Zinc in PDB 4ngq: Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor

All present enzymatic activity of Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor:
3.4.17.21;

The structure of Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor, PDB code: 4ngq was solved by J.Tykvart, P.Pachl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.89 / 2.08
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	101.088, 130.347, 158.784, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 21.3

The structure of Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Chlorine	(Cl)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor (pdb code 4ngq). 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 Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor, PDB code: 4ngq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor


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 Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn816 b:17.4 occ:1.00 O A:HOH1095 1.7 12.3 1.0 NE2 A:HIS377 2.0 12.9 1.0 OD2 A:ASP453 2.1 18.1 1.0 OD1 A:ASP387 2.1 17.7 1.0 CG A:ASP453 2.8 17.8 1.0 OD1 A:ASP453 2.9 18.2 1.0 CG A:ASP387 2.9 15.2 1.0 CE1 A:HIS377 2.9 12.7 1.0 CD2 A:HIS377 3.0 13.1 1.0 OD2 A:ASP387 3.1 16.8 1.0 ZN A:ZN817 3.2 17.4 1.0 OE2 A:GLU425 3.6 11.6 1.0 OE1 A:GLU424 3.8 14.1 1.0 ND1 A:HIS377 4.1 12.7 1.0 CD A:GLU424 4.1 12.8 1.0 CG A:HIS377 4.2 13.1 1.0 OE2 A:GLU424 4.2 12.1 1.0 ND2 A:ASN519 4.3 13.9 1.0 CB A:ASP387 4.3 15.9 1.0 CB A:ASP453 4.3 15.5 1.0 CD A:GLU425 4.4 11.8 1.0 CB A:PRO388 4.4 14.6 1.0 C2 A:J37820 4.5 17.8 1.0 O6 A:J37820 4.5 15.1 1.0 N A:J37820 4.6 16.5 1.0 CA A:PRO388 4.6 15.4 1.0 CA A:ASP387 4.7 14.3 1.0 C A:ASP387 4.7 14.4 1.0 N A:PRO388 4.7 14.6 1.0 OE1 A:GLU425 4.7 13.5 1.0 C1 A:J37820 4.7 20.0 1.0 OG A:SER454 4.8 19.3 1.0 N1 A:J37820 4.9 16.9 1.0 O A:HOH1087 4.9 22.3 1.0 C A:J37820 5.0 17.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor


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 Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn817 b:17.4 occ:1.00 OD2 A:ASP387 2.0 16.8 1.0 O A:HOH1095 2.0 12.3 1.0 NE2 A:HIS553 2.1 17.2 1.0 OE2 A:GLU425 2.1 11.6 1.0 OE1 A:GLU425 2.5 13.5 1.0 O6 A:J37820 2.5 15.1 1.0 CD A:GLU425 2.6 11.8 1.0 CE1 A:HIS553 3.0 15.2 1.0 CG A:ASP387 3.0 15.2 1.0 CD2 A:HIS553 3.2 16.3 1.0 ZN A:ZN816 3.2 17.4 1.0 C2 A:J37820 3.3 17.8 1.0 OD1 A:ASP387 3.4 17.7 1.0 N1 A:J37820 3.8 16.9 1.0 C3 A:J37820 4.0 15.5 1.0 CE1 A:TYR552 4.0 14.6 1.0 OE1 A:GLU424 4.1 14.1 1.0 CG A:GLU425 4.1 11.7 1.0 ND1 A:HIS553 4.1 15.4 1.0 N A:J37820 4.2 16.5 1.0 O A:HOH989 4.2 15.0 1.0 CG A:HIS553 4.3 15.7 1.0 OH A:TYR552 4.3 15.2 1.0 CB A:ASP387 4.4 15.9 1.0 C1 A:J37820 4.5 20.0 1.0 NE2 A:HIS377 4.5 12.9 1.0 C7 A:J37820 4.6 15.4 1.0 CZ A:TYR552 4.6 14.0 1.0 CE1 A:HIS377 4.7 12.7 1.0 CD1 A:TRP381 4.7 18.1 1.0 O4 A:J37820 4.8 15.8 1.0 NE1 A:TRP381 4.8 18.8 1.0 CD A:GLU424 5.0 12.8 1.0 OD2 A:ASP453 5.0 18.1 1.0 CD1 A:TYR552 5.0 15.1 1.0

J.Tykvart, J.Schimer, J.Barinkova, P.Pachl, L.Postova-Slavetinska, P.Majer, J.Konvalinka, P.Sacha. Rational Design of Urea-Based Glutamate Carboxypeptidase II (Gcpii) Inhibitors As Versatile Tools For Specific Drug Targeting and Delivery Bioorg.Med.Chem. 2014.
ISSN: ESSN 1464-3391
DOI: 10.1016/J.BMC.2014.05.061