Copper in PDB 8p9u: Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus

All present enzymatic activity of Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus:
1.10.3.2;

The structure of Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus, PDB code: 8p9u was solved by I.A.Kolyadenko, S.V.Tishchenko, A.G.Gabdulkhakov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.54 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.302, 94.026, 118.927, 90, 91.1, 90
R / Rfree (%)	20.1 / 24.2

The structure of Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus (pdb code 8p9u). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 20 binding sites of Copper where determined in the Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus, PDB code: 8p9u:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 20 in the Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:18.4 occ:0.80 ND1 A:HIS232 1.9 14.6 1.0 ND1 A:HIS294 2.1 19.2 1.0 SG A:CYS289 2.2 19.4 1.0 CE1 A:HIS232 2.8 15.9 1.0 CG A:HIS232 2.9 17.5 1.0 CG A:HIS294 3.0 17.4 1.0 CB A:CYS289 3.2 27.6 1.0 CE1 A:HIS294 3.2 22.1 1.0 CB A:HIS294 3.2 20.6 1.0 SD A:MET299 3.3 27.0 1.0 CB A:HIS232 3.3 16.8 1.0 CA A:HIS232 3.8 17.3 1.0 NE2 A:HIS232 4.0 21.6 1.0 CE A:MET299 4.0 18.6 1.0 CD2 A:HIS232 4.0 22.2 1.0 CB A:VAL291 4.2 21.0 1.0 O A:TYR231 4.2 17.2 1.0 CG2 A:VAL291 4.2 21.1 1.0 CD2 A:HIS294 4.2 19.1 1.0 NE2 A:HIS294 4.3 18.9 1.0 CA A:CYS289 4.6 14.9 1.0 N A:THR233 4.7 13.4 1.0 CA A:HIS294 4.8 20.9 1.0 N A:HIS232 4.8 12.5 1.0 CG A:MET299 4.8 30.4 1.0 C A:HIS232 4.9 21.0 1.0 CD2 A:PHE196 4.9 21.9 1.0 C A:TYR231 4.9 14.8 1.0 CG1 A:VAL291 5.0 20.7 1.0

Copper binding site 2 out of 20 in the Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:31.2 occ:0.57 O1 A:OXY404 2.0 25.9 0.8 NE2 A:HIS237 2.1 21.8 1.0 O2 A:OXY404 2.2 18.4 0.8 NE2 A:HIS288 2.2 22.5 1.0 NE2 C:HIS159 2.3 20.5 1.0 CE1 A:HIS237 2.7 23.0 1.0 CE1 A:HIS288 3.0 25.9 1.0 CD2 A:HIS288 3.2 18.8 1.0 CD2 C:HIS159 3.2 22.4 1.0 CE1 C:HIS159 3.3 23.4 1.0 CD2 A:HIS237 3.3 19.8 1.0 O A:HOH550 3.8 24.3 1.0 CD2 A:HIS235 3.9 16.2 1.0 ND1 A:HIS237 4.0 19.1 1.0 ND1 A:HIS288 4.1 22.5 1.0 CE A:MET286 4.2 28.2 1.0 CG A:HIS288 4.2 18.4 1.0 NE2 A:HIS235 4.2 26.9 1.0 CG A:HIS237 4.2 22.4 1.0 NE2 C:HIS103 4.3 23.1 1.0 ND1 C:HIS159 4.4 27.3 1.0 CG C:HIS159 4.4 27.4 1.0 ND1 C:HIS165 4.4 29.1 1.0 CU C:CU402 4.5 24.2 0.5 CU C:CU404 4.6 20.6 0.1 SD A:MET286 4.7 36.1 1.0 CD2 C:HIS103 4.7 23.7 1.0 CE1 C:HIS103 4.7 21.6 1.0 NE2 A:HIS290 4.7 23.4 1.0 CD2 A:HIS290 4.9 24.5 1.0 CE1 C:HIS165 5.0 25.0 1.0 O A:HOH654 5.0 25.5 1.0

