Copper in PDB 6l4c: Crystal Structure of Vicilin From Corylus Avellana (Hazelnut)

The structure of Crystal Structure of Vicilin From Corylus Avellana (Hazelnut), PDB code: 6l4c was solved by M.Shikhi, D.M.Salunke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.12 / 3.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.000, 91.137, 266.872, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 28.3

The binding sites of Copper atom in the Crystal Structure of Vicilin From Corylus Avellana (Hazelnut) (pdb code 6l4c). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Crystal Structure of Vicilin From Corylus Avellana (Hazelnut), PDB code: 6l4c:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in the Crystal Structure of Vicilin From Corylus Avellana (Hazelnut)


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 Vicilin From Corylus Avellana (Hazelnut) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:57.4 occ:1.00 NE2 A:HIS305 2.1 56.7 1.0 ND1 A:HIS278 2.1 54.1 1.0 SG A:CYS276 2.3 62.0 1.0 CG A:HIS278 2.9 57.5 1.0 CE1 A:HIS305 2.9 61.7 1.0 CE1 A:HIS278 3.1 55.2 1.0 CB A:HIS278 3.1 67.8 1.0 CD2 A:HIS305 3.2 52.8 1.0 N A:HIS278 3.2 73.1 1.0 OH A:TYR5 3.4 61.9 1.0 CB A:CYS276 3.5 70.8 1.0 CD A:PRO277 3.5 68.8 1.0 CA A:CYS276 3.6 61.3 1.0 N A:PRO277 3.6 55.1 1.0 C A:CYS276 3.7 63.3 1.0 CA A:HIS278 3.8 71.8 1.0 CD2 A:HIS278 4.0 63.6 1.0 NE2 A:HIS278 4.1 58.0 1.0 ND1 A:HIS305 4.1 63.2 1.0 CG A:PRO277 4.2 60.6 1.0 C A:PRO277 4.2 62.1 1.0 CG A:HIS305 4.2 62.7 1.0 CA A:PRO277 4.5 60.0 1.0 CZ A:TYR5 4.6 49.5 1.0 O A:CYS276 4.6 76.5 1.0 N A:LEU279 4.7 66.4 1.0 C A:HIS278 4.8 63.8 1.0 N A:CYS276 5.0 57.8 1.0

Copper binding site 2 out of 3 in the Crystal Structure of Vicilin From Corylus Avellana (Hazelnut)


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 Vicilin From Corylus Avellana (Hazelnut) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu401 b:0.6 occ:1.00 CD2 B:HIS278 2.1 89.6 1.0 SG B:CYS276 2.3 76.9 1.0 NE2 B:HIS305 2.4 72.1 1.0 CG B:HIS278 2.9 96.1 1.0 CE1 B:HIS305 3.0 63.8 1.0 OH B:TYR5 3.2 80.7 1.0 CD2 B:HIS305 3.2 59.4 1.0 NE2 B:HIS278 3.3 0.7 1.0 CB B:HIS278 3.3 93.5 1.0 CB B:CYS276 3.6 66.5 1.0 N B:HIS278 3.8 88.5 1.0 CA B:CYS276 3.9 66.1 1.0 ND1 B:HIS305 3.9 65.8 1.0 CG B:HIS305 4.0 51.8 1.0 CD B:PRO277 4.0 81.0 1.0 ND1 B:HIS278 4.2 0.2 1.0 CA B:HIS278 4.2 90.4 1.0 N B:PRO277 4.3 77.3 1.0 CE1 B:HIS278 4.3 84.8 1.0 CZ B:TYR5 4.3 70.0 1.0 C B:CYS276 4.4 74.1 1.0 C B:PRO277 4.9 82.2 1.0 N B:LEU279 5.0 79.0 1.0

Copper binding site 3 out of 3 in the Crystal Structure of Vicilin From Corylus Avellana (Hazelnut)


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 Vicilin From Corylus Avellana (Hazelnut) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu401 b:91.3 occ:1.00 NE2 C:HIS305 2.0 79.5 1.0 SG C:CYS276 2.4 98.3 1.0 CD2 C:HIS278 2.5 0.9 1.0 CE1 C:HIS305 2.7 81.1 1.0 NE2 C:HIS278 2.8 0.3 1.0 CG C:HIS278 3.1 96.1 1.0 CD2 C:HIS305 3.1 89.6 1.0 CB C:CYS276 3.3 92.4 1.0 CA C:CYS276 3.4 97.4 1.0 CE1 C:HIS278 3.4 0.3 1.0 CD C:PRO277 3.5 73.5 1.0 ND1 C:HIS278 3.6 0.7 1.0 N C:PRO277 3.6 79.6 1.0 C C:CYS276 3.7 92.4 1.0 N C:HIS278 3.7 0.9 1.0 OH C:TYR5 3.7 0.9 1.0 ND1 C:HIS305 3.8 87.0 1.0 CB C:HIS278 3.9 92.9 1.0 CG C:HIS305 4.1 88.6 1.0 CA C:HIS278 4.4 0.2 1.0 O C:CYS276 4.5 0.6 1.0 CA C:PRO277 4.6 86.6 1.0 C C:PRO277 4.6 98.4 1.0 CG C:PRO277 4.7 77.4 1.0 CZ C:TYR5 4.7 0.5 1.0 N C:CYS276 4.7 97.3 1.0 CZ B:PHE131 4.8 0.7 1.0 O C:ALA275 4.8 87.9 1.0 CB C:PRO277 5.0 88.6 1.0

M.Shikhi, A.Jain, D.M.Salunke. Comparative Study of 7S Globulin From Corylus Avellana and Solanum Lycopersicum Revealed Importance of Salicylic Acid and Cu-Binding Loop in Modulating Their Function. Biochem.Biophys.Res.Commun. 2019.
ISSN: ESSN 1090-2104
PubMed: 31753489
DOI: 10.1016/J.BBRC.2019.11.072