Copper in PDB 1kya: Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine

All present enzymatic activity of Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine:
1.10.3.2;

The structure of Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine, PDB code: 1kya was solved by T.Bertrand, C.Jolivalt, P.Briozzo, E.Caminade, N.Joly, C.Madzak, C.Mougin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.720, 110.520, 123.201, 90.00, 103.44, 90.00
R / Rfree (%)	25.3 / 27.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Copper atom in the Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine (pdb code 1kya). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 16 binding sites of Copper where determined in the Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine, PDB code: 1kya:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 16 in the Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu500 b:47.3 occ:1.00 SG A:CYS453 2.2 41.0 1.0 ND1 A:HIS458 2.2 45.9 1.0 ND1 A:HIS395 2.4 38.6 1.0 CE1 A:HIS458 3.1 46.3 1.0 CG A:HIS458 3.2 44.0 1.0 CG A:HIS395 3.2 37.2 1.0 CB A:CYS453 3.3 36.7 1.0 CE1 A:HIS395 3.3 38.4 1.0 CB A:HIS395 3.4 36.1 1.0 CD1 A:ILE455 3.5 35.0 1.0 CB A:HIS458 3.6 41.3 1.0 CD2 A:PHE463 3.7 38.2 1.0 CB A:ILE455 3.8 36.0 1.0 CE2 A:PHE463 3.8 37.7 1.0 CG1 A:ILE455 3.9 37.4 1.0 CA A:HIS395 3.9 35.5 1.0 NE2 A:HIS458 4.3 46.9 1.0 CD2 A:HIS458 4.3 45.8 1.0 CD2 A:HIS395 4.4 37.9 1.0 NE2 A:HIS395 4.4 40.2 1.0 CD A:PRO396 4.5 34.0 1.0 CG2 A:ILE455 4.6 34.8 1.0 CA A:CYS453 4.7 36.2 1.0 N A:ILE455 4.8 35.9 1.0 C A:HIS395 4.8 35.2 1.0 CA A:ILE455 4.9 36.2 1.0 O A:GLY392 4.9 42.1 1.0 N A:HIS395 5.0 35.6 1.0 N A:PRO396 5.0 34.8 1.0 O A:ILE455 5.0 35.5 1.0 CG A:PHE463 5.0 37.1 1.0

Copper binding site 2 out of 16 in the Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu501 b:43.8 occ:1.00 O A:HOH1505 1.8 38.1 1.0 NE2 A:HIS400 2.1 30.7 1.0 NE2 A:HIS452 2.2 36.0 1.0 NE2 A:HIS111 2.3 31.4 1.0 CE1 A:HIS400 2.9 28.9 1.0 CE1 A:HIS452 3.0 35.6 1.0 CD2 A:HIS111 3.2 31.6 1.0 CD2 A:HIS400 3.2 30.7 1.0 CE1 A:HIS111 3.3 31.3 1.0 CD2 A:HIS452 3.4 36.2 1.0 CD2 A:HIS398 3.6 37.7 1.0 CU A:CU502 3.8 48.3 1.0 CU A:CU503 4.0 76.1 1.0 ND1 A:HIS400 4.1 31.2 1.0 ND1 A:HIS452 4.2 35.6 1.0 NE2 A:HIS398 4.2 39.6 1.0 CG A:HIS400 4.3 32.0 1.0 CG A:HIS111 4.4 31.1 1.0 ND1 A:HIS111 4.4 31.4 1.0 CG A:HIS452 4.4 35.4 1.0 CD2 A:HIS64 4.4 37.5 1.0 NE2 A:HIS64 4.7 39.3 1.0 CG A:HIS398 4.7 38.2 1.0 NE2 A:HIS454 4.8 32.8 1.0 CD2 A:HIS454 4.8 32.3 1.0 CD2 A:PHE450 4.8 33.5 1.0 CG A:HIS64 4.9 37.1 1.0 CB A:PHE450 5.0 34.9 1.0

