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Copper in PDB 4gxf: Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor

Protein crystallography data

The structure of Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor, PDB code: 4gxf was solved by I.Nederlof, A.Gupta, G.W.Canters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.01 / 2.73
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 176.660, 176.660, 176.850, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 19.9

Copper Binding Sites:

Pages:

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

Binding sites:

The binding sites of Copper atom in the Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor (pdb code 4gxf). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor, PDB code: 4gxf:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in 4gxf

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Copper binding site 1 out of 12 in the Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:36.0
occ:1.00
ND1 A:HIS293 2.0 30.5 1.0
ND1 A:HIS231 2.0 27.9 1.0
SG A:CYS288 2.2 30.5 1.0
CE1 A:HIS293 2.9 30.4 1.0
CG A:HIS231 3.0 27.8 1.0
CG A:HIS293 3.0 31.4 1.0
CE1 A:HIS231 3.0 27.4 1.0
CB A:CYS288 3.2 30.5 1.0
CB A:HIS231 3.3 28.2 1.0
CB A:HIS293 3.4 30.9 1.0
CA A:HIS231 3.6 27.6 1.0
SD A:MET298 3.7 35.8 1.0
CE A:MET298 3.9 32.4 1.0
O A:TYR230 4.0 27.8 1.0
CG2 A:VAL290 4.0 31.7 1.0
NE2 A:HIS293 4.0 31.5 1.0
CB A:VAL290 4.1 30.8 1.0
CD2 A:HIS293 4.1 31.6 1.0
NE2 A:HIS231 4.1 27.8 1.0
CD2 A:HIS231 4.1 27.4 1.0
N A:THR232 4.6 28.9 1.0
N A:HIS231 4.6 28.0 1.0
CA A:CYS288 4.6 31.3 1.0
C A:HIS231 4.6 28.1 1.0
C A:TYR230 4.7 27.6 1.0
CA A:HIS293 4.9 32.8 1.0
CG1 A:VAL290 5.0 31.1 1.0
CD2 A:PHE195 5.0 30.9 1.0
N A:VAL290 5.0 31.6 1.0

Copper binding site 2 out of 12 in 4gxf

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Copper binding site 2 out of 12 in the Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:58.5
occ:1.00
NE2 A:HIS236 2.0 35.8 1.0
NE2 C:HIS158 2.2 37.3 1.0
NE2 A:HIS287 2.4 38.0 1.0
O C:O402 2.5 13.2 0.4
CE1 A:HIS236 2.9 35.7 1.0
CE1 C:HIS158 3.1 35.8 1.0
CD2 C:HIS158 3.2 35.7 1.0
CD2 A:HIS236 3.2 35.6 1.0
CE1 A:HIS287 3.3 37.2 1.0
CD2 A:HIS287 3.3 37.2 1.0
O C:HOH536 3.4 34.1 1.0
CU A:CU403 3.6 46.6 0.4
ND1 A:HIS236 4.1 34.8 1.0
CD2 A:HIS234 4.1 33.8 1.0
NE2 C:HIS102 4.2 41.3 1.0
CG A:HIS236 4.2 35.1 1.0
ND1 C:HIS158 4.3 35.7 1.0
CG C:HIS158 4.3 35.0 1.0
ND1 A:HIS287 4.3 36.8 1.0
CE A:MET285 4.4 45.0 1.0
CG A:HIS287 4.4 35.5 1.0
ND1 C:HIS164 4.4 35.5 1.0
NE2 A:HIS234 4.4 34.4 1.0
CD2 C:HIS102 4.6 38.9 1.0
NE2 A:HIS289 4.7 34.2 1.0
CU C:CU401 4.8 43.0 1.0
SD A:MET285 4.8 48.8 1.0
CE1 C:HIS102 4.8 39.8 1.0
CD2 A:HIS289 4.9 33.3 1.0

