Copper in PDB 8u8r: Y229F/V290N/S292F Streptomyces Coelicolor Laccase

The structure of Y229F/V290N/S292F Streptomyces Coelicolor Laccase, PDB code: 8u8r was solved by J.-X.Wang, Y.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.70 / 2.86
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	177.355, 177.355, 176.956, 90, 90, 90
R / Rfree (%)	18.2 / 21.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Copper atom in the Y229F/V290N/S292F Streptomyces Coelicolor Laccase (pdb code 8u8r). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Y229F/V290N/S292F Streptomyces Coelicolor Laccase, PDB code: 8u8r:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in the Y229F/V290N/S292F Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Y229F/V290N/S292F Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:56.3 occ:1.00 ND1 A:HIS293 2.0 48.9 1.0 ND1 A:HIS231 2.1 49.8 1.0 SG A:CYS288 2.1 58.0 1.0 CG A:HIS231 3.0 44.8 1.0 CG A:HIS293 3.0 53.3 1.0 CE1 A:HIS293 3.0 52.0 1.0 CE1 A:HIS231 3.1 42.6 1.0 CB A:CYS288 3.2 46.1 1.0 CB A:HIS231 3.2 46.0 1.0 CB A:HIS293 3.3 46.0 1.0 CA A:HIS231 3.6 46.7 1.0 O A:TYR230 3.7 47.2 1.0 SD A:MET298 3.8 62.2 1.0 CB A:ASN290 3.9 43.6 1.0 CE A:MET298 4.1 52.6 1.0 NE2 A:HIS293 4.1 59.5 1.0 CD2 A:HIS293 4.2 57.9 1.0 CD2 A:HIS231 4.2 46.8 1.0 NE2 A:HIS231 4.2 46.5 1.0 OH C:TYR230 4.4 60.6 1.0 N A:HIS231 4.5 48.9 1.0 C A:TYR230 4.5 49.6 1.0 CA A:CYS288 4.6 53.3 1.0 N A:THR232 4.6 46.2 1.0 C A:HIS231 4.7 51.0 1.0 CG A:ASN290 4.7 57.7 1.0 CA A:HIS293 4.9 52.0 1.0 CD2 A:PHE195 4.9 54.8 1.0 N A:ASN290 5.0 46.3 1.0 ND2 A:ASN290 5.0 58.4 1.0

Copper binding site 2 out of 12 in the Y229F/V290N/S292F Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Y229F/V290N/S292F Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:52.5 occ:0.31 O A:OH405 2.0 54.2 0.9 NE2 A:HIS236 2.1 53.2 1.0 NE2 C:HIS158 2.3 48.4 1.0 NE2 A:HIS287 2.4 63.7 1.0 CE1 A:HIS236 2.8 40.5 1.0 CE1 A:HIS287 3.1 51.9 1.0 CE1 C:HIS158 3.1 53.0 1.0 CD2 A:HIS236 3.4 54.3 1.0 O A:HOH527 3.4 61.9 1.0 CD2 C:HIS158 3.4 56.8 1.0 CD2 A:HIS287 3.4 63.7 1.0 CD2 A:HIS234 4.0 49.5 1.0 SD A:MET285 4.0 74.2 1.0 ND1 A:HIS236 4.0 61.6 1.0 ND1 A:HIS287 4.2 57.3 1.0 CU A:CU403 4.2 54.1 0.1 NE2 C:HIS102 4.3 59.7 1.0 ND1 C:HIS158 4.3 51.4 1.0 CG A:HIS236 4.3 53.0 1.0 CG A:HIS287 4.4 54.8 1.0 NE2 A:HIS234 4.4 56.0 1.0 CG C:HIS158 4.4 60.2 1.0 CD2 C:HIS102 4.5 53.5 1.0 NE2 A:HIS289 4.7 57.4 1.0 O A:HOH526 4.8 59.8 1.0 CE A:MET285 4.9 46.7 1.0 CE1 C:HIS102 4.9 54.6 1.0 CD2 A:HIS289 5.0 50.3 1.0 CU A:CU404 5.0 50.1 0.8 CG A:MET285 5.0 58.8 1.0