Copper binding site 3 out of 16 in the Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:48.3 occ:1.00 O A:HOH1505 2.1 38.1 1.0 NE2 A:HIS454 2.3 32.8 1.0 ND1 A:HIS66 2.3 35.2 1.0 NE2 A:HIS109 2.5 30.1 1.0 CE1 A:HIS66 2.9 34.6 1.0 CD2 A:HIS454 3.1 32.3 1.0 CE1 A:HIS109 3.3 29.6 1.0 CE1 A:HIS454 3.4 31.8 1.0 CG A:HIS66 3.4 33.6 1.0 CD2 A:HIS109 3.7 28.9 1.0 CD2 A:HIS64 3.7 37.5 1.0 CU A:CU503 3.8 76.1 1.0 CU A:CU501 3.8 43.8 1.0 CD2 A:HIS398 4.0 37.7 1.0 CB A:HIS66 4.0 32.8 1.0 NE2 A:HIS66 4.1 34.2 1.0 NE2 A:HIS398 4.1 39.6 1.0 CZ2 A:TRP107 4.2 30.6 1.0 NE2 A:HIS64 4.3 39.3 1.0 CG A:HIS454 4.3 33.0 1.0 CD2 A:HIS66 4.4 33.9 1.0 ND1 A:HIS454 4.4 32.1 1.0 ND1 A:HIS109 4.5 31.0 1.0 CB A:ALA241 4.6 28.9 1.0 CE2 A:TRP107 4.6 29.7 1.0 CG A:HIS109 4.7 30.0 1.0 CH2 A:TRP107 4.8 28.9 1.0 CG A:HIS64 4.8 37.1 1.0 NE1 A:TRP107 4.8 28.0 1.0 CA A:HIS66 4.9 32.2 1.0 CD2 A:HIS111 4.9 31.6 1.0 CG A:HIS398 4.9 38.2 1.0 NE2 A:HIS111 4.9 31.4 1.0

Copper binding site 4 out of 16 in the Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu503 b:76.1 occ:1.00 NE2 A:HIS398 2.0 39.6 1.0 NE2 A:HIS64 2.1 39.3 1.0 O A:HOH1540 2.6 36.9 1.0 CD2 A:HIS398 2.9 37.7 1.0 CE1 A:HIS64 3.0 37.1 1.0 CE1 A:HIS398 3.0 38.7 1.0 CD2 A:HIS64 3.0 37.5 1.0 CE1 A:HIS400 3.3 28.9 1.0 O A:HOH1505 3.4 38.1 1.0 NE2 A:HIS400 3.5 30.7 1.0 ND1 A:HIS400 3.5 31.2 1.0 ND1 A:HIS66 3.7 35.2 1.0 CG A:HIS66 3.8 33.6 1.0 CU A:CU502 3.8 48.3 1.0 CD2 A:HIS400 3.8 30.7 1.0 CG A:HIS400 3.8 32.0 1.0 CE1 A:HIS66 3.9 34.6 1.0 CA A:HIS66 4.0 32.2 1.0 CU A:CU501 4.0 43.8 1.0 CD2 A:HIS66 4.0 33.9 1.0 ND1 A:HIS64 4.0 37.9 1.0 CG A:HIS64 4.1 37.1 1.0 ND1 A:HIS398 4.1 38.7 1.0 CG A:HIS398 4.1 38.2 1.0 NE2 A:HIS66 4.1 34.2 1.0 N A:GLY67 4.2 32.9 1.0 CB A:HIS66 4.3 32.8 1.0 C A:HIS66 4.6 32.6 1.0 CA A:HIS400 4.7 34.0 1.0 CB A:HIS400 4.8 32.9 1.0 N A:HIS66 4.8 32.2 1.0 O A:LEU399 4.9 35.5 1.0

Copper binding site 5 out of 16 in the Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu500 b:48.8 occ:1.00 ND1 B:HIS458 2.2 45.0 1.0 SG B:CYS453 2.2 41.0 1.0 ND1 B:HIS395 2.4 38.4 1.0 CE1 B:HIS458 3.1 45.2 1.0 CG B:HIS458 3.2 43.6 1.0 CG B:HIS395 3.3 38.1 1.0 CE1 B:HIS395 3.3 37.6 1.0 CB B:CYS453 3.3 36.2 1.0 CB B:HIS458 3.5 41.6 1.0 CB B:HIS395 3.5 36.5 1.0 CD1 B:ILE455 3.6 34.3 1.0 CD2 B:PHE463 3.7 37.6 1.0 CB B:ILE455 3.8 36.1 1.0 CE2 B:PHE463 3.8 37.4 1.0 CG1 B:ILE455 3.9 35.8 1.0 CA B:HIS395 4.0 35.9 1.0 NE2 B:HIS458 4.2 45.4 1.0 CD2 B:HIS458 4.3 44.7 1.0 NE2 B:HIS395 4.4 39.9 1.0 CD2 B:HIS395 4.4 37.7 1.0 CG2 B:ILE455 4.5 36.4 1.0 CD B:PRO396 4.6 34.9 1.0 CA B:CYS453 4.7 36.1 1.0 N B:ILE455 4.8 36.1 1.0 CA B:ILE455 4.8 36.7 1.0 O B:ILE455 4.9 36.2 1.0 C B:HIS395 4.9 36.0 1.0 CG B:PHE463 5.0 38.0 1.0 CA B:HIS458 5.0 39.9 1.0

