Copper in PDB 4q89: Crystal Structure of the Cota Native Enzyme

The structure of Crystal Structure of the Cota Native Enzyme, PDB code: 4q89 was solved by T.Xie, Z.C.Liu, G.G.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.62 / 2.31
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.013, 119.864, 84.136, 90.00, 93.99, 90.00
R / Rfree (%)	15 / 21.5

The structure of Crystal Structure of the Cota Native Enzyme also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Copper atom in the Crystal Structure of the Cota Native Enzyme (pdb code 4q89). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Crystal Structure of the Cota Native Enzyme, PDB code: 4q89:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in the Crystal Structure of the Cota Native Enzyme


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 the Cota Native Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu601 b:23.6 occ:1.00 ND1 A:HIS497 2.0 18.4 1.0 ND1 A:HIS419 2.1 27.9 1.0 SG A:CYS492 2.2 20.6 1.0 CE1 A:HIS419 3.0 25.8 1.0 CE1 A:HIS497 3.0 17.5 1.0 CG A:HIS497 3.0 19.2 1.0 CG A:HIS419 3.1 26.2 1.0 CB A:CYS492 3.2 19.4 1.0 SD A:MET502 3.3 22.7 1.0 CB A:HIS497 3.4 20.4 1.0 CB A:HIS419 3.5 24.1 1.0 CD1 A:ILE494 3.9 18.4 1.0 NE2 A:HIS497 4.1 18.4 1.0 NE2 A:HIS419 4.1 26.8 1.0 CA A:HIS419 4.1 22.8 1.0 CD2 A:HIS497 4.2 18.1 1.0 CD2 A:HIS419 4.2 26.9 1.0 CE A:MET502 4.3 24.6 1.0 CB A:ILE494 4.3 17.5 1.0 CG1 A:ILE494 4.6 17.6 1.0 CA A:CYS492 4.6 19.2 1.0 CD1 A:LEU386 4.6 32.0 1.0 O A:HOH840 4.7 29.7 1.0 CD A:PRO420 4.7 17.7 1.0 CG A:MET502 4.8 23.0 1.0 O A:THR418 4.9 25.3 1.0 CA A:HIS497 4.9 20.3 1.0 N A:ILE494 5.0 16.3 1.0 CG2 A:ILE494 5.0 16.2 1.0

Copper binding site 2 out of 8 in the Crystal Structure of the Cota Native Enzyme


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 the Cota Native Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu602 b:22.6 occ:0.76 NE2 A:HIS422 1.9 18.4 1.0 NE2 A:HIS105 2.0 18.6 1.0 CD2 A:HIS105 2.8 16.8 1.0 CE1 A:HIS422 2.8 17.3 1.0 CD2 A:HIS422 2.9 17.2 1.0 CE1 A:HIS105 3.0 17.2 1.0 O A:HOH895 3.1 29.1 1.0 O A:HOH962 3.1 6.3 1.0 NE2 A:HIS424 3.3 20.5 1.0 CD2 A:HIS424 3.4 20.3 1.0 ND1 A:HIS107 3.5 16.7 1.0 CG A:HIS107 3.6 16.8 1.0 CE1 A:HIS424 3.6 22.0 1.0 CA A:HIS107 3.7 17.7 1.0 CG A:HIS424 3.8 20.9 1.0 CU A:CU603 3.8 27.0 0.9 CB A:HIS107 3.9 16.8 1.0 ND1 A:HIS424 3.9 22.2 1.0 ND1 A:HIS422 4.0 17.9 1.0 CE1 A:HIS107 4.0 15.2 1.0 CG A:HIS105 4.0 17.1 1.0 CG A:HIS422 4.0 18.1 1.0 ND1 A:HIS105 4.0 17.7 1.0 CD2 A:HIS107 4.1 16.1 1.0 N A:GLY108 4.1 19.8 1.0 CU A:CU604 4.1 21.4 1.0 NE2 A:HIS107 4.3 16.1 1.0 C A:HIS107 4.5 18.6 1.0 CA A:HIS424 4.5 19.8 1.0 CB A:HIS424 4.6 20.1 1.0 N A:HIS107 4.7 17.2 1.0 O A:LEU106 4.8 18.9 1.0 O A:HOH1051 4.9 24.1 1.0 N A:HIS424 5.0 18.9 1.0

Copper binding site 3 out of 8 in the Crystal Structure of the Cota Native Enzyme


