Zinc in PDB 5f09: Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate

All present enzymatic activity of Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate:
3.4.17.21;

The structure of Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate, PDB code: 5f09 was solved by J.Tykvart, M.Navratil, P.Pachl, J.Konvalinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.85
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	100.901, 130.923, 159.136, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 18.1

The structure of Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate (pdb code 5f09). 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 Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate, PDB code: 5f09:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn815 b:28.0 occ:1.00 OD2 A:ASP387 2.0 28.7 1.0 OE2 A:GLU425 2.1 25.6 1.0 NE2 A:HIS553 2.1 26.9 1.0 O A:HOH933 2.2 24.4 0.3 O A:HOH902 2.2 28.4 1.0 OE1 A:GLU425 2.5 28.1 1.0 CD A:GLU425 2.6 25.9 1.0 OAK A:BC8819 2.6 37.6 0.7 CG A:ASP387 3.0 26.2 1.0 CE1 A:HIS553 3.0 26.5 1.0 CD2 A:HIS553 3.1 27.3 1.0 OD1 A:ASP387 3.2 25.6 1.0 ZN A:ZN816 3.4 26.7 1.0 O A:HOH1197 3.7 17.6 0.3 CAJ A:BC8819 3.7 38.1 0.7 CE1 A:TYR552 4.0 29.4 1.0 O A:HOH967 4.1 21.9 1.0 CG A:GLU425 4.1 24.6 1.0 ND1 A:HIS553 4.2 27.7 1.0 CA A:BC8819 4.2 32.2 0.7 CG A:HIS553 4.2 27.6 1.0 OH A:TYR552 4.2 31.4 1.0 O A:HOH1335 4.2 27.0 0.3 CB A:ASP387 4.3 26.9 1.0 N A:BC8819 4.4 37.4 0.7 CZ A:TYR552 4.5 30.0 1.0 NE2 A:HIS377 4.5 23.1 1.0 C A:BC8819 4.6 29.7 0.7 CD1 A:TRP381 4.6 28.7 1.0 OAI A:BC8819 4.6 37.2 0.7 CE1 A:HIS377 4.6 23.3 1.0 NE1 A:TRP381 4.7 29.2 1.0 OXT A:BC8819 4.7 25.8 0.7 CAD A:BC8819 4.8 37.0 0.7

Zinc binding site 2 out of 2 in the Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn816 b:26.7 occ:1.00 OD1 A:ASP387 1.9 25.6 1.0 OD2 A:ASP453 2.0 24.3 1.0 NE2 A:HIS377 2.1 23.1 1.0 O A:HOH902 2.2 28.4 1.0 O A:HOH1197 2.5 17.6 0.3 CG A:ASP453 2.7 24.7 1.0 OD1 A:ASP453 2.7 25.6 1.0 CG A:ASP387 2.9 26.2 1.0 CE1 A:HIS377 3.0 23.3 1.0 CD2 A:HIS377 3.1 22.2 1.0 OD2 A:ASP387 3.3 28.7 1.0 ZN A:ZN815 3.4 28.0 1.0 OE2 A:GLU425 3.8 25.6 1.0 OAI A:BC8819 4.1 37.2 0.7 OAK A:BC8819 4.1 37.6 0.7 ND1 A:HIS377 4.2 22.9 1.0 CB A:ASP453 4.2 24.3 1.0 CG A:HIS377 4.2 21.5 1.0 CB A:ASP387 4.2 26.9 1.0 O A:HOH933 4.3 24.4 0.3 ND2 A:ASN519 4.3 25.7 1.0 CB A:PRO388 4.4 23.6 1.0 O A:HOH1335 4.4 27.0 0.3 CAJ A:BC8819 4.5 38.1 0.7 CD A:GLU425 4.5 25.9 1.0 CA A:ASP387 4.6 26.6 1.0 CA A:PRO388 4.6 24.1 1.0 OG A:SER454 4.7 28.5 1.0 C A:ASP387 4.7 25.7 1.0 N A:PRO388 4.7 24.2 1.0 O A:HOH1090 4.8 45.6 1.0 OE1 A:GLU425 4.8 28.1 1.0 CAD A:BC8819 4.9 37.0 0.7 O A:HOH983 4.9 21.1 0.3

M.Navratil, J.Tykvart, J.Schimer, P.Pachl, V.Navratil, T.A.Rokob, K.Hlouchova, L.Rulisek, J.Konvalinka. Comparison of Human Glutamate Carboxypeptidases II and III Reveals Their Divergent Substrate Specificities. Febs J. V. 283 2528 2016.
ISSN: ISSN 1742-464X
PubMed: 27208881
DOI: 10.1111/FEBS.13761