Copper binding site 6 out of 16 in the Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu501 b:46.2 occ:1.00 O B:HOH1502 1.9 45.9 1.0 NE2 B:HIS400 2.2 31.2 1.0 NE2 B:HIS452 2.2 34.8 1.0 NE2 B:HIS111 2.3 30.4 1.0 CE1 B:HIS452 2.9 35.5 1.0 CE1 B:HIS400 3.0 29.0 1.0 CD2 B:HIS111 3.2 30.3 1.0 CD2 B:HIS400 3.3 30.1 1.0 CE1 B:HIS111 3.4 30.9 1.0 CD2 B:HIS452 3.4 35.5 1.0 CD2 B:HIS398 3.5 38.4 1.0 CU B:CU503 3.9 74.7 1.0 CU B:CU502 4.0 50.4 1.0 ND1 B:HIS452 4.1 36.6 1.0 ND1 B:HIS400 4.2 30.3 1.0 NE2 B:HIS398 4.2 41.3 1.0 CG B:HIS400 4.3 31.7 1.0 CG B:HIS111 4.4 30.9 1.0 CD2 B:HIS64 4.4 37.9 1.0 ND1 B:HIS111 4.4 31.7 1.0 CG B:HIS452 4.4 35.5 1.0 NE2 B:HIS64 4.6 39.7 1.0 CG B:HIS398 4.7 38.2 1.0 NE2 B:HIS454 4.7 30.7 1.0 CD2 B:HIS454 4.7 31.3 1.0 CD2 B:PHE450 4.9 33.8 1.0 CG B:HIS64 4.9 36.9 1.0 CE1 B:HIS109 5.0 29.3 1.0

Copper binding site 7 out of 16 in the Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu502 b:50.4 occ:1.00 O B:HOH1502 2.1 45.9 1.0 ND1 B:HIS66 2.2 33.9 1.0 NE2 B:HIS454 2.2 30.7 1.0 NE2 B:HIS109 2.4 30.3 1.0 CE1 B:HIS66 2.9 34.9 1.0 CD2 B:HIS454 3.1 31.3 1.0 CE1 B:HIS454 3.2 31.0 1.0 CE1 B:HIS109 3.3 29.3 1.0 CG B:HIS66 3.3 32.8 1.0 CD2 B:HIS109 3.5 30.1 1.0 CD2 B:HIS64 3.8 37.9 1.0 CU B:CU503 3.9 74.7 1.0 CB B:HIS66 3.9 33.2 1.0 CZ2 B:TRP107 3.9 30.5 1.0 CU B:CU501 4.0 46.2 1.0 NE2 B:HIS66 4.1 34.9 1.0 CD2 B:HIS398 4.2 38.4 1.0 CG B:HIS454 4.3 32.8 1.0 CD2 B:HIS66 4.3 34.5 1.0 NE2 B:HIS398 4.3 41.3 1.0 ND1 B:HIS454 4.3 31.9 1.0 CE2 B:TRP107 4.4 28.9 1.0 NE2 B:HIS64 4.4 39.7 1.0 CB B:ALA241 4.4 28.9 1.0 ND1 B:HIS109 4.5 29.9 1.0 CH2 B:TRP107 4.5 29.0 1.0 NE1 B:TRP107 4.6 27.2 1.0 CG B:HIS109 4.6 29.5 1.0 CA B:HIS66 4.8 33.0 1.0 CG B:HIS64 5.0 36.9 1.0

Copper binding site 8 out of 16 in the Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu503 b:74.7 occ:1.00 NE2 B:HIS398 2.0 41.3 1.0 NE2 B:HIS64 2.0 39.7 1.0 O B:HOH1304 2.3 68.8 1.0 CD2 B:HIS64 2.9 37.9 1.0 CD2 B:HIS398 2.9 38.4 1.0 CE1 B:HIS64 3.0 38.0 1.0 CE1 B:HIS398 3.1 39.7 1.0 CE1 B:HIS400 3.2 29.0 1.0 ND1 B:HIS400 3.5 30.3 1.0 NE2 B:HIS400 3.5 31.2 1.0 O B:HOH1502 3.5 45.9 1.0 ND1 B:HIS66 3.7 33.9 1.0 CG B:HIS66 3.8 32.8 1.0 CD2 B:HIS400 3.8 30.1 1.0 CE1 B:HIS66 3.9 34.9 1.0 CG B:HIS400 3.9 31.7 1.0 CU B:CU502 3.9 50.4 1.0 CU B:CU501 3.9 46.2 1.0 CA B:HIS66 3.9 33.0 1.0 ND1 B:HIS64 4.0 38.0 1.0 CG B:HIS64 4.0 36.9 1.0 CD2 B:HIS66 4.0 34.5 1.0 NE2 B:HIS66 4.1 34.9 1.0 CG B:HIS398 4.1 38.2 1.0 ND1 B:HIS398 4.1 39.7 1.0 CB B:HIS66 4.3 33.2 1.0 N B:GLY67 4.3 32.2 1.0 C B:HIS66 4.7 32.5 1.0 CA B:HIS400 4.8 34.0 1.0 N B:HIS66 4.8 32.5 1.0 CB B:HIS400 4.8 33.7 1.0 O B:LEU399 5.0 34.8 1.0