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 the Cota Native Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu603 b:27.0 occ:0.91 NE2 A:HIS424 2.0 20.5 1.0 NE2 A:HIS491 2.0 25.8 1.0 NE2 A:HIS155 2.1 15.3 1.0 O A:HOH962 2.3 6.3 1.0 CE1 A:HIS424 2.8 22.0 1.0 CD2 A:HIS491 2.9 24.2 1.0 O A:HOH1058 3.0 45.5 1.0 CE1 A:HIS491 3.1 25.1 1.0 CD2 A:HIS155 3.1 15.7 1.0 CE1 A:HIS155 3.1 15.7 1.0 CD2 A:HIS424 3.1 20.3 1.0 CD2 A:HIS422 3.8 17.2 1.0 CU A:CU602 3.8 22.6 0.8 ND1 A:HIS424 4.0 22.2 1.0 CG2 A:VAL489 4.0 23.7 1.0 CG A:HIS491 4.1 22.1 1.0 ND1 A:HIS491 4.1 23.8 1.0 CG A:HIS424 4.2 20.9 1.0 ND1 A:HIS155 4.2 16.2 1.0 CG A:HIS155 4.2 16.1 1.0 NE2 A:HIS422 4.2 18.4 1.0 CD2 A:HIS105 4.2 16.8 1.0 NE2 A:HIS105 4.4 18.6 1.0 OE2 A:GLU498 4.5 26.5 1.0 O A:HOH779 4.7 18.6 1.0 CG A:HIS105 4.8 17.1 1.0 CU A:CU604 4.9 21.4 1.0 CE1 A:HIS105 5.0 17.2 1.0 CD A:GLU498 5.0 22.4 1.0 CD2 A:HIS493 5.0 17.5 1.0

Copper binding site 4 out of 8 in the Crystal Structure of the Cota Native Enzyme


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 the Cota Native Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu604 b:21.4 occ:1.00 NE2 A:HIS153 2.0 17.8 1.0 ND1 A:HIS107 2.1 16.7 1.0 NE2 A:HIS493 2.2 17.5 1.0 O A:HOH962 2.6 6.3 1.0 CD2 A:HIS153 3.0 16.8 1.0 CG A:HIS107 3.0 16.8 1.0 CE1 A:HIS153 3.0 16.1 1.0 CE1 A:HIS107 3.1 15.2 1.0 CE1 A:HIS493 3.2 16.8 1.0 CD2 A:HIS493 3.2 17.5 1.0 CB A:HIS107 3.3 16.8 1.0 CZ2 A:TRP151 3.8 18.1 1.0 O A:HOH1058 3.8 45.5 1.0 CE2 A:TRP151 4.1 17.0 1.0 ND1 A:HIS153 4.1 16.9 1.0 CG A:HIS153 4.1 16.5 1.0 CU A:CU602 4.1 22.6 0.8 NE2 A:HIS107 4.2 16.1 1.0 CD2 A:HIS107 4.2 16.1 1.0 CD2 A:HIS105 4.2 16.8 1.0 ND1 A:HIS493 4.3 15.7 1.0 NE1 A:TRP151 4.3 16.5 1.0 CB A:ALA297 4.3 15.5 1.0 CG A:HIS493 4.3 16.1 1.0 CD2 A:HIS422 4.4 17.2 1.0 CH2 A:TRP151 4.5 17.7 1.0 NE2 A:HIS422 4.5 18.4 1.0 CA A:HIS107 4.5 17.7 1.0 NE2 A:HIS105 4.8 18.6 1.0 CU A:CU603 4.9 27.0 0.9

Copper binding site 5 out of 8 in the Crystal Structure of the Cota Native Enzyme


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of the Cota Native Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu601 b:20.5 occ:1.00 ND1 B:HIS497 2.1 19.7 1.0 SG B:CYS492 2.1 19.6 1.0 ND1 B:HIS419 2.2 21.8 1.0 CG B:HIS497 3.0 18.7 1.0 CE1 B:HIS497 3.0 21.4 1.0 SD B:MET502 3.1 22.2 1.0 CE1 B:HIS419 3.1 23.9 1.0 CG B:HIS419 3.2 20.1 1.0 CB B:CYS492 3.2 16.5 1.0 CB B:HIS497 3.3 18.4 1.0 CB B:HIS419 3.5 17.6 1.0 CE B:MET502 3.9 25.9 1.0 CA B:HIS419 4.0 17.9 1.0 CD1 B:ILE494 4.1 16.1 1.0 NE2 B:HIS497 4.2 22.9 1.0 CD2 B:HIS497 4.2 21.0 1.0 CB B:ILE494 4.2 16.6 1.0 NE2 B:HIS419 4.2 23.0 1.0 CD2 B:HIS419 4.3 22.2 1.0 O B:HOH850 4.5 23.6 1.0 CG1 B:ILE494 4.5 15.9 1.0 CA B:CYS492 4.6 16.8 1.0 CD B:PRO420 4.6 17.4 1.0 CG B:MET502 4.7 20.8 1.0 CA B:HIS497 4.9 18.5 1.0 CG2 B:ILE494 4.9 15.2 1.0 N B:ILE494 5.0 17.3 1.0

Copper binding site 6 out of 8 in the Crystal Structure of the Cota Native Enzyme


