Copper in PDB 5e1r: Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen

The structure of Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen, PDB code: 5e1r was solved by Y.Z.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.60 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.691, 151.610, 342.782, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 26.2

The binding sites of Copper atom in the Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen (pdb code 5e1r). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen, PDB code: 5e1r:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in the Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu801 b:12.9 occ:1.00 NE2 A:HIS698 1.9 12.4 1.0 ND1 A:HIS654 2.2 13.7 1.0 OH A:TYR379 2.3 21.9 1.0 SG A:CYS652 2.3 16.6 1.0 CE1 A:HIS698 2.7 14.3 1.0 CE1 A:HIS654 2.9 6.7 1.0 CD2 A:HIS698 3.1 9.2 1.0 CZ A:TYR379 3.2 16.4 1.0 CB A:CYS652 3.3 9.5 1.0 CG A:HIS654 3.4 9.0 1.0 CE2 A:TYR379 3.7 19.0 1.0 CA A:CYS652 3.8 7.1 1.0 ND1 A:HIS698 3.9 10.8 1.0 CB A:HIS654 3.9 11.9 1.0 CD A:PRO653 3.9 9.3 1.0 NE2 A:HIS654 4.1 5.5 1.0 CG A:HIS698 4.1 7.2 1.0 CE1 A:TYR379 4.1 9.8 1.0 N A:PRO653 4.3 10.2 1.0 CD2 A:HIS654 4.3 8.5 1.0 N A:HIS654 4.4 13.8 1.0 C A:CYS652 4.4 13.2 1.0 CA A:HIS654 4.8 14.2 1.0 CE A:MET650 4.9 13.5 1.0 CD2 A:TYR379 4.9 20.5 1.0 CG A:PRO653 4.9 10.7 1.0 OH B:TYR505 4.9 10.8 1.0

Copper binding site 2 out of 6 in the Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu801 b:16.0 occ:1.00 NE2 B:HIS698 1.9 14.0 1.0 OH B:TYR379 2.1 22.2 1.0 ND1 B:HIS654 2.2 12.8 1.0 SG B:CYS652 2.3 20.9 1.0 CE1 B:HIS698 2.6 10.6 1.0 CZ B:TYR379 3.0 16.7 1.0 CE1 B:HIS654 3.0 10.1 1.0 CD2 B:HIS698 3.1 15.0 1.0 CG B:HIS654 3.2 13.4 1.0 CB B:CYS652 3.4 10.7 1.0 CE2 B:TYR379 3.6 22.0 1.0 CB B:HIS654 3.6 18.6 1.0 ND1 B:HIS698 3.8 10.9 1.0 CE1 B:TYR379 3.9 14.6 1.0 CA B:CYS652 4.0 10.7 1.0 CG B:HIS698 4.1 12.0 1.0 NE2 B:HIS654 4.2 15.1 1.0 CD B:PRO653 4.2 15.2 1.0 N B:HIS654 4.2 16.1 1.0 CD2 B:HIS654 4.3 15.9 1.0 N B:PRO653 4.4 17.9 1.0 C B:CYS652 4.5 19.2 1.0 CA B:HIS654 4.5 18.0 1.0 CD2 B:TYR379 4.8 21.2 1.0 OH C:TYR505 4.9 15.1 1.0 CG B:PRO695 5.0 9.5 1.0

Copper binding site 3 out of 6 in the Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu801 b:11.6 occ:1.00 NE2 C:HIS698 1.9 15.1 1.0 OH C:TYR379 2.0 17.1 1.0 SG C:CYS652 2.3 18.9 1.0 ND1 C:HIS654 2.3 14.0 1.0 CE1 C:HIS698 2.7 11.1 1.0 CZ C:TYR379 3.0 13.6 1.0 CD2 C:HIS698 3.1 17.1 1.0 CE1 C:HIS654 3.1 9.8 1.0 CE2 C:TYR379 3.2 12.7 1.0 CB C:CYS652 3.3 10.1 1.0 CG C:HIS654 3.4 13.4 1.0 CB C:HIS654 3.7 12.5 1.0 ND1 C:HIS698 3.8 13.0 1.0 CA C:CYS652 3.9 9.3 1.0 CG C:HIS698 4.1 12.7 1.0 CD C:PRO653 4.1 14.5 1.0 CE1 C:TYR379 4.2 13.9 1.0 N C:HIS654 4.2 13.9 1.0 NE2 C:HIS654 4.3 10.7 1.0 N C:PRO653 4.4 17.9 1.0 CD2 C:HIS654 4.4 10.2 1.0 C C:CYS652 4.5 12.6 1.0 CD2 C:TYR379 4.6 12.3 1.0 CA C:HIS654 4.6 11.2 1.0 CG C:PRO695 4.9 13.2 1.0

