Copper in PDB 6fdj: Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy

All present enzymatic activity of Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy:
1.10.3.2;

The structure of Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy, PDB code: 6fdj was solved by A.G.Gabdulkhakov, T.V.Tishchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.71 / 2.31
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	77.369, 95.118, 116.475, 90.13, 90.11, 91.85
R / Rfree (%)	17.1 / 22.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy (pdb code 6fdj). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 48 binding sites of Copper where determined in the Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy, PDB code: 6fdj:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy


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 H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:26.9 occ:1.00 ND1 A:HIS294 1.9 20.5 1.0 ND1 A:HIS232 2.0 26.0 1.0 SG A:CYS289 2.2 25.9 1.0 CG A:HIS294 2.8 25.5 1.0 CE1 A:HIS232 2.9 25.8 1.0 CE1 A:HIS294 2.9 24.7 1.0 CG A:HIS232 3.1 24.8 1.0 CB A:HIS294 3.2 23.4 1.0 CB A:CYS289 3.3 24.1 1.0 CB A:HIS232 3.5 24.6 1.0 SD A:MET299 3.5 26.5 1.0 CA A:HIS232 3.8 24.1 1.0 CD2 A:HIS294 4.0 23.2 1.0 NE2 A:HIS294 4.0 18.5 1.0 NE2 A:HIS232 4.0 24.4 1.0 O A:TYR231 4.1 24.8 1.0 CE A:MET299 4.1 22.4 1.0 CB A:VAL291 4.1 23.2 1.0 CG2 A:VAL291 4.2 20.1 1.0 CD2 A:HIS232 4.2 23.4 1.0 CA A:HIS294 4.7 23.8 1.0 CA A:CYS289 4.7 24.5 1.0 N A:THR233 4.7 26.0 1.0 CD2 A:PHE196 4.8 24.7 1.0 N A:HIS232 4.8 25.4 1.0 C A:TYR231 4.8 25.6 1.0 C A:HIS232 4.9 24.9 1.0 CG1 A:VAL291 4.9 20.8 1.0 CE2 A:PHE196 5.0 23.6 1.0 CG A:MET299 5.0 23.8 1.0

Copper binding site 2 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy


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 H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:37.6 occ:1.00 NE2 A:HIS237 2.0 33.8 1.0 NE2 C:HIS159 2.1 32.6 1.0 NE2 A:HIS288 2.2 28.1 1.0 CE1 A:HIS237 2.8 32.8 1.0 CE1 A:HIS288 2.9 24.4 1.0 CE1 C:HIS159 3.1 29.9 1.0 CD2 C:HIS159 3.2 27.7 1.0 CD2 A:HIS237 3.2 32.2 1.0 CD2 A:HIS288 3.3 29.0 1.0 O C:HOH512 3.7 33.8 1.0 CD2 A:HIS235 3.8 29.6 1.0 CU A:CU403 3.8 41.3 0.6 NE2 C:HIS103 3.9 29.7 1.0 ND1 A:HIS237 4.0 31.1 1.0 NE2 A:HIS235 4.0 28.6 1.0 ND1 A:HIS288 4.1 29.4 1.0 CU A:CU409 4.1 37.7 1.0 ND1 C:HIS159 4.2 32.2 1.0 CG A:HIS237 4.2 27.2 1.0 CG C:HIS159 4.3 26.3 1.0 CG A:HIS288 4.3 22.3 1.0 CD2 C:HIS103 4.3 25.6 1.0 CE1 C:HIS103 4.4 33.8 1.0 NE2 A:HIS290 4.5 25.2 1.0 SD A:MET286 4.7 51.5 1.0 CD2 A:HIS290 4.7 21.9 1.0 CE1 C:HIS157 5.0 26.4 1.0