Copper binding site 3 out of 12 in the Y229F/V290N/S292F Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Y229F/V290N/S292F Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:54.1 occ:0.15 NE2 C:HIS102 1.8 59.7 1.0 NE2 A:HIS234 1.8 56.0 1.0 CE1 C:HIS102 2.4 54.6 1.0 CE1 A:HIS234 2.6 51.9 1.0 O C:HOH502 2.7 60.5 1.0 CD2 A:HIS234 3.0 49.5 1.0 CD2 C:HIS102 3.0 53.5 1.0 O A:OH405 3.2 54.2 0.9 CD2 A:HIS236 3.2 54.3 1.0 NE2 A:HIS236 3.3 53.2 1.0 ND1 C:HIS102 3.7 64.8 1.0 CG A:HIS236 3.7 53.0 1.0 NE2 C:HIS104 3.8 47.8 1.0 ND1 A:HIS234 3.8 50.5 1.0 CE1 A:HIS236 3.9 40.5 1.0 CU A:CU404 3.9 50.1 0.8 CG C:HIS102 4.0 60.9 1.0 CG A:HIS234 4.0 57.2 1.0 CD2 C:HIS104 4.0 56.0 1.0 ND1 A:HIS236 4.1 61.6 1.0 CU A:CU402 4.2 52.5 0.3 CE1 C:HIS104 4.2 47.6 1.0 OH C:TYR108 4.2 55.4 1.0 O C:VAL103 4.3 44.1 1.0 CA A:HIS236 4.4 43.4 1.0 CG C:HIS104 4.5 46.2 1.0 CB A:HIS236 4.5 50.0 1.0 ND1 C:HIS104 4.6 48.2 1.0 OD2 A:ASP259 4.7 53.4 1.0 N A:HIS236 4.7 46.1 1.0 O A:HOH529 4.8 47.6 1.0 O A:MET235 4.9 51.6 1.0

Copper binding site 4 out of 12 in the Y229F/V290N/S292F Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Y229F/V290N/S292F Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:50.1 occ:0.76 NE2 C:HIS104 2.0 47.8 1.0 NE2 A:HIS289 2.0 57.4 1.0 NE2 C:HIS156 2.1 65.0 1.0 O A:OH405 2.9 54.2 0.9 CD2 A:HIS289 3.0 50.3 1.0 CE1 C:HIS156 3.0 55.8 1.0 CD2 C:HIS104 3.0 56.0 1.0 CE1 C:HIS104 3.0 47.6 1.0 CE1 A:HIS289 3.0 51.5 1.0 CD2 C:HIS156 3.1 50.0 1.0 CD2 C:HIS102 3.5 53.5 1.0 NE2 C:HIS102 3.8 59.7 1.0 CU A:CU403 3.9 54.1 0.1 ND1 A:HIS289 4.1 61.4 1.0 ND1 C:HIS104 4.1 48.2 1.0 CG A:HIS289 4.1 51.1 1.0 ND1 C:HIS156 4.1 52.2 1.0 CG C:HIS104 4.1 46.2 1.0 NE2 A:HIS234 4.1 56.0 1.0 CB C:ALA266 4.1 43.4 1.0 CG C:HIS156 4.2 46.1 1.0 CE1 C:HIS154 4.2 45.4 1.0 O A:HOH527 4.3 61.9 1.0 CD2 A:HIS234 4.3 49.5 1.0 NE2 C:HIS154 4.8 46.7 1.0 CE1 A:HIS234 4.8 51.9 1.0 CG C:HIS102 4.8 60.9 1.0 CE1 C:HIS226 4.9 46.9 1.0 CU A:CU402 5.0 52.5 0.3

Copper binding site 5 out of 12 in the Y229F/V290N/S292F Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Y229F/V290N/S292F Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu404 b:42.0 occ:0.68 NE2 B:HIS289 2.0 52.3 1.0 NE2 A:HIS104 2.0 45.2 1.0 NE2 A:HIS156 2.1 61.6 1.0 O B:OH405 2.6 49.9 0.9 CE1 A:HIS156 2.9 54.9 1.0 CD2 B:HIS289 3.0 45.2 1.0 CE1 A:HIS104 3.0 42.1 1.0 CE1 B:HIS289 3.0 46.8 1.0 CD2 A:HIS104 3.0 51.8 1.0 CD2 A:HIS156 3.2 50.6 1.0 CD2 A:HIS102 3.5 44.9 1.0 CU B:CU403 3.8 48.8 0.1 NE2 A:HIS102 3.8 52.1 1.0 ND1 A:HIS156 4.0 53.1 1.0 ND1 B:HIS289 4.1 50.3 1.0 ND1 A:HIS104 4.1 52.1 1.0 CG B:HIS289 4.1 56.1 1.0 O B:HOH532 4.1 51.5 1.0 CG A:HIS104 4.2 48.9 1.0 NE2 B:HIS234 4.2 54.3 1.0 CB A:ALA266 4.2 41.0 1.0 CG A:HIS156 4.2 47.1 1.0 CE1 A:HIS154 4.3 43.5 1.0 CD2 B:HIS234 4.3 52.4 1.0 CU B:CU402 4.7 55.1 0.4 CE1 B:HIS234 4.8 49.1 1.0 CG A:HIS102 4.8 56.8 1.0 NE2 A:HIS154 4.9 45.7 1.0 CE1 A:HIS226 5.0 50.5 1.0 CG B:HIS234 5.0 51.4 1.0

