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Calcium in PDB 3d7d: A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor

Enzymatic activity of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor

All present enzymatic activity of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor:
3.4.17.21;

Protein crystallography data

The structure of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor, PDB code: 3d7d was solved by J.Lubkowski, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.69
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.930, 130.497, 159.187, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 19.9

Other elements in 3d7d:

The structure of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor (pdb code 3d7d). 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 A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor, PDB code: 3d7d:

Calcium binding site 1 out of 1 in 3d7d

Go back to Calcium Binding Sites List in 3d7d
Calcium binding site 1 out of 1 in the A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A 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 A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1753

b:16.0
occ:1.00
 OE2 A:GLU436 2.3 19.3 1.0
O A:TYR272 2.3 17.6 1.0
O A:HOH1774 2.4 18.6 1.0
O A:THR269 2.5 16.3 1.0
OE1 A:GLU433 2.5 16.0 1.0
OG1 A:THR269 2.5 16.8 1.0
OE2 A:GLU433 2.5 16.3 1.0
CD A:GLU433 2.8 16.1 1.0
C A:THR269 3.3 17.2 1.0
CB A:THR269 3.4 17.6 1.0
C A:TYR272 3.4 17.2 1.0
CD A:GLU436 3.4 17.3 1.0
CA A:THR269 3.9 17.4 1.0
OE1 A:GLU436 4.0 16.5 1.0
N A:TYR272 4.0 16.9 1.0
CA A:PRO273 4.2 17.9 1.0
N A:ALA274 4.3 18.0 1.0
CB A:ASP266 4.3 16.6 1.0
N A:PRO270 4.3 17.5 1.0
N A:PRO273 4.3 18.2 1.0
CG A:GLU433 4.3 14.8 1.0
CA A:TYR272 4.3 18.0 1.0
C A:PRO273 4.4 18.2 1.0
N A:ASP266 4.5 14.7 1.0
CA A:PRO270 4.5 16.6 1.0
N A:GLY271 4.5 17.4 1.0
O A:ASP266 4.6 17.4 1.0
O A:ALA264 4.6 19.3 1.0
N A:THR269 4.6 17.5 1.0
CG A:GLU436 4.7 14.2 1.0
CG2 A:THR269 4.7 17.0 1.0
OD2 A:ASP266 4.7 18.6 1.0
C A:PRO270 4.8 18.4 1.0
CA A:ASP266 4.9 15.8 1.0
CB A:ALA274 4.9 19.5 1.0
CB A:GLU436 4.9 14.6 1.0
C A:GLY271 5.0 18.8 1.0
CA A:GLU433 5.0 14.8 1.0

Reference:

C.Barinka, Y.Byun, C.L.Dusich, S.R.Banerjee, Y.Chen, M.Castanares, A.P.Kozikowski, R.C.Mease, M.G.Pomper, J.Lubkowski. Interactions Between Human Glutamate Carboxypeptidase II and Urea-Based Inhibitors: Structural Characterization J.Med.Chem. V. 51 7737 2008.
ISSN: ISSN 0022-2623
PubMed: 19053759
DOI: 10.1021/JM800765E
Page generated: Tue Jul 8 11:32:24 2025

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