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of the Cota Native Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu602 b:25.5 occ:0.74 NE2 B:HIS105 2.0 18.5 1.0 NE2 B:HIS422 2.0 25.8 1.0 O B:HOH791 2.7 17.7 1.0 CD2 B:HIS105 2.8 18.1 1.0 CE1 B:HIS422 2.8 24.3 1.0 CD2 B:HIS422 3.1 25.8 1.0 CE1 B:HIS105 3.1 20.0 1.0 O B:HOH994 3.3 9.0 1.0 CD2 B:HIS424 3.3 22.6 1.0 NE2 B:HIS424 3.3 23.3 1.0 ND1 B:HIS107 3.5 15.9 1.0 CA B:HIS107 3.7 14.7 1.0 CG B:HIS107 3.7 16.1 1.0 CU B:CU603 3.7 29.6 0.9 CE1 B:HIS424 3.8 21.1 1.0 CG B:HIS424 3.8 21.9 1.0 CE1 B:HIS107 4.0 16.6 1.0 CG B:HIS105 4.0 19.1 1.0 ND1 B:HIS422 4.0 26.9 1.0 ND1 B:HIS424 4.0 22.2 1.0 ND1 B:HIS105 4.1 19.5 1.0 CB B:HIS107 4.1 15.3 1.0 N B:GLY108 4.1 17.5 1.0 CG B:HIS422 4.1 25.0 1.0 CD2 B:HIS107 4.2 16.9 1.0 CU B:CU604 4.2 21.5 1.0 NE2 B:HIS107 4.3 18.3 1.0 C B:HIS107 4.4 16.5 1.0 CA B:HIS424 4.6 20.7 1.0 N B:HIS107 4.7 15.8 1.0 CB B:HIS424 4.7 21.1 1.0 O B:HOH858 4.7 19.1 1.0 O B:LEU106 4.8 12.7 1.0 O B:HOH714 4.9 13.3 1.0

Copper binding site 7 out of 8 in the Crystal Structure of the Cota Native Enzyme


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of the Cota Native Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu603 b:29.6 occ:0.88 NE2 B:HIS424 2.1 23.3 1.0 NE2 B:HIS155 2.1 22.3 1.0 NE2 B:HIS491 2.1 19.8 1.0 O B:HOH994 2.1 9.0 1.0 CE1 B:HIS424 2.9 21.1 1.0 CE1 B:HIS491 3.0 20.2 1.0 CD2 B:HIS155 3.0 21.6 1.0 CD2 B:HIS424 3.2 22.6 1.0 CD2 B:HIS491 3.2 20.6 1.0 CE1 B:HIS155 3.2 22.8 1.0 CD2 B:HIS422 3.7 25.8 1.0 CU B:CU602 3.7 25.5 0.7 CD2 B:HIS105 3.9 18.1 1.0 NE2 B:HIS422 4.0 25.8 1.0 NE2 B:HIS105 4.1 18.5 1.0 ND1 B:HIS424 4.1 22.2 1.0 ND1 B:HIS491 4.1 20.3 1.0 CG B:HIS155 4.2 21.1 1.0 ND1 B:HIS155 4.2 21.5 1.0 CG2 B:VAL489 4.2 26.4 1.0 CG B:HIS491 4.2 19.1 1.0 CG B:HIS424 4.2 21.9 1.0 OE2 B:GLU498 4.6 22.5 1.0 CG B:HIS105 4.6 19.1 1.0 CU B:CU604 4.7 21.5 1.0 CD2 B:HIS493 4.8 15.9 1.0 O B:HOH1052 4.9 26.0 1.0 CE1 B:HIS105 4.9 20.0 1.0 NE2 B:HIS493 4.9 14.2 1.0 CG B:HIS422 5.0 25.0 1.0

Copper binding site 8 out of 8 in the Crystal Structure of the Cota Native Enzyme


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of the Cota Native Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu604 b:21.5 occ:1.00 ND1 B:HIS107 2.0 15.9 1.0 NE2 B:HIS493 2.1 14.2 1.0 NE2 B:HIS153 2.1 21.7 1.0 O B:HOH994 2.5 9.0 1.0 CE1 B:HIS107 2.9 16.6 1.0 CE1 B:HIS493 3.0 16.0 1.0 CE1 B:HIS153 3.0 19.8 1.0 CG B:HIS107 3.1 16.1 1.0 CD2 B:HIS493 3.1 15.9 1.0 CD2 B:HIS153 3.1 20.3 1.0 CB B:HIS107 3.5 15.3 1.0 CZ2 B:TRP151 3.9 15.8 1.0 NE2 B:HIS107 4.0 18.3 1.0 CD2 B:HIS105 4.1 18.1 1.0 ND1 B:HIS493 4.1 16.5 1.0 CD2 B:HIS107 4.1 16.9 1.0 ND1 B:HIS153 4.2 20.6 1.0 CU B:CU602 4.2 25.5 0.7 CG B:HIS493 4.2 16.9 1.0 CG B:HIS153 4.2 20.2 1.0 CE2 B:TRP151 4.2 17.2 1.0 NE1 B:TRP151 4.4 18.9 1.0 CB B:ALA297 4.5 16.8 1.0 CA B:HIS107 4.5 14.7 1.0 NE2 B:HIS422 4.5 25.8 1.0 CH2 B:TRP151 4.6 15.8 1.0 CD2 B:HIS422 4.6 25.8 1.0 CU B:CU603 4.7 29.6 0.9 NE2 B:HIS105 4.8 18.5 1.0

T.Xie, Z.C.Liu, G.G.Wang. The Crystal Structure of Cota Laccase Complexed with Sinapic Acid To Be Published.