Zinc in PDB 6f5l: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor JHU2379

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor JHU2379:
3.4.17.21;

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor JHU2379, PDB code: 6f5l was solved by C.Barinka, Z.Novakova, L.Motlova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.63
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	101.099, 130.270, 158.584, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 17.4

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor JHU2379 also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Inhibitor JHU2379 (pdb code 6f5l). 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 JHU2379, PDB code: 6f5l:
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 JHU2379


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 JHU2379 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn816 b:23.3 occ:1.00 OD2 A:ASP387 2.0 25.5 1.0 NE2 A:HIS553 2.0 22.0 1.0 O A:HOH1064 2.1 22.6 1.0 OE2 A:GLU425 2.1 22.8 1.0 OE1 A:GLU425 2.4 22.7 1.0 CD A:GLU425 2.6 22.3 1.0 OAF A:CQB823 2.7 23.8 1.0 CG A:ASP387 2.9 24.2 1.0 CE1 A:HIS553 2.9 21.8 1.0 CD2 A:HIS553 3.1 23.0 1.0 ZN A:ZN817 3.3 23.9 1.0 OD1 A:ASP387 3.3 22.6 1.0 CAR A:CQB823 3.4 27.2 1.0 OAN A:CQB823 3.8 24.3 1.0 CAU A:CQB823 4.0 25.2 1.0 CE1 A:TYR552 4.0 23.8 1.0 O A:HOH1016 4.1 24.6 1.0 ND1 A:HIS553 4.1 22.2 1.0 OE1 A:GLU424 4.1 21.1 1.0 CG A:GLU425 4.1 21.4 1.0 CG A:HIS553 4.2 22.2 1.0 CB A:ASP387 4.2 23.5 1.0 N A:CQB823 4.4 23.8 1.0 OH A:TYR552 4.4 25.0 1.0 NE2 A:HIS377 4.5 21.6 1.0 CAQ A:CQB823 4.6 26.3 1.0 CZ A:TYR552 4.6 24.9 1.0 CD1 A:TRP381 4.6 23.8 1.0 CE1 A:HIS377 4.7 21.5 1.0 NE1 A:TRP381 4.8 23.4 1.0 CA A:CQB823 4.8 25.6 1.0 OAI A:CQB823 4.8 24.8 1.0 O A:HOH1107 4.9 34.1 1.0 CD1 A:TYR552 4.9 24.6 1.0 OD2 A:ASP453 4.9 25.2 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 JHU2379


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 JHU2379 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn817 b:23.9 occ:1.00 O A:HOH1064 1.8 22.6 1.0 NE2 A:HIS377 2.0 21.6 1.0 OD2 A:ASP453 2.0 25.2 1.0 OD1 A:ASP387 2.0 22.6 1.0 CG A:ASP453 2.7 26.1 1.0 OD1 A:ASP453 2.8 28.6 1.0 CG A:ASP387 2.9 24.2 1.0 CE1 A:HIS377 2.9 21.5 1.0 CD2 A:HIS377 3.0 21.8 1.0 OD2 A:ASP387 3.3 25.5 1.0 ZN A:ZN816 3.3 23.3 1.0 OE1 A:GLU424 3.6 21.1 1.0 OE2 A:GLU425 3.6 22.8 1.0 CD A:GLU424 4.0 21.2 1.0 ND1 A:HIS377 4.1 22.2 1.0 CG A:HIS377 4.1 20.5 1.0 CB A:ASP453 4.2 23.9 1.0 CB A:ASP387 4.2 23.5 1.0 ND2 A:ASN519 4.2 22.5 1.0 CB A:PRO388 4.3 22.7 1.0 OE2 A:GLU424 4.3 22.2 1.0 CD A:GLU425 4.4 22.3 1.0 O A:HOH1107 4.4 34.1 1.0 CAR A:CQB823 4.5 27.2 1.0 CA A:ASP387 4.5 23.5 1.0 CA A:PRO388 4.5 22.7 1.0 OAF A:CQB823 4.6 23.8 1.0 OE1 A:GLU425 4.6 22.7 1.0 C A:ASP387 4.6 23.5 1.0 N A:PRO388 4.7 23.4 1.0 OG A:SER454 4.7 26.1 1.0 N A:CQB823 4.7 23.8 1.0 OAN A:CQB823 4.7 24.3 1.0 O A:CQB823 5.0 28.1 1.0 CG A:GLU424 5.0 19.9 1.0

C.Barinka, Z.Novakova, N.Hin, D.Bim, D.V.Ferraris, B.Duvall, G.Kabarriti, R.Tsukamoto, M.Budesinsky, L.Motlova, C.Rojas, B.S.Slusher, T.A.Rokob, L.Rulisek, T.Tsukamoto. Structural and Computational Basis For Potent Inhibition of Glutamate Carboxypeptidase II By Carbamate-Based Inhibitors. Bioorg.Med.Chem. V. 27 255 2019.
ISSN: ESSN 1464-3391
PubMed: 30552009
DOI: 10.1016/J.BMC.2018.11.022