Copper in PDB 9nji: M298L Streptomyces Coelicolor Laccase

The structure of M298L Streptomyces Coelicolor Laccase, PDB code: 9nji was solved by J.-X.Wang, Y.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.31 / 2.60
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	177.228, 177.228, 177.228, 90, 90, 90
R / Rfree (%)	18.6 / 20.2

The binding sites of Copper atom in the M298L Streptomyces Coelicolor Laccase (pdb code 9nji). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the M298L Streptomyces Coelicolor Laccase, PDB code: 9nji:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the M298L Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of M298L Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:41.0 occ:1.00 ND1 A:HIS293 2.0 39.4 1.0 ND1 A:HIS231 2.1 40.1 1.0 SG A:CYS288 2.3 39.0 1.0 O A:HOH554 2.5 43.4 1.0 CG A:HIS231 2.9 34.3 1.0 CE1 A:HIS293 2.9 39.5 1.0 CG A:HIS293 3.1 41.2 1.0 CE1 A:HIS231 3.1 37.9 1.0 CB A:HIS231 3.1 32.5 1.0 CB A:CYS288 3.2 35.1 1.0 CB A:HIS293 3.4 38.9 1.0 CA A:HIS231 3.8 37.1 1.0 NE2 A:HIS293 4.1 39.4 1.0 CD2 A:HIS231 4.1 38.9 1.0 CD1 A:LEU298 4.1 48.6 1.0 CD2 A:HIS293 4.2 41.8 1.0 NE2 A:HIS231 4.2 39.8 1.0 O A:TYR230 4.2 39.3 1.0 CG2 A:VAL290 4.4 37.0 1.0 CB A:VAL290 4.5 39.8 1.0 O A:HOH504 4.5 43.0 1.0 CD2 A:PHE195 4.6 43.0 1.0 CA A:CYS288 4.6 38.3 1.0 N A:THR232 4.7 36.4 1.0 N A:HIS231 4.8 39.7 1.0 CE2 A:PHE195 4.8 39.2 1.0 C A:HIS231 4.8 39.6 1.0 C A:TYR230 4.9 38.4 1.0 CA A:HIS293 4.9 41.1 1.0

Copper binding site 2 out of 4 in the M298L Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of M298L Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:46.6 occ:0.72 NE2 A:HIS289 2.1 43.1 1.0 O A:OH405 2.4 34.4 1.0 CE1 A:HIS289 3.0 36.8 1.0 CD2 A:HIS289 3.1 40.6 1.0 CU A:CU404 3.5 46.0 0.2 O A:HOH573 4.0 56.5 1.0 NE2 A:HIS234 4.1 46.4 1.0 ND1 A:HIS289 4.1 36.7 1.0 CG A:HIS289 4.2 40.1 1.0 CD2 A:HIS234 4.3 42.5 1.0 CU A:CU403 4.6 53.3 0.7 CE1 A:HIS234 4.8 40.5 1.0

Copper binding site 3 out of 4 in the M298L Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of M298L Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:53.3 occ:0.73 NE2 A:HIS236 2.1 44.9 1.0 O A:OH405 2.3 34.4 1.0 NE2 A:HIS287 2.3 47.0 1.0 CE1 A:HIS236 2.8 47.2 1.0 CE1 A:HIS287 3.2 41.9 1.0 CD2 A:HIS287 3.3 42.8 1.0 CD2 A:HIS236 3.3 47.6 1.0 O A:HOH573 3.4 56.5 1.0 CU A:CU404 3.9 46.0 0.2 ND1 A:HIS236 4.0 47.9 1.0 CD2 A:HIS234 4.1 42.5 1.0 ND1 A:HIS287 4.3 41.4 1.0 CG A:HIS236 4.3 46.2 1.0 CE A:MET285 4.4 46.7 1.0 CG A:HIS287 4.4 41.6 1.0 NE2 A:HIS234 4.4 46.4 1.0 NE2 A:HIS289 4.6 43.1 1.0 CU A:CU402 4.6 46.6 0.7 CD2 A:HIS289 4.9 40.6 1.0 SD A:MET285 5.0 69.6 1.0

Copper binding site 4 out of 4 in the M298L Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of M298L Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:46.0 occ:0.16 NE2 A:HIS234 1.9 46.4 1.0 O A:OH405 2.8 34.4 1.0 CE1 A:HIS234 2.8 40.5 1.0 CD2 A:HIS234 3.0 42.5 1.0 CD2 A:HIS236 3.3 47.6 1.0 NE2 A:HIS236 3.3 44.9 1.0 CU A:CU402 3.5 46.6 0.7 CG A:HIS236 3.9 46.2 1.0 CU A:CU403 3.9 53.3 0.7 ND1 A:HIS234 3.9 42.6 1.0 CE1 A:HIS236 4.0 47.2 1.0 CG A:HIS234 4.0 44.2 1.0 ND1 A:HIS236 4.3 47.9 1.0 CA A:HIS236 4.6 40.5 1.0 NE2 A:HIS289 4.7 43.1 1.0 CB A:HIS236 4.8 40.7 1.0 O A:MET235 4.9 39.6 1.0 N A:HIS236 5.0 42.0 1.0 CD2 A:HIS289 5.0 40.6 1.0 NE2 A:HIS287 5.0 47.0 1.0

J.X.Wang, A.C.Vilbert, L.H.Williams, E.N.Mirts, C.Cui, Y.Lu. Unexpected Effect of An Axial Ligand Mutation in the Type 1 Copper Center in Small Laccase: Structure-Based Analyses and Engineering to Increase Reduction Potential and Activity Chem Sci 2025.
ISSN: ESSN 2041-6539
DOI: 10.1039/D5SC02177D