Copper in PDB 7b4y: Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand

The structure of Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand, PDB code: 7b4y was solved by K.Zovo, S.Majumdar, T.Lukk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.65 / 2.19
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	177.2, 177.2, 177.2, 90, 90, 90
R / Rfree (%)	15 / 15.8

The binding sites of Copper atom in the Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand (pdb code 7b4y). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand, PDB code: 7b4y:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in the Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:55.9 occ:1.00 SG A:CYS288 2.1 27.6 1.0 ND1 A:HIS231 2.1 27.9 1.0 ND1 A:HIS293 2.2 30.6 1.0 CB A:CYS288 3.0 22.3 1.0 CE1 A:HIS231 3.1 25.9 1.0 CG A:HIS231 3.1 23.8 1.0 CG A:HIS293 3.1 31.5 1.0 CE1 A:HIS293 3.2 28.6 1.0 CB A:HIS293 3.4 25.0 1.0 CB A:HIS231 3.4 20.1 1.0 CA A:HIS231 3.9 23.7 1.0 NE2 A:HIS231 4.2 31.3 1.0 CD1 A:LEU298 4.2 42.8 1.0 CD2 A:HIS231 4.2 27.6 1.0 CD2 A:HIS293 4.3 32.1 1.0 NE2 A:HIS293 4.3 33.1 1.0 O A:TYR230 4.3 26.4 1.0 CG2 A:VAL290 4.4 22.5 1.0 CA A:CYS288 4.4 27.2 1.0 O A:HOH515 4.5 40.2 1.0 CB A:VAL290 4.5 26.6 1.0 CD2 A:PHE195 4.7 27.6 1.0 N A:THR232 4.7 23.8 1.0 CA A:HIS293 4.9 28.1 1.0 C A:HIS231 4.9 25.8 1.0 CE2 A:PHE195 4.9 28.6 1.0 N A:HIS231 4.9 25.3 1.0

Copper binding site 2 out of 8 in the Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:17.0 occ:0.64 NE2 A:HIS104 2.0 25.2 1.0 NE2 A:HIS156 2.1 26.1 1.0 CE1 A:HIS104 2.9 26.0 1.0 CE1 A:HIS156 3.0 24.5 1.0 CD2 A:HIS104 3.0 23.2 1.0 CD2 A:HIS156 3.2 23.4 1.0 CU A:CU404 3.8 28.4 0.4 CD2 A:HIS102 3.9 24.0 1.0 ND1 A:HIS104 4.0 24.8 1.0 NE2 A:HIS102 4.1 31.2 1.0 ND1 A:HIS156 4.1 24.1 1.0 CG A:HIS104 4.1 27.8 1.0 CB A:ALA266 4.2 22.3 1.0 CG A:HIS156 4.3 25.9 1.0 CE1 A:HIS154 4.3 22.4 1.0 O A:HOH652 4.5 40.7 1.0 CU A:CU403 4.8 28.4 0.6

Copper binding site 3 out of 8 in the Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:28.4 occ:0.62 NE2 A:HIS158 2.3 30.8 1.0 CD2 A:HIS158 3.2 25.5 1.0 CE1 A:HIS158 3.3 27.1 1.0 O A:HOH652 3.7 40.7 1.0 CU A:CU404 4.1 28.4 0.4 NE2 A:HIS102 4.3 31.2 1.0 ND1 A:HIS158 4.4 28.9 1.0 CG A:HIS158 4.4 28.3 1.0 CD2 A:HIS164 4.4 29.3 1.0 CD2 A:HIS102 4.7 24.0 1.0 CE1 A:HIS102 4.7 27.4 1.0 CU A:CU402 4.8 17.0 0.6

Copper binding site 4 out of 8 in the Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:28.4 occ:0.39 NE2 A:HIS102 1.9 31.2 1.0 CE1 A:HIS102 2.7 27.4 1.0 O A:HOH541 2.7 31.5 1.0 CD2 A:HIS102 3.1 24.0 1.0 NE2 A:HIS104 3.7 25.2 1.0 CU A:CU402 3.8 17.0 0.6 CD2 A:HIS104 3.8 23.2 1.0 ND1 A:HIS102 3.9 28.0 1.0 CE1 A:HIS104 4.0 26.0 1.0 CU A:CU403 4.1 28.4 0.6 CG A:HIS102 4.1 25.5 1.0 CG A:HIS104 4.3 27.8 1.0 O A:VAL103 4.3 24.9 1.0 ND1 A:HIS104 4.3 24.8 1.0 OH A:TYR108 4.4 31.9 1.0 CA A:HIS104 4.9 23.8 1.0 C A:VAL103 4.9 24.9 1.0

