Zinc in PDB 4ngt: 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: 4ngt 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)	47.19 / 2.31
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	101.543, 130.297, 159.864, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 22.3

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

Bromine	(Br)	2 atoms
Calcium	(Ca)	1 atom
Chlorine	(Cl)	1 atom
Sodium	(Na)	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 4ngt). 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: 4ngt:
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:Zn810 b:21.0 occ:1.00 O A:HOH951 1.7 6.1 1.0 OD2 A:ASP453 1.9 18.6 1.0 OD1 A:ASP387 1.9 27.1 1.0 NE2 A:HIS377 2.0 20.0 1.0 CG A:ASP387 2.7 20.1 1.0 CG A:ASP453 2.8 20.4 1.0 CE1 A:HIS377 2.8 18.2 1.0 OD2 A:ASP387 3.0 15.5 1.0 OD1 A:ASP453 3.1 20.9 1.0 CD2 A:HIS377 3.1 18.7 1.0 ZN A:ZN811 3.2 20.7 1.0 OE2 A:GLU425 3.4 13.3 1.0 OE1 A:GLU424 3.6 18.4 1.0 CD A:GLU424 4.0 20.0 1.0 ND1 A:HIS377 4.0 17.6 1.0 CB A:ASP387 4.1 19.9 1.0 OE2 A:GLU424 4.1 19.4 1.0 CG A:HIS377 4.2 17.8 1.0 CD A:GLU425 4.2 14.0 1.0 CB A:ASP453 4.2 18.5 1.0 ND2 A:ASN519 4.3 20.0 1.0 CB A:PRO388 4.3 18.1 1.0 C11 A:J42815 4.4 22.9 0.5 N2 A:J42815 4.5 24.5 0.5 C11 A:J42815 4.5 21.5 0.5 O6 A:J42815 4.5 23.5 0.5 CA A:ASP387 4.5 21.2 1.0 CA A:PRO388 4.6 17.4 1.0 C A:ASP387 4.6 20.4 1.0 OE1 A:GLU425 4.6 13.7 1.0 O A:HOH1039 4.7 21.2 1.0 OG A:SER454 4.7 16.8 1.0 N A:PRO388 4.7 18.5 1.0 O6 A:J42815 4.7 24.8 0.5 N3 A:J42815 4.7 21.5 0.5 N2 A:J42815 4.8 22.6 0.5 N3 A:J42815 4.9 20.5 0.5 CG A:GLU424 4.9 18.4 1.0 C9 A:J42815 5.0 27.6 0.5

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:Zn811 b:20.7 occ:1.00 OD2 A:ASP387 1.9 15.5 1.0 O A:HOH951 2.1 6.1 1.0 OE2 A:GLU425 2.1 13.3 1.0 NE2 A:HIS553 2.1 19.3 1.0 OE1 A:GLU425 2.4 13.7 1.0 O6 A:J42815 2.5 23.5 0.5 CD A:GLU425 2.6 14.0 1.0 O6 A:J42815 2.6 24.8 0.5 CG A:ASP387 3.0 20.1 1.0 CE1 A:HIS553 3.0 20.6 1.0 C11 A:J42815 3.2 22.9 0.5 ZN A:ZN810 3.2 21.0 1.0 CD2 A:HIS553 3.2 18.1 1.0 C11 A:J42815 3.3 21.5 0.5 OD1 A:ASP387 3.5 27.1 1.0 N3 A:J42815 3.7 21.5 0.5 N3 A:J42815 3.8 20.5 0.5 C12 A:J42815 3.9 19.7 0.5 C12 A:J42815 3.9 20.5 0.5 N2 A:J42815 4.0 24.5 0.5 OE1 A:GLU424 4.1 18.4 1.0 CG A:GLU425 4.1 15.4 1.0 CE1 A:TYR552 4.1 16.9 1.0 ND1 A:HIS553 4.2 20.2 1.0 CB A:ASP387 4.2 19.9 1.0 O A:HOH946 4.2 14.3 1.0 N2 A:J42815 4.3 22.6 0.5 OH A:TYR552 4.3 15.2 1.0 CG A:HIS553 4.3 21.1 1.0 C16 A:J42815 4.5 19.6 0.5 C16 A:J42815 4.5 20.3 0.5 C9 A:J42815 4.5 27.6 0.5 CZ A:TYR552 4.6 16.4 1.0 NE2 A:HIS377 4.7 20.0 1.0 CE1 A:HIS377 4.7 18.2 1.0 CD1 A:TRP381 4.7 20.3 1.0 C9 A:J42815 4.8 25.1 0.5 OD2 A:ASP453 4.8 18.6 1.0 O4 A:J42815 4.8 20.4 0.5 O4 A:J42815 4.8 21.1 0.5 NE1 A:TRP381 4.8 20.3 1.0 CD A:GLU424 4.9 20.0 1.0 OE2 A:GLU424 4.9 19.4 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