Copper in PDB 6zip: Crystal Structure of Two-Domain Laccase Mutant R240A From Streptomyces Griseoflavus

All present enzymatic activity of Crystal Structure of Two-Domain Laccase Mutant R240A From Streptomyces Griseoflavus:
1.10.3.2;

The structure of Crystal Structure of Two-Domain Laccase Mutant R240A From Streptomyces Griseoflavus, PDB code: 6zip was solved by A.G.Gabdulkhakov, T.V.Tishchenko, I.A.Kolyadenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.40 / 2.05
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	76.873, 94.838, 116.106, 90.21, 90.24, 91.46
R / Rfree (%)	18.8 / 20.8

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 R240A From Streptomyces Griseoflavus (pdb code 6zip). 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 R240A From Streptomyces Griseoflavus, PDB code: 6zip:
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 R240A 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 R240A From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:29.9 occ:1.00 ND1 A:HIS294 2.0 20.7 1.0 ND1 A:HIS232 2.1 29.8 1.0 SG A:CYS289 2.2 25.5 1.0 CG A:HIS294 3.0 29.5 1.0 CE1 A:HIS232 3.0 26.8 1.0 CE1 A:HIS294 3.0 25.8 1.0 CG A:HIS232 3.1 27.4 1.0 CB A:CYS289 3.2 31.7 1.0 CB A:HIS294 3.3 23.6 1.0 SD A:MET299 3.3 31.1 1.0 CB A:HIS232 3.4 24.1 1.0 CA A:HIS232 3.8 29.1 1.0 CE A:MET299 3.9 26.6 1.0 CB A:VAL291 4.0 29.0 1.0 CG2 A:VAL291 4.1 25.7 1.0 CD2 A:HIS294 4.1 30.9 1.0 NE2 A:HIS294 4.1 22.3 1.0 NE2 A:HIS232 4.1 29.2 1.0 CD2 A:HIS232 4.2 23.4 1.0 O A:TYR231 4.2 28.7 1.0 CA A:CYS289 4.6 31.6 1.0 N A:THR233 4.7 27.1 1.0 CA A:HIS294 4.8 25.0 1.0 N A:HIS232 4.8 28.9 1.0 C A:HIS232 4.9 28.4 1.0 CG A:MET299 4.9 26.0 1.0 C A:TYR231 4.9 27.2 1.0 CG1 A:VAL291 4.9 28.4 1.0 N A:VAL291 5.0 27.2 1.0

Copper binding site 2 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant R240A 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 R240A From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:30.9 occ:0.31 NE2 A:HIS237 2.0 28.8 1.0 O1 C:OXY406 2.1 34.2 0.6 NE2 A:HIS288 2.3 35.2 1.0 O2 C:OXY406 2.4 32.4 0.6 NE2 C:HIS159 2.5 40.7 1.0 CE1 A:HIS237 2.6 32.3 1.0 CE1 A:HIS288 3.0 32.7 1.0 CD2 A:HIS237 3.3 32.3 1.0 CE1 C:HIS159 3.4 29.9 1.0 CD2 A:HIS288 3.4 37.9 1.0 CD2 C:HIS159 3.6 36.8 1.0 O C:HOH524 3.6 34.4 1.0 ND1 A:HIS237 3.9 34.7 1.0 CU A:CU403 3.9 33.3 0.7 CD2 A:HIS235 4.0 31.5 1.0 NE2 C:HIS103 4.1 37.3 1.0 ND1 A:HIS288 4.2 33.3 1.0 CG A:HIS237 4.2 29.9 1.0 CU C:CU401 4.3 35.6 1.0 CE A:MET286 4.4 41.0 1.0 NE2 A:HIS290 4.4 25.6 1.0 CG A:HIS288 4.4 36.4 1.0 NE2 A:HIS235 4.4 40.4 1.0 CD2 C:HIS103 4.5 34.8 1.0 ND1 C:HIS159 4.6 33.5 1.0 CD2 A:HIS290 4.6 21.9 1.0 CD2 C:HIS165 4.6 33.5 1.0 CG C:HIS159 4.7 35.9 1.0 CE1 C:HIS103 4.8 31.4 1.0 SD A:MET286 4.8 60.6 1.0

