Copper in PDB 6l2d: Crystal Structure of A Cupin Protein (TM1459) in Copper (Cu) Substituted Form

The structure of Crystal Structure of A Cupin Protein (TM1459) in Copper (Cu) Substituted Form, PDB code: 6l2d was solved by N.Fujieda, H.Ichihashi, Y.Nishikawa, G.Kurisu, S.Itoh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.521, 57.808, 74.963, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Copper atom in the Crystal Structure of A Cupin Protein (TM1459) in Copper (Cu) Substituted Form (pdb code 6l2d). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of A Cupin Protein (TM1459) in Copper (Cu) Substituted Form, PDB code: 6l2d:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Crystal Structure of A Cupin Protein (TM1459) in Copper (Cu) Substituted Form


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 A Cupin Protein (TM1459) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1201 b:13.2 occ:0.94 O A:HOH1312 1.9 24.7 1.0 NE2 A:HIS58 2.0 14.0 1.0 NE2 A:HIS52 2.0 14.1 1.0 NE2 A:HIS92 2.1 13.3 1.0 NE2 A:HIS54 2.1 14.6 1.0 O A:HOH1383 2.8 50.4 1.0 CE1 A:HIS92 3.0 12.7 1.0 CE1 A:HIS52 3.0 15.1 1.0 CD2 A:HIS58 3.0 13.7 1.0 CE1 A:HIS58 3.0 17.8 1.0 CE1 A:HIS54 3.0 12.9 1.0 CD2 A:HIS52 3.1 15.1 1.0 HE1 A:HIS92 3.1 15.2 1.0 HE1 A:HIS52 3.1 18.1 1.0 CD2 A:HIS92 3.1 13.6 1.0 HE1 A:HIS54 3.2 15.4 1.0 HD2 A:HIS58 3.2 16.4 1.0 HE1 A:HIS58 3.2 21.3 1.0 CD2 A:HIS54 3.2 13.1 1.0 HD2 A:HIS52 3.3 18.1 1.0 HD2 A:HIS92 3.4 16.3 1.0 HD2 A:HIS54 3.4 15.7 1.0 ND1 A:HIS58 4.1 17.5 1.0 ND1 A:HIS52 4.1 16.2 1.0 O A:HOH1388 4.1 44.1 1.0 CG A:HIS58 4.1 13.2 1.0 ND1 A:HIS92 4.1 12.4 1.0 CG A:HIS52 4.2 13.3 1.0 ND1 A:HIS54 4.2 13.1 1.0 CG A:HIS92 4.2 12.3 1.0 O A:HOH1374 4.3 18.9 1.0 CG A:HIS54 4.3 12.5 1.0 HE2 A:PHE94 4.3 23.4 1.0 HD1 A:HIS52 4.9 19.4 1.0 HD1 A:HIS58 4.9 21.1 1.0 HD1 A:HIS92 4.9 14.9 1.0 HE1 A:TRP56 4.9 15.9 1.0 HD1 A:HIS54 4.9 15.7 1.0

Copper binding site 2 out of 2 in the Crystal Structure of A Cupin Protein (TM1459) in Copper (Cu) Substituted Form


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 A Cupin Protein (TM1459) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu2201 b:13.2 occ:0.94 NE2 B:HIS52 2.0 14.2 1.0 NE2 B:HIS58 2.0 13.6 1.0 NE2 B:HIS92 2.0 13.2 1.0 O B:HOH2357 2.1 26.9 1.0 NE2 B:HIS54 2.2 16.2 1.0 CE1 B:HIS52 3.0 14.4 1.0 CE1 B:HIS92 3.0 12.6 1.0 CD2 B:HIS58 3.0 13.8 1.0 CD2 B:HIS52 3.0 14.3 1.0 CE1 B:HIS58 3.0 16.6 1.0 CE1 B:HIS54 3.0 16.8 1.0 CD2 B:HIS92 3.1 13.5 1.0 HE1 B:HIS54 3.1 20.1 1.0 HE1 B:HIS92 3.1 15.1 1.0 HE1 B:HIS52 3.2 17.3 1.0 HD2 B:HIS58 3.2 16.6 1.0 HD2 B:HIS52 3.2 17.2 1.0 HE1 B:HIS58 3.2 20.0 1.0 HD2 B:HIS92 3.3 16.2 1.0 CD2 B:HIS54 3.3 17.1 1.0 HD2 B:HIS54 3.6 20.5 1.0 O B:HOH2399 4.1 56.4 1.0 ND1 B:HIS52 4.1 13.8 1.0 ND1 B:HIS92 4.1 12.1 1.0 ND1 B:HIS58 4.1 15.8 1.0 CG B:HIS52 4.1 12.6 1.0 CG B:HIS58 4.2 14.5 1.0 ND1 B:HIS54 4.2 18.7 1.0 CG B:HIS92 4.2 12.1 1.0 O B:HOH2361 4.3 23.1 1.0 HE2 B:PHE94 4.3 17.2 1.0 CG B:HIS54 4.4 16.6 1.0 HD1 B:HIS52 4.8 16.5 1.0 HD1 B:HIS92 4.9 14.5 1.0 HD1 B:HIS58 4.9 18.9 1.0 HD1 B:HIS54 5.0 22.4 1.0

N.Fujieda, H.Ichihashi, M.Yuasa, Y.Nishikawa, G.Kurisu, S.Itoh. Cupin Variants As A Macromolecular Ligand Library For Stereoselective Michael Addition of Nitroalkanes. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32073197
DOI: 10.1002/ANIE.202000129