Copper binding site 3 out of 20 in the Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:27.0 occ:0.52 NE2 A:HIS105 2.1 13.1 1.0 NE2 B:HIS290 2.2 17.9 1.0 NE2 A:HIS157 2.2 19.1 1.0 O1 B:OXY404 2.3 16.3 0.7 O2 B:OXY404 2.3 19.8 0.7 CE1 A:HIS157 2.9 16.4 1.0 CE1 A:HIS105 3.0 17.2 1.0 CD2 B:HIS290 3.1 20.9 1.0 CE1 B:HIS290 3.2 16.3 1.0 CD2 A:HIS105 3.2 11.1 1.0 CD2 A:HIS103 3.2 15.9 1.0 CD2 A:HIS157 3.5 8.7 1.0 NE2 A:HIS103 3.5 19.7 1.0 NE2 B:HIS235 3.9 22.3 1.0 CD2 B:HIS235 3.9 19.4 1.0 ND1 A:HIS157 4.1 12.6 1.0 ND1 A:HIS105 4.2 13.6 1.0 CG A:HIS105 4.3 14.5 1.0 ND1 B:HIS290 4.3 15.3 1.0 CG B:HIS290 4.3 21.8 1.0 CU B:CU402 4.4 35.3 0.8 CG A:HIS157 4.4 9.3 1.0 O B:HOH505 4.4 26.8 1.0 CG A:HIS103 4.5 20.7 1.0 CB A:ALA267 4.6 12.4 1.0 CE1 B:HIS235 4.7 18.5 1.0 CG B:HIS235 4.8 21.9 1.0 CE1 A:HIS103 4.8 21.9 1.0

Copper binding site 4 out of 20 in the Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu401 b:22.6 occ:0.97 ND1 B:HIS294 1.9 14.0 1.0 ND1 B:HIS232 2.1 21.4 1.0 SG B:CYS289 2.2 21.7 1.0 CG B:HIS294 2.9 12.9 1.0 CE1 B:HIS294 3.0 22.4 1.0 CG B:HIS232 3.0 21.5 1.0 CE1 B:HIS232 3.1 28.9 1.0 CB B:CYS289 3.2 22.3 1.0 CB B:HIS294 3.2 22.3 1.0 CB B:HIS232 3.3 17.0 1.0 SD B:MET299 3.4 34.4 1.0 CE B:MET299 3.8 23.1 1.0 CA B:HIS232 3.9 22.1 1.0 CD2 B:HIS294 4.0 20.0 1.0 NE2 B:HIS294 4.0 28.9 1.0 CB B:VAL291 4.1 15.2 1.0 NE2 B:HIS232 4.2 30.1 1.0 CD2 B:HIS232 4.2 21.7 1.0 CG2 B:VAL291 4.2 12.7 1.0 O B:TYR231 4.2 16.6 1.0 CA B:CYS289 4.6 18.2 1.0 CA B:HIS294 4.7 27.2 1.0 N B:HIS232 4.8 18.2 1.0 N B:THR233 4.8 15.3 1.0 C B:TYR231 4.9 22.0 1.0 C B:HIS232 4.9 21.0 1.0 CD2 B:PHE196 4.9 29.1 1.0 CG1 B:VAL291 5.0 11.7 1.0 CG B:MET299 5.0 27.6 1.0

Copper binding site 5 out of 20 in the Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu402 b:35.3 occ:0.78 NE2 B:HIS237 2.0 17.8 1.0 NE2 B:HIS288 2.1 22.4 1.0 O1 B:OXY404 2.1 16.3 0.7 NE2 A:HIS159 2.3 12.1 1.0 O2 B:OXY404 2.7 19.8 0.7 CE1 B:HIS237 2.7 12.0 1.0 CE1 B:HIS288 2.9 20.3 1.0 CD2 B:HIS288 3.1 27.9 1.0 CD2 A:HIS159 3.2 15.4 1.0 CD2 B:HIS237 3.2 25.7 1.0 CE1 A:HIS159 3.3 21.0 1.0 CD2 B:HIS235 3.9 19.4 1.0 O B:HOH505 3.9 26.8 1.0 ND1 B:HIS237 3.9 20.0 1.0 ND1 B:HIS288 4.0 19.0 1.0 CG B:HIS288 4.2 21.1 1.0 CG B:HIS237 4.2 17.4 1.0 NE2 B:HIS235 4.2 22.3 1.0 CE B:MET286 4.3 23.0 1.0 NE2 A:HIS103 4.3 19.7 1.0 SD B:MET286 4.3 29.0 1.0 ND1 A:HIS159 4.3 21.0 1.0 CG A:HIS159 4.3 25.0 1.0 CU A:CU403 4.4 27.0 0.5 CD2 A:HIS165 4.4 22.2 1.0 CD2 A:HIS103 4.5 15.9 1.0 NE2 B:HIS290 4.7 17.9 1.0 CE1 A:HIS103 4.8 21.9 1.0 CB B:MET286 5.0 24.6 1.0 CD2 B:HIS290 5.0 20.9 1.0

