Copper in PDB 9bd5: Laccase From Bacillus Licheniformis

The structure of Laccase From Bacillus Licheniformis, PDB code: 9bd5 was solved by M.H.Habib, T.J.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.70 / 2.70
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	94.8, 94.8, 271.658, 90, 90, 120
R / Rfree (%)	18.9 / 23.2

The binding sites of Copper atom in the Laccase From Bacillus Licheniformis (pdb code 9bd5). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Laccase From Bacillus Licheniformis, PDB code: 9bd5:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in the Laccase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Laccase From Bacillus Licheniformis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu607 b:22.3 occ:1.00 ND1 A:HIS495 2.2 16.5 1.0 ND1 A:HIS417 2.2 16.4 1.0 SG A:CYS490 2.3 19.6 1.0 CE1 A:HIS417 3.0 17.3 1.0 CE1 A:HIS495 3.1 18.8 1.0 CG A:HIS495 3.2 19.7 1.0 CG A:HIS417 3.3 16.1 1.0 SD A:MET500 3.3 23.9 1.0 CB A:CYS490 3.4 11.8 1.0 CB A:HIS495 3.5 21.5 1.0 CB A:HIS417 3.8 12.2 1.0 CD1 A:ILE492 3.8 18.0 1.0 CB A:ILE492 4.1 16.8 1.0 CA A:HIS417 4.1 14.9 1.0 CG1 A:ILE492 4.2 15.4 1.0 NE2 A:HIS417 4.2 18.3 1.0 NE2 A:HIS495 4.2 22.9 1.0 CD2 A:HIS495 4.3 21.8 1.0 CD2 A:HIS417 4.4 18.1 1.0 O A:HOH795 4.5 19.5 1.0 CD2 A:LEU384 4.5 25.5 1.0 CE A:MET500 4.5 21.6 1.0 CD A:PRO418 4.6 11.9 1.0 CA A:CYS490 4.8 15.4 1.0 CG A:MET500 4.8 18.1 1.0 O A:ILE416 4.9 17.5 1.0 CG2 A:ILE492 4.9 13.2 1.0 C A:HIS417 5.0 14.8 1.0 N A:ILE492 5.0 14.2 1.0

Copper binding site 2 out of 8 in the Laccase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Laccase From Bacillus Licheniformis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu613 b:19.1 occ:1.00 NE2 A:HIS489 2.1 13.9 1.0 NE2 A:HIS422 2.1 13.7 1.0 NE2 A:HIS153 2.3 13.9 1.0 CE1 A:HIS422 2.9 16.1 1.0 CD2 A:HIS489 3.0 12.4 1.0 CE1 A:HIS489 3.1 12.2 1.0 CD2 A:HIS153 3.1 14.6 1.0 CD2 A:HIS422 3.3 14.2 1.0 CE1 A:HIS153 3.3 18.1 1.0 CU A:CU614 3.7 18.5 1.0 CD2 A:HIS420 3.8 10.1 1.0 CD2 A:HIS103 4.1 15.6 1.0 ND1 A:HIS422 4.1 14.6 1.0 ND1 A:HIS489 4.2 10.9 1.0 CG A:HIS489 4.2 13.9 1.0 NE2 A:HIS103 4.2 15.0 1.0 CG A:HIS153 4.3 16.1 1.0 CG A:HIS422 4.3 13.9 1.0 NE2 A:HIS420 4.3 14.2 1.0 CG2 A:VAL487 4.4 7.3 1.0 ND1 A:HIS153 4.4 14.6 1.0 OE2 A:GLU496 4.7 21.9 1.0 CU A:CU615 4.7 23.2 1.0 CG A:HIS103 4.9 20.0 1.0 CE1 A:HIS103 5.0 15.6 1.0

Copper binding site 3 out of 8 in the Laccase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Laccase From Bacillus Licheniformis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu614 b:18.5 occ:1.00 NE2 A:HIS420 2.0 14.2 1.0 NE2 A:HIS103 2.1 15.0 1.0 CD2 A:HIS420 2.9 10.1 1.0 CD2 A:HIS103 3.0 15.6 1.0 O A:HOH837 3.0 15.8 1.0 CE1 A:HIS420 3.1 12.6 1.0 CE1 A:HIS103 3.2 15.6 1.0 NE2 A:HIS422 3.2 13.7 1.0 CD2 A:HIS422 3.3 14.2 1.0 ND1 A:HIS105 3.3 12.1 1.0 CE1 A:HIS422 3.6 16.1 1.0 CU A:CU613 3.7 19.1 1.0 CA A:HIS105 3.7 10.7 1.0 CG A:HIS105 3.7 12.4 1.0 CG A:HIS422 3.8 13.9 1.0 CE1 A:HIS105 3.8 14.4 1.0 ND1 A:HIS422 3.9 14.6 1.0 CB A:HIS105 4.1 9.2 1.0 CU A:CU615 4.1 23.2 1.0 CG A:HIS420 4.1 15.2 1.0 N A:GLY106 4.1 15.5 1.0 ND1 A:HIS420 4.1 15.3 1.0 CG A:HIS103 4.2 20.0 1.0 ND1 A:HIS103 4.2 17.5 1.0 CD2 A:HIS105 4.4 12.4 1.0 C A:HIS105 4.5 13.6 1.0 NE2 A:HIS105 4.5 17.8 1.0 CA A:HIS422 4.6 13.6 1.0 N A:HIS105 4.7 15.1 1.0 CB A:HIS422 4.7 14.3 1.0 O A:LEU104 4.8 11.8 1.0 O A:LEU421 4.9 16.2 1.0

