Zinc in PDB 2c6p: Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Phosphate Anion

All present enzymatic activity of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Phosphate Anion:
3.4.17.21;

The structure of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Phosphate Anion, PDB code: 2c6p was solved by J.R.Mesters, C.Barinka, W.Li, T.Tsukamoto, P.Majer, B.S.Slusher, J.Konvalinka, R.Hilgenfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.14 / 2.39
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.573, 130.365, 159.414, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.1

The structure of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Phosphate Anion also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Phosphate Anion (pdb code 2c6p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Phosphate Anion, PDB code: 2c6p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Phosphate Anion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Phosphate Anion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1751 b:30.5 occ:1.00 OE2 A:GLU425 1.8 19.5 1.0 OD2 A:ASP387 1.9 24.2 1.0 O3 A:PO41764 2.0 41.8 1.0 NE2 A:HIS553 2.1 35.4 1.0 CD A:GLU425 2.4 24.3 1.0 OE1 A:GLU425 2.5 27.0 1.0 P A:PO41764 2.9 38.0 1.0 O1 A:PO41764 2.9 35.6 1.0 CG A:ASP387 3.0 32.1 1.0 CE1 A:HIS553 3.1 36.4 1.0 CD2 A:HIS553 3.1 34.8 1.0 OD1 A:ASP387 3.4 35.6 1.0 ZN A:ZN1752 3.6 30.8 1.0 O4 A:PO41764 3.7 38.4 1.0 O A:HOH2024 3.9 37.0 1.0 CG A:GLU425 4.0 25.4 1.0 CE1 A:TYR552 4.0 39.3 1.0 OH A:TYR552 4.1 36.7 1.0 O2 A:PO41764 4.1 41.2 1.0 ND1 A:HIS553 4.2 36.5 1.0 CG A:HIS553 4.2 36.6 1.0 OE1 A:GLU424 4.3 27.3 1.0 CB A:ASP387 4.3 31.7 1.0 O A:HOH2087 4.3 30.9 1.0 CZ A:TYR552 4.4 36.8 1.0 NE2 A:HIS377 4.4 40.9 1.0 CD1 A:TRP381 4.5 35.4 1.0 NE1 A:TRP381 4.6 36.1 1.0 CB A:GLU425 4.9 27.2 1.0 CD1 A:TYR552 5.0 39.7 1.0 CE1 A:HIS377 5.0 44.7 1.0

Zinc binding site 2 out of 2 in the Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Phosphate Anion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Phosphate Anion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1752 b:30.8 occ:1.00 O1 A:PO41764 1.8 35.6 1.0 OD1 A:ASP387 2.0 35.6 1.0 OD2 A:ASP453 2.0 33.0 1.0 NE2 A:HIS377 2.1 40.9 1.0 CE1 A:HIS377 2.5 44.7 1.0 OD1 A:ASP453 2.6 30.3 1.0 CG A:ASP453 2.7 30.8 1.0 CG A:ASP387 3.0 32.1 1.0 P A:PO41764 3.2 38.0 1.0 OD2 A:ASP387 3.3 24.2 1.0 CD2 A:HIS377 3.3 45.1 1.0 O4 A:PO41764 3.5 38.4 1.0 ZN A:ZN1751 3.6 30.5 1.0 ND1 A:HIS377 3.7 45.8 1.0 OE2 A:GLU425 3.7 19.5 1.0 OE1 A:GLU424 3.9 27.3 1.0 O3 A:PO41764 4.0 41.8 1.0 CG A:HIS377 4.1 37.5 1.0 ND2 A:ASN519 4.1 31.4 1.0 CD A:GLU424 4.2 28.1 1.0 OE2 A:GLU424 4.2 31.5 1.0 CB A:ASP453 4.2 31.3 1.0 O2 A:PO41764 4.3 41.2 1.0 CB A:ASP387 4.3 31.7 1.0 CB A:PRO388 4.3 29.4 1.0 CD A:GLU425 4.6 24.3 1.0 CA A:PRO388 4.6 29.8 1.0 N A:PRO388 4.6 30.5 1.0 CA A:ASP387 4.6 32.2 1.0 C A:ASP387 4.6 31.6 1.0 OG A:SER454 4.7 35.2 1.0 OD1 A:ASN519 4.9 31.6 1.0 CG A:ASN519 5.0 32.1 1.0

J.R.Mesters, C.Barinka, W.Li, T.Tsukamoto, P.Majer, B.S.Slusher, J.Konvalinka, R.Hilgenfeld. Structure of Glutamate Carboxypeptidase II, A Drug Target in Neuronal Damage and Prostate Cancer. Embo J. V. 25 1375 2006.
ISSN: ISSN 0261-4189
PubMed: 16467855
DOI: 10.1038/SJ.EMBOJ.7600969