Copper in PDB 8zyh: Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/H54A/C106D Mutant) in Copper (Cu) Substituted Form

The structure of Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/H54A/C106D Mutant) in Copper (Cu) Substituted Form, PDB code: 8zyh was solved by Y.Morita, H.Kubo, R.Matsumoto, N.Fujieda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.07
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.57, 58.5, 71.96, 90, 90, 90
R / Rfree (%)	n/a / n/a

The binding sites of Copper atom in the Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/H54A/C106D Mutant) in Copper (Cu) Substituted Form (pdb code 8zyh). 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, I49C-4PY/H52A/H54A/C106D Mutant) in Copper (Cu) Substituted Form, PDB code: 8zyh:
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, I49C-4PY/H52A/H54A/C106D 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, I49C-4PY/H52A/H54A/C106D Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu202 b:23.0 occ:0.68 O A:HOH365 1.9 51.8 1.0 NE2 A:HIS58 2.0 20.5 1.0 NE2 A:HIS92 2.1 23.8 1.0 O A:HOH363 2.4 39.0 1.0 CE1 A:HIS58 2.9 19.1 1.0 CE1 A:HIS92 3.0 23.5 1.0 CD2 A:HIS58 3.0 19.6 1.0 HE1 A:HIS58 3.0 23.0 1.0 HE1 A:HIS92 3.1 28.2 1.0 CD2 A:HIS92 3.2 23.8 1.0 HD2 A:HIS58 3.3 23.5 1.0 HD2 A:HIS92 3.5 28.6 1.0 O A:HOH359 3.6 47.5 1.0 HB2 A:ALA54 3.7 38.1 1.0 ND1 A:HIS58 4.0 17.2 1.0 O A:HOH353 4.0 40.1 1.0 HB3 A:ALA54 4.0 38.1 1.0 CG A:HIS58 4.1 15.5 1.0 HE1 A:TRP56 4.1 25.2 1.0 ND1 A:HIS92 4.1 21.8 1.0 CG A:HIS92 4.3 21.8 1.0 CB A:ALA54 4.3 25.4 1.0 HD1 A:HIS58 4.7 20.7 1.0 NE1 A:TRP56 4.8 21.0 1.0 HB1 A:ALA54 4.9 38.1 1.0 HB3 A:ALA52 4.9 45.7 1.0 HD1 A:HIS92 4.9 26.2 1.0

Copper binding site 2 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/H54A/C106D 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, I49C-4PY/H52A/H54A/C106D Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu203 b:34.4 occ:0.26 OE1 A:GLU90 1.8 38.0 1.0 CD A:GLU90 2.7 29.3 1.0 HA3 B:GLY0 3.0 42.5 1.0 OE2 A:GLU90 3.0 39.1 1.0 H B:GLY0 3.5 70.1 1.0 CA B:GLY0 3.8 35.5 1.0 O A:HOH369 3.8 54.5 1.0 N B:GLY0 3.9 46.7 1.0 O A:HOH305 3.9 36.3 1.0 CG A:GLU90 4.1 27.0 1.0 HA2 B:GLY0 4.3 42.5 1.0 HA A:GLU90 4.3 23.5 1.0 HB2 A:GLU90 4.3 26.5 1.0 HG2 A:GLU90 4.4 32.4 1.0 OE1 A:GLU72 4.4 44.4 1.0 CB A:GLU90 4.6 22.1 1.0 HG3 A:GLU90 4.7 32.4 1.0 C B:GLY0 4.8 24.4 1.0 CA A:GLU90 5.0 19.6 1.0

