Zinc in PDB 3sjf: X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with A Urea-Based Inhibitor (A25)

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with A Urea-Based Inhibitor (A25):
3.4.17.21;

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with A Urea-Based Inhibitor (A25), PDB code: 3sjf was solved by A.Plechanovova, Y.Byun, G.Alquicer, L.Skultetyova, P.Mlcochova, A.Nemcova, H.Kim, M.Navratil, R.Mease, J.Lubkowski, M.Pomper, J.Konvalinka, L.Rulisek, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.52 / 1.65
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	101.545, 130.431, 159.156, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 17.8

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with A Urea-Based Inhibitor (A25) also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with A Urea-Based Inhibitor (A25) (pdb code 3sjf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with A Urea-Based Inhibitor (A25), PDB code: 3sjf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with A Urea-Based Inhibitor (A25)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with A Urea-Based Inhibitor (A25) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1751 b:15.5 occ:1.00 O A:HOH2476 2.0 14.0 1.0 NE2 A:HIS553 2.0 17.2 1.0 OD2 A:ASP387 2.1 20.1 1.0 OE2 A:GLU425 2.1 18.6 1.0 OE1 A:GLU425 2.4 17.9 1.0 CD A:GLU425 2.6 17.3 1.0 OAD A:JRG1 2.6 20.9 1.0 CE1 A:HIS553 3.0 17.8 1.0 CG A:ASP387 3.0 18.5 1.0 CD2 A:HIS553 3.1 18.8 1.0 OD1 A:ASP387 3.3 18.4 1.0 ZN A:ZN1752 3.3 14.9 1.0 CAY A:JRG1 3.4 23.1 1.0 NAU A:JRG1 4.0 22.5 1.0 CBD A:JRG1 4.0 20.9 1.0 CE1 A:TYR552 4.0 18.6 1.0 OE1 A:GLU424 4.1 18.1 1.0 ND1 A:HIS553 4.1 16.4 1.0 O A:HOH1783 4.2 15.1 1.0 CG A:GLU425 4.2 18.3 1.0 CG A:HIS553 4.2 17.8 1.0 N A:JRG1 4.3 21.9 1.0 CB A:ASP387 4.3 18.4 1.0 OH A:TYR552 4.4 20.6 1.0 CA A:JRG1 4.5 23.7 1.0 NE2 A:HIS377 4.5 17.1 1.0 CAX A:JRG1 4.6 26.4 1.0 CZ A:TYR552 4.6 19.2 1.0 CD1 A:TRP381 4.7 19.5 1.0 CE1 A:HIS377 4.7 16.8 1.0 NE1 A:TRP381 4.8 18.6 1.0 OD2 A:ASP453 4.8 18.3 1.0 OAG A:JRG1 4.8 26.4 1.0 CD1 A:TYR552 5.0 20.2 1.0

Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with A Urea-Based Inhibitor (A25)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with A Urea-Based Inhibitor (A25) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1752 b:14.9 occ:1.00 O A:HOH2476 1.9 14.0 1.0 OD2 A:ASP453 1.9 18.3 1.0 OD1 A:ASP387 2.0 18.4 1.0 NE2 A:HIS377 2.0 17.1 1.0 CG A:ASP453 2.7 20.3 1.0 OD1 A:ASP453 2.8 22.4 1.0 CG A:ASP387 2.9 18.5 1.0 CE1 A:HIS377 3.0 16.8 1.0 CD2 A:HIS377 3.0 17.0 1.0 OD2 A:ASP387 3.3 20.1 1.0 ZN A:ZN1751 3.3 15.5 1.0 OE2 A:GLU425 3.6 18.6 1.0 OE1 A:GLU424 3.7 18.1 1.0 CD A:GLU424 4.0 18.8 1.0 ND1 A:HIS377 4.1 17.1 1.0 CB A:ASP453 4.1 18.9 1.0 CG A:HIS377 4.2 15.8 1.0 CB A:ASP387 4.2 18.4 1.0 OE2 A:GLU424 4.2 19.5 1.0 ND2 A:ASN519 4.2 18.1 1.0 CB A:PRO388 4.3 17.0 1.0 CD A:GLU425 4.3 17.3 1.0 CA A:PRO388 4.5 16.8 1.0 CA A:ASP387 4.5 18.7 1.0 CAY A:JRG1 4.6 23.1 1.0 C A:ASP387 4.6 19.0 1.0 OAD A:JRG1 4.6 20.9 1.0 N A:PRO388 4.6 18.1 1.0 OE1 A:GLU425 4.7 17.9 1.0 N A:JRG1 4.7 21.9 1.0 O A:HOH2477 4.7 24.6 1.0 OG A:SER454 4.7 19.9 0.8 CA A:JRG1 4.9 23.7 1.0 OXT A:JRG1 4.9 25.6 1.0 NAU A:JRG1 5.0 22.5 1.0 CG A:GLU424 5.0 16.4 1.0

A.Plechanovova, Y.Byun, G.Alquicer, L.Skultetyova, P.Mlcochova, A.Nemcova, H.J.Kim, M.Navratil, R.Mease, J.Lubkowski, M.Pomper, J.Konvalinka, L.Rulisek, C.Barinka. Novel Substrate-Based Inhibitors of Human Glutamate Carboxypeptidase II with Enhanced Lipophilicity. J.Med.Chem. V. 54 7535 2011.
ISSN: ISSN 0022-2623
PubMed: 21923190
DOI: 10.1021/JM200807M