Zinc in PDB 2xej: Human Glutamate Carboxypeptidase II in Complex with Arm-M4, Urea-Based Inhibitor

All present enzymatic activity of Human Glutamate Carboxypeptidase II in Complex with Arm-M4, Urea-Based Inhibitor:
3.4.17.21;

The structure of Human Glutamate Carboxypeptidase II in Complex with Arm-M4, Urea-Based Inhibitor, PDB code: 2xej was solved by A.X.Zhang, R.Murelli, C.Barinka, J.Michel, A.Cocleaza, W.L.Jorgensen, J.Lubkowski, D.A.Spiegel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.78
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	101.508, 129.958, 159.246, 90.00, 90.00, 90.00
R / Rfree (%)	15.665 / 18.467

The structure of Human Glutamate Carboxypeptidase II in Complex with Arm-M4, Urea-Based Inhibitor also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Human Glutamate Carboxypeptidase II in Complex with Arm-M4, Urea-Based Inhibitor (pdb code 2xej). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Glutamate Carboxypeptidase II in Complex with Arm-M4, Urea-Based Inhibitor, PDB code: 2xej:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Glutamate Carboxypeptidase II in Complex with Arm-M4, 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 Human Glutamate Carboxypeptidase II in Complex with Arm-M4, Urea-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1751 b:19.5 occ:1.00 OD2 A:ASP387 2.1 21.1 1.0 NE2 A:HIS553 2.1 15.3 1.0 O A:HOH2542 2.1 12.3 1.0 OE2 A:GLU425 2.2 16.9 1.0 OE1 A:GLU425 2.4 16.1 1.0 OAE A:OKD1768 2.6 17.2 1.0 CD A:GLU425 2.6 16.5 1.0 CE1 A:HIS553 3.0 17.3 1.0 CG A:ASP387 3.0 17.6 1.0 CD2 A:HIS553 3.1 17.4 1.0 ZN A:ZN1752 3.3 18.8 1.0 OD1 A:ASP387 3.4 17.3 1.0 CBK A:OKD1768 3.4 20.6 1.0 NBB A:OKD1768 3.9 16.7 1.0 CBN A:OKD1768 3.9 17.2 1.0 CE1 A:TYR552 4.0 17.6 1.0 OE1 A:GLU424 4.1 15.4 1.0 ND1 A:HIS553 4.1 15.7 1.0 O A:HOH2273 4.1 15.1 1.0 CG A:GLU425 4.2 15.2 1.0 CG A:HIS553 4.2 15.7 1.0 N A:OKD1768 4.3 18.0 1.0 CB A:ASP387 4.3 18.7 1.0 OH A:TYR552 4.3 17.9 1.0 NE2 A:HIS377 4.5 17.1 1.0 CBJ A:OKD1768 4.5 18.9 1.0 CA A:OKD1768 4.6 20.7 1.0 CZ A:TYR552 4.6 18.1 1.0 CD1 A:TRP381 4.6 17.0 1.0 CE1 A:HIS377 4.7 17.2 1.0 NE1 A:TRP381 4.8 17.3 1.0 OAH A:OKD1768 4.8 19.8 1.0 OD2 A:ASP453 4.9 18.9 1.0 CD1 A:TYR552 5.0 18.7 1.0 CD A:GLU424 5.0 14.6 1.0

Zinc binding site 2 out of 2 in the Human Glutamate Carboxypeptidase II in Complex with Arm-M4, 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 Human Glutamate Carboxypeptidase II in Complex with Arm-M4, Urea-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1752 b:18.8 occ:1.00 O A:HOH2542 1.8 12.3 1.0 OD2 A:ASP453 2.0 18.9 1.0 OD1 A:ASP387 2.0 17.3 1.0 NE2 A:HIS377 2.0 17.1 1.0 CG A:ASP453 2.7 18.0 1.0 OD1 A:ASP453 2.8 21.2 1.0 CG A:ASP387 2.9 17.6 1.0 CE1 A:HIS377 3.0 17.2 1.0 CD2 A:HIS377 3.0 15.4 1.0 OD2 A:ASP387 3.2 21.1 1.0 ZN A:ZN1751 3.3 19.5 1.0 OE2 A:GLU425 3.6 16.9 1.0 OE1 A:GLU424 3.6 15.4 1.0 CD A:GLU424 4.0 14.6 1.0 ND1 A:HIS377 4.1 17.7 1.0 CG A:HIS377 4.1 15.4 1.0 OE2 A:GLU424 4.2 15.7 1.0 CB A:ASP453 4.2 15.5 1.0 CB A:ASP387 4.2 18.7 1.0 ND2 A:ASN519 4.2 14.7 1.0 CB A:PRO388 4.3 15.4 1.0 CD A:GLU425 4.3 16.5 1.0 CBK A:OKD1768 4.6 20.6 1.0 CA A:PRO388 4.6 16.6 1.0 CA A:ASP387 4.6 17.6 1.0 OAE A:OKD1768 4.6 17.2 1.0 C A:ASP387 4.6 17.1 1.0 OE1 A:GLU425 4.6 16.1 1.0 N A:PRO388 4.6 17.1 1.0 N A:OKD1768 4.7 18.0 1.0 OG A:SER454 4.8 19.8 1.0 O A:HOH2307 4.8 22.9 1.0 NBB A:OKD1768 4.8 16.7 1.0 CA A:OKD1768 4.9 20.7 1.0 CG A:GLU424 5.0 14.8 1.0

A.X.Zhang, R.P.Murelli, C.Barinka, J.Michel, A.Cocleaza, W.L.Jorgensen, J.Lubkowski, D.A.Spiegel. A Remote Arene-Binding Site on Prostate Specific Membrane Antigen Revealed By Antibody-Recruiting Small Molecules. J.Am.Chem.Soc. V. 132 12711 2010.
ISSN: ISSN 0002-7863
PubMed: 20726553
DOI: 10.1021/JA104591M