Copper binding site 3 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant R240A 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 R240A From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:33.3 occ:0.67 NE2 C:HIS103 1.9 37.3 1.0 NE2 A:HIS235 2.0 40.4 1.0 O2 C:OXY406 2.4 32.4 0.6 CE1 C:HIS103 2.9 31.4 1.0 CD2 C:HIS103 2.9 34.8 1.0 CE1 A:HIS235 3.0 28.8 1.0 CD2 A:HIS235 3.0 31.5 1.0 NE2 A:HIS237 3.3 28.8 1.0 CD2 A:HIS237 3.4 32.3 1.0 CU C:CU401 3.4 35.6 1.0 O C:HOH536 3.5 41.6 1.0 O1 C:OXY406 3.6 34.2 0.6 NE2 C:HIS105 3.6 35.3 1.0 CE1 A:HIS237 3.8 32.3 1.0 CG A:HIS237 3.8 29.9 1.0 CE1 C:HIS105 3.9 31.2 1.0 CU A:CU402 3.9 30.9 0.3 CD2 C:HIS105 3.9 38.4 1.0 ND1 C:HIS103 4.0 34.4 1.0 CG C:HIS103 4.1 36.2 1.0 ND1 A:HIS237 4.1 34.7 1.0 ND1 A:HIS235 4.1 32.5 1.0 CG A:HIS235 4.1 33.6 1.0 ND1 C:HIS105 4.2 35.2 1.0 CG C:HIS105 4.3 32.6 1.0 O C:VAL104 4.4 30.3 1.0 CA A:HIS237 4.6 30.5 1.0 CB A:HIS237 4.7 36.2 1.0 OH C:TYR109 4.8 37.3 1.0 C C:VAL104 4.9 35.9 1.0 NE2 C:HIS157 4.9 31.0 1.0 CA C:HIS105 4.9 26.8 1.0 NE2 A:HIS290 4.9 25.6 1.0

Copper binding site 4 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant R240A 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 R240A From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:31.1 occ:1.00 NE2 A:HIS105 2.1 24.6 1.0 NE2 A:HIS157 2.1 25.3 1.0 NE2 B:HIS290 2.1 28.4 1.0 O A:HOH571 2.2 41.0 1.0 CE1 A:HIS157 3.0 21.9 1.0 CD2 B:HIS290 3.0 28.4 1.0 CE1 A:HIS105 3.0 23.6 1.0 CD2 A:HIS105 3.1 21.9 1.0 CE1 B:HIS290 3.2 27.0 1.0 CD2 A:HIS157 3.2 26.9 1.0 CU B:CU403 3.6 36.5 0.8 CD2 A:HIS103 3.7 30.9 1.0 NE2 A:HIS103 3.8 28.1 1.0 NE2 B:HIS235 4.0 22.9 1.0 CD2 B:HIS235 4.1 26.9 1.0 ND1 A:HIS105 4.2 28.4 1.0 ND1 A:HIS157 4.2 31.5 1.0 CU B:CU402 4.2 38.9 0.4 CG A:HIS105 4.2 25.6 1.0 CG B:HIS290 4.2 33.1 1.0 ND1 B:HIS290 4.3 27.9 1.0 CG A:HIS157 4.3 32.4 1.0 O A:HOH579 4.3 33.0 1.0 CB A:ALA267 4.4 31.7 1.0 CE1 A:HIS155 4.6 33.4 1.0 CE1 B:HIS235 4.8 28.8 1.0 CG B:HIS235 4.9 24.8 1.0

Copper binding site 5 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant R240A 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 R240A From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu401 b:30.5 occ:1.00 ND1 B:HIS232 2.0 29.9 1.0 ND1 B:HIS294 2.1 31.4 1.0 SG B:CYS289 2.1 29.8 1.0 CG B:HIS294 3.0 28.2 1.0 CE1 B:HIS232 3.0 33.0 1.0 CG B:HIS232 3.0 35.2 1.0 CE1 B:HIS294 3.1 23.9 1.0 CB B:CYS289 3.1 29.8 1.0 CB B:HIS294 3.3 24.7 1.0 CB B:HIS232 3.4 26.8 1.0 SD B:MET299 3.4 35.8 1.0 CA B:HIS232 3.7 28.7 1.0 CG2 B:VAL291 3.9 24.9 1.0 O B:TYR231 4.0 24.9 1.0 NE2 B:HIS232 4.1 32.0 1.0 CD2 B:HIS294 4.1 28.8 1.0 NE2 B:HIS294 4.2 28.5 1.0 CD2 B:HIS232 4.2 32.0 1.0 CB B:VAL291 4.2 29.5 1.0 CE B:MET299 4.2 23.9 1.0 CA B:CYS289 4.6 30.2 1.0 N B:HIS232 4.7 23.6 1.0 C B:TYR231 4.7 28.7 1.0 N B:THR233 4.8 16.9 1.0 CA B:HIS294 4.8 26.4 1.0 C B:HIS232 4.8 28.7 1.0 CG B:MET299 4.9 30.0 1.0

