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Calcium in PDB 4ngm: Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor

Enzymatic activity of Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor

All present enzymatic activity of Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor:
3.4.17.21;

Protein crystallography data

The structure of Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor, PDB code: 4ngm was solved by J.Tykvart, P.Pachl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.03 / 1.84
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.300, 130.193, 158.789, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.6

Other elements in 4ngm:

The structure of Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor also contains other interesting chemical elements:

Bromine (Br) 1 atom
Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor (pdb code 4ngm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor, PDB code: 4ngm:

Calcium binding site 1 out of 1 in 4ngm

Go back to Calcium Binding Sites List in 4ngm
Calcium binding site 1 out of 1 in the Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Glutamate Carboxypeptidase II in A Complex with Urea-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca820

b:14.2
occ:1.00
 O A:TYR272 2.3 15.6 1.0
O A:HOH902 2.3 14.8 1.0
OE2 A:GLU436 2.4 16.0 1.0
O A:THR269 2.4 14.3 1.0
OG1 A:THR269 2.5 13.9 1.0
OE1 A:GLU433 2.5 14.4 1.0
OE2 A:GLU433 2.5 13.1 1.0
CD A:GLU433 2.8 13.3 1.0
C A:THR269 3.3 15.6 1.0
CB A:THR269 3.3 15.4 1.0
C A:TYR272 3.4 15.2 1.0
CD A:GLU436 3.5 14.7 1.0
OE1 A:GLU436 3.9 13.2 1.0
CA A:THR269 3.9 15.9 1.0
N A:TYR272 4.0 14.6 1.0
CA A:PRO273 4.2 16.2 1.0
CB A:ASP266 4.2 15.8 1.0
N A:ALA274 4.2 15.5 1.0
CG A:GLU433 4.2 14.3 1.0
N A:PRO270 4.2 15.9 1.0
N A:PRO273 4.3 15.6 1.0
CA A:TYR272 4.4 15.2 1.0
C A:PRO273 4.4 16.4 1.0
CA A:PRO270 4.5 15.6 1.0
O A:ASP266 4.5 14.5 1.0
N A:GLY271 4.5 16.5 1.0
N A:ASP266 4.5 14.9 1.0
O A:ALA264 4.6 15.2 1.0
CG2 A:THR269 4.6 16.1 1.0
N A:THR269 4.6 15.6 1.0
CG A:GLU436 4.7 14.0 1.0
OD2 A:ASP266 4.8 17.0 1.0
C A:PRO270 4.8 15.8 1.0
CA A:ASP266 4.8 14.9 1.0
CB A:ALA274 4.9 18.0 1.0
CB A:GLU436 4.9 14.3 1.0
CA A:ALA274 5.0 18.0 1.0

Reference:

J.Tykvart, J.Schimer, J.Barinkova, P.Pachl, L.Postova-Slavetinska, P.Majer, J.Konvalinka, P.Sacha. Rational Design of Urea-Based Glutamate Carboxypeptidase II (Gcpii) Inhibitors As Versatile Tools For Specific Drug Targeting and Delivery Bioorg.Med.Chem. 2014.
ISSN: ESSN 1464-3391
DOI: 10.1016/J.BMC.2014.05.061
Page generated: Wed Jul 9 00:50:44 2025

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