Copper binding site 3 out of 12 in 4gxf

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Copper binding site 3 out of 12 in the Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:46.6
occ:0.40
NE2 C:HIS102 2.0 41.3 1.0
NE2 A:HIS234 2.0 34.4 1.0
O C:O402 2.4 13.2 0.4
CE1 C:HIS102 2.8 39.8 1.0
CD2 A:HIS234 2.9 33.8 1.0
CE1 A:HIS234 3.1 33.3 1.0
CD2 C:HIS102 3.1 38.9 1.0
CU C:CU401 3.3 43.0 1.0
NE2 A:HIS236 3.3 35.8 1.0
NE2 C:HIS104 3.4 29.8 1.0
CD2 A:HIS236 3.4 35.6 1.0
CU A:CU402 3.6 58.5 1.0
CE1 A:HIS236 3.7 35.7 1.0
CE1 C:HIS104 3.7 30.1 1.0
CD2 C:HIS104 3.8 29.7 1.0
CG A:HIS236 4.0 35.1 1.0
ND1 C:HIS102 4.0 39.2 1.0
CG A:HIS234 4.1 33.4 1.0
ND1 A:HIS234 4.1 33.2 1.0
ND1 A:HIS236 4.1 34.8 1.0
CG C:HIS102 4.2 38.7 1.0
ND1 C:HIS104 4.3 30.2 1.0
CG C:HIS104 4.4 30.1 1.0
NE2 A:HIS289 4.4 34.2 1.0
CD2 A:HIS289 4.6 33.3 1.0
NE2 C:HIS156 4.6 34.6 1.0
NE2 A:HIS287 4.7 38.0 1.0
O C:VAL103 4.7 32.8 1.0
CA A:HIS236 4.8 34.2 1.0
CD2 C:HIS158 4.8 35.7 1.0
NE2 C:HIS158 4.8 37.3 1.0
CB A:HIS236 4.9 34.9 1.0

Copper binding site 4 out of 12 in 4gxf

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Copper binding site 4 out of 12 in the Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:41.4
occ:1.00
NE2 B:HIS289 2.0 33.2 1.0
NE2 A:HIS104 2.0 30.3 1.0
NE2 A:HIS156 2.1 32.0 1.0
O A:O407 2.5 9.5 0.4
CD2 B:HIS289 2.9 32.8 1.0
CE1 A:HIS156 2.9 32.3 1.0
CE1 A:HIS104 2.9 30.1 1.0
CE1 B:HIS289 3.1 32.5 1.0
CD2 A:HIS104 3.1 29.4 1.0
CD2 A:HIS156 3.2 32.1 1.0
CU A:CU406 3.6 53.4 0.4
CD2 A:HIS102 3.9 35.3 1.0
CG B:HIS289 4.1 33.2 1.0
ND1 A:HIS104 4.1 30.0 1.0
NE2 A:HIS102 4.1 37.5 1.0
ND1 A:HIS156 4.1 32.4 1.0
ND1 B:HIS289 4.1 33.6 1.0
NE2 B:HIS234 4.1 34.0 1.0
CB A:ALA266 4.2 26.4 1.0
CG A:HIS104 4.2 29.6 1.0
CE1 A:HIS154 4.2 28.2 1.0
CD2 B:HIS234 4.3 32.9 1.0
CG A:HIS156 4.3 31.9 1.0
O A:HOH533 4.4 36.9 1.0
CU B:CU402 4.7 52.3 1.0
CE1 B:HIS234 5.0 32.7 1.0
NE2 A:HIS154 5.0 27.8 1.0

Copper binding site 5 out of 12 in 4gxf

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Copper binding site 5 out of 12 in the Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:53.4
occ:0.40
NE2 A:HIS102 2.0 37.5 1.0
NE2 B:HIS234 2.2 34.0 1.0
O A:O407 2.8 9.5 0.4
CE1 A:HIS102 2.9 35.9 1.0
CD2 A:HIS102 3.1 35.3 1.0
CE1 B:HIS234 3.1 32.7 1.0
CD2 B:HIS234 3.2 32.9 1.0
NE2 A:HIS104 3.4 30.3 1.0
CU A:CU405 3.6 41.4 1.0
NE2 B:HIS236 3.6 34.6 1.0
CD2 B:HIS236 3.7 34.1 1.0
CD2 A:HIS104 3.7 29.4 1.0
CE1 A:HIS104 3.8 30.1 1.0
CE1 B:HIS236 3.8 33.9 1.0
CU B:CU402 3.9 52.3 1.0
CG B:HIS236 4.0 32.8 1.0
ND1 B:HIS236 4.0 33.9 1.0
ND1 A:HIS102 4.0 35.5 1.0
CG A:HIS102 4.2 34.7 1.0
ND1 A:HIS104 4.2 30.0 1.0
CG A:HIS104 4.2 29.6 1.0
ND1 B:HIS234 4.3 33.5 1.0
O A:VAL103 4.3 31.5 1.0
CG B:HIS234 4.3 32.6 1.0
CA B:HIS236 4.6 32.6 1.0
CB B:HIS236 4.8 33.1 1.0
NE2 B:HIS289 4.9 33.2 1.0
C A:VAL103 4.9 30.1 1.0
OD2 B:ASP259 4.9 30.2 1.0
NE2 A:HIS156 4.9 32.0 1.0
N B:HIS236 5.0 33.5 1.0