Copper binding site 5 out of 8 in the Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu401 b:28.7 occ:0.89 NE2 B:HIS289 2.0 25.0 1.0 O B:HOH654 2.4 32.0 1.0 CD2 B:HIS289 3.0 22.4 1.0 CE1 B:HIS289 3.0 22.3 1.0 CU B:CU402 3.7 31.1 0.4 ND1 B:HIS289 4.1 25.4 1.0 CG B:HIS289 4.1 27.1 1.0 NE2 B:HIS234 4.2 28.1 1.0 CD2 B:HIS234 4.3 27.3 1.0 CU B:CU403 4.8 31.9 0.7 CE1 B:HIS234 4.8 23.2 1.0

Copper binding site 6 out of 8 in the Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu402 b:31.1 occ:0.39 NE2 B:HIS234 2.0 28.1 1.0 O B:HOH654 2.8 32.0 1.0 CE1 B:HIS234 2.9 23.2 1.0 CD2 B:HIS234 3.1 27.3 1.0 CD2 B:HIS236 3.3 25.5 1.0 NE2 B:HIS236 3.4 25.8 1.0 CU B:CU401 3.7 28.7 0.9 CG B:HIS236 3.8 30.3 1.0 CE1 B:HIS236 4.0 26.4 1.0 CU B:CU403 4.0 31.9 0.7 ND1 B:HIS234 4.0 24.8 1.0 CG B:HIS234 4.1 23.7 1.0 ND1 B:HIS236 4.2 30.2 1.0 CA B:HIS236 4.5 23.1 1.0 CB B:HIS236 4.7 24.3 1.0 N B:HIS236 4.9 22.3 1.0 O B:HOH509 4.9 27.2 1.0 OD2 B:ASP259 4.9 21.8 1.0 O B:MET235 5.0 26.0 1.0

Copper binding site 7 out of 8 in the Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu403 b:31.9 occ:0.67 NE2 B:HIS236 2.0 25.8 1.0 NE2 B:HIS287 2.3 31.7 1.0 O B:HOH654 2.4 32.0 1.0 CE1 B:HIS236 2.8 26.4 1.0 CE1 B:HIS287 3.2 25.3 1.0 CD2 B:HIS236 3.2 25.5 1.0 CD2 B:HIS287 3.3 29.1 1.0 CU B:CU402 4.0 31.1 0.4 ND1 B:HIS236 4.0 30.2 1.0 CD2 B:HIS234 4.1 27.3 1.0 CG B:HIS236 4.2 30.3 1.0 ND1 B:HIS287 4.3 29.7 1.0 CG B:HIS287 4.4 29.3 1.0 SD B:MET285 4.5 54.0 1.0 NE2 B:HIS234 4.5 28.1 1.0 CE B:MET285 4.6 38.6 1.0 CU B:CU401 4.8 28.7 0.9 NE2 B:HIS289 4.8 25.0 1.0

Copper binding site 8 out of 8 in the Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Structure of the M298L Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Axial Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu404 b:53.1 occ:1.00 ND1 B:HIS231 2.1 28.2 1.0 SG B:CYS288 2.2 28.2 1.0 ND1 B:HIS293 2.2 30.0 1.0 CB B:CYS288 3.0 22.8 1.0 CE1 B:HIS231 3.1 24.8 1.0 CG B:HIS231 3.1 24.5 1.0 CG B:HIS293 3.1 30.7 1.0 CE1 B:HIS293 3.2 28.6 1.0 CB B:HIS293 3.4 24.1 1.0 CB B:HIS231 3.4 23.8 1.0 CA B:HIS231 3.9 24.2 1.0 NE2 B:HIS231 4.2 30.7 1.0 CD2 B:HIS231 4.2 28.6 1.0 CD1 B:LEU298 4.2 41.5 1.0 CD2 B:HIS293 4.3 32.0 1.0 NE2 B:HIS293 4.3 31.8 1.0 O B:TYR230 4.3 27.3 1.0 CG2 B:VAL290 4.4 21.5 1.0 CA B:CYS288 4.4 29.3 1.0 CB B:VAL290 4.5 27.0 1.0 O B:HOH552 4.5 39.4 1.0 CD2 B:PHE195 4.7 26.4 1.0 N B:THR232 4.7 22.6 1.0 CA B:HIS293 4.9 28.6 1.0 C B:HIS231 4.9 26.6 1.0 N B:HIS231 4.9 24.7 1.0 CE2 B:PHE195 4.9 27.9 1.0

K.Zovo, H.Pupart, A.Van Wieren, R.E.Gillilan, Q.Huang, S.Majumdar, T.Lukk. Substitution of the Methionine Axial Ligand of the T1 Copper For the Fungal-Like Phenylalanine Ligand (M298F) Causes Local Structural Perturbations That Lead to Thermal Instability and Reduced Catalytic Efficiency of the Small Laccase From Streptomyces Coelicolor A3(2). Acs Omega V. 7 6184 2022.
ISSN: ESSN 2470-1343
PubMed: 35224382
DOI: 10.1021/ACSOMEGA.1C06668