Copper in PDB 8hjy: Crystal Structure of A Cupin Protein (TM1459, H52A/H58E/F104W Mutant) in Copper (Cu) Substituted Form

The structure of Crystal Structure of A Cupin Protein (TM1459, H52A/H58E/F104W Mutant) in Copper (Cu) Substituted Form, PDB code: 8hjy was solved by R.Matsumoto, G.Kurisu, N.Fujieda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	99.00 / 1.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.7, 57.72, 75.82, 90, 90, 90
R / Rfree (%)	n/a / n/a

The binding sites of Copper atom in the Crystal Structure of A Cupin Protein (TM1459, H52A/H58E/F104W Mutant) in Copper (Cu) Substituted Form (pdb code 8hjy). 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, H52A/H58E/F104W Mutant) in Copper (Cu) Substituted Form, PDB code: 8hjy:
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, H52A/H58E/F104W 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/H58E/F104W Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:22.3 occ:0.73 NE2 A:HIS92 2.0 16.4 1.0 NE2 A:HIS54 2.1 19.8 1.0 OE2 A:GLU58 2.3 44.5 1.0 O A:HOH379 2.4 52.8 1.0 CE1 A:HIS92 2.9 14.1 1.0 HE1 A:HIS92 3.0 16.9 1.0 CD2 A:HIS54 3.0 17.1 1.0 CE1 A:HIS54 3.1 19.0 1.0 CD2 A:HIS92 3.2 18.0 1.0 HD2 A:HIS54 3.2 20.5 1.0 HE1 A:HIS54 3.3 22.8 1.0 CD A:GLU58 3.4 35.9 1.0 HD2 A:HIS92 3.4 21.6 1.0 O A:HOH353 3.7 22.3 1.0 OE1 A:GLU58 3.9 52.1 1.0 ND1 A:HIS92 4.1 13.3 1.0 CG A:HIS54 4.2 15.3 1.0 ND1 A:HIS54 4.2 17.2 1.0 CG A:HIS92 4.2 13.6 1.0 O A:HOH337 4.3 25.8 1.0 HB2 A:GLU58 4.3 21.4 1.0 O A:HOH393 4.4 44.9 1.0 HE2 A:PHE94 4.5 24.4 1.0 CG A:GLU58 4.7 21.7 1.0 HD1 A:HIS92 4.8 16.0 1.0 HE1 A:TRP56 4.9 15.7 1.0 CB A:GLU58 4.9 17.9 1.0 HB3 A:GLU58 4.9 21.4 1.0 HD1 A:HIS54 5.0 20.6 1.0

Copper binding site 2 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, H52A/H58E/F104W 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/H58E/F104W Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu202 b:24.7 occ:0.23 OE2 A:GLU90 1.8 36.8 1.0 CD A:GLU90 2.7 34.5 1.0 HA3 B:GLY0 2.9 51.0 1.0 OE1 A:GLU90 2.9 52.2 1.0 CA B:GLY0 3.8 42.5 1.0 O A:HOH356 3.8 29.7 1.0 O A:HOH311 3.8 29.5 1.0 N B:GLY0 4.0 38.5 1.0 CG A:GLU90 4.1 16.7 1.0 HA A:GLU90 4.2 15.5 1.0 HA2 B:GLY0 4.2 51.0 1.0 HB2 A:GLU90 4.3 16.8 1.0 OE1 A:GLU72 4.4 49.0 1.0 HG2 A:GLU90 4.4 20.1 1.0 CB A:GLU90 4.6 14.0 1.0 HG3 A:GLU90 4.7 20.1 1.0 C B:GLY0 4.8 34.5 1.0 CA A:GLU90 4.9 12.9 1.0

