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

The structure of Crystal Structure of A Cupin Protein (TM1459, H52A/H58E Mutant) in Copper (Cu) Substituted Form, PDB code: 8hjx 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 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.71, 57.76, 75.32, 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 Mutant) in Copper (Cu) Substituted Form (pdb code 8hjx). 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 Mutant) in Copper (Cu) Substituted Form, PDB code: 8hjx:
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 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 Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:18.7 occ:0.79 O A:HOH332 2.0 41.4 1.0 NE2 A:HIS92 2.0 17.2 1.0 NE2 A:HIS54 2.1 19.3 1.0 O A:HOH384 2.2 40.3 1.0 OE2 A:GLU58 2.3 33.3 1.0 CE1 A:HIS92 2.9 14.3 1.0 HE1 A:HIS92 3.0 17.2 1.0 CD2 A:HIS54 3.1 18.0 1.0 CE1 A:HIS54 3.1 19.6 1.0 CD2 A:HIS92 3.1 16.1 1.0 HD2 A:HIS54 3.2 21.6 1.0 HE1 A:HIS54 3.3 23.5 1.0 CD A:GLU58 3.3 29.3 1.0 HD2 A:HIS92 3.3 19.4 1.0 OE1 A:GLU58 3.7 36.7 1.0 O A:HOH368 3.9 26.4 1.0 O A:HOH352 4.1 22.5 1.0 ND1 A:HIS92 4.1 13.8 1.0 CG A:HIS92 4.2 13.6 1.0 ND1 A:HIS54 4.2 17.1 1.0 CG A:HIS54 4.2 15.8 1.0 O A:HOH302 4.3 53.5 1.0 HB2 A:GLU58 4.4 20.8 1.0 HE2 A:PHE94 4.5 23.5 1.0 O A:HOH418 4.6 50.7 1.0 CG A:GLU58 4.7 20.8 1.0 O A:HOH419 4.8 63.1 1.0 HD1 A:HIS92 4.8 16.5 1.0 HE1 A:TRP56 4.9 16.5 1.0 CB A:GLU58 5.0 17.3 1.0 HB3 A:ALA52 5.0 27.5 1.0 HB3 A:GLU58 5.0 20.8 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 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 Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu202 b:21.6 occ:0.25 OE2 A:GLU90 1.8 31.1 1.0 CD A:GLU90 2.7 22.8 1.0 OE1 A:GLU90 2.8 28.8 1.0 HA3 B:GLY0 3.2 39.7 1.0 O A:HOH360 3.9 28.7 1.0 O A:HOH304 3.9 31.5 1.0 CA B:GLY0 4.0 33.1 1.0 OE2 A:GLU87 4.0 60.2 1.0 CG A:GLU90 4.1 18.1 1.0 N B:GLY0 4.1 40.6 1.0 HA A:GLU90 4.2 16.6 1.0 HB2 A:GLU90 4.2 18.5 1.0 OE1 A:GLU72 4.4 57.4 1.0 HG2 A:GLU90 4.5 21.7 1.0 HA2 B:GLY0 4.6 39.7 1.0 CB A:GLU90 4.6 15.4 1.0 HG2 A:GLU87 4.6 47.6 1.0 HG3 A:GLU90 4.7 21.7 1.0 CD A:GLU87 4.8 46.3 1.0 CA A:GLU90 4.9 13.9 1.0 C B:GLY0 4.9 26.4 1.0

Copper binding site 3 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, H52A/H58E 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 Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu201 b:20.5 occ:0.47 CU B:CU201 0.0 20.5 0.5 CU B:CU201 0.5 23.6 0.4 NE2 B:HIS92 2.0 16.7 1.0 O B:HOH310 2.0 35.9 1.0 O B:HOH362 2.1 31.9 1.0 NE2 B:HIS54 2.1 20.1 0.5 NE2 B:HIS54 2.1 17.0 0.6 OE1 B:GLU58 2.2 32.8 1.0 HD2 B:HIS54 2.7 21.4 0.5 CD2 B:HIS54 2.7 17.9 0.5 CE1 B:HIS92 2.9 15.4 1.0 HE1 B:HIS92 3.1 18.5 1.0 CD2 B:HIS92 3.1 17.6 1.0 CE1 B:HIS54 3.1 17.0 0.6 CD2 B:HIS54 3.1 14.4 0.6 CD B:GLU58 3.2 28.2 1.0 CE1 B:HIS54 3.3 18.5 0.5 HE1 B:HIS54 3.3 20.4 0.6 HD2 B:HIS54 3.3 17.2 0.6 HD2 B:HIS92 3.3 21.1 1.0 OE2 B:GLU58 3.5 32.8 1.0 HE1 B:HIS54 3.6 22.2 0.5 O B:HOH368 3.8 30.4 1.0 CG B:HIS54 4.0 17.8 0.5 ND1 B:HIS92 4.1 14.3 1.0 ND1 B:HIS54 4.2 21.2 0.5 CG B:HIS92 4.2 14.6 1.0 ND1 B:HIS54 4.2 15.6 0.6 CG B:HIS54 4.3 14.6 0.6 HB2 B:GLU58 4.3 21.5 1.0 O B:HOH331 4.4 20.0 1.0 HE2 B:PHE94 4.5 19.8 1.0 CG B:GLU58 4.6 22.8 1.0 O B:HOH398 4.7 63.8 1.0 HD1 B:HIS92 4.8 17.2 1.0 HE1 B:TRP56 4.8 19.4 1.0 CB B:GLU58 4.9 17.9 1.0 HG3 B:GLU58 4.9 27.4 1.0

Copper binding site 4 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, H52A/H58E 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 Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu201 b:23.6 occ:0.37 CU B:CU201 0.0 23.6 0.4 CU B:CU201 0.5 20.5 0.5 NE2 B:HIS54 1.9 20.1 0.5 O B:HOH310 1.9 35.9 1.0 O B:HOH362 2.0 31.9 1.0 NE2 B:HIS92 2.0 16.7 1.0 NE2 B:HIS54 2.3 17.0 0.6 OE1 B:GLU58 2.7 32.8 1.0 CD2 B:HIS54 2.8 17.9 0.5 HD2 B:HIS54 2.9 21.4 0.5 CE1 B:HIS92 2.9 15.4 1.0 CE1 B:HIS54 3.0 18.5 0.5 HE1 B:HIS92 3.1 18.5 1.0 CD2 B:HIS92 3.1 17.6 1.0 CD2 B:HIS54 3.1 14.4 0.6 HD2 B:HIS54 3.1 17.2 0.6 HE1 B:HIS54 3.3 22.2 0.5 HD2 B:HIS92 3.3 21.1 1.0 CE1 B:HIS54 3.4 17.0 0.6 CD B:GLU58 3.6 28.2 1.0 HE1 B:HIS54 3.7 20.4 0.6 OE2 B:GLU58 3.9 32.8 1.0 O B:HOH331 3.9 20.0 1.0 O B:HOH368 3.9 30.4 1.0 CG B:HIS54 4.0 17.8 0.5 ND1 B:HIS54 4.1 21.2 0.5 ND1 B:HIS92 4.1 14.3 1.0 CG B:HIS92 4.2 14.6 1.0 CG B:HIS54 4.3 14.6 0.6 ND1 B:HIS54 4.5 15.6 0.6 HE2 B:PHE94 4.5 19.8 1.0 HB3 B:ALA52 4.5 24.6 1.0 O B:HOH398 4.6 63.8 1.0 HD1 B:HIS92 4.8 17.2 1.0 HD1 B:HIS54 4.9 25.5 0.5 HB2 B:GLU58 4.9 21.5 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