Zinc in PDB 3s2n: Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Tyr-D-Asp

The structure of Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Tyr-D-Asp, PDB code: 3s2n 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)	32.23 / 1.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.922, 96.922, 104.711, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 16.4

The binding sites of Zinc atom in the Crystal Structure of Dipeptidase From Streptomyces Coelicolor Complexed with Phosphinate Pseudodipeptide L-Tyr-D-Asp (pdb code 3s2n). 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-Tyr-D-Asp, PDB code: 3s2n:
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-Tyr-D-Asp


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-Tyr-D-Asp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:10.2 occ:1.00 OD2 A:ASP22 2.1 9.9 1.0 O31 A:P4D401 2.1 9.6 1.0 OE1 A:GLU123 2.1 10.0 1.0 NE2 A:HIS20 2.1 8.4 1.0 N1 A:P4D401 2.2 10.9 1.0 CG A:ASP22 2.8 9.9 1.0 OD1 A:ASP22 2.9 10.9 1.0 CD A:GLU123 3.0 9.2 1.0 P3 A:P4D401 3.0 11.1 1.0 C2 A:P4D401 3.1 9.3 1.0 CE1 A:HIS20 3.1 8.7 1.0 CD2 A:HIS20 3.1 9.2 1.0 OE2 A:GLU123 3.1 9.9 1.0 O32 A:P4D401 3.6 10.6 1.0 ZN A:ZN403 3.7 10.4 1.0 OD1 A:ASP320 3.9 10.7 1.0 OG A:SER66 4.0 9.3 1.0 ND1 A:HIS20 4.2 9.5 1.0 CB A:ASP22 4.3 10.3 1.0 CG A:HIS20 4.3 8.4 1.0 NE2 A:HIS212 4.3 8.4 1.0 CG A:GLU123 4.4 9.2 1.0 CB A:TYR68 4.4 10.6 1.0 O A:HOH836 4.4 19.3 1.0 C1 A:P4D401 4.5 13.7 1.0 CB A:SER66 4.6 9.5 1.0 C4 A:P4D401 4.6 11.6 1.0 CG A:TYR68 4.6 9.3 1.0 CE1 A:HIS212 4.7 9.6 1.0 CD1 A:TYR68 4.8 10.0 1.0 CB A:GLU123 4.8 10.2 1.0

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


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-Tyr-D-Asp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:10.4 occ:1.00 NE2 A:HIS191 2.0 11.2 1.0 OE2 A:GLU123 2.1 9.9 1.0 NE2 A:HIS212 2.1 8.4 1.0 O32 A:P4D401 2.1 10.6 1.0 O62 A:P4D401 2.2 10.3 1.0 O31 A:P4D401 2.7 9.6 1.0 P3 A:P4D401 2.8 11.1 1.0 CE1 A:HIS212 3.0 9.6 1.0 CD2 A:HIS191 3.0 9.4 1.0 CE1 A:HIS191 3.0 10.2 1.0 C6 A:P4D401 3.1 12.2 1.0 CD2 A:HIS212 3.1 9.3 1.0 CD A:GLU123 3.2 9.2 1.0 ZN A:ZN402 3.7 10.2 1.0 O61 A:P4D401 3.8 11.3 1.0 NH2 A:ARG223 3.8 10.3 1.0 OE1 A:GLU123 3.8 10.0 1.0 C4 A:P4D401 3.8 11.6 1.0 C5 A:P4D401 4.0 13.9 1.0 NE2 A:HIS150 4.0 10.7 1.0 ND1 A:HIS191 4.1 10.3 1.0 CD2 A:HIS150 4.1 10.6 1.0 ND1 A:HIS212 4.2 8.8 1.0 CG A:HIS191 4.2 8.8 1.0 NE2 A:HIS20 4.2 8.4 1.0 CG A:HIS212 4.2 9.4 1.0 CG A:GLU123 4.4 9.2 1.0 C2 A:P4D401 4.4 9.3 1.0 N1 A:P4D401 4.4 10.9 1.0 OD1 A:ASP320 4.6 10.7 1.0 CZ A:ARG223 4.6 10.7 1.0 CD2 A:HIS20 4.7 9.2 1.0 CE1 A:HIS20 4.8 8.7 1.0 NE A:ARG223 4.8 9.5 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-Tyr-D-Asp To Be Published.