Zinc in PDB 6hkz: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 2-49-1

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 2-49-1:
3.4.17.21;

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 2-49-1, PDB code: 6hkz was solved by L.Motlova, Z.Novakova, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.59 / 2.09
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.956, 132.259, 161.589, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.3

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 2-49-1 also contains other interesting chemical elements:

Fluorine	(F)	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 (Gcpii) in Complex with A Inhibitor Rna 2-49-1 (pdb code 6hkz). 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 (Gcpii) in Complex with A Inhibitor Rna 2-49-1, PDB code: 6hkz:
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 (Gcpii) in Complex with A Inhibitor Rna 2-49-1


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 (Gcpii) in Complex with A Inhibitor Rna 2-49-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:48.3 occ:1.00 OD2 A:ASP387 2.1 46.8 1.0 OE2 A:GLU425 2.1 50.4 1.0 NE2 A:HIS553 2.1 45.5 1.0 O A:HOH1055 2.1 43.6 1.0 OE1 A:GLU425 2.5 46.5 1.0 OBE A:GBZ818 2.5 46.2 1.0 CD A:GLU425 2.6 47.0 1.0 CG A:ASP387 3.0 48.9 1.0 CE1 A:HIS553 3.1 49.9 1.0 CD2 A:HIS553 3.1 46.0 1.0 ZN A:ZN802 3.3 48.0 1.0 OD1 A:ASP387 3.3 54.1 1.0 CAU A:GBZ818 3.4 48.4 1.0 NAV A:GBZ818 4.0 48.9 1.0 CAW A:GBZ818 4.1 47.6 1.0 CG A:GLU425 4.1 45.1 1.0 OE1 A:GLU424 4.2 43.0 1.0 O A:HOH1003 4.2 41.1 1.0 ND1 A:HIS553 4.2 46.6 1.0 CE1 A:TYR552 4.2 50.1 1.0 CG A:HIS553 4.3 46.1 1.0 N A:GBZ818 4.3 47.0 1.0 CB A:ASP387 4.4 46.9 1.0 OH A:TYR552 4.4 46.5 1.0 CAX A:GBZ818 4.6 47.9 1.0 CA A:GBZ818 4.6 49.9 1.0 NE2 A:HIS377 4.7 43.0 1.0 CZ A:TYR552 4.8 48.6 1.0 OBG A:GBZ818 4.8 51.0 1.0 CE1 A:HIS377 4.9 47.4 1.0 CD1 A:TRP381 4.9 50.7 1.0 OD2 A:ASP453 4.9 48.8 1.0

Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 2-49-1


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 (Gcpii) in Complex with A Inhibitor Rna 2-49-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:48.0 occ:1.00 O A:HOH1055 1.9 43.6 1.0 OD2 A:ASP453 2.0 48.8 1.0 OD1 A:ASP387 2.0 54.1 1.0 NE2 A:HIS377 2.1 43.0 1.0 CG A:ASP453 2.8 47.3 1.0 OD1 A:ASP453 2.8 45.3 1.0 CG A:ASP387 2.9 48.9 1.0 CE1 A:HIS377 3.1 47.4 1.0 OD2 A:ASP387 3.1 46.8 1.0 CD2 A:HIS377 3.1 46.2 1.0 ZN A:ZN801 3.3 48.3 1.0 OE2 A:GLU425 3.6 50.4 1.0 OE1 A:GLU424 3.8 43.0 1.0 CD A:GLU424 4.1 46.1 1.0 ND1 A:HIS377 4.2 43.8 1.0 OE2 A:GLU424 4.2 43.1 1.0 CG A:HIS377 4.3 43.1 1.0 CB A:ASP453 4.3 45.9 1.0 CB A:ASP387 4.3 46.9 1.0 ND2 A:ASN519 4.3 42.3 1.0 CB A:PRO388 4.4 46.0 1.0 CD A:GLU425 4.4 47.0 1.0 OBE A:GBZ818 4.5 46.2 1.0 CAU A:GBZ818 4.6 48.4 1.0 CA A:PRO388 4.6 44.9 1.0 C A:ASP387 4.6 50.0 1.0 CA A:ASP387 4.7 50.8 1.0 N A:PRO388 4.7 45.5 1.0 OE1 A:GLU425 4.7 46.5 1.0 N A:GBZ818 4.8 47.0 1.0 OG A:SER454 4.8 46.8 1.0 CA A:GBZ818 4.9 49.9 1.0 O A:HOH1053 5.0 52.1 1.0

R.Nakajima, Z.Novakova, W.Tueckmantel, L.Motlova, C.Barinka, A.P.Kozikowski. 2-Aminoadipic Acid-C(O)-Glutamate Based Prostate-Specific Membrane Antigen Ligands For Potential Use As Theranostics. Acs Med Chem Lett V. 9 1099 2018.
ISSN: ISSN 1948-5875
PubMed: 30429952
DOI: 10.1021/ACSMEDCHEMLETT.8B00318