Copper binding site 6 out of 12 in the Y229F/V290N/S292F Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Y229F/V290N/S292F Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu401 b:55.5 occ:1.00 ND1 B:HIS231 2.1 46.4 1.0 SG B:CYS288 2.1 63.5 1.0 ND1 B:HIS293 2.1 53.9 1.0 CG B:HIS231 3.0 42.1 1.0 CG B:HIS293 3.1 53.0 1.0 CE1 B:HIS231 3.1 44.5 1.0 CB B:CYS288 3.2 50.9 1.0 CE1 B:HIS293 3.2 54.7 1.0 CB B:HIS293 3.3 43.6 1.0 CB B:HIS231 3.3 43.2 1.0 CA B:HIS231 3.6 45.7 1.0 SD B:MET298 3.8 62.2 1.0 O B:TYR230 3.8 49.5 1.0 CB B:ASN290 3.8 43.9 1.0 CE B:MET298 4.1 46.6 1.0 CD2 B:HIS231 4.2 46.7 1.0 NE2 B:HIS231 4.2 44.9 1.0 CD2 B:HIS293 4.2 58.3 1.0 NE2 B:HIS293 4.2 62.1 1.0 OH A:TYR230 4.4 69.4 1.0 N B:HIS231 4.5 46.5 1.0 C B:TYR230 4.5 53.1 1.0 CA B:CYS288 4.6 50.1 1.0 N B:THR232 4.6 53.8 1.0 CG B:ASN290 4.7 55.9 1.0 C B:HIS231 4.7 55.1 1.0 CA B:HIS293 4.8 56.0 1.0 N B:ASN290 4.9 46.0 1.0 CA B:ASN290 5.0 51.8 1.0 ND2 B:ASN290 5.0 55.1 1.0

Copper binding site 7 out of 12 in the Y229F/V290N/S292F Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Y229F/V290N/S292F Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu402 b:55.1 occ:0.37 O B:OH405 2.1 49.9 0.9 NE2 B:HIS236 2.2 53.7 1.0 NE2 A:HIS158 2.4 55.4 1.0 NE2 B:HIS287 2.5 56.9 1.0 CE1 B:HIS236 3.0 48.8 1.0 CE1 B:HIS287 3.1 45.3 1.0 O B:HOH532 3.3 51.5 1.0 CE1 A:HIS158 3.3 55.4 1.0 CD2 B:HIS236 3.4 54.2 1.0 CD2 A:HIS158 3.4 59.0 1.0 CD2 B:HIS287 3.5 57.8 1.0 CD2 B:HIS234 3.8 52.4 1.0 NE2 A:HIS102 4.1 52.1 1.0 SD B:MET285 4.1 82.2 1.0 CU B:CU403 4.2 48.8 0.1 ND1 B:HIS236 4.2 65.8 1.0 NE2 B:HIS234 4.2 54.3 1.0 ND1 B:HIS287 4.3 55.5 1.0 CG B:HIS236 4.4 54.3 1.0 NE2 B:HIS289 4.4 52.3 1.0 CD2 A:HIS102 4.4 44.9 1.0 ND1 A:HIS158 4.4 58.9 1.0 CG B:HIS287 4.5 54.3 1.0 CG A:HIS158 4.5 63.6 1.0 CD2 B:HIS289 4.7 45.2 1.0 CU B:CU404 4.7 42.0 0.7 CE1 A:HIS102 4.8 55.3 1.0 CG B:MET285 5.0 62.4 1.0

Copper binding site 8 out of 12 in the Y229F/V290N/S292F Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Y229F/V290N/S292F Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu403 b:48.8 occ:0.12 NE2 A:HIS102 1.8 52.1 1.0 NE2 B:HIS234 1.8 54.3 1.0 CE1 B:HIS234 2.6 49.1 1.0 CE1 A:HIS102 2.6 55.3 1.0 O A:HOH503 2.6 58.3 1.0 O B:OH405 2.9 49.9 0.9 CD2 B:HIS234 3.0 52.4 1.0 CD2 A:HIS102 3.0 44.9 1.0 CD2 B:HIS236 3.5 54.2 1.0 NE2 B:HIS236 3.6 53.7 1.0 NE2 A:HIS104 3.6 45.2 1.0 ND1 B:HIS234 3.8 49.2 1.0 CU B:CU404 3.8 42.0 0.7 ND1 A:HIS102 3.8 72.2 1.0 CE1 A:HIS104 3.9 42.1 1.0 CD2 A:HIS104 3.9 51.8 1.0 CG B:HIS236 4.0 54.3 1.0 CG B:HIS234 4.0 51.4 1.0 CG A:HIS102 4.0 56.8 1.0 O A:VAL103 4.1 44.6 1.0 CE1 B:HIS236 4.1 48.8 1.0 CU B:CU402 4.2 55.1 0.4 ND1 A:HIS104 4.2 52.1 1.0 CG A:HIS104 4.2 48.9 1.0 ND1 B:HIS236 4.3 65.8 1.0 OH A:TYR108 4.5 53.8 1.0 CA B:HIS236 4.5 39.2 1.0 O B:HOH514 4.6 44.0 1.0 OD2 B:ASP259 4.7 44.0 1.0 CB B:HIS236 4.7 50.3 1.0 C A:VAL103 4.8 43.6 1.0 N B:HIS236 4.9 50.5 1.0 NE2 B:HIS289 4.9 52.3 1.0 CA A:HIS104 5.0 39.4 1.0