Copper binding site 3 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy


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 H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:41.3 occ:0.62 NE2 C:HIS103 1.9 29.7 1.0 NE2 A:HIS235 2.0 28.6 1.0 CE1 C:HIS103 2.5 33.8 1.0 O C:HOH511 2.5 28.6 1.0 CE1 A:HIS235 2.8 29.1 1.0 CD2 A:HIS235 3.1 29.6 1.0 CD2 C:HIS103 3.2 25.6 1.0 CD2 A:HIS237 3.2 32.2 1.0 NE2 A:HIS237 3.3 33.8 1.0 NE2 C:HIS105 3.6 27.0 1.0 CU A:CU409 3.7 37.7 1.0 CE1 C:HIS105 3.7 24.9 1.0 CG A:HIS237 3.7 27.2 1.0 ND1 C:HIS103 3.8 30.9 1.0 CE1 A:HIS237 3.8 32.8 1.0 CU A:CU402 3.8 37.6 1.0 CD2 C:HIS105 3.8 29.1 1.0 ND1 A:HIS235 4.0 29.1 1.0 ND1 A:HIS237 4.1 31.1 1.0 ND1 C:HIS105 4.1 24.8 1.0 CG C:HIS103 4.1 32.0 1.0 CG C:HIS105 4.1 26.5 1.0 OH C:TYR109 4.1 34.6 1.0 CG A:HIS235 4.2 26.6 1.0 O C:VAL104 4.2 26.8 1.0 CA A:HIS237 4.4 30.3 1.0 CB A:HIS237 4.6 29.8 1.0 O A:HOH508 4.8 24.3 1.0 CA C:HIS105 4.8 25.7 1.0 N A:HIS237 4.8 31.5 1.0 O A:MET236 4.8 28.1 1.0 C C:VAL104 4.9 29.4 1.0 NE2 C:HIS157 4.9 24.4 1.0 NE2 A:HIS288 5.0 28.1 1.0

Copper binding site 4 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy


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 H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:32.5 occ:0.97 NE2 B:HIS290 1.9 16.8 1.0 NE2 A:HIS105 2.0 20.1 1.0 O1 A:OXY407 2.2 26.7 0.8 NE2 A:HIS157 2.3 28.9 1.0 O2 A:OXY407 2.4 24.9 0.8 CE1 B:HIS290 2.9 23.9 1.0 CD2 B:HIS290 2.9 21.7 1.0 CE1 A:HIS105 2.9 19.9 1.0 CD2 A:HIS105 3.0 21.7 1.0 CE1 A:HIS157 3.2 25.5 1.0 CD2 A:HIS157 3.3 27.5 1.0 NE2 A:HIS103 3.5 27.1 1.0 CD2 A:HIS103 3.6 27.3 1.0 CU A:CU405 3.9 42.9 0.7 ND1 B:HIS290 4.0 22.7 1.0 CG B:HIS290 4.0 21.2 1.0 ND1 A:HIS105 4.1 18.7 1.0 NE2 B:HIS235 4.1 18.4 1.0 CG A:HIS105 4.1 17.6 1.0 CD2 B:HIS235 4.2 22.1 1.0 ND1 A:HIS157 4.3 31.0 1.0 CU A:CU408 4.4 35.6 1.0 CG A:HIS157 4.4 30.1 1.0 CE1 A:HIS155 4.5 20.5 1.0 CB A:ALA267 4.5 21.9 1.0 CE1 B:HIS235 4.7 20.6 1.0 CE1 A:HIS103 4.8 27.5 1.0 CG B:HIS235 4.9 16.4 1.0 CG A:HIS103 4.9 29.0 1.0 CE1 B:HIS288 5.0 22.9 1.0

Copper binding site 5 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy


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 H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu405 b:42.9 occ:0.70 NE2 A:HIS103 2.1 27.1 1.0 NE2 B:HIS235 2.2 18.4 1.0 CE1 A:HIS103 2.3 27.5 1.0 O2 A:OXY407 2.7 24.9 0.8 CE1 B:HIS235 3.0 20.6 1.0 CD2 B:HIS235 3.3 22.1 1.0 CD2 A:HIS103 3.4 27.3 1.0 CD2 A:HIS105 3.5 21.7 1.0 CD2 B:HIS237 3.5 26.3 1.0 NE2 A:HIS105 3.6 20.1 1.0 ND1 A:HIS103 3.6 31.1 1.0 NE2 B:HIS237 3.7 27.6 1.0 CU A:CU404 3.9 32.5 1.0 O1 A:OXY407 3.9 26.7 0.8 CG B:HIS237 4.0 27.0 1.0 O A:VAL104 4.0 30.1 1.0 OH A:TYR109 4.1 30.8 1.0 CG A:HIS105 4.1 17.6 1.0 CG A:HIS103 4.1 29.0 1.0 ND1 B:HIS235 4.2 18.3 1.0 CE1 A:HIS105 4.2 19.9 1.0 CE1 B:HIS237 4.2 28.4 1.0 CG B:HIS235 4.4 16.4 1.0 ND1 B:HIS237 4.4 27.6 1.0 CA B:HIS237 4.4 27.1 1.0 CU A:CU408 4.4 35.6 1.0 CA A:HIS105 4.5 26.2 1.0 ND1 A:HIS105 4.5 18.7 1.0 O B:HOH519 4.5 24.9 1.0 C A:VAL104 4.6 27.0 1.0 O B:MET236 4.7 29.4 1.0 N A:HIS105 4.7 27.8 1.0 CB B:HIS237 4.8 28.7 1.0 N B:HIS237 4.9 23.8 1.0 CB A:HIS105 4.9 19.0 1.0 OD2 B:ASP260 4.9 26.5 1.0