Copper binding site 6 out of 12 in 4gxf

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Copper binding site 6 out of 12 in the Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:33.6
occ:1.00
ND1 B:HIS293 1.9 29.4 1.0
ND1 B:HIS231 2.0 30.4 1.0
SG B:CYS288 2.2 34.9 1.0
CE1 B:HIS293 2.9 29.4 1.0
CE1 B:HIS231 2.9 30.7 1.0
CG B:HIS293 3.0 30.3 1.0
CG B:HIS231 3.0 30.2 1.0
CB B:CYS288 3.2 34.0 1.0
CB B:HIS231 3.4 30.2 1.0
CB B:HIS293 3.4 30.4 1.0
SD B:MET298 3.6 37.4 1.0
CA B:HIS231 3.7 29.3 1.0
NE2 B:HIS293 4.0 29.6 1.0
NE2 B:HIS231 4.1 30.9 1.0
CG2 B:VAL290 4.1 30.5 1.0
CD2 B:HIS293 4.1 29.8 1.0
CD2 B:HIS231 4.1 30.4 1.0
O B:TYR230 4.1 28.1 1.0
CB B:VAL290 4.2 30.7 1.0
CE B:MET298 4.2 34.4 1.0
N B:THR232 4.4 29.9 1.0
CA B:CYS288 4.6 32.6 1.0
C B:HIS231 4.6 29.6 1.0
N B:HIS231 4.8 28.0 1.0
C B:TYR230 4.9 27.8 1.0
CD2 B:PHE195 4.9 30.6 1.0
CA B:HIS293 4.9 32.2 1.0

Copper binding site 7 out of 12 in 4gxf

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Copper binding site 7 out of 12 in the Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:52.3
occ:1.00
NE2 B:HIS236 2.0 34.6 1.0
NE2 A:HIS158 2.1 36.7 1.0
O A:O407 2.2 9.5 0.4
NE2 B:HIS287 2.4 34.4 1.0
CE1 B:HIS236 2.8 33.9 1.0
CE1 A:HIS158 3.0 35.1 1.0
CD2 B:HIS236 3.1 34.1 1.0
CE1 B:HIS287 3.2 33.3 1.0
CD2 A:HIS158 3.2 35.3 1.0
O A:HOH533 3.3 36.9 1.0
CD2 B:HIS287 3.4 35.0 1.0
CU A:CU406 3.9 53.4 0.4
ND1 B:HIS236 4.0 33.9 1.0
NE2 A:HIS102 4.0 37.5 1.0
CD2 B:HIS234 4.2 32.9 1.0
CG B:HIS236 4.2 32.8 1.0
ND1 A:HIS158 4.2 35.6 1.0
CG A:HIS158 4.3 34.5 1.0
ND1 B:HIS287 4.3 33.1 1.0
CD2 A:HIS164 4.4 38.0 1.0
CD2 A:HIS102 4.4 35.3 1.0
CG B:HIS287 4.5 33.7 1.0
NE2 B:HIS234 4.5 34.0 1.0
SD B:MET285 4.7 50.8 1.0
NE2 B:HIS289 4.7 33.2 1.0
CU A:CU405 4.7 41.4 1.0
CE1 A:HIS102 4.8 35.9 1.0
CD2 B:HIS289 4.9 32.8 1.0

Copper binding site 8 out of 12 in 4gxf

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Copper binding site 8 out of 12 in the Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu405

b:40.9
occ:1.00
NE2 C:HIS289 2.0 29.8 1.0
NE2 B:HIS156 2.1 33.4 1.0
NE2 B:HIS104 2.1 27.8 1.0
O B:O406 2.4 9.7 0.4
CE1 B:HIS156 2.9 33.0 1.0
CE1 C:HIS289 3.0 29.1 1.0
CD2 C:HIS289 3.0 29.5 1.0
CD2 B:HIS104 3.1 27.8 1.0
CE1 B:HIS104 3.1 27.9 1.0
CD2 B:HIS156 3.1 32.2 1.0
CU C:CU405 3.6 41.0 0.4
CD2 B:HIS102 3.8 34.4 1.0
NE2 B:HIS102 4.0 35.4 1.0
ND1 B:HIS156 4.1 32.4 1.0
O B:HOH536 4.1 39.1 1.0
ND1 C:HIS289 4.1 30.2 1.0
CB B:ALA266 4.1 26.7 1.0
CG C:HIS289 4.2 29.9 1.0
CG B:HIS156 4.2 31.6 1.0
NE2 C:HIS234 4.2 30.1 1.0
ND1 B:HIS104 4.2 27.6 1.0
CG B:HIS104 4.2 28.0 1.0
CE1 B:HIS154 4.2 25.6 1.0
CD2 C:HIS234 4.4 29.3 1.0
CU C:CU404 4.7 56.3 1.0
NE2 B:HIS154 4.8 25.3 1.0
CE1 C:HIS234 4.9 29.1 1.0

