Zinc in PDB 6h7y: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 1-79-1

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 1-79-1:
3.4.17.21;

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 1-79-1, PDB code: 6h7y 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)	47.26 / 1.81
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	102.258, 131.376, 159.874, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 17.8

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 1-79-1 also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Calcium	(Ca)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor Rna 1-79-1 (pdb code 6h7y). 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 1-79-1, PDB code: 6h7y:
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 1-79-1


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 1-79-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn817 b:33.1 occ:1.00 O A:HOH1165 1.9 30.8 1.0 OD2 A:ASP387 2.1 36.1 1.0 NE2 A:HIS553 2.1 32.6 1.0 OE2 A:GLU425 2.1 31.9 1.0 OE1 A:GLU425 2.5 33.3 1.0 OAT A:FVZ833 2.5 33.1 1.0 CD A:GLU425 2.6 33.7 1.0 CE1 A:HIS553 3.0 32.7 1.0 CG A:ASP387 3.0 35.6 1.0 CD2 A:HIS553 3.1 32.4 1.0 ZN A:ZN818 3.3 32.1 1.0 OD1 A:ASP387 3.3 34.6 1.0 CAA A:FVZ833 3.4 34.2 1.0 NAU A:FVZ833 4.0 32.9 1.0 CAV A:FVZ833 4.1 33.2 1.0 CE1 A:TYR552 4.1 33.2 1.0 OE1 A:GLU424 4.1 29.6 1.0 ND1 A:HIS553 4.1 34.1 1.0 CG A:GLU425 4.1 30.7 1.0 O A:HOH971 4.2 33.3 1.0 CG A:HIS553 4.2 31.9 1.0 N A:FVZ833 4.3 32.0 1.0 CB A:ASP387 4.4 34.1 1.0 OH A:TYR552 4.4 31.9 1.0 NE2 A:HIS377 4.5 29.8 1.0 CA A:FVZ833 4.6 33.7 1.0 CAW A:FVZ833 4.6 34.0 1.0 CZ A:TYR552 4.7 33.8 1.0 CE1 A:HIS377 4.8 31.6 1.0 CD1 A:TRP381 4.8 35.0 1.0 OAY A:FVZ833 4.9 34.0 1.0 OD2 A:ASP453 4.9 34.2 1.0 NE1 A:TRP381 4.9 33.4 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 1-79-1


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 1-79-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn818 b:32.1 occ:1.00 O A:HOH1165 1.9 30.8 1.0 OD2 A:ASP453 2.0 34.2 1.0 NE2 A:HIS377 2.0 29.8 1.0 OD1 A:ASP387 2.0 34.6 1.0 CG A:ASP453 2.7 32.3 1.0 OD1 A:ASP453 2.8 34.2 1.0 CG A:ASP387 2.9 35.6 1.0 CE1 A:HIS377 3.0 31.6 1.0 CD2 A:HIS377 3.0 30.4 1.0 OD2 A:ASP387 3.3 36.1 1.0 ZN A:ZN817 3.3 33.1 1.0 OE2 A:GLU425 3.6 31.9 1.0 OE1 A:GLU424 3.7 29.6 1.0 CD A:GLU424 4.1 30.3 1.0 ND1 A:HIS377 4.1 31.3 1.0 CG A:HIS377 4.1 30.6 1.0 CB A:ASP453 4.2 30.2 1.0 OE2 A:GLU424 4.2 30.3 1.0 ND2 A:ASN519 4.3 30.1 1.0 CB A:ASP387 4.3 34.1 1.0 CD A:GLU425 4.3 33.7 1.0 CB A:PRO388 4.4 32.7 1.0 OAT A:FVZ833 4.5 33.1 1.0 CAA A:FVZ833 4.5 34.2 1.0 CA A:PRO388 4.6 31.5 1.0 OE1 A:GLU425 4.7 33.3 1.0 CA A:ASP387 4.7 34.0 1.0 O A:HOH948 4.7 35.6 1.0 C A:ASP387 4.7 32.0 1.0 N A:PRO388 4.7 31.1 1.0 N A:FVZ833 4.7 32.0 1.0 OG A:SER454 4.8 29.2 0.7 CA A:FVZ833 4.9 33.7 1.0 NAU A:FVZ833 4.9 32.9 1.0 CG A:GLU424 5.0 31.0 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