Copper binding site 6 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy


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 H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu408 b:35.6 occ:0.97 NE2 A:HIS159 2.2 21.6 1.0 O1 A:OXY407 2.2 26.7 0.8 NE2 B:HIS288 2.3 20.2 1.0 O2 A:OXY407 2.3 24.9 0.8 NE2 B:HIS237 2.3 27.6 1.0 CD2 B:HIS288 3.2 23.4 1.0 CE1 A:HIS159 3.2 20.1 1.0 CD2 A:HIS159 3.2 23.8 1.0 CE1 B:HIS288 3.2 22.9 1.0 CD2 B:HIS237 3.3 26.3 1.0 CE1 B:HIS237 3.3 28.4 1.0 NE2 A:HIS103 3.9 27.1 1.0 O A:HOH517 4.0 25.0 1.0 CD2 B:HIS235 4.2 22.1 1.0 ND1 A:HIS159 4.3 25.2 1.0 CD2 A:HIS103 4.3 27.3 1.0 CG B:HIS288 4.3 23.2 1.0 ND1 B:HIS288 4.3 23.8 1.0 CG A:HIS159 4.3 26.8 1.0 CU A:CU404 4.4 32.5 1.0 ND1 B:HIS237 4.4 27.6 1.0 CG B:HIS237 4.4 27.0 1.0 CU A:CU405 4.4 42.9 0.7 NE2 B:HIS235 4.6 18.4 1.0 CE1 A:HIS103 4.6 27.5 1.0 SD B:MET286 4.6 47.4 1.0 NE2 B:HIS290 4.7 16.8 1.0

Copper binding site 7 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy


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 H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu409 b:37.7 occ:1.00 NE2 C:HIS157 2.0 24.4 1.0 NE2 C:HIS105 2.1 27.0 1.0 NE2 A:HIS290 2.1 25.2 1.0 CE1 C:HIS157 2.7 26.4 1.0 CD2 A:HIS290 3.0 21.9 1.0 CD2 C:HIS105 3.0 29.1 1.0 CE1 C:HIS105 3.1 24.9 1.0 CE1 A:HIS290 3.2 22.9 1.0 CD2 C:HIS157 3.3 27.2 1.0 CD2 C:HIS103 3.6 25.6 1.0 NE2 C:HIS103 3.7 29.7 1.0 CU A:CU403 3.7 41.3 0.6 ND1 C:HIS157 3.9 24.3 1.0 NE2 A:HIS235 3.9 28.6 1.0 CD2 A:HIS235 4.0 29.6 1.0 CU A:CU402 4.1 37.6 1.0 CG C:HIS105 4.1 26.5 1.0 ND1 C:HIS105 4.2 24.8 1.0 CG A:HIS290 4.2 21.3 1.0 CG C:HIS157 4.2 23.0 1.0 ND1 A:HIS290 4.2 24.2 1.0 O C:HOH512 4.2 33.8 1.0 CB C:ALA267 4.6 23.5 1.0 CE1 C:HIS155 4.7 21.1 1.0 CE1 A:HIS235 4.8 29.1 1.0 CG C:HIS103 4.9 32.0 1.0 CG A:HIS235 5.0 26.6 1.0 CE1 A:HIS288 5.0 24.4 1.0 CD2 C:HIS159 5.0 27.7 1.0 CE1 C:HIS103 5.0 33.8 1.0 NE2 C:HIS159 5.0 32.6 1.0

Copper binding site 8 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy


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 H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu401 b:27.1 occ:0.95 SG B:CYS289 1.9 25.9 1.0 ND1 B:HIS294 2.0 24.4 1.0 ND1 B:HIS232 2.1 21.6 1.0 CG B:HIS294 2.9 24.5 1.0 CB B:CYS289 3.0 20.4 1.0 CE1 B:HIS232 3.1 20.9 1.0 CE1 B:HIS294 3.1 27.8 1.0 CG B:HIS232 3.1 19.0 1.0 CB B:HIS294 3.2 21.9 1.0 CB B:HIS232 3.5 21.9 1.0 SD B:MET299 3.5 22.5 1.0 CE B:MET299 3.6 17.8 1.0 CA B:HIS232 3.8 19.7 1.0 CG2 B:VAL291 4.0 15.2 1.0 CB B:VAL291 4.0 21.1 1.0 CD2 B:HIS294 4.1 20.4 1.0 NE2 B:HIS294 4.1 20.3 1.0 NE2 B:HIS232 4.2 20.0 1.0 O B:TYR231 4.2 19.5 1.0 CD2 B:HIS232 4.2 20.4 1.0 CA B:CYS289 4.4 21.1 1.0 N B:THR233 4.6 16.7 1.0 CA B:HIS294 4.7 26.3 1.0 CG B:MET299 4.8 22.2 1.0 C B:HIS232 4.8 21.0 1.0 CG1 B:VAL291 4.8 19.1 1.0 N B:HIS232 4.9 19.1 1.0 N B:VAL291 4.9 20.7 1.0 C B:CYS289 4.9 22.8 1.0 C B:TYR231 5.0 22.3 1.0 O B:VAL291 5.0 27.6 1.0 CD2 B:PHE196 5.0 23.6 1.0 CB B:MET299 5.0 22.3 1.0

