Copper in PDB 6l2f: Crystal Structure of A Cupin Protein (TM1459, H54AH58A Mutant) in Copper (Cu) Substituted Form

The structure of Crystal Structure of A Cupin Protein (TM1459, H54AH58A Mutant) in Copper (Cu) Substituted Form, PDB code: 6l2f 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 / 1.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.635, 57.797, 74.402, 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, H54AH58A Mutant) in Copper (Cu) Substituted Form (pdb code 6l2f). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of A Cupin Protein (TM1459, H54AH58A Mutant) in Copper (Cu) Substituted Form, PDB code: 6l2f:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, H54AH58A 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, H54AH58A Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1201 b:18.5 occ:0.73 CU A:CU1201 0.0 18.5 0.7 CU A:CU1201 1.8 27.1 0.2 O A:HOH1334 1.8 29.5 1.0 NE2 A:HIS52 2.0 16.9 1.0 NE2 A:HIS92 2.1 16.8 1.0 O A:HOH1358 2.2 28.5 1.0 O A:HOH1379 2.4 21.6 1.0 CE1 A:HIS52 2.9 18.9 1.0 CE1 A:HIS92 2.9 16.5 1.0 HE1 A:HIS52 3.0 22.7 1.0 HE1 A:HIS92 3.0 19.8 1.0 CD2 A:HIS52 3.1 16.0 1.0 CD2 A:HIS92 3.2 15.3 1.0 HD2 A:HIS52 3.3 19.2 1.0 O A:HOH1366 3.4 45.3 1.0 HD2 A:HIS92 3.5 18.3 1.0 ND1 A:HIS52 4.0 17.9 1.0 O A:HOH1348 4.1 51.8 1.0 ND1 A:HIS92 4.1 13.5 1.0 O A:HOH1363 4.1 22.7 1.0 CG A:HIS52 4.1 14.7 1.0 CG A:HIS92 4.3 13.3 1.0 HB2 A:ALA54 4.3 28.1 1.0 HE2 A:PHE94 4.7 19.0 1.0 HB3 A:ALA54 4.7 28.1 1.0 HD1 A:HIS52 4.8 21.4 1.0 HD1 A:HIS92 4.8 16.1 1.0 O A:HOH1396 4.9 47.5 1.0 CB A:ALA54 5.0 18.8 1.0 HG23 A:ILE49 5.0 28.0 1.0

Copper binding site 2 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, H54AH58A 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, H54AH58A Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu1201 b:27.1 occ:0.16 CU A:CU1201 0.0 27.1 0.2 O A:HOH1379 1.6 21.6 1.0 CU A:CU1201 1.8 18.5 0.7 O A:HOH1366 1.9 45.3 1.0 NE2 A:HIS92 2.0 16.8 1.0 HD2 A:HIS92 2.2 18.3 1.0 CD2 A:HIS92 2.4 15.3 1.0 O A:HOH1358 2.5 28.5 1.0 HE2 A:PHE94 3.1 19.0 1.0 HE1 A:HIS52 3.2 22.7 1.0 CE1 A:HIS92 3.2 16.5 1.0 NE2 A:HIS52 3.3 16.9 1.0 O A:HOH1334 3.4 29.5 1.0 CE1 A:HIS52 3.5 18.9 1.0 CG A:HIS92 3.7 13.3 1.0 HE1 A:HIS92 3.7 19.8 1.0 O A:HOH1348 3.9 51.8 1.0 CE2 A:PHE94 4.0 15.8 1.0 ND1 A:HIS92 4.1 13.5 1.0 HZ A:PHE94 4.4 21.6 1.0 OD1 A:CSD106 4.5 25.6 1.0 CD2 A:HIS52 4.5 16.0 1.0 HG23 A:ILE49 4.5 28.0 1.0 O A:HOH1323 4.6 38.9 1.0 HD11 A:ILE60 4.6 22.6 1.0 HB2 A:ALA58 4.6 16.0 1.0 HG22 A:VAL86 4.6 21.4 1.0 CZ A:PHE94 4.7 18.0 1.0 HG13 A:VAL86 4.7 21.5 1.0 ND1 A:HIS52 4.8 17.9 1.0 HB3 A:ALA58 4.8 16.0 1.0 HD2 A:PHE94 4.9 16.8 1.0 HD1 A:HIS92 4.9 16.1 1.0 HD2 A:HIS52 4.9 19.2 1.0 CD2 A:PHE94 4.9 14.0 1.0 O A:HOH1363 5.0 22.7 1.0 HB2 A:HIS92 5.0 16.2 1.0 CB A:HIS92 5.0 13.5 1.0