Copper binding site 3 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, H52A/H58E/F104W 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/H58E/F104W Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu201 b:24.7 occ:0.39 CU B:CU201 0.0 24.7 0.4 CU B:CU201 0.8 26.2 0.4 OE2 B:GLU58 1.9 38.0 1.0 NE2 B:HIS92 1.9 20.5 1.0 O B:HOH337 2.0 33.9 1.0 NE2 B:HIS54 2.3 20.0 0.6 NE2 B:HIS54 2.3 20.5 0.4 HD2 B:HIS54 2.7 22.4 0.4 CD2 B:HIS54 2.8 18.7 0.4 CD B:GLU58 2.9 28.5 1.0 CE1 B:HIS92 2.9 18.5 1.0 CD2 B:HIS92 3.0 19.3 1.0 HE1 B:HIS92 3.0 22.2 1.0 OE1 B:GLU58 3.1 41.9 1.0 CE1 B:HIS54 3.2 19.2 0.6 HD2 B:HIS92 3.2 23.1 1.0 CD2 B:HIS54 3.3 17.1 0.6 HE1 B:HIS54 3.3 23.0 0.6 HD2 B:HIS54 3.5 20.6 0.6 CE1 B:HIS54 3.6 17.9 0.4 O B:HOH353 3.9 29.8 1.0 HE1 B:HIS54 4.0 21.5 0.4 ND1 B:HIS92 4.0 14.3 1.0 HB2 B:GLU58 4.1 21.9 1.0 CG B:HIS54 4.1 18.9 0.4 CG B:HIS92 4.1 15.8 1.0 CG B:GLU58 4.3 26.3 1.0 HE2 B:PHE94 4.3 22.2 1.0 ND1 B:HIS54 4.4 16.5 0.6 CG B:HIS54 4.4 15.7 0.6 ND1 B:HIS54 4.4 19.3 0.4 HB3 B:GLU58 4.6 21.9 1.0 CB B:GLU58 4.6 18.2 1.0 HG3 B:GLU58 4.7 31.6 1.0 O B:HOH311 4.7 25.9 1.0 HD1 B:HIS92 4.8 17.2 1.0 HG2 B:GLU58 4.9 31.6 1.0 HG13 B:VAL86 4.9 21.9 1.0 HE1 B:TRP56 5.0 19.6 1.0

Copper binding site 4 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, H52A/H58E/F104W 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, H52A/H58E/F104W Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu201 b:26.2 occ:0.43 CU B:CU201 0.0 26.2 0.4 CU B:CU201 0.8 24.7 0.4 NE2 B:HIS54 1.9 20.5 0.4 O B:HOH337 2.0 33.9 1.0 NE2 B:HIS92 2.1 20.5 1.0 NE2 B:HIS54 2.4 20.0 0.6 OE2 B:GLU58 2.7 38.0 1.0 CD2 B:HIS54 2.7 18.7 0.4 HD2 B:HIS54 2.8 22.4 0.4 CE1 B:HIS92 2.9 18.5 1.0 CE1 B:HIS54 3.0 17.9 0.4 HD2 B:HIS54 3.0 20.6 0.6 CD2 B:HIS54 3.0 17.1 0.6 HE1 B:HIS92 3.0 22.2 1.0 CD2 B:HIS92 3.2 19.3 1.0 HE1 B:HIS54 3.3 21.5 0.4 HD2 B:HIS92 3.5 23.1 1.0 CE1 B:HIS54 3.5 19.2 0.6 CD B:GLU58 3.6 28.5 1.0 OE1 B:GLU58 3.8 41.9 1.0 HE1 B:HIS54 3.8 23.0 0.6 CG B:HIS54 3.9 18.9 0.4 O B:HOH353 3.9 29.8 1.0 ND1 B:HIS54 4.0 19.3 0.4 O B:HOH311 4.1 25.9 1.0 ND1 B:HIS92 4.1 14.3 1.0 CG B:HIS54 4.3 15.7 0.6 CG B:HIS92 4.3 15.8 1.0 HE2 B:PHE94 4.4 22.2 1.0 ND1 B:HIS54 4.5 16.5 0.6 HB3 B:ALA52 4.6 28.8 1.0 HD1 B:HIS54 4.8 23.2 0.4 HB2 B:GLU58 4.8 21.9 1.0 HD1 B:HIS92 4.9 17.2 1.0

R.Matsumoto, S.Yoshioka, M.Yuasa, Y.Morita, G.Kurisu, N.Fujieda. An Artificial Metallolyase with Pliable 2-His-1-Carboxylate Facial Triad For Stereoselective Michael Addition. Chem Sci V. 14 3932 2023.
ISSN: ISSN 2041-6520
PubMed: 37035687
DOI: 10.1039/D2SC06809E