Zinc in PDB 4ngm: 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: 4ngm 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)	49.03 / 1.84
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	101.300, 130.193, 158.789, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.6

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 4ngm). 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: 4ngm:
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:Zn817 b:16.3 occ:1.00 O A:HOH901 1.7 13.4 1.0 NE2 A:HIS377 2.0 16.9 1.0 OD2 A:ASP453 2.0 18.7 1.0 OD1 A:ASP387 2.0 19.2 1.0 CG A:ASP453 2.8 17.9 1.0 CG A:ASP387 2.9 15.9 1.0 OD1 A:ASP453 2.9 19.5 1.0 CE1 A:HIS377 3.0 16.3 1.0 CD2 A:HIS377 3.0 15.6 1.0 OD2 A:ASP387 3.1 18.4 1.0 ZN A:ZN818 3.3 17.0 1.0 OE2 A:GLU425 3.6 14.5 1.0 OE1 A:GLU424 3.7 14.2 1.0 CD A:GLU424 4.1 16.5 1.0 ND1 A:HIS377 4.1 15.5 1.0 CG A:HIS377 4.1 14.3 1.0 OE2 A:GLU424 4.2 15.0 1.0 CB A:ASP453 4.3 15.5 1.0 CB A:ASP387 4.3 16.8 1.0 CB A:PRO388 4.3 17.5 1.0 ND2 A:ASN519 4.3 15.1 1.0 CD A:GLU425 4.3 14.1 1.0 C6 A:JB7821 4.4 19.0 1.0 O5 A:JB7821 4.5 15.9 1.0 CA A:PRO388 4.6 18.0 1.0 N A:PRO388 4.6 17.4 1.0 OE1 A:GLU425 4.6 15.0 1.0 C A:ASP387 4.6 15.2 1.0 CA A:ASP387 4.6 16.8 1.0 N2 A:JB7821 4.7 16.8 1.0 OG A:SER454 4.8 17.5 1.0 N1 A:JB7821 4.8 15.5 1.0 O A:HOH1025 4.9 26.2 1.0 CG A:GLU424 5.0 14.4 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:Zn818 b:17.0 occ:1.00 OD2 A:ASP387 2.0 18.4 1.0 NE2 A:HIS553 2.0 16.9 1.0 O A:HOH901 2.1 13.4 1.0 OE2 A:GLU425 2.2 14.5 1.0 OE1 A:GLU425 2.4 15.0 1.0 O5 A:JB7821 2.6 15.9 1.0 CD A:GLU425 2.6 14.1 1.0 CE1 A:HIS553 3.0 15.5 1.0 CG A:ASP387 3.0 15.9 1.0 CD2 A:HIS553 3.1 17.5 1.0 ZN A:ZN817 3.3 16.3 1.0 C6 A:JB7821 3.3 19.0 1.0 OD1 A:ASP387 3.4 19.2 1.0 N1 A:JB7821 3.9 15.5 1.0 C2 A:JB7821 3.9 16.2 1.0 CE1 A:TYR552 4.0 14.8 1.0 ND1 A:HIS553 4.1 16.5 1.0 O A:HOH911 4.1 14.3 1.0 CG A:GLU425 4.1 12.9 1.0 OE1 A:GLU424 4.1 14.2 1.0 CG A:HIS553 4.2 16.2 1.0 N2 A:JB7821 4.3 16.8 1.0 OH A:TYR552 4.3 17.8 1.0 CB A:ASP387 4.4 16.8 1.0 NE2 A:HIS377 4.5 16.9 1.0 C1 A:JB7821 4.5 16.8 1.0 CZ A:TYR552 4.6 16.7 1.0 CD1 A:TRP381 4.7 19.3 1.0 C7 A:JB7821 4.7 18.8 1.0 CE1 A:HIS377 4.7 16.3 1.0 O1 A:JB7821 4.8 16.2 1.0 NE1 A:TRP381 4.8 18.0 1.0 OD2 A:ASP453 4.9 18.7 1.0 CD1 A:TYR552 5.0 16.8 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