Copper binding site 3 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, H54AH58A 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, H54AH58A Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu2201 b:15.9 occ:0.65 CU B:CU2201 0.0 15.9 0.7 CU B:CU2201 1.5 25.1 0.2 NE2 B:HIS52 2.0 16.0 1.0 O B:HOH2382 2.1 32.8 1.0 O B:HOH2379 2.1 38.4 1.0 NE2 B:HIS92 2.2 17.4 1.0 O B:HOH2386 2.4 22.9 1.0 CE1 B:HIS52 2.9 14.2 1.0 CE1 B:HIS92 3.0 15.8 1.0 HE1 B:HIS52 3.0 17.0 1.0 CD2 B:HIS52 3.0 15.0 1.0 HE1 B:HIS92 3.1 19.0 1.0 CD2 B:HIS92 3.2 17.0 1.0 HD2 B:HIS52 3.3 18.0 1.0 HD2 B:HIS92 3.5 20.4 1.0 ND1 B:HIS52 4.0 13.9 1.0 O B:HOH2385 4.0 46.0 1.0 CG B:HIS52 4.1 13.3 1.0 ND1 B:HIS92 4.1 12.7 1.0 O B:HOH2350 4.1 26.3 1.0 CG B:HIS92 4.3 13.7 1.0 HE2 B:PHE94 4.5 14.6 1.0 HB2 B:ALA54 4.7 22.6 1.0 HD1 B:HIS52 4.8 16.7 1.0 HD1 B:HIS92 4.8 15.2 1.0 HG23 B:ILE49 5.0 21.3 1.0

Copper binding site 4 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, H54AH58A 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 4 of Crystal Structure of A Cupin Protein (TM1459, H54AH58A Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu2201 b:25.1 occ:0.23 CU B:CU2201 0.0 25.1 0.2 CU B:CU2201 1.5 15.9 0.7 NE2 B:HIS92 1.8 17.4 1.0 O B:HOH2386 1.9 22.9 1.0 O B:HOH2382 2.3 32.8 1.0 HD2 B:HIS92 2.4 20.4 1.0 CD2 B:HIS92 2.4 17.0 1.0 NE2 B:HIS52 3.0 16.0 1.0 CE1 B:HIS92 3.1 15.8 1.0 HE1 B:HIS52 3.2 17.0 1.0 HE2 B:PHE94 3.2 14.6 1.0 CE1 B:HIS52 3.4 14.2 1.0 O B:HOH2379 3.4 38.4 1.0 HE1 B:HIS92 3.5 19.0 1.0 CG B:HIS92 3.7 13.7 1.0 ND1 B:HIS92 4.0 12.7 1.0 CE2 B:PHE94 4.1 12.2 1.0 CD2 B:HIS52 4.2 15.0 1.0 O B:HOH2385 4.2 46.0 1.0 O B:HOH2360 4.4 48.0 1.0 HZ B:PHE94 4.5 14.7 1.0 OD1 B:CSD106 4.5 27.9 1.0 HB2 B:ALA58 4.5 16.1 1.0 HD2 B:HIS52 4.6 18.0 1.0 ND1 B:HIS52 4.6 13.9 1.0 HD11 B:ILE60 4.7 21.5 1.0 CZ B:PHE94 4.7 12.2 1.0 HG23 B:ILE49 4.8 21.3 1.0 HD1 B:HIS92 4.8 15.2 1.0 O B:HOH2350 4.9 26.3 1.0 HB3 B:ALA58 4.9 16.1 1.0 HG22 B:VAL86 4.9 16.3 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