Copper binding site 9 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy


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 H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu402 b:34.3 occ:1.00 NE2 B:HIS105 1.9 25.4 1.0 O1 B:OXY403 2.0 22.9 1.0 NE2 B:HIS157 2.2 24.8 1.0 NE2 C:HIS290 2.2 34.1 1.0 O2 B:OXY403 2.4 28.8 1.0 CE1 B:HIS105 2.8 26.9 1.0 CD2 B:HIS105 2.9 27.5 1.0 CE1 B:HIS157 3.1 25.1 1.0 CD2 C:HIS290 3.1 30.1 1.0 CE1 B:HIS103 3.2 33.6 1.0 CE1 C:HIS290 3.2 30.6 1.0 CD2 B:HIS157 3.2 22.4 1.0 ND1 B:HIS103 3.4 31.6 1.0 ND1 B:HIS105 3.9 28.9 1.0 CG B:HIS105 4.0 29.1 1.0 CU B:CU405 4.0 34.8 0.3 ND1 B:HIS157 4.2 21.8 1.0 CG C:HIS290 4.3 32.3 1.0 ND1 C:HIS290 4.3 33.9 1.0 CU B:CU404 4.3 44.2 0.8 NE2 C:HIS235 4.3 25.6 1.0 CG B:HIS157 4.3 25.9 1.0 CB B:ALA267 4.3 26.2 1.0 CE1 B:HIS155 4.3 22.0 1.0 NE2 B:HIS103 4.4 33.9 1.0 CD2 C:HIS235 4.5 24.4 1.0 CE1 C:HIS235 4.6 25.2 1.0 CG B:HIS103 4.7 36.2 1.0 NE2 B:HIS155 4.9 20.0 1.0 CG C:HIS235 5.0 25.1 1.0

Copper binding site 10 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy


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 H165A From Streptomyces Griseoflavus with High Copper Ions Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu404 b:44.2 occ:0.83 NE2 C:HIS237 2.1 28.4 1.0 NE2 B:HIS159 2.2 28.1 1.0 O1 B:OXY403 2.3 22.9 1.0 O2 B:OXY403 2.6 28.8 1.0 NE2 C:HIS288 2.6 32.5 1.0 CE1 C:HIS237 2.9 26.7 1.0 CD2 B:HIS159 3.0 27.2 1.0 CE1 C:HIS288 3.0 27.3 1.0 CD2 C:HIS237 3.3 30.8 1.0 CE1 B:HIS159 3.3 31.7 1.0 CU B:CU405 3.5 34.8 0.3 CD2 C:HIS288 3.7 31.4 1.0 CE1 B:HIS103 4.0 33.6 1.0 ND1 C:HIS237 4.1 28.1 1.0 ND1 C:HIS288 4.2 26.0 1.0 CG B:HIS159 4.2 34.6 1.0 CD2 C:HIS235 4.2 24.4 1.0 NE2 B:HIS103 4.3 33.9 1.0 CU B:CU402 4.3 34.3 1.0 CG C:HIS237 4.3 26.6 1.0 ND1 B:HIS159 4.3 31.6 1.0 ND1 B:HIS103 4.4 31.6 1.0 NE2 C:HIS290 4.4 34.1 1.0 CG C:HIS288 4.5 30.1 1.0 NE2 C:HIS235 4.6 25.6 1.0 CD2 C:HIS290 4.8 30.1 1.0 CD2 B:HIS103 4.8 36.8 1.0 SD C:MET286 4.8 52.6 1.0 CG B:HIS103 4.9 36.2 1.0

A.Gabdulkhakov, I.Kolyadenko, O.Kostareva, A.Mikhaylina, P.Oliveira, P.Tamagnini, A.Lisov, S.Tishchenko. Investigations of Accessibility of T2/T3 Copper Center of Two-Domain Laccase Fromstreptomyces Griseoflavusac-993. Int J Mol Sci V. 20 2019.
ISSN: ESSN 1422-0067
PubMed: 31261802
DOI: 10.3390/IJMS20133184