Copper in PDB 7bdn: Structure of the Streptomyces Coelicolor Small Laccase - Cubic Crystal Form

The structure of Structure of the Streptomyces Coelicolor Small Laccase - Cubic Crystal Form, PDB code: 7bdn 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)	29.50 / 2.70
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	176.981, 176.981, 176.981, 90, 90, 90
R / Rfree (%)	20 / 22.2

The binding sites of Copper atom in the Structure of the Streptomyces Coelicolor Small Laccase - Cubic Crystal Form (pdb code 7bdn). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Structure of the Streptomyces Coelicolor Small Laccase - Cubic Crystal Form, PDB code: 7bdn:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in the Structure of the Streptomyces Coelicolor Small Laccase - Cubic Crystal Form


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 Streptomyces Coelicolor Small Laccase - Cubic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:45.6 occ:1.00 NE2 A:HIS104 2.1 32.3 1.0 NE2 A:HIS156 2.2 37.4 1.0 CE1 A:HIS102 2.9 36.0 1.0 CE1 A:HIS156 3.0 34.3 1.0 CE1 A:HIS104 3.0 31.3 1.0 CD2 A:HIS104 3.2 30.2 1.0 CD2 A:HIS156 3.3 33.0 1.0 ND1 A:HIS102 3.3 35.2 1.0 CU A:CU402 3.4 75.3 1.0 NE2 A:HIS102 4.1 42.2 1.0 ND1 A:HIS156 4.1 32.0 1.0 ND1 A:HIS104 4.2 33.6 1.0 O A:HOH592 4.2 34.3 1.0 CG A:HIS104 4.3 31.6 1.0 CG A:HIS156 4.3 34.0 1.0 CG A:HIS102 4.6 39.0 1.0 CB A:ALA266 4.7 27.4 1.0 CE1 A:HIS154 4.7 28.3 1.0

Copper binding site 2 out of 6 in the Structure of the Streptomyces Coelicolor Small Laccase - Cubic Crystal Form


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 Streptomyces Coelicolor Small Laccase - Cubic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:75.3 occ:1.00 NE2 A:HIS158 2.6 38.7 1.0 O A:HOH592 3.3 34.3 1.0 CD2 A:HIS158 3.4 35.8 1.0 CU A:CU401 3.4 45.6 1.0 CE1 A:HIS102 3.6 36.0 1.0 CE1 A:HIS158 3.6 36.1 1.0 NE2 A:HIS102 3.9 42.2 1.0 ND1 A:HIS102 4.2 35.2 1.0 CG A:HIS158 4.5 37.2 1.0 ND1 A:HIS158 4.6 37.0 1.0 CD2 A:HIS102 4.6 38.2 1.0 CE1 A:HIS156 4.7 34.3 1.0 NE2 A:HIS156 4.8 37.4 1.0 CG A:HIS102 4.8 39.0 1.0

Copper binding site 3 out of 6 in the Structure of the Streptomyces Coelicolor Small Laccase - Cubic Crystal Form


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 Streptomyces Coelicolor Small Laccase - Cubic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:34.6 occ:1.00 ND1 A:HIS231 2.0 31.7 1.0 ND1 A:HIS293 2.1 30.5 1.0 SG A:CYS288 2.2 33.2 1.0 CG A:HIS231 2.9 31.0 1.0 CE1 A:HIS231 3.0 29.7 1.0 CG A:HIS293 3.0 34.3 1.0 CE1 A:HIS293 3.1 33.9 1.0 CB A:CYS288 3.1 31.8 1.0 CB A:HIS231 3.2 28.2 1.0 CB A:HIS293 3.3 31.7 1.0 SD A:MET298 3.5 36.0 1.0 CA A:HIS231 3.7 28.6 1.0 CE A:MET298 3.7 30.2 1.0 CD2 A:HIS231 4.1 31.9 1.0 NE2 A:HIS231 4.1 33.4 1.0 O A:TYR230 4.1 29.2 1.0 NE2 A:HIS293 4.2 32.9 1.0 CD2 A:HIS293 4.2 36.2 1.0 CG2 A:VAL290 4.2 27.6 1.0 CB A:VAL290 4.2 30.3 1.0 CA A:CYS288 4.5 31.1 1.0 N A:THR232 4.6 28.2 1.0 N A:HIS231 4.7 29.9 1.0 C A:HIS231 4.7 27.6 1.0 C A:TYR230 4.8 29.6 1.0 CA A:HIS293 4.8 30.8 1.0 CD2 A:PHE195 4.9 33.1 1.0

Copper binding site 4 out of 6 in the Structure of the Streptomyces Coelicolor Small Laccase - Cubic Crystal Form


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 Streptomyces Coelicolor Small Laccase - Cubic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu401 b:45.2 occ:1.00 NE2 B:HIS104 2.1 32.5 1.0 NE2 B:HIS156 2.2 36.1 1.0 CE1 B:HIS102 2.8 36.3 1.0 CE1 B:HIS156 2.9 33.9 1.0 CE1 B:HIS104 3.1 30.5 1.0 CD2 B:HIS104 3.1 31.4 1.0 ND1 B:HIS102 3.3 34.1 1.0 CD2 B:HIS156 3.3 31.1 1.0 CU B:CU402 3.5 77.7 1.0 NE2 B:HIS102 4.0 41.3 1.0 ND1 B:HIS156 4.1 30.9 1.0 ND1 B:HIS104 4.2 33.4 1.0 CG B:HIS104 4.2 32.0 1.0 O B:HOH600 4.3 34.9 1.0 CG B:HIS156 4.3 33.3 1.0 CG B:HIS102 4.6 38.8 1.0 CB B:ALA266 4.7 27.3 1.0 CE1 B:HIS154 4.7 27.5 1.0 CD2 B:HIS102 4.9 37.5 1.0

Copper binding site 5 out of 6 in the Structure of the Streptomyces Coelicolor Small Laccase - Cubic Crystal Form


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 Streptomyces Coelicolor Small Laccase - Cubic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu402 b:77.7 occ:1.00 NE2 B:HIS158 2.6 39.6 1.0 CD2 B:HIS158 3.4 34.1 1.0 O B:HOH600 3.4 34.9 1.0 CU B:CU401 3.5 45.2 1.0 CE1 B:HIS158 3.6 34.3 1.0 CE1 B:HIS102 3.7 36.3 1.0 NE2 B:HIS102 3.9 41.3 1.0 ND1 B:HIS102 4.2 34.1 1.0 CG B:HIS158 4.5 35.3 1.0 ND1 B:HIS158 4.6 36.2 1.0 CD2 B:HIS102 4.7 37.5 1.0 CE1 B:HIS156 4.8 33.9 1.0 CG B:HIS102 4.8 38.8 1.0 CD2 B:HIS164 4.9 35.0 1.0 NE2 B:HIS156 5.0 36.1 1.0

Copper binding site 6 out of 6 in the Structure of the Streptomyces Coelicolor Small Laccase - Cubic Crystal Form


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 Streptomyces Coelicolor Small Laccase - Cubic Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu403 b:36.0 occ:1.00 ND1 B:HIS231 2.0 31.9 1.0 ND1 B:HIS293 2.0 28.9 1.0 SG B:CYS288 2.1 32.8 1.0 CG B:HIS231 3.0 31.7 1.0 CE1 B:HIS231 3.0 28.8 1.0 CG B:HIS293 3.0 34.1 1.0 CE1 B:HIS293 3.0 34.2 1.0 CB B:CYS288 3.1 31.9 1.0 CB B:HIS231 3.3 27.4 1.0 CB B:HIS293 3.3 31.0 1.0 SD B:MET298 3.5 37.0 1.0 CA B:HIS231 3.7 28.1 1.0 CE B:MET298 3.7 29.6 1.0 O B:TYR230 4.1 28.2 1.0 NE2 B:HIS231 4.1 32.5 1.0 CD2 B:HIS231 4.1 32.6 1.0 NE2 B:HIS293 4.1 31.7 1.0 CD2 B:HIS293 4.1 35.6 1.0 CB B:VAL290 4.2 30.4 1.0 CG2 B:VAL290 4.2 26.4 1.0 CA B:CYS288 4.5 29.7 1.0 N B:THR232 4.7 28.0 1.0 N B:HIS231 4.7 30.0 1.0 C B:HIS231 4.8 27.2 1.0 CA B:HIS293 4.8 30.5 1.0 C B:TYR230 4.8 29.2 1.0 CD2 B:PHE195 4.9 31.1 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