Copper in PDB 5yjs: Structure of Vicilin From Capsicum Annuum

The structure of Structure of Vicilin From Capsicum Annuum, PDB code: 5yjs was solved by M.Shikhi, D.T.Nair, D.M.Salunke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.16
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	148.030, 148.030, 148.030, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21.7

The structure of Structure of Vicilin From Capsicum Annuum also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Copper atom in the Structure of Vicilin From Capsicum Annuum (pdb code 5yjs). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Structure of Vicilin From Capsicum Annuum, PDB code: 5yjs:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Structure of Vicilin From Capsicum Annuum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Vicilin From Capsicum Annuum within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu604 b:31.2 occ:1.00 NE2 A:HIS464 2.1 21.0 1.0 ND1 A:HIS419 2.2 36.3 1.0 SG A:CYS417 2.2 25.3 1.0 CD2 A:HIS464 3.0 21.8 1.0 OH A:TYR148 3.1 42.6 1.0 CG A:HIS419 3.1 38.6 1.0 CE1 A:HIS419 3.2 39.6 1.0 CE1 A:HIS464 3.2 24.1 1.0 CB A:CYS417 3.3 23.3 1.0 CB A:HIS419 3.4 34.6 1.0 CD A:PRO418 3.6 23.9 1.0 N A:HIS419 3.7 32.2 1.0 CA A:CYS417 3.7 24.7 1.0 N A:PRO418 3.9 25.3 1.0 C A:CYS417 4.1 25.9 1.0 CA A:HIS419 4.2 36.0 1.0 CG A:HIS464 4.2 22.6 1.0 ND1 A:HIS464 4.3 24.7 1.0 NE2 A:HIS419 4.3 46.7 1.0 CZ A:TYR148 4.3 36.9 1.0 CD2 A:HIS419 4.3 41.8 1.0 CG A:PRO418 4.4 25.5 1.0 C A:PRO418 4.8 29.9 1.0 C A:HIS419 4.9 37.1 1.0 CA A:PRO418 4.9 28.9 1.0 O A:CYS417 5.0 27.6 1.0

Copper binding site 2 out of 2 in the Structure of Vicilin From Capsicum Annuum


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Vicilin From Capsicum Annuum within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu602 b:46.3 occ:1.00 ND1 B:HIS419 2.1 55.6 1.0 NE2 B:HIS464 2.2 34.8 1.0 SG B:CYS417 2.4 40.2 1.0 CE1 B:HIS419 2.9 55.4 1.0 OH B:TYR148 3.1 69.0 1.0 CD2 B:HIS464 3.1 34.7 1.0 CG B:HIS419 3.1 57.6 1.0 CE1 B:HIS464 3.2 27.7 1.0 CB B:CYS417 3.5 38.3 1.0 CB B:HIS419 3.6 58.6 1.0 CD B:PRO418 3.7 43.1 1.0 CA B:CYS417 3.8 40.9 1.0 N B:HIS419 3.9 52.5 1.0 N B:PRO418 4.0 47.3 1.0 NE2 B:HIS419 4.1 57.7 1.0 CD2 B:HIS419 4.2 55.9 1.0 C B:CYS417 4.2 48.0 1.0 CZ B:TYR148 4.2 61.0 1.0 CG B:HIS464 4.3 34.4 1.0 ND1 B:HIS464 4.3 34.3 1.0 CA B:HIS419 4.4 59.4 1.0 CG B:PRO418 4.6 44.4 1.0 C B:PRO418 4.8 48.7 1.0 CA B:PRO418 5.0 47.5 1.0 CE1 B:TYR148 5.0 54.2 1.0

M.Shikhi, D.T.Nair, D.M.Salunke. Structure-Guided Identification of Function: Role Ofcapsicum Annuumvicilin During Oxidative Stress. Biochem. J. V. 475 3057 2018.
ISSN: ESSN 1470-8728
PubMed: 30181145
DOI: 10.1042/BCJ20180520