Zinc in PDB 3gip: Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc, Acetate and Formate Ions.

All present enzymatic activity of Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc, Acetate and Formate Ions.:
3.5.1.82;

The structure of Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc, Acetate and Formate Ions., PDB code: 3gip 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)	24.95 / 1.50
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.988, 90.988, 507.134, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 21.5

The binding sites of Zinc atom in the Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc, Acetate and Formate Ions. (pdb code 3gip). 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 N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc, Acetate and Formate Ions., PDB code: 3gip:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc, Acetate and Formate Ions.


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 N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc, Acetate and Formate Ions. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn484 b:14.1 occ:1.00 ND1 A:HIS218 2.0 13.6 1.0 NE2 A:HIS248 2.1 11.6 1.0 SG A:CYS95 2.2 13.8 1.0 O A:ACY481 2.3 19.6 1.0 OXT A:ACY481 2.3 21.3 1.0 C A:ACY481 2.7 20.0 1.0 CE1 A:HIS218 2.9 13.5 1.0 CG A:HIS218 3.0 12.8 1.0 CE1 A:HIS248 3.0 16.0 1.0 CD2 A:HIS248 3.1 14.5 1.0 CB A:CYS95 3.3 13.3 1.0 CB A:HIS218 3.4 13.7 1.0 NE2 A:HIS218 4.0 14.5 1.0 NE2 A:HIS66 4.1 13.4 1.0 CD2 A:HIS218 4.1 13.7 1.0 CH3 A:ACY481 4.2 20.2 1.0 ND1 A:HIS248 4.2 13.1 1.0 CG A:HIS248 4.3 13.0 1.0 OH A:TYR190 4.3 17.2 1.0 CE1 A:HIS66 4.4 13.1 1.0 CA A:CYS95 4.5 13.4 1.0 CE2 A:TYR190 4.5 18.4 1.0 OD2 A:ASP365 4.6 17.6 1.0 CA A:HIS218 4.6 13.2 1.0 NE2 A:HIS68 4.7 15.9 1.0 C A:FMT482 4.8 14.7 1.0 CZ A:TYR190 4.9 18.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc, Acetate and Formate Ions.


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 N-Acyl-D-Glutamate Deacylase From Bordetella Bronchiseptica Complexed with Zinc, Acetate and Formate Ions. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn484 b:13.2 occ:1.00 ND1 B:HIS218 2.1 13.1 1.0 NE2 B:HIS248 2.1 12.0 1.0 O B:ACY481 2.2 15.9 1.0 SG B:CYS95 2.2 13.7 1.0 OXT B:ACY481 2.3 18.5 1.0 C B:ACY481 2.6 15.5 1.0 CE1 B:HIS218 3.0 12.2 1.0 CG B:HIS218 3.1 12.5 1.0 CE1 B:HIS248 3.1 13.2 1.0 CD2 B:HIS248 3.1 12.7 1.0 CB B:CYS95 3.3 12.5 1.0 CB B:HIS218 3.4 11.9 1.0 NE2 B:HIS218 4.1 12.8 1.0 CH3 B:ACY481 4.1 16.9 1.0 NE2 B:HIS66 4.1 12.4 1.0 CD2 B:HIS218 4.1 12.1 1.0 ND1 B:HIS248 4.2 11.4 1.0 CG B:HIS248 4.3 13.1 1.0 OH B:TYR190 4.3 14.2 1.0 CE1 B:HIS66 4.4 13.7 1.0 CE2 B:TYR190 4.5 13.4 1.0 CA B:CYS95 4.5 11.1 1.0 CA B:HIS218 4.6 12.3 1.0 OD2 B:ASP365 4.6 16.7 1.0 NE2 B:HIS68 4.7 15.0 1.0 C B:FMT482 4.8 15.5 1.0 CZ B:TYR190 4.9 13.2 1.0

J.A.Cummings, A.A.Fedorov, C.Xu, S.Brown, E.Fedorov, P.C.Babbitt, S.C.Almo, F.M.Raushel. Annotating Enzymes of Uncertain Function: the Deacylation of D-Amino Acids By Members of the Amidohydrolase Superfamily. Biochemistry V. 48 6469 2009.
ISSN: ISSN 0006-2960
PubMed: 19518059
DOI: 10.1021/BI900661B