Copper in PDB 6l2e: Crystal Structure of A Cupin Protein (TM1459, H52A Mutant) in Copper (Cu) Substituted Form

The structure of Crystal Structure of A Cupin Protein (TM1459, H52A Mutant) in Copper (Cu) Substituted Form, PDB code: 6l2e 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 (°)	50.625, 57.763, 75.035, 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, H52A Mutant) in Copper (Cu) Substituted Form (pdb code 6l2e). 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 A Cupin Protein (TM1459, H52A Mutant) in Copper (Cu) Substituted Form, PDB code: 6l2e:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in the Crystal Structure of A Cupin Protein (TM1459, H52A Mutant) 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, H52A Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1201 b:10.1 occ:0.90 O A:HOH1386 2.0 30.9 1.0 O A:HOH1333 2.0 25.6 1.0 NE2 A:HIS58 2.0 11.8 1.0 NE2 A:HIS54 2.0 10.3 1.0 NE2 A:HIS92 2.1 9.9 1.0 CE1 A:HIS92 2.9 9.6 1.0 CD2 A:HIS58 3.0 10.9 1.0 CE1 A:HIS54 3.0 10.4 1.0 CE1 A:HIS58 3.0 14.5 1.0 HE1 A:HIS92 3.1 11.5 1.0 CD2 A:HIS54 3.1 10.0 1.0 HD2 A:HIS58 3.1 13.1 1.0 HE1 A:HIS54 3.2 12.4 1.0 CD2 A:HIS92 3.2 10.2 1.0 HE1 A:HIS58 3.3 17.4 1.0 HD2 A:HIS54 3.3 12.0 1.0 HD2 A:HIS92 3.4 12.3 1.0 O A:HOH1364 3.9 14.4 1.0 ND1 A:HIS92 4.1 9.7 1.0 ND1 A:HIS54 4.1 9.9 1.0 ND1 A:HIS58 4.1 12.6 1.0 CG A:HIS58 4.2 10.2 1.0 O A:HOH1419 4.2 22.8 1.0 O A:HOH1385 4.2 17.5 1.0 CG A:HIS54 4.2 9.4 1.0 O A:HOH1442 4.3 30.9 1.0 CG A:HIS92 4.3 9.0 1.0 HE2 A:PHE94 4.6 17.2 1.0 O A:HOH1343 4.7 44.3 1.0 HB3 A:ALA52 4.8 22.2 1.0 HE1 A:TRP56 4.8 12.9 1.0 HD1 A:HIS92 4.9 11.6 1.0 HD1 A:HIS54 4.9 11.8 1.0 O A:HOH1301 4.9 28.6 1.0 HD1 A:HIS58 4.9 15.1 1.0

Copper binding site 2 out of 3 in the Crystal Structure of A Cupin Protein (TM1459, H52A Mutant) 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, H52A Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1202 b:18.3 occ:0.28 OE2 A:GLU90 1.7 26.0 1.0 CD A:GLU90 2.6 20.8 1.0 OE1 A:GLU90 2.8 33.7 1.0 HA3 B:GLY0 3.1 34.9 1.0 H B:GLY0 3.7 47.2 1.0 O A:HOH1350 3.8 22.6 1.0 CA B:GLY0 3.9 29.1 1.0 CG A:GLU90 4.0 13.7 1.0 N B:GLY0 4.1 39.3 1.0 HA A:GLU90 4.2 12.3 1.0 O A:HOH1349 4.2 26.1 1.0 HB2 A:GLU90 4.4 14.5 1.0 HG2 A:GLU90 4.4 16.5 1.0 HA2 B:GLY0 4.4 34.9 1.0 OE2 A:GLU87 4.4 46.8 1.0 CB A:GLU90 4.6 12.1 1.0 HG3 A:GLU90 4.6 16.5 1.0 OE1 A:GLU72 4.7 30.3 1.0 HG2 A:GLU87 4.7 37.7 1.0 HB2 B:SER-1 4.8 65.8 1.0 CD A:GLU87 4.9 35.6 1.0 CA A:GLU90 4.9 10.3 1.0 C B:GLY0 5.0 22.7 1.0

Copper binding site 3 out of 3 in the Crystal Structure of A Cupin Protein (TM1459, H52A Mutant) 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 3 of Crystal Structure of A Cupin Protein (TM1459, H52A Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu2201 b:10.8 occ:0.90 O B:HOH2372 1.9 32.0 1.0 NE2 B:HIS92 2.0 9.8 1.0 NE2 B:HIS58 2.0 12.0 1.0 O B:HOH2383 2.1 27.0 1.0 NE2 B:HIS54 2.1 12.2 1.0 CE1 B:HIS92 2.9 9.8 1.0 CD2 B:HIS58 3.0 10.9 1.0 CE1 B:HIS54 3.1 13.6 1.0 CE1 B:HIS58 3.1 13.2 1.0 CD2 B:HIS92 3.1 10.0 1.0 HE1 B:HIS92 3.1 11.7 1.0 HE1 B:HIS54 3.2 16.3 1.0 HD2 B:HIS58 3.2 13.1 1.0 CD2 B:HIS54 3.2 12.8 1.0 HE1 B:HIS58 3.3 15.8 1.0 HD2 B:HIS92 3.3 12.0 1.0 HD2 B:HIS54 3.4 15.4 1.0 O B:HOH2357 4.0 13.6 1.0 O B:HOH2376 4.0 21.2 1.0 O B:HOH2409 4.0 23.2 0.5 ND1 B:HIS92 4.1 8.9 1.0 ND1 B:HIS58 4.2 13.6 1.0 CG B:HIS92 4.2 9.4 1.0 CG B:HIS58 4.2 10.6 1.0 ND1 B:HIS54 4.2 12.5 1.0 CG B:HIS54 4.3 10.7 1.0 O B:HOH2415 4.3 44.1 1.0 HE2 B:PHE94 4.5 14.2 1.0 HB3 B:ALA52 4.7 19.4 1.0 HD1 B:HIS92 4.8 10.7 1.0 HE1 B:TRP56 4.9 13.5 1.0 O B:HOH2313 4.9 28.8 1.0 HD1 B:HIS58 4.9 16.4 1.0 HD1 B:HIS54 5.0 15.0 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