Copper binding site 3 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/H54A/C106D 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, I49C-4PY/H52A/H54A/C106D Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu2201 b:21.7 occ:0.51 CU B:CU2201 0.0 21.7 0.5 CU B:CU2201 0.9 31.8 0.3 O B:HOH2364 1.8 43.0 1.0 NE2 B:HIS58 2.0 19.7 1.0 NE2 B:HIS92 2.1 21.8 1.0 O B:HOH2377 2.2 35.1 1.0 N5 B:4GJ49 2.6 36.5 1.0 CE1 B:HIS58 2.8 18.2 1.0 CE1 B:HIS92 2.9 20.6 1.0 HE1 B:HIS58 3.0 21.9 1.0 HE1 B:HIS92 3.0 24.7 1.0 CD2 B:HIS58 3.0 19.2 1.0 CD2 B:HIS92 3.2 21.8 1.0 C6 B:4GJ49 3.3 44.1 1.0 HD2 B:HIS58 3.3 23.0 1.0 HB2 B:ALA54 3.5 31.2 1.0 HD2 B:HIS92 3.5 26.1 1.0 C4 B:4GJ49 3.6 39.4 1.0 ND1 B:HIS58 3.9 16.9 1.0 HE1 B:TRP56 4.0 24.8 1.0 HB3 B:ALA54 4.0 31.2 1.0 CG B:HIS58 4.1 15.7 1.0 ND1 B:HIS92 4.1 18.1 1.0 CB B:ALA54 4.2 20.8 1.0 O B:HOH2350 4.2 47.4 1.0 O B:HOH2370 4.2 54.4 1.0 CG B:HIS92 4.3 17.9 1.0 HB1 B:ALA54 4.6 31.2 1.0 NE1 B:TRP56 4.6 20.7 1.0 HD1 B:HIS58 4.7 20.2 1.0 C1 B:4GJ49 4.7 45.3 1.0 HE2 B:PHE94 4.8 24.6 1.0 HD1 B:HIS92 4.8 21.7 1.0 C3 B:4GJ49 4.9 35.5 1.0

Copper binding site 4 out of 4 in the Crystal Structure of A Cupin Protein (TM1459, I49C-4PY/H52A/H54A/C106D 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, I49C-4PY/H52A/H54A/C106D Mutant) in Copper (Cu) Substituted Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu2201 b:31.8 occ:0.30 CU B:CU2201 0.0 31.8 0.3 CU B:CU2201 0.9 21.7 0.5 NE2 B:HIS92 1.9 21.8 1.0 N5 B:4GJ49 2.0 36.5 1.0 NE2 B:HIS58 2.0 19.7 1.0 O B:HOH2364 2.5 43.0 1.0 CE1 B:HIS58 2.7 18.2 1.0 CD2 B:HIS92 2.8 21.8 1.0 C6 B:4GJ49 2.8 44.1 1.0 O B:HOH2377 2.8 35.1 1.0 HE1 B:HIS58 2.8 21.9 1.0 HD2 B:HIS92 2.9 26.1 1.0 CD2 B:HIS58 3.0 19.2 1.0 C4 B:4GJ49 3.0 39.4 1.0 CE1 B:HIS92 3.1 20.6 1.0 HD2 B:HIS58 3.4 23.0 1.0 HE1 B:HIS92 3.4 24.7 1.0 ND1 B:HIS58 3.6 16.9 1.0 CG B:HIS58 3.8 15.7 1.0 HE2 B:PHE94 4.0 24.6 1.0 O B:HOH2350 4.0 47.4 1.0 CG B:HIS92 4.0 17.9 1.0 ND1 B:HIS92 4.1 18.1 1.0 C1 B:4GJ49 4.1 45.3 1.0 C3 B:4GJ49 4.3 35.5 1.0 HB2 B:ALA54 4.3 31.2 1.0 HD1 B:HIS58 4.3 20.2 1.0 O B:HOH2370 4.5 54.4 1.0 HE1 B:TRP56 4.6 24.8 1.0 C2 B:4GJ49 4.7 34.9 1.0 HB3 B:ALA54 4.8 31.2 1.0 CE2 B:PHE94 4.9 20.5 1.0 HD1 B:HIS92 4.9 21.7 1.0

Y.Morita, H.Kubo, R.Matsumoto, N.Fujieda. Copper Center in Artificial Non-Heme Metalloenzyme To Be Published.