Copper binding site 9 out of 12 in 4gxf

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Copper binding site 9 out of 12 in the Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu401

b:43.0
occ:1.00
NE2 C:HIS104 2.0 29.8 1.0
NE2 A:HIS289 2.1 34.2 1.0
NE2 C:HIS156 2.1 34.6 1.0
O C:O402 2.3 13.2 0.4
CE1 C:HIS104 2.9 30.1 1.0
CD2 C:HIS104 3.1 29.7 1.0
CD2 A:HIS289 3.1 33.3 1.0
CE1 C:HIS156 3.1 33.7 1.0
CE1 A:HIS289 3.1 33.0 1.0
CD2 C:HIS156 3.1 32.8 1.0
CU A:CU403 3.3 46.6 0.4
CD2 C:HIS102 3.7 38.9 1.0
NE2 C:HIS102 3.7 41.3 1.0
ND1 C:HIS104 4.1 30.2 1.0
CG C:HIS104 4.2 30.1 1.0
ND1 C:HIS156 4.2 33.1 1.0
ND1 A:HIS289 4.2 33.0 1.0
CB C:ALA266 4.2 26.5 1.0
CG A:HIS289 4.2 32.7 1.0
CE1 C:HIS154 4.2 27.7 1.0
CG C:HIS156 4.3 32.2 1.0
NE2 A:HIS234 4.3 34.4 1.0
CD2 A:HIS234 4.5 33.8 1.0
O C:HOH536 4.5 34.1 1.0
CU A:CU402 4.8 58.5 1.0
NE2 C:HIS154 4.8 28.0 1.0
CE1 A:HIS234 4.9 33.3 1.0

Copper binding site 10 out of 12 in 4gxf

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Copper binding site 10 out of 12 in the Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Role of the Biradical Intermediate Observed During the Turnover of Slac: A Two-Domain Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu403

b:32.3
occ:1.00
ND1 C:HIS231 2.0 26.6 1.0
ND1 C:HIS293 2.0 30.1 1.0
SG C:CYS288 2.1 30.1 1.0
CG C:HIS231 3.0 25.8 1.0
CE1 C:HIS293 3.0 29.9 1.0
CE1 C:HIS231 3.0 25.9 1.0
CG C:HIS293 3.1 30.5 1.0
CB C:CYS288 3.2 30.2 1.0
CB C:HIS231 3.3 26.1 1.0
CB C:HIS293 3.5 30.5 1.0
SD C:MET298 3.5 36.7 1.0
CA C:HIS231 3.6 26.4 1.0
CE C:MET298 3.7 35.0 1.0
O C:TYR230 4.1 26.6 1.0
CG2 C:VAL290 4.1 30.1 1.0
CD2 C:HIS231 4.1 25.5 1.0
NE2 C:HIS231 4.1 25.7 1.0
NE2 C:HIS293 4.1 30.3 1.0
CB C:VAL290 4.2 29.6 1.0
CD2 C:HIS293 4.2 30.4 1.0
N C:THR232 4.5 26.5 1.0
CA C:CYS288 4.6 29.4 1.0
N C:HIS231 4.6 26.7 1.0
C C:HIS231 4.6 26.6 1.0
C C:TYR230 4.7 27.0 1.0
CD2 C:PHE195 4.9 30.8 1.0
CA C:HIS293 4.9 31.7 1.0

Reference:

A.Gupta, I.Nederlof, S.Sottini, A.W.Tepper, E.J.Groenen, E.A.Thomassen, G.W.Canters. Involvement of TYR108 in the Enzyme Mechanism of the Small Laccase From Streptomyces Coelicolor J.Am.Chem.Soc. V. 134 18213 2012.
ISSN: ISSN 0002-7863
PubMed: 23094962
DOI: 10.1021/JA3088604
Page generated: Sun Dec 13 11:14:33 2020

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