Zinc in PDB 2pvv: Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate

All present enzymatic activity of Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate:
3.4.17.21;

The structure of Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate, PDB code: 2pvv was solved by C.Barinka, J.Lubkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.11
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	101.617, 130.220, 158.975, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.2

The structure of Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate (pdb code 2pvv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate, PDB code: 2pvv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1751 b:24.1 occ:1.00 OE2 A:GLU425 2.0 14.4 1.0 OD2 A:ASP387 2.0 21.9 1.0 NE2 A:HIS553 2.1 19.4 1.0 O A:HOH2263 2.2 17.3 1.0 OE1 A:GLU425 2.4 19.2 1.0 CD A:GLU425 2.5 15.0 1.0 CG A:ASP387 2.9 21.2 1.0 CD2 A:HIS553 3.1 17.4 1.0 CE1 A:HIS553 3.1 19.4 1.0 OD1 A:ASP387 3.2 22.9 1.0 ZN A:ZN1752 3.2 21.3 1.0 O A:HOH2264 3.5 27.5 1.0 O A:HOH1784 4.0 16.4 1.0 CG A:GLU425 4.0 14.1 1.0 CE1 A:TYR552 4.1 20.1 1.0 OE1 A:GLU424 4.1 15.8 1.0 OH A:TYR552 4.2 24.8 1.0 ND1 A:HIS553 4.2 18.8 1.0 N A:OSE1768 4.2 23.9 1.0 CG A:HIS553 4.2 20.5 1.0 CB A:ASP387 4.3 19.6 1.0 NE2 A:HIS377 4.4 14.4 1.0 CA A:OSE1768 4.4 22.8 1.0 CE1 A:HIS377 4.5 17.2 1.0 CZ A:TYR552 4.5 20.2 1.0 CD1 A:TRP381 4.6 18.6 1.0 C A:OSE1768 4.6 22.6 1.0 NE1 A:TRP381 4.7 22.3 1.0 OXT A:OSE1768 4.7 22.4 1.0 OD2 A:ASP453 4.9 17.0 1.0

Zinc binding site 2 out of 2 in the Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1752 b:21.3 occ:1.00 O A:HOH2263 1.8 17.3 1.0 NE2 A:HIS377 2.0 14.4 1.0 OD2 A:ASP453 2.0 17.0 1.0 OD1 A:ASP387 2.1 22.9 1.0 OD1 A:ASP453 2.7 21.1 1.0 CG A:ASP453 2.7 20.2 1.0 CE1 A:HIS377 2.9 17.2 1.0 CD2 A:HIS377 3.0 13.9 1.0 CG A:ASP387 3.0 21.2 1.0 ZN A:ZN1751 3.2 24.1 1.0 OD2 A:ASP387 3.3 21.9 1.0 OE2 A:GLU425 3.6 14.4 1.0 OE1 A:GLU424 3.7 15.8 1.0 O A:HOH2272 3.9 35.6 1.0 O A:HOH2264 4.0 27.5 1.0 ND1 A:HIS377 4.0 16.7 1.0 CD A:GLU424 4.1 19.8 1.0 CG A:HIS377 4.1 14.7 1.0 CB A:ASP453 4.2 18.6 1.0 ND2 A:ASN519 4.3 17.7 1.0 CB A:PRO388 4.3 20.7 1.0 CB A:ASP387 4.3 19.6 1.0 CD A:GLU425 4.4 15.0 1.0 OE2 A:GLU424 4.4 16.6 1.0 CA A:PRO388 4.6 19.8 1.0 CA A:ASP387 4.6 19.8 1.0 N A:PRO388 4.6 19.8 1.0 N A:OSE1768 4.6 23.9 1.0 OG A:SER454 4.6 19.7 1.0 C A:ASP387 4.6 18.7 1.0 OE1 A:GLU425 4.7 19.2 1.0

C.Barinka, M.Rovenska, P.Mlcochova, K.Hlouchova, A.Plechanovova, P.Majer, T.Tsukamoto, B.S.Slusher, J.Konvalinka, J.Lubkowski. Structural Insight Into the Pharmacophore Pocket of Human Glutamate Carboxypeptidase II. J.Med.Chem. V. 50 3267 2007.
ISSN: ISSN 0022-2623
PubMed: 17567119
DOI: 10.1021/JM070133W