Copper binding site 6 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant R240A 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 R240A From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu402 b:38.9 occ:0.43 O A:HOH571 2.1 41.0 1.0 NE2 B:HIS237 2.3 33.4 1.0 NE2 B:HIS288 2.4 28.8 1.0 NE2 A:HIS159 2.6 36.0 1.0 CE1 B:HIS288 3.2 34.7 1.0 CE1 B:HIS237 3.2 35.2 1.0 CD2 B:HIS288 3.4 36.4 1.0 CD2 B:HIS237 3.4 33.0 1.0 CD2 A:HIS159 3.4 35.4 1.0 O A:HOH579 3.5 33.0 1.0 CE1 A:HIS159 3.6 35.9 1.0 CU B:CU403 4.0 36.5 0.8 CD2 B:HIS235 4.0 26.9 1.0 CU A:CU404 4.2 31.1 1.0 NE2 A:HIS103 4.2 28.1 1.0 ND1 B:HIS288 4.3 31.2 1.0 ND1 B:HIS237 4.4 29.6 1.0 NE2 B:HIS290 4.4 28.4 1.0 CG B:HIS288 4.4 35.7 1.0 NE2 B:HIS235 4.5 22.9 1.0 CG B:HIS237 4.5 36.1 1.0 CD2 A:HIS165 4.5 29.9 1.0 CE B:MET286 4.6 40.4 1.0 CD2 A:HIS103 4.6 30.9 1.0 CG A:HIS159 4.6 30.6 1.0 CD2 B:HIS290 4.7 28.4 1.0 ND1 A:HIS159 4.7 32.4 1.0 CE1 A:HIS103 4.8 25.2 1.0 SD B:MET286 4.9 55.3 1.0

Copper binding site 7 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant R240A 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 R240A From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu403 b:36.5 occ:0.84 NE2 A:HIS103 1.9 28.1 1.0 NE2 B:HIS235 2.1 22.9 1.0 CE1 A:HIS103 2.7 25.2 1.0 O A:HOH571 2.9 41.0 1.0 CE1 B:HIS235 3.1 28.8 1.0 CD2 B:HIS235 3.1 26.9 1.0 CD2 A:HIS103 3.1 30.9 1.0 O A:HOH501 3.5 38.9 1.0 NE2 B:HIS237 3.5 33.4 1.0 CD2 B:HIS237 3.5 33.0 1.0 NE2 A:HIS105 3.5 24.6 1.0 CU A:CU404 3.6 31.1 1.0 CD2 A:HIS105 3.7 21.9 1.0 ND1 A:HIS103 3.9 34.3 1.0 CE1 B:HIS237 3.9 35.2 1.0 CE1 A:HIS105 3.9 23.6 1.0 CG B:HIS237 3.9 36.1 1.0 CU B:CU402 4.0 38.9 0.4 CG A:HIS103 4.1 37.6 1.0 ND1 B:HIS237 4.2 29.6 1.0 ND1 B:HIS235 4.2 27.2 1.0 CG B:HIS235 4.2 24.8 1.0 CG A:HIS105 4.3 25.6 1.0 ND1 A:HIS105 4.3 28.4 1.0 O A:VAL104 4.4 32.1 1.0 CA B:HIS237 4.6 32.0 1.0 OH A:TYR109 4.6 33.7 1.0 O B:HOH529 4.7 42.3 1.0 CB B:HIS237 4.8 35.6 1.0 CA A:HIS105 4.9 30.7 1.0 C A:VAL104 4.9 26.3 1.0 OD2 B:ASP260 4.9 30.3 1.0

Copper binding site 8 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant R240A 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 R240A From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu404 b:33.2 occ:0.83 O C:HOH540 1.9 32.4 1.0 NE2 B:HIS157 2.1 31.3 1.0 NE2 B:HIS105 2.1 24.6 1.0 NE2 C:HIS290 2.1 34.7 1.0 CE1 B:HIS157 2.8 32.8 1.0 CE1 B:HIS105 3.0 24.1 1.0 CD2 C:HIS290 3.0 30.6 1.0 CE1 C:HIS290 3.1 33.1 1.0 CD2 B:HIS105 3.1 32.8 1.0 CD2 B:HIS157 3.2 28.2 1.0 CU C:CU404 3.5 39.6 0.7 CD2 B:HIS103 3.6 36.6 1.0 NE2 B:HIS103 3.8 39.7 1.0 NE2 C:HIS235 4.0 32.1 1.0 ND1 B:HIS157 4.0 33.2 1.0 ND1 B:HIS105 4.1 27.2 1.0 CD2 C:HIS235 4.1 31.9 1.0 ND1 C:HIS290 4.2 30.0 1.0 CG C:HIS290 4.2 33.5 1.0 CG B:HIS105 4.2 26.3 1.0 O B:HOH575 4.2 36.3 1.0 CU C:CU403 4.2 36.7 0.5 CG B:HIS157 4.2 26.9 1.0 CB B:ALA267 4.4 25.1 1.0 CE1 B:HIS155 4.6 28.6 1.0 CE1 C:HIS235 4.8 32.9 1.0 CG B:HIS103 4.9 35.7 1.0 CE1 C:HIS288 5.0 32.9 1.0

