Zinc in PDB 3k5x: Crystal Structure of Dipeptidase From Streptomics Coelicolor Complexed with Phosphinate Pseudodipeptide L-Ala-D-Asp at 1.4A Resolution.

The structure of Crystal Structure of Dipeptidase From Streptomics Coelicolor Complexed with Phosphinate Pseudodipeptide L-Ala-D-Asp at 1.4A Resolution., PDB code: 3k5x 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)	24.88 / 1.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	96.910, 96.910, 104.190, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 20.6

The binding sites of Zinc atom in the Crystal Structure of Dipeptidase From Streptomics Coelicolor Complexed with Phosphinate Pseudodipeptide L-Ala-D-Asp at 1.4A Resolution. (pdb code 3k5x). 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 Streptomics Coelicolor Complexed with Phosphinate Pseudodipeptide L-Ala-D-Asp at 1.4A Resolution., PDB code: 3k5x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Dipeptidase From Streptomics Coelicolor Complexed with Phosphinate Pseudodipeptide L-Ala-D-Asp at 1.4A Resolution.


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 Streptomics Coelicolor Complexed with Phosphinate Pseudodipeptide L-Ala-D-Asp at 1.4A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:11.2 occ:1.00 OD2 A:ASP22 2.0 11.8 1.0 NE2 A:HIS20 2.1 9.6 1.0 OE1 A:GLU123 2.1 11.1 1.0 O31 A:P8D401 2.2 11.9 1.0 N1 A:P8D401 2.3 11.5 1.0 CG A:ASP22 2.8 11.3 1.0 OD1 A:ASP22 2.9 11.3 1.0 P3 A:P8D401 3.0 12.2 1.0 CD A:GLU123 3.0 10.6 1.0 CE1 A:HIS20 3.1 11.5 1.0 C2 A:P8D401 3.1 11.2 1.0 CD2 A:HIS20 3.1 9.8 1.0 OE2 A:GLU123 3.2 10.5 1.0 O32 A:P8D401 3.6 11.5 1.0 ZN A:ZN403 3.7 11.7 1.0 OD1 A:ASP320 3.8 12.1 1.0 OG A:SER66 4.0 10.3 1.0 ND1 A:HIS20 4.2 10.3 1.0 CG A:HIS20 4.2 9.5 1.0 NE2 A:HIS212 4.2 9.7 1.0 CB A:ASP22 4.3 11.3 1.0 CB A:TYR68 4.3 11.7 1.0 O A:HOH614 4.4 23.1 1.0 CG A:GLU123 4.4 11.1 1.0 C1 A:P8D401 4.5 13.1 1.0 CG A:TYR68 4.5 11.8 1.0 CB A:SER66 4.5 11.2 1.0 C4 A:P8D401 4.6 12.9 1.0 CE1 A:HIS212 4.6 11.0 1.0 CD1 A:TYR68 4.8 11.8 1.0 CB A:GLU123 4.8 11.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Dipeptidase From Streptomics Coelicolor Complexed with Phosphinate Pseudodipeptide L-Ala-D-Asp at 1.4A Resolution.


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 Streptomics Coelicolor Complexed with Phosphinate Pseudodipeptide L-Ala-D-Asp at 1.4A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:11.7 occ:1.00 OE2 A:GLU123 2.0 10.5 1.0 NE2 A:HIS191 2.0 10.8 1.0 O32 A:P8D401 2.1 11.5 1.0 NE2 A:HIS212 2.1 9.7 1.0 O62 A:P8D401 2.3 12.0 1.0 O31 A:P8D401 2.6 11.9 1.0 P3 A:P8D401 2.8 12.2 1.0 CD2 A:HIS191 3.0 10.6 1.0 CE1 A:HIS212 3.0 11.0 1.0 CE1 A:HIS191 3.1 11.2 1.0 C6 A:P8D401 3.1 12.4 1.0 CD2 A:HIS212 3.1 10.0 1.0 CD A:GLU123 3.2 10.6 1.0 ZN A:ZN402 3.7 11.2 1.0 OE1 A:GLU123 3.8 11.1 1.0 O61 A:P8D401 3.8 6.8 1.0 C4 A:P8D401 3.8 12.9 1.0 NH2 A:ARG223 3.8 11.1 1.0 C5 A:P8D401 4.0 13.1 1.0 NE2 A:HIS150 4.1 12.0 1.0 ND1 A:HIS191 4.2 10.9 1.0 CG A:HIS191 4.2 10.6 1.0 ND1 A:HIS212 4.2 10.2 1.0 CD2 A:HIS150 4.2 11.1 1.0 NE2 A:HIS20 4.2 9.6 1.0 CG A:HIS212 4.3 9.8 1.0 CG A:GLU123 4.4 11.1 1.0 C2 A:P8D401 4.4 11.2 1.0 N1 A:P8D401 4.5 11.5 1.0 OD1 A:ASP320 4.5 12.1 1.0 CZ A:ARG223 4.6 11.9 1.0 CD2 A:HIS20 4.7 9.8 1.0 NE A:ARG223 4.8 11.6 1.0 CE1 A:HIS20 4.8 11.5 1.0

J.A.Cummings, T.T.Nguyen, A.A.Fedorov, P.Kolb, C.Xu, E.V.Fedorov, B.K.Shoichet, D.P.Barondeau, S.C.Almo, F.M.Raushel. Structure, Mechanism, and Substrate Profile For SCO3058: the Closest Bacterial Homologue to Human Renal Dipeptidase . Biochemistry V. 49 611 2010.
ISSN: ISSN 0006-2960
PubMed: 20000809
DOI: 10.1021/BI901935Y