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Copper in PDB 3cg8: Laccase From Streptomyces Coelicolor

Enzymatic activity of Laccase From Streptomyces Coelicolor

All present enzymatic activity of Laccase From Streptomyces Coelicolor:
1.10.3.2;

Protein crystallography data

The structure of Laccase From Streptomyces Coelicolor, PDB code: 3cg8 was solved by T.Skalova, J.Dohnalek, L.H.Ostergaard, P.R.Ostergaard, P.Kolenko, J.Duskova, J.Hasek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.54 / 2.68
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 180.868, 180.868, 177.111, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.4

Copper Binding Sites:

The binding sites of Copper atom in the Laccase From Streptomyces Coelicolor (pdb code 3cg8). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Laccase From Streptomyces Coelicolor, PDB code: 3cg8:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12;

Copper binding site 1 out of 12 in 3cg8

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Copper binding site 1 out of 12 in the 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 Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu411

b:30.2
occ:1.00
ND1 A:HIS293 1.9 28.4 1.0
ND1 A:HIS231 2.0 27.3 1.0
SG A:CYS288 2.2 26.6 1.0
CE1 A:HIS293 2.9 26.7 1.0
CG A:HIS293 2.9 29.3 1.0
CE1 A:HIS231 3.0 26.0 1.0
CG A:HIS231 3.0 25.5 1.0
CB A:CYS288 3.3 26.6 1.0
CB A:HIS293 3.3 29.4 1.0
CB A:HIS231 3.3 25.2 1.0
SD A:MET298 3.5 32.9 1.0
CA A:HIS231 3.7 25.1 1.0
CE A:MET298 3.9 35.4 1.0
NE2 A:HIS293 4.0 25.7 1.0
O A:TYR230 4.0 23.5 1.0
CD2 A:HIS293 4.0 28.0 1.0
CG2 A:VAL290 4.1 22.0 1.0
NE2 A:HIS231 4.1 24.0 1.0
CB A:VAL290 4.1 25.0 1.0
CD2 A:HIS231 4.1 23.9 1.0
N A:THR232 4.6 24.9 1.0
N A:HIS231 4.6 24.6 1.0
CA A:CYS288 4.7 26.5 1.0
C A:HIS231 4.7 24.6 1.0
C A:TYR230 4.8 24.8 1.0
CA A:HIS293 4.8 30.2 1.0
CG A:MET298 5.0 32.9 1.0
CG1 A:VAL290 5.0 21.2 1.0

Copper binding site 2 out of 12 in 3cg8

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Copper binding site 2 out of 12 in the 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 Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu412

b:30.3
occ:1.00
NE2 C:HIS104 1.9 23.1 1.0
NE2 A:HIS289 2.0 22.3 1.0
NE2 C:HIS156 2.1 31.5 1.0
O A:O501 2.4 2.0 0.4
CE1 C:HIS104 2.8 25.9 1.0
CE1 A:HIS289 2.9 26.1 1.0
CD2 A:HIS289 2.9 22.5 1.0
CD2 C:HIS104 3.0 25.9 1.0
CE1 C:HIS156 3.0 28.8 1.0
CD2 C:HIS156 3.0 29.1 1.0
CD2 C:HIS102 3.9 35.0 1.0
CU A:CU414 3.9 52.7 0.4
ND1 C:HIS104 4.0 24.2 1.0
ND1 A:HIS289 4.0 24.7 1.0
CB C:ALA266 4.0 22.1 1.0
CG A:HIS289 4.0 23.7 1.0
CG C:HIS104 4.1 25.2 1.0
ND1 C:HIS156 4.1 28.0 1.0
CG C:HIS156 4.2 28.6 1.0
NE2 C:HIS102 4.2 37.5 1.0
NE2 A:HIS234 4.2 28.0 1.0
CE1 C:HIS154 4.2 27.5 1.0
CD2 A:HIS234 4.4 26.7 1.0
O C:HOH681 4.7 46.5 1.0
NE2 C:HIS154 4.9 27.0 1.0
CE1 A:HIS234 4.9 28.3 1.0
CU A:CU413 5.0 54.3 1.0
CE1 C:HIS226 5.0 27.6 1.0

Copper binding site 3 out of 12 in 3cg8

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Copper binding site 3 out of 12 in the 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 Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu413

b:54.3
occ:1.00
NE2 A:HIS236 2.1 25.7 1.0
NE2 A:HIS287 2.3 33.5 1.0
NE2 C:HIS158 2.3 33.9 1.0
O A:O501 2.5 2.0 0.4
CE1 A:HIS236 2.9 27.7 1.0
CD2 A:HIS236 3.2 25.4 1.0
CE1 A:HIS287 3.3 32.7 1.0
CD2 A:HIS287 3.3 32.1 1.0
CE1 C:HIS158 3.3 33.8 1.0
CD2 C:HIS158 3.3 32.4 1.0
O C:HOH681 3.6 46.5 1.0
CU A:CU414 3.6 52.7 0.4
CD2 A:HIS234 4.0 26.7 1.0
NE2 C:HIS102 4.0 37.5 1.0
ND1 A:HIS236 4.1 27.6 1.0
CG A:HIS236 4.2 25.5 1.0
NE2 A:HIS234 4.3 28.0 1.0
CD2 C:HIS102 4.4 35.0 1.0
ND1 A:HIS287 4.4 32.3 1.0
CG A:HIS287 4.4 29.1 1.0
ND1 C:HIS158 4.4 34.4 1.0
CG C:HIS158 4.5 33.5 1.0
CE1 C:HIS102 4.6 35.9 1.0
SD A:MET285 4.7 44.3 1.0
NE2 A:HIS289 4.7 22.3 1.0
ND1 C:HIS164 4.7 33.3 1.0
CU A:CU412 5.0 30.3 1.0

Copper binding site 4 out of 12 in 3cg8

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Copper binding site 4 out of 12 in the 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 Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu414

b:52.7
occ:0.40
NE2 C:HIS102 1.8 37.5 1.0
NE2 A:HIS234 1.9 28.0 1.0
O A:O501 2.6 2.0 0.4
CE1 C:HIS102 2.7 35.9 1.0
O C:HOH613 2.8 36.3 1.0
CD2 C:HIS102 2.9 35.0 1.0
CD2 A:HIS234 2.9 26.7 1.0
CE1 A:HIS234 2.9 28.3 1.0
CD2 A:HIS236 3.1 25.4 1.0
NE2 A:HIS236 3.2 25.7 1.0
CU A:CU413 3.6 54.3 1.0
NE2 C:HIS104 3.7 23.1 1.0
ND1 C:HIS102 3.8 35.0 1.0
CG A:HIS236 3.9 25.5 1.0
CU A:CU412 3.9 30.3 1.0
CG C:HIS102 4.0 32.1 1.0
CE1 C:HIS104 4.0 25.9 1.0
ND1 A:HIS234 4.0 27.2 1.0
CG A:HIS234 4.0 27.0 1.0
CE1 A:HIS236 4.0 27.7 1