Copper binding site 9 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant R240A 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 R240A From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu401 b:35.6 occ:1.00 O2 C:OXY406 2.0 32.4 0.6 NE2 A:HIS290 2.1 25.6 1.0 NE2 C:HIS105 2.1 35.3 1.0 NE2 C:HIS157 2.2 31.0 1.0 O1 C:OXY406 2.5 34.2 0.6 CD2 A:HIS290 2.9 21.9 1.0 CE1 C:HIS105 2.9 31.2 1.0 CE1 C:HIS157 3.1 26.3 1.0 CE1 A:HIS290 3.2 25.2 1.0 CD2 C:HIS105 3.2 38.4 1.0 CD2 C:HIS157 3.3 27.0 1.0 CU A:CU403 3.4 33.3 0.7 CD2 C:HIS103 3.8 34.8 1.0 NE2 A:HIS235 3.9 40.4 1.0 NE2 C:HIS103 4.0 37.3 1.0 ND1 C:HIS105 4.1 35.2 1.0 CD2 A:HIS235 4.1 31.5 1.0 CG A:HIS290 4.1 25.9 1.0 ND1 A:HIS290 4.2 27.1 1.0 CG C:HIS105 4.2 32.6 1.0 ND1 C:HIS157 4.2 31.0 1.0 CU A:CU402 4.3 30.9 0.3 O C:HOH524 4.3 34.4 1.0 CB C:ALA267 4.3 27.3 1.0 CG C:HIS157 4.4 30.6 1.0 CE1 C:HIS155 4.7 34.3 1.0 CE1 A:HIS235 4.7 28.8 1.0 CG A:HIS235 4.9 33.6 1.0

Copper binding site 10 out of 48 in the Crystal Structure of Two-Domain Laccase Mutant R240A 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 R240A From Streptomyces Griseoflavus within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu402 b:30.7 occ:1.00 ND1 C:HIS294 2.0 25.9 1.0 ND1 C:HIS232 2.0 32.7 1.0 SG C:CYS289 2.1 31.4 1.0 CE1 C:HIS294 2.9 32.3 1.0 CE1 C:HIS232 2.9 22.5 1.0 CG C:HIS232 3.0 26.4 1.0 CG C:HIS294 3.0 28.6 1.0 CB C:CYS289 3.2 29.3 1.0 CB C:HIS232 3.3 21.1 1.0 CB C:HIS294 3.3 31.1 1.0 SD C:MET299 3.5 33.9 1.0 CA C:HIS232 3.7 29.4 1.0 CE C:MET299 3.8 28.8 1.0 O C:TYR231 4.0 28.7 1.0 NE2 C:HIS232 4.0 31.2 1.0 NE2 C:HIS294 4.0 35.7 1.0 CG2 C:VAL291 4.1 22.8 1.0 CD2 C:HIS232 4.1 21.8 1.0 CB C:VAL291 4.1 23.2 1.0 CD2 C:HIS294 4.1 27.9 1.0 CA C:CYS289 4.5 31.3 1.0 N C:THR233 4.6 24.1 1.0 N C:HIS232 4.7 29.9 1.0 C C:HIS232 4.8 26.7 1.0 C C:TYR231 4.8 24.3 1.0 CA C:HIS294 4.8 29.8 1.0 CG1 C:VAL291 5.0 19.9 1.0 N C:VAL291 5.0 29.1 1.0 CD2 C:PHE196 5.0 28.0 1.0

A.Gabdulkhakov, I.Kolyadenko, P.Oliveira, P.Tamagnini, A.Mikhaylina, S.Tishchenko. The Role of Positive Charged Residue in the Proton-Transfer Mechanism of Two-Domain Laccase From Streptomyces Griseoflavus Ac-993. J.Biomol.Struct.Dyn. 1 2021.
ISSN: ESSN 1538-0254
PubMed: 33870857
DOI: 10.1080/07391102.2021.1911852