Copper binding site 9 out of 12 in the Y229F/V290N/S292F Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Y229F/V290N/S292F Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu404 b:44.6 occ:0.71 NE2 C:HIS289 2.0 56.1 1.0 NE2 B:HIS104 2.0 48.9 1.0 NE2 B:HIS156 2.1 59.9 1.0 CE1 B:HIS156 2.8 52.3 1.0 O C:OH405 2.9 50.0 0.9 CD2 C:HIS289 3.0 50.4 1.0 CE1 C:HIS289 3.0 48.0 1.0 CD2 B:HIS104 3.0 48.8 1.0 CE1 B:HIS104 3.0 41.7 1.0 CD2 B:HIS156 3.2 50.8 1.0 CD2 B:HIS102 3.4 48.3 1.0 CU C:CU403 3.5 49.4 0.1 NE2 B:HIS102 3.7 56.1 1.0 ND1 B:HIS156 4.0 45.0 1.0 ND1 C:HIS289 4.1 58.1 1.0 CG C:HIS289 4.1 53.5 1.0 ND1 B:HIS104 4.1 50.6 1.0 NE2 C:HIS234 4.1 56.9 1.0 CG B:HIS104 4.1 40.9 1.0 CD2 C:HIS234 4.2 52.1 1.0 CB B:ALA266 4.2 47.4 1.0 CG B:HIS156 4.2 49.7 1.0 O B:HOH512 4.3 56.0 1.0 CE1 B:HIS154 4.3 44.3 1.0 CG B:HIS102 4.7 56.5 1.0 CU C:CU402 4.8 50.3 0.3 NE2 B:HIS154 4.9 40.4 1.0 CE1 C:HIS234 4.9 49.3 1.0 CG C:HIS234 5.0 48.4 1.0

Copper binding site 10 out of 12 in the Y229F/V290N/S292F Streptomyces Coelicolor Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Y229F/V290N/S292F Streptomyces Coelicolor Laccase within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu401 b:56.6 occ:1.00 ND1 C:HIS293 2.0 56.9 1.0 ND1 C:HIS231 2.1 45.1 1.0 SG C:CYS288 2.1 58.4 1.0 CG C:HIS293 3.0 55.0 1.0 CG C:HIS231 3.1 41.9 1.0 CE1 C:HIS293 3.1 60.2 1.0 CE1 C:HIS231 3.1 46.2 1.0 CB C:CYS288 3.2 50.5 1.0 CB C:HIS293 3.3 38.2 1.0 CB C:HIS231 3.3 42.0 1.0 CA C:HIS231 3.6 48.4 1.0 O C:TYR230 3.7 49.0 1.0 SD C:MET298 3.7 66.1 1.0 CB C:ASN290 3.8 45.5 1.0 CE C:MET298 4.1 45.8 1.0 CD2 C:HIS293 4.1 57.9 1.0 NE2 C:HIS293 4.2 61.5 1.0 CD2 C:HIS231 4.2 51.0 1.0 NE2 C:HIS231 4.2 45.4 1.0 OH B:TYR230 4.4 65.9 1.0 C C:TYR230 4.5 48.6 1.0 N C:HIS231 4.5 47.5 1.0 CA C:CYS288 4.6 49.7 1.0 N C:THR232 4.6 44.0 1.0 CG C:ASN290 4.6 56.1 1.0 C C:HIS231 4.7 50.5 1.0 CA C:HIS293 4.8 54.3 1.0 ND2 C:ASN290 4.9 59.1 1.0 N C:ASN290 4.9 45.3 1.0 CD2 C:PHE195 5.0 48.2 1.0 CA C:ASN290 5.0 50.9 1.0

J.X.Wang, A.C.Vilbert, C.Cui, E.N.Mirts, L.H.Williams, W.Kim, Y.J.Zhang, Y.Lu. Increasing Reduction Potentials of Type 1 Copper Center and Catalytic Efficiency of Small Laccase From Streptomyces Coelicolor Through Secondary Coordination Sphere Mutations. Angew.Chem.Int.Ed.Engl. 14019 2023.
ISSN: ESSN 1521-3773
PubMed: 37926680
DOI: 10.1002/ANIE.202314019