Copper binding site 4 out of 8 in the Laccase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Laccase From Bacillus Licheniformis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu615 b:23.2 occ:1.00 ND1 A:HIS105 2.1 12.1 1.0 NE2 A:HIS151 2.1 8.0 1.0 NE2 A:HIS491 2.1 13.1 1.0 CE1 A:HIS105 3.0 14.4 1.0 CG A:HIS105 3.0 12.4 1.0 CE1 A:HIS491 3.1 11.5 1.0 CE1 A:HIS151 3.1 9.5 1.0 CD2 A:HIS151 3.1 10.7 1.0 CD2 A:HIS491 3.2 11.9 1.0 CB A:HIS105 3.4 9.2 1.0 CZ2 A:TRP149 3.7 8.9 1.0 NE2 A:HIS105 4.0 17.8 1.0 CU A:CU614 4.1 18.5 1.0 CD2 A:HIS105 4.1 12.4 1.0 CE2 A:TRP149 4.1 10.8 1.0 ND1 A:HIS151 4.2 12.0 1.0 ND1 A:HIS491 4.2 15.6 1.0 CG A:HIS151 4.3 11.7 1.0 CG A:HIS491 4.3 14.0 1.0 CD2 A:HIS103 4.3 15.6 1.0 NE1 A:TRP149 4.3 9.9 1.0 CH2 A:TRP149 4.4 11.5 1.0 CB A:ALA295 4.4 10.7 1.0 CA A:HIS105 4.5 10.7 1.0 CD2 A:HIS420 4.6 10.1 1.0 NE2 A:HIS420 4.6 14.2 1.0 CU A:CU613 4.7 19.1 1.0 NE2 A:HIS103 4.8 15.0 1.0

Copper binding site 5 out of 8 in the Laccase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Laccase From Bacillus Licheniformis within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu606 b:24.8 occ:1.00 ND1 B:HIS495 2.2 14.0 1.0 ND1 B:HIS417 2.2 20.3 1.0 SG B:CYS490 2.4 19.3 1.0 CE1 B:HIS417 3.0 18.7 1.0 CE1 B:HIS495 3.1 17.1 1.0 CG B:HIS495 3.2 18.5 1.0 SD B:MET500 3.2 20.7 1.0 CB B:CYS490 3.3 13.2 1.0 CG B:HIS417 3.4 15.7 1.0 CB B:HIS495 3.5 19.3 1.0 CD1 B:ILE492 3.8 17.1 1.0 CB B:HIS417 3.8 12.3 1.0 CE B:MET500 4.0 23.9 1.0 CB B:ILE492 4.1 15.2 1.0 NE2 B:HIS417 4.2 17.6 1.0 CA B:HIS417 4.2 13.7 1.0 CG1 B:ILE492 4.2 15.7 1.0 NE2 B:HIS495 4.2 21.7 1.0 CD2 B:HIS495 4.3 17.7 1.0 CD2 B:LEU384 4.3 24.2 1.0 O B:HOH863 4.3 16.7 1.0 CD2 B:HIS417 4.4 18.3 1.0 CD B:PRO418 4.7 14.9 1.0 CA B:CYS490 4.8 16.6 1.0 CG B:MET500 4.8 18.8 1.0 CG2 B:ILE492 4.9 13.1 1.0 O B:ILE416 5.0 18.4 1.0 CA B:HIS495 5.0 16.5 1.0

Copper binding site 6 out of 8 in the Laccase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Laccase From Bacillus Licheniformis within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu613 b:21.8 occ:1.00 NE2 B:HIS489 2.0 14.4 1.0 NE2 B:HIS422 2.1 15.9 1.0 NE2 B:HIS153 2.2 12.4 1.0 CE1 B:HIS422 2.8 15.7 1.0 CE1 B:HIS489 3.0 14.2 1.0 CD2 B:HIS153 3.0 12.3 1.0 CD2 B:HIS489 3.1 18.8 1.0 CD2 B:HIS422 3.3 16.0 1.0 CE1 B:HIS153 3.3 17.7 1.0 CU B:CU614 3.6 19.5 1.0 CD2 B:HIS420 3.8 11.3 1.0 CD2 B:HIS103 4.0 15.5 1.0 ND1 B:HIS422 4.0 15.8 1.0 NE2 B:HIS103 4.1 13.4 1.0 ND1 B:HIS489 4.1 14.0 1.0 NE2 B:HIS420 4.2 15.6 1.0 CG B:HIS489 4.2 17.2 1.0 CG2 B:VAL487 4.2 10.4 1.0 CG B:HIS153 4.3 16.9 1.0 CG B:HIS422 4.3 15.0 1.0 ND1 B:HIS153 4.3 16.5 1.0 OE2 B:GLU496 4.5 21.1 1.0 CU B:CU615 4.6 23.6 1.0 O B:HOH740 4.7 16.0 1.0 CG B:HIS103 4.8 17.2 1.0 CE1 B:HIS103 4.9 16.1 1.0