Copper binding site 9 out of 16 in the Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu500 b:45.9 occ:1.00 ND1 C:HIS458 2.1 44.5 1.0 SG C:CYS453 2.3 39.6 1.0 ND1 C:HIS395 2.4 38.8 1.0 CE1 C:HIS458 3.1 44.7 1.0 CG C:HIS458 3.1 43.5 1.0 CG C:HIS395 3.3 37.9 1.0 CE1 C:HIS395 3.3 38.3 1.0 CB C:CYS453 3.4 36.1 1.0 CB C:HIS458 3.5 41.1 1.0 CB C:HIS395 3.5 36.7 1.0 CD1 C:ILE455 3.6 34.6 1.0 CD2 C:PHE463 3.7 38.1 1.0 CB C:ILE455 3.8 36.0 1.0 CE2 C:PHE463 3.8 37.8 1.0 CG1 C:ILE455 3.9 36.2 1.0 CA C:HIS395 4.0 35.4 1.0 NE2 C:HIS458 4.2 46.0 1.0 CD2 C:HIS458 4.2 44.7 1.0 NE2 C:HIS395 4.4 40.3 1.0 CD2 C:HIS395 4.4 38.7 1.0 CG2 C:ILE455 4.6 35.0 1.0 CD C:PRO396 4.6 34.7 1.0 CA C:CYS453 4.8 35.8 1.0 O C:GLY392 4.8 42.5 1.0 N C:ILE455 4.8 35.8 1.0 CA C:ILE455 4.9 35.8 1.0 C C:HIS395 5.0 35.2 1.0 O C:ILE455 5.0 36.0 1.0 CG C:PHE463 5.0 37.1 1.0 CA C:HIS458 5.0 40.2 1.0

Copper binding site 10 out of 16 in the Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Active Laccase From Trametes Versicolor Complexed with 2,5-Xylidine within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu501 b:43.8 occ:1.00 O C:HOH1492 1.9 35.0 1.0 NE2 C:HIS452 2.2 34.9 1.0 NE2 C:HIS400 2.2 30.9 1.0 NE2 C:HIS111 2.3 30.4 1.0 CE1 C:HIS452 2.9 34.7 1.0 CE1 C:HIS400 3.0 28.7 1.0 CD2 C:HIS111 3.2 32.0 1.0 CD2 C:HIS400 3.3 30.2 1.0 CE1 C:HIS111 3.3 30.6 1.0 CD2 C:HIS452 3.4 35.5 1.0 CD2 C:HIS398 3.5 38.6 1.0 CU C:CU502 3.9 47.6 1.0 CU C:CU503 3.9 72.5 1.0 ND1 C:HIS452 4.1 34.4 1.0 ND1 C:HIS400 4.2 30.6 1.0 NE2 C:HIS398 4.2 41.5 1.0 CG C:HIS400 4.4 31.4 1.0 CG C:HIS111 4.4 32.2 1.0 CG C:HIS452 4.4 35.5 1.0 ND1 C:HIS111 4.4 31.2 1.0 CD2 C:HIS64 4.4 38.2 1.0 NE2 C:HIS454 4.7 31.1 1.0 CG C:HIS398 4.7 38.9 1.0 CD2 C:HIS454 4.7 31.8 1.0 NE2 C:HIS64 4.7 39.3 1.0 CD2 C:PHE450 4.9 33.8 1.0 CG C:HIS64 5.0 37.0 1.0

T.Bertrand, C.Jolivalt, P.Briozzo, E.Caminade, N.Joly, C.Madzak, C.Mougin. Crystal Structure of A Four-Copper Laccase Complexed with An Arylamine: Insights Into Substrate Recognition and Correlation with Kinetics. Biochemistry V. 41 7325 2002.
ISSN: ISSN 0006-2960
PubMed: 12044164
DOI: 10.1021/BI0201318