Copper binding site 6 out of 20 in the Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu403 b:32.8 occ:0.77 NE2 B:HIS157 1.9 31.6 1.0 NE2 C:HIS290 2.2 29.7 1.0 NE2 B:HIS105 2.2 21.1 1.0 CE1 B:HIS157 2.7 27.2 1.0 O2 C:OXY405 2.8 36.8 0.8 O1 C:OXY405 2.8 36.3 0.8 CD2 B:HIS103 3.1 29.1 1.0 CD2 B:HIS157 3.1 26.0 1.0 CE1 C:HIS290 3.2 31.0 1.0 CD2 B:HIS105 3.2 14.6 1.0 CD2 C:HIS290 3.2 21.6 1.0 CE1 B:HIS105 3.2 22.7 1.0 NE2 B:HIS103 3.2 33.6 1.0 ND1 B:HIS157 3.9 28.5 1.0 NE2 C:HIS235 4.1 26.8 1.0 CG B:HIS157 4.1 27.1 1.0 CD2 C:HIS235 4.2 22.1 1.0 ND1 C:HIS290 4.3 23.1 1.0 CG C:HIS290 4.3 26.9 1.0 ND1 B:HIS105 4.3 19.3 1.0 CG B:HIS105 4.3 19.2 1.0 CG B:HIS103 4.4 32.4 1.0 CE1 B:HIS103 4.5 38.0 1.0 CB B:ALA267 4.6 23.2 1.0 CE1 B:HIS155 4.7 17.3 1.0 CU C:CU403 4.7 39.8 0.5 CE1 C:HIS235 4.9 16.8 1.0

Copper binding site 7 out of 20 in the Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu401 b:27.2 occ:0.88 ND1 C:HIS232 1.9 22.7 1.0 ND1 C:HIS294 2.1 27.8 1.0 SG C:CYS289 2.1 23.5 1.0 CE1 C:HIS232 2.8 26.0 1.0 CE C:MET299 2.9 26.5 1.0 CG C:HIS232 2.9 21.3 1.0 CG C:HIS294 3.0 28.9 1.0 CB C:CYS289 3.1 27.8 1.0 CE1 C:HIS294 3.1 29.1 1.0 CB C:HIS294 3.2 25.6 1.0 CB C:HIS232 3.3 17.3 1.0 SD C:MET299 3.5 44.2 1.0 CA C:HIS232 3.8 23.4 1.0 NE2 C:HIS232 3.9 28.8 1.0 CD2 C:HIS232 4.0 23.8 1.0 CD2 C:HIS294 4.1 23.0 1.0 O C:TYR231 4.2 23.9 1.0 NE2 C:HIS294 4.2 24.8 1.0 CA C:CYS289 4.5 28.0 1.0 CG2 C:VAL291 4.5 26.1 1.0 CB C:VAL291 4.6 25.4 1.0 CD2 C:PHE196 4.7 29.1 1.0 CA C:HIS294 4.7 25.5 1.0 N C:THR233 4.7 13.7 1.0 N C:HIS232 4.8 18.9 1.0 C C:HIS232 4.9 30.8 1.0 CE2 C:PHE196 4.9 27.7 1.0 CG C:MET299 4.9 45.1 1.0 C C:TYR231 4.9 24.2 1.0 CB C:MET299 5.0 27.1 1.0

Copper binding site 8 out of 20 in the Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu402 b:24.2 occ:0.52 NE2 C:HIS157 2.1 27.4 1.0 NE2 A:HIS290 2.2 23.4 1.0 NE2 C:HIS105 2.2 13.3 1.0 O1 A:OXY404 2.6 25.9 0.8 O2 A:OXY404 2.7 18.4 0.8 CE1 C:HIS157 2.8 20.3 1.0 CE1 C:HIS105 3.1 15.4 1.0 CD2 A:HIS290 3.1 24.5 1.0 NE2 C:HIS103 3.2 23.1 1.0 CE1 A:HIS290 3.2 27.1 1.0 CD2 C:HIS105 3.2 17.7 1.0 CD2 C:HIS157 3.3 23.3 1.0 CD2 C:HIS103 3.3 23.7 1.0 CU C:CU404 3.4 20.6 0.1 NE2 A:HIS235 3.8 26.9 1.0 CD2 A:HIS235 4.0 16.2 1.0 ND1 C:HIS157 4.0 31.4 1.0 ND1 C:HIS105 4.2 17.0 1.0 ND1 A:HIS290 4.3 24.7 1.0 CG C:HIS157 4.3 28.6 1.0 CG A:HIS290 4.3 25.8 1.0 CG C:HIS105 4.3 20.3 1.0 O A:HOH550 4.3 24.3 1.0 CB C:ALA267 4.4 15.6 1.0 CE1 C:HIS103 4.5 21.6 1.0 CU A:CU402 4.5 31.2 0.6 CE1 A:HIS235 4.5 20.9 1.0 CG C:HIS103 4.6 19.4 1.0 CG A:HIS235 4.8 18.8 1.0 CE1 C:HIS155 4.8 19.6 1.0