Copper binding site 7 out of 8 in the Laccase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Laccase From Bacillus Licheniformis within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu614 b:19.5 occ:1.00 NE2 B:HIS420 2.1 15.6 1.0 NE2 B:HIS103 2.1 13.4 1.0 CD2 B:HIS103 3.0 15.5 1.0 CE1 B:HIS420 3.0 14.1 1.0 O B:HOH813 3.0 11.9 1.0 CD2 B:HIS420 3.0 11.3 1.0 NE2 B:HIS422 3.1 15.9 1.0 CE1 B:HIS103 3.2 16.1 1.0 ND1 B:HIS105 3.3 12.7 1.0 CD2 B:HIS422 3.3 16.0 1.0 CE1 B:HIS422 3.6 15.7 1.0 CU B:CU613 3.6 21.8 1.0 CG B:HIS105 3.7 12.7 1.0 CA B:HIS105 3.7 11.0 1.0 CE1 B:HIS105 3.8 13.2 1.0 CG B:HIS422 3.8 15.0 1.0 CU B:CU615 3.9 23.6 1.0 ND1 B:HIS422 4.0 15.8 1.0 ND1 B:HIS420 4.1 13.2 1.0 CB B:HIS105 4.1 10.7 1.0 N B:GLY106 4.1 16.3 1.0 CG B:HIS420 4.1 14.1 1.0 CG B:HIS103 4.1 17.2 1.0 ND1 B:HIS103 4.2 16.8 1.0 CD2 B:HIS105 4.4 11.7 1.0 NE2 B:HIS105 4.4 14.0 1.0 C B:HIS105 4.5 15.2 1.0 N B:HIS105 4.7 13.4 1.0 CA B:HIS422 4.8 13.4 1.0 CB B:HIS422 4.8 13.9 1.0 O B:LEU104 4.9 14.4 1.0 O B:LEU421 4.9 11.9 1.0 O B:HOH764 5.0 13.7 1.0 O B:HOH790 5.0 10.0 1.0

Copper binding site 8 out of 8 in the Laccase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Laccase From Bacillus Licheniformis within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu615 b:23.6 occ:1.00 ND1 B:HIS105 2.0 12.7 1.0 NE2 B:HIS151 2.1 11.9 1.0 NE2 B:HIS491 2.2 14.7 1.0 CE1 B:HIS105 2.9 13.2 1.0 CE1 B:HIS151 3.0 12.9 1.0 CG B:HIS105 3.1 12.7 1.0 CE1 B:HIS491 3.1 12.9 1.0 CD2 B:HIS151 3.2 12.3 1.0 CD2 B:HIS491 3.2 12.2 1.0 CB B:HIS105 3.5 10.7 1.0 CZ2 B:TRP149 3.9 10.0 1.0 CU B:CU614 3.9 19.5 1.0 NE2 B:HIS105 4.0 14.0 1.0 CD2 B:HIS105 4.1 11.7 1.0 ND1 B:HIS151 4.1 15.2 1.0 CD2 B:HIS103 4.2 15.5 1.0 ND1 B:HIS491 4.2 13.1 1.0 CG B:HIS151 4.3 14.7 1.0 CG B:HIS491 4.3 11.9 1.0 CE2 B:TRP149 4.3 10.6 1.0 NE1 B:TRP149 4.5 8.9 1.0 CA B:HIS105 4.5 11.0 1.0 CH2 B:TRP149 4.6 10.6 1.0 CU B:CU613 4.6 21.8 1.0 CB B:ALA295 4.6 12.1 1.0 NE2 B:HIS420 4.6 15.6 1.0 NE2 B:HIS103 4.7 13.4 1.0 CD2 B:HIS420 4.7 11.3 1.0

M.Refaat, M.T.Elrakaiby, M.Elhariri Elnokab, J.Es Sayed, A.Elshewy, K.O.Sebakhy, N.Moneib, T.Wang, T.J.Smith, M.H.Habib. Polymerization Potential of A Bacterial Cota-Laccase For B-Naphthol: Enzyme Structure and Comprehensive Polymer Characterization. Front Microbiol 2024.
ISSN: ESSN 1664-302X
DOI: 10.3389/FMICB.2024.1501112