Copper in PDB 7bfm: Structure of the M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site

The structure of Structure of the M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site, PDB code: 7bfm 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)	29.77 / 2.00
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	178.638, 178.638, 178.638, 90, 90, 90
R / Rfree (%)	14.6 / 15.8

The binding sites of Copper atom in the Structure of the M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site (pdb code 7bfm). 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 M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site, PDB code: 7bfm:
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 M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site


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 M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:18.4 occ:0.56 NE2 A:HIS104 1.9 26.5 1.0 NE2 A:HIS156 2.0 26.2 1.0 CE1 A:HIS104 2.9 25.4 1.0 CE1 A:HIS156 2.9 24.8 1.0 CD2 A:HIS104 3.0 24.3 1.0 CD2 A:HIS156 3.1 24.1 1.0 O A:HOH704 3.2 39.1 1.0 CD2 A:HIS102 3.8 30.7 1.0 CU A:CU404 3.9 49.8 0.2 NE2 A:HIS102 3.9 33.0 1.0 CB A:ALA266 4.0 24.2 1.0 ND1 A:HIS104 4.0 24.6 1.0 ND1 A:HIS156 4.0 26.2 1.0 CG A:HIS104 4.1 24.3 1.0 CE1 A:HIS154 4.2 26.6 1.0 CG A:HIS156 4.2 25.3 1.0 O A:HOH702 4.6 37.7 1.0 NE2 A:HIS154 4.9 24.9 1.0

Copper binding site 2 out of 8 in the Structure of the M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site


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 M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:36.5 occ:0.42 O A:HOH704 2.1 39.1 1.0 NE2 A:HIS158 2.4 29.5 1.0 CE1 A:HIS158 3.3 32.9 1.0 CD2 A:HIS158 3.4 30.0 1.0 O A:HOH702 3.9 37.7 1.0 CU A:CU404 3.9 49.8 0.2 NE2 A:HIS102 4.2 33.0 1.0 CD2 A:HIS164 4.4 29.2 1.0 ND1 A:HIS158 4.5 28.7 1.0 CE1 A:HIS102 4.5 36.3 1.0 CG A:HIS158 4.6 28.6 1.0 CD2 A:HIS102 4.8 30.7 1.0 NE2 A:HIS164 5.0 35.0 1.0

Copper binding site 3 out of 8 in the Structure of the M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site


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 M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:49.8 occ:0.18 NE2 A:HIS102 1.8 33.0 1.0 CE1 A:HIS102 2.5 36.3 1.0 O A:HOH527 2.8 32.6 1.0 CD2 A:HIS102 3.0 30.7 1.0 O A:HOH704 3.5 39.1 1.0 NE2 A:HIS104 3.6 26.5 1.0 ND1 A:HIS102 3.7 34.6 1.0 CU A:CU402 3.9 18.4 0.6 CU A:CU403 3.9 36.5 0.4 CE1 A:HIS104 3.9 25.4 1.0 CD2 A:HIS104 3.9 24.3 1.0 CG A:HIS102 4.0 29.5 1.0 ND1 A:HIS104 4.4 24.6 1.0 CG A:HIS104 4.4 24.3 1.0 O A:VAL103 4.4 24.7 1.0 OH A:TYR108 4.5 30.1 1.0

Copper binding site 4 out of 8 in the Structure of the M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site


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 M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu405 b:29.4 occ:1.00 ND1 A:HIS293 2.0 28.5 1.0 ND1 A:HIS231 2.1 25.4 1.0 SG A:CYS288 2.2 24.9 1.0 O A:HOH725 2.7 44.5 1.0 CE1 A:HIS293 2.9 31.9 1.0 CG A:HIS293 3.0 27.3 1.0 CE1 A:HIS231 3.0 26.7 1.0 CB A:CYS288 3.0 26.5 1.0 CG A:HIS231 3.1 24.1 1.0 CB A:HIS293 3.4 27.0 1.0 CB A:HIS231 3.4 22.5 1.0 CA A:HIS231 3.8 23.9 1.0 NE2 A:HIS293 4.0 31.0 1.0 CD2 A:HIS293 4.1 29.7 1.0 CG2 A:VAL290 4.1 23.2 1.0 O A:TYR230 4.1 25.1 1.0 NE2 A:HIS231 4.2 27.1 1.0 CB A:VAL290 4.2 23.8 1.0 CD2 A:HIS231 4.2 24.1 1.0 CA A:CYS288 4.5 25.4 1.0 N A:THR232 4.7 21.7 1.0 O A:HOH578 4.7 30.6 1.0 N A:HIS231 4.8 22.1 1.0 C A:HIS231 4.8 23.4 1.0 C A:TYR230 4.9 25.7 1.0 CA A:HIS293 4.9 27.8 1.0 CD2 A:PHE195 5.0 28.0 1.0

