 3.0 11.6 1.0 P3 A:LDE401 3.0 13.1 1.0 C2 A:LDE401 3.0 12.8 1.0 CE1 A:HIS20 3.1 10.7 1.0 CD2 A:HIS20 3.1 9.9 1.0 OE2 A:GLU123 3.1 12.1 1.0 O32 A:LDE401 3.6 14.0 1.0 ZN A:ZN403 3.7 12.4 1.0 OD1 A:ASP320 3.9 12.9 1.0 OG A:SER66 3.9 10.6 1.0 NE2 A:HIS212 4.2 11.4 1.0 ND1 A:HIS20 4.2 11.3 1.0 CB A:ASP22 4.2 12.2 1.0 CG A:HIS20 4.3 9.6 1.0 CG A:GLU123 4.4 11.2 1.0 CB A:TYR68 4.4 12.9 1.0 C1 A:LDE401 4.5 15.6 1.0 CB A:SER66 4.5 10.0 1.0 C4 A:LDE401 4.6 14.1 1.0 CE1 A:HIS212 4.6 11.3 1.0 CG A:TYR68 4.7 12.2 1.0 CB A:GLU123 4.8 11.6 1.0 CD1 A:TYR68 4.9 10.8 1.0 CD2 A:HIS212 4.9 10.8 1.0 O62 A:LDE401 5.0 12.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Leu-D-Glu


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 Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Leu-D-Glu within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:12.4 occ:1.00 OE2 A:GLU123 2.1 12.1 1.0 NE2 A:HIS191 2.1 11.5 1.0 NE2 A:HIS212 2.1 11.4 1.0 O32 A:LDE401 2.1 14.0 1.0 O62 A:LDE401 2.2 12.3 1.0 O31 A:LDE401 2.6 13.5 1.0 P3 A:LDE401 2.8 13.1 1.0 CE1 A:HIS212 3.0 11.3 1.0 CD2 A:HIS191 3.0 11.9 1.0 CE1 A:HIS191 3.1 10.6 1.0 C6 A:LDE401 3.1 13.1 1.0 CD2 A:HIS212 3.1 10.8 1.0 CD A:GLU123 3.2 11.6 1.0 ZN A:ZN402 3.7 11.8 1.0 NH2 A:ARG223 3.7 12.1 1.0 O61 A:LDE401 3.7 12.9 1.0 OE1 A:GLU123 3.8 11.5 1.0 C4 A:LDE401 3.9 14.1 1.0 C5 A:LDE401 4.0 17.2 1.0 NE2 A:HIS150 4.1 13.3 1.0 ND1 A:HIS212 4.2 10.5 1.0 ND1 A:HIS191 4.2 12.5 1.0 CG A:HIS191 4.2 11.7 1.0 NE2 A:HIS20 4.2 10.8 1.0 CD2 A:HIS150 4.2 11.8 1.0 CG A:HIS212 4.2 10.8 1.0 N1 A:LDE401 4.4 12.3 1.0 C2 A:LDE401 4.4 12.8 1.0 CG A:GLU123 4.4 11.2 1.0 OD1 A:ASP320 4.4 12.9 1.0 CZ A:ARG223 4.6 13.5 1.0 CD2 A:HIS20 4.7 9.9 1.0 NE A:ARG223 4.7 12.6 1.0 CE1 A:HIS20 4.8 10.7 1.0

A.A.Fedorov, E.V.Fedorov, J.Cummings, F.M.Raushel, S.C.Almo. Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Leu-D-Glu To Be Published.