Copper binding site 4 out of 6 in the Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu801 b:11.5 occ:1.00 NE2 D:HIS698 2.0 8.3 1.0 ND1 D:HIS654 2.0 9.5 1.0 OH D:TYR379 2.2 22.1 1.0 SG D:CYS652 2.4 29.6 1.0 CE1 D:HIS654 2.8 9.8 1.0 CE1 D:HIS698 2.8 16.2 1.0 CZ D:TYR379 3.1 19.6 1.0 CD2 D:HIS698 3.1 15.3 1.0 CG D:HIS654 3.2 12.7 1.0 CE2 D:TYR379 3.2 17.9 1.0 CB D:CYS652 3.5 8.5 1.0 CB D:HIS654 3.8 22.9 1.0 CD D:PRO653 3.9 13.2 1.0 ND1 D:HIS698 4.0 9.4 1.0 NE2 D:HIS654 4.0 4.5 1.0 CA D:CYS652 4.0 9.1 1.0 CG D:HIS698 4.1 9.9 1.0 CD2 D:HIS654 4.2 6.8 1.0 N D:HIS654 4.2 19.2 1.0 CE1 D:TYR379 4.3 14.9 1.0 N D:PRO653 4.3 12.4 1.0 C D:CYS652 4.5 12.2 1.0 CD2 D:TYR379 4.6 11.1 1.0 CA D:HIS654 4.6 20.6 1.0 CG D:PRO653 4.8 7.3 1.0

Copper binding site 5 out of 6 in the Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu801 b:18.7 occ:1.00 NE2 E:HIS698 1.9 12.0 1.0 OH E:TYR379 2.0 51.2 1.0 ND1 E:HIS654 2.2 19.0 1.0 SG E:CYS652 2.2 20.3 1.0 CE1 E:HIS698 2.6 12.2 1.0 CE1 E:HIS654 3.0 16.6 1.0 CZ E:TYR379 3.0 21.3 1.0 CD2 E:HIS698 3.1 17.3 1.0 CG E:HIS654 3.2 17.2 1.0 CB E:CYS652 3.4 10.4 1.0 CE2 E:TYR379 3.6 19.8 1.0 CB E:HIS654 3.7 18.9 1.0 ND1 E:HIS698 3.8 13.6 1.0 CA E:CYS652 3.9 14.4 1.0 CD E:PRO653 4.0 15.7 1.0 CE1 E:TYR379 4.0 21.3 1.0 CG E:HIS698 4.1 13.4 1.0 NE2 E:HIS654 4.1 18.7 1.0 N E:HIS654 4.1 18.9 1.0 N E:PRO653 4.2 15.9 1.0 CD2 E:HIS654 4.3 16.9 1.0 C E:CYS652 4.4 17.8 1.0 CA E:HIS654 4.6 16.4 1.0 CD2 E:TYR379 4.8 21.7 1.0 CG E:PRO653 4.9 12.4 1.0 CD1 E:LEU409 5.0 19.8 1.0 CG E:PRO695 5.0 11.4 1.0

Copper binding site 6 out of 6 in the Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Pecan (Carya Illinoinensis) Vicilin, A New Food Allergen within 5.0Å range: probe atom residue distance (Å) B Occ F:Cu801 b:22.6 occ:1.00 OH F:TYR379 2.0 18.9 1.0 NE2 F:HIS698 2.0 16.8 1.0 ND1 F:HIS654 2.1 13.9 1.0 SG F:CYS652 2.3 25.8 1.0 CE1 F:HIS698 2.8 13.9 1.0 CE1 F:HIS654 3.0 11.6 1.0 CZ F:TYR379 3.0 19.4 1.0 CD2 F:HIS698 3.1 16.3 1.0 CG F:HIS654 3.2 15.6 1.0 CE2 F:TYR379 3.3 22.6 1.0 CB F:CYS652 3.5 15.7 1.0 CB F:HIS654 3.6 18.6 1.0 ND1 F:HIS698 4.0 12.4 1.0 CA F:CYS652 4.0 16.0 1.0 NE2 F:HIS654 4.1 14.1 1.0 CG F:HIS698 4.1 14.8 1.0 CD F:PRO653 4.2 15.1 1.0 CD2 F:HIS654 4.2 15.5 1.0 N F:HIS654 4.2 18.4 1.0 CE1 F:TYR379 4.3 14.0 1.0 N F:PRO653 4.5 16.6 1.0 C F:CYS652 4.5 16.6 1.0 CA F:HIS654 4.5 20.4 1.0 CD2 F:TYR379 4.7 23.0 1.0

Y.Zhang, B.Lee, W.X.Du, S.C.Lyu, K.C.Nadeau, L.J.Grauke, Y.Zhang, S.Wang, Y.Fan, J.Yi, T.H.Mchugh. Identification and Characterization of A New Pecan [Carya Illinoinensis (Wangenh.) K. Koch] Allergen, Car I 2. J.Agric.Food Chem. V. 64 4146 2016.
ISSN: ESSN 1520-5118
PubMed: 27128197
DOI: 10.1021/ACS.JAFC.6B00884