Copper binding site 5 out of 8 in the Structure of the M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site


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 M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu402 b:21.3 occ:0.62 NE2 C:HIS104 1.9 24.6 1.0 NE2 C:HIS156 2.0 25.3 1.0 CE1 C:HIS104 2.9 24.5 1.0 CE1 C:HIS156 2.9 25.9 1.0 CD2 C:HIS104 3.0 24.1 1.0 CD2 C:HIS156 3.1 23.8 1.0 CD2 C:HIS102 3.6 31.5 1.0 CU C:CU404 3.7 49.8 0.2 NE2 C:HIS102 3.8 40.0 1.0 ND1 C:HIS104 4.0 22.7 1.0 CB C:ALA266 4.0 24.0 1.0 ND1 C:HIS156 4.1 25.1 1.0 CG C:HIS104 4.1 23.4 1.0 CE1 C:HIS154 4.2 26.4 1.0 CG C:HIS156 4.2 25.1 1.0 O C:HOH676 4.7 38.4 1.0 NE2 C:HIS154 4.9 23.9 1.0 CG C:HIS102 5.0 30.3 1.0

Copper binding site 6 out of 8 in the Structure of the M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site


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 M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu403 b:37.5 occ:0.44 NE2 C:HIS158 2.4 29.2 1.0 CE1 C:HIS158 3.3 32.3 1.0 CD2 C:HIS158 3.4 32.2 1.0 CU C:CU404 3.9 49.8 0.2 O C:HOH676 4.0 38.4 1.0 NE2 C:HIS102 4.1 40.0 1.0 CD2 C:HIS164 4.4 29.3 1.0 ND1 C:HIS158 4.5 28.7 1.0 CG C:HIS158 4.6 28.4 1.0 CE1 C:HIS102 4.6 31.1 1.0 CD2 C:HIS102 4.6 31.5 1.0 NE2 C:HIS164 4.9 36.9 1.0

Copper binding site 7 out of 8 in the Structure of the M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site


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 M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu404 b:49.8 occ:0.17 NE2 C:HIS102 1.8 40.0 1.0 CE1 C:HIS102 2.5 31.1 1.0 O C:HOH511 2.9 32.4 1.0 CD2 C:HIS102 3.0 31.5 1.0 NE2 C:HIS104 3.4 24.6 1.0 CU C:CU402 3.7 21.3 0.6 ND1 C:HIS102 3.8 35.8 1.0 CE1 C:HIS104 3.8 24.5 1.0 CD2 C:HIS104 3.8 24.1 1.0 CU C:CU403 3.9 37.5 0.4 CG C:HIS102 4.0 30.3 1.0 ND1 C:HIS104 4.2 22.7 1.0 CG C:HIS104 4.3 23.4 1.0 O C:VAL103 4.5 24.9 1.0 OH C:TYR108 4.7 29.8 1.0

Copper binding site 8 out of 8 in the Structure of the M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site


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 M198F M298F Double Mutant of the Streptomyces Coelicolor Small Laccase T1 Copper Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu405 b:28.9 occ:1.00 ND1 C:HIS293 2.0 28.7 1.0 ND1 C:HIS231 2.1 26.2 1.0 SG C:CYS288 2.2 24.2 1.0 O C:HOH734 2.7 43.1 1.0 CE1 C:HIS293 2.9 31.9 1.0 CG C:HIS293 3.0 26.8 1.0 CB C:CYS288 3.0 27.1 1.0 CE1 C:HIS231 3.1 26.2 1.0 CG C:HIS231 3.1 24.8 1.0 CB C:HIS293 3.4 26.1 1.0 CB C:HIS231 3.4 22.1 1.0 CA C:HIS231 3.8 24.2 1.0 NE2 C:HIS293 4.0 30.6 1.0 CD2 C:HIS293 4.1 29.6 1.0 CG2 C:VAL290 4.1 22.5 1.0 O C:TYR230 4.2 25.0 1.0 NE2 C:HIS231 4.2 26.5 1.0 CB C:VAL290 4.2 23.7 1.0 CD2 C:HIS231 4.2 25.0 1.0 CA C:CYS288 4.5 25.5 1.0 O C:HOH587 4.7 30.9 1.0 N C:THR232 4.7 21.9 1.0 N C:HIS231 4.8 22.8 1.0 C C:HIS231 4.8 22.7 1.0 CA C:HIS293 4.9 27.2 1.0 C C:TYR230 4.9 25.1 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