Copper in PDB 5vf5: Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement

The structure of Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement, PDB code: 5vf5 was solved by P.J.Porebski, A.Wlodawer, Z.Dauter, W.Minor, R.Stanfield, M.Jaskolski, E.Pozharski, C.X.Weichenberger, B.Rupp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.71 / 1.49
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	119.330, 119.330, 158.190, 90.00, 90.00, 120.00
R / Rfree (%)	13.1 / 16.3

The structure of Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Copper atom in the Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement (pdb code 5vf5). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total only one binding site of Copper was determined in the Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement, PDB code: 5vf5:

Copper binding site 1 out of 1 in the Crystal Structure of the Vicilin From Solanum Melongena, Re-Refinement


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 the Vicilin From Solanum Melongena, Re-Refinement within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu503 b:15.1 occ:0.50 ND1 A:HIS283 1.9 16.8 0.5 NE2 A:HIS325 2.0 12.4 1.0 SG A:CYS281 2.2 22.2 1.0 CE1 A:HIS283 2.8 17.6 0.5 CD A:PRO282 2.9 18.0 0.5 CD2 A:HIS325 2.9 14.8 1.0 CE1 A:HIS325 3.0 12.0 1.0 CG A:HIS283 3.0 16.2 0.5 OH A:TYR12 3.3 30.8 1.0 CB A:CYS281 3.4 20.2 1.0 CB A:HIS283 3.5 15.7 0.5 N A:HIS283 3.6 16.0 0.5 N A:PRO282 3.6 17.7 0.5 CG A:PRO282 3.6 20.0 0.5 CA A:CYS281 3.7 16.4 1.0 CD A:PRO282 3.7 15.5 0.5 N A:PRO282 3.7 15.4 0.5 O A:HOH907 3.9 36.9 1.0 C A:CYS281 3.9 16.3 1.0 NE2 A:HIS283 4.0 22.1 0.5 ND1 A:HIS325 4.0 13.5 1.0 CG A:HIS325 4.1 12.5 1.0 O A:PRO282 4.1 24.4 0.5 CD2 A:HIS283 4.1 17.4 0.5 CA A:HIS283 4.1 17.9 0.5 CG A:PRO282 4.3 14.0 0.5 CZ A:TYR12 4.4 22.3 1.0 C A:PRO282 4.6 17.2 0.5 CA A:PRO282 4.7 16.9 0.5 CA A:PRO282 4.7 19.8 0.5 CE2 A:TYR12 4.8 26.9 1.0 O A:CYS281 4.8 20.6 1.0 CB A:PRO282 4.8 21.5 0.5 C A:PRO282 4.8 23.1 0.5 N A:LEU284 4.9 19.1 0.5

A.Wlodawer, Z.Dauter, P.J.Porebski, W.Minor, R.Stanfield, M.Jaskolski, E.Pozharski, C.X.Weichenberger, B.Rupp. Detect, Correct, Retract: How to Manage Incorrect Structural Models. Febs J. V. 285 444 2018.
ISSN: ISSN 1742-4658
PubMed: 29113027
DOI: 10.1111/FEBS.14320