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Calcium in PDB 4oc1: X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid

Enzymatic activity of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid

All present enzymatic activity of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid, PDB code: 4oc1 was solved by J.Pavlicek, J.Ptacek, J.Cerny, Y.Byun, L.Skultetyova, M.Pomper, J.Lubkowski, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.48 / 1.75
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.396, 130.353, 158.944, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 19.3

Other elements in 4oc1:

The structure of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid also contains other interesting chemical elements:

Iodine (I) 2 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid (pdb code 4oc1). 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 X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid, PDB code: 4oc1:

Calcium binding site 1 out of 1 in 4oc1

Go back to Calcium Binding Sites List in 4oc1
Calcium binding site 1 out of 1 in the X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Coibzl, A Urea-Based Inhibitor (2S)-2-[({(1S)-1-Carboxy- 2-[(2S)-Oxiran-2-Yl]Ethyl}Carbamoyl)Amino]-6-[(4-Iodobenzoyl) Amino]Hexanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca816

b:16.4
occ:1.00
 O A:TYR272 2.3 17.4 1.0
OE2 A:GLU436 2.3 18.7 1.0
OE1 A:GLU433 2.4 17.0 1.0
O A:HOH906 2.4 18.6 1.0
O A:THR269 2.5 16.2 1.0
OE2 A:GLU433 2.5 16.5 1.0
OG1 A:THR269 2.5 15.3 1.0
CD A:GLU433 2.8 17.5 1.0
C A:THR269 3.3 16.4 1.0
CB A:THR269 3.3 16.5 1.0
C A:TYR272 3.4 16.4 1.0
CD A:GLU436 3.5 18.7 1.0
OE1 A:GLU436 3.9 16.8 1.0
CA A:THR269 3.9 16.9 1.0
N A:TYR272 4.0 17.1 1.0
CA A:PRO273 4.2 17.0 1.0
N A:ALA274 4.2 17.4 1.0
N A:PRO273 4.2 18.4 1.0
N A:PRO270 4.3 17.6 1.0
CB A:ASP266 4.3 18.3 1.0
CA A:TYR272 4.3 17.9 1.0
CG A:GLU433 4.3 17.6 1.0
C A:PRO273 4.4 17.8 1.0
CA A:PRO270 4.5 17.5 1.0
N A:GLY271 4.5 18.1 1.0
N A:ASP266 4.5 16.4 1.0
O A:ASP266 4.5 19.3 1.0
O A:ALA264 4.6 19.4 1.0
N A:THR269 4.6 16.8 1.0
CG2 A:THR269 4.7 16.7 1.0
CG A:GLU436 4.7 15.3 1.0
C A:PRO270 4.8 18.0 1.0
OD2 A:ASP266 4.8 20.4 1.0
CB A:ALA274 4.9 18.6 1.0
CA A:ASP266 4.9 17.5 1.0
C A:GLY271 5.0 19.1 1.0
CB A:GLU436 5.0 15.7 1.0
CA A:GLU433 5.0 13.9 1.0

Reference:

J.Pavlicek, J.Ptacek, J.Cerny, Y.Byun, L.Skultetyova, M.G.Pomper, J.Lubkowski, C.Barinka. Structural Characterization of P1'-Diversified Urea-Based Inhibitors of Glutamate Carboxypeptidase II. Bioorg.Med.Chem.Lett. V. 24 2340 2014.
ISSN: ISSN 0960-894X
PubMed: 24731280
DOI: 10.1016/J.BMCL.2014.03.066
Page generated: Sun Jul 14 11:20:42 2024

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