Copper binding site 9 out of 20 in the Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu403 b:39.8 occ:0.54 NE2 C:HIS288 2.0 30.6 1.0 NE2 C:HIS237 2.0 27.0 1.0 O2 C:OXY405 2.1 36.8 0.8 O1 C:OXY405 2.1 36.3 0.8 NE2 B:HIS159 2.3 34.5 1.0 CE1 C:HIS237 2.6 20.7 1.0 CD2 C:HIS288 2.9 26.4 1.0 CE1 C:HIS288 3.0 20.2 1.0 CE1 B:HIS159 3.2 36.0 1.0 CD2 C:HIS237 3.3 27.6 1.0 CD2 B:HIS159 3.3 31.4 1.0 ND1 C:HIS237 3.9 22.8 1.0 CD2 C:HIS235 4.0 22.1 1.0 CG C:HIS288 4.0 23.7 1.0 ND1 C:HIS288 4.1 24.9 1.0 CG C:HIS237 4.2 23.9 1.0 CD2 B:HIS165 4.2 34.6 1.0 ND1 B:HIS159 4.4 27.4 1.0 CE C:MET286 4.4 26.0 1.0 CG B:HIS159 4.5 25.9 1.0 NE2 C:HIS235 4.5 26.8 1.0 NE2 B:HIS103 4.6 33.6 1.0 CU B:CU403 4.7 32.8 0.8 SD C:MET286 4.8 34.7 1.0 NE2 C:HIS290 4.8 29.7 1.0 NE2 B:HIS165 4.9 38.5 1.0 CD2 B:HIS103 4.9 29.1 1.0 CD2 C:HIS290 4.9 21.6 1.0 CB C:MET286 4.9 27.8 1.0 CE1 B:HIS103 4.9 38.0 1.0

Copper binding site 10 out of 20 in the Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of Two-Domain Laccase Mutant M199A/D268N From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu404 b:20.6 occ:0.15 NE2 A:HIS235 1.9 26.9 1.0 NE2 C:HIS103 2.0 23.1 1.0 CE1 A:HIS235 2.3 20.9 1.0 CE1 C:HIS103 2.4 21.6 1.0 O C:HOH506 2.7 25.2 1.0 CD2 A:HIS235 3.1 16.2 1.0 O1 A:OXY404 3.2 25.9 0.8 NE2 C:HIS105 3.2 13.3 1.0 CD2 C:HIS103 3.3 23.7 1.0 CU C:CU402 3.4 24.2 0.5 CD2 C:HIS105 3.4 17.7 1.0 ND1 A:HIS235 3.5 22.5 1.0 CE1 C:HIS105 3.6 15.4 1.0 ND1 C:HIS103 3.7 24.4 1.0 CG C:HIS105 3.8 20.3 1.0 ND1 C:HIS105 3.9 17.0 1.0 CG A:HIS235 3.9 18.8 1.0 O C:VAL104 3.9 17.6 1.0 NE2 A:HIS237 4.1 21.8 1.0 CD2 A:HIS237 4.1 19.8 1.0 CG C:HIS103 4.1 19.4 1.0 O2 A:OXY404 4.1 18.4 0.8 OD2 A:ASP260 4.3 17.8 1.0 CE1 A:HIS237 4.3 23.0 1.0 CG A:HIS237 4.3 22.4 1.0 ND1 A:HIS237 4.5 19.1 1.0 C C:VAL104 4.5 13.0 1.0 CA C:HIS105 4.5 17.1 1.0 OH C:TYR109 4.5 21.7 1.0 CU A:CU402 4.6 31.2 0.6 CA A:HIS237 4.7 20.0 1.0 N C:HIS105 4.8 14.3 1.0 CB C:HIS105 4.8 15.2 1.0 O A:HOH604 4.8 16.7 1.0 NE2 C:HIS157 4.9 27.4 1.0 NE2 A:HIS290 5.0 23.4 1.0

I.Kolyadenko, S.Tishchenko, A.Gabdulkhakov. Structural Insight Into the Amino Acid Environment of the Two-Domain Laccase'S Trinuclear Copper Cluster. Int J Mol Sci V. 24 2023.
ISSN: ESSN 1422-0067
PubMed: 37569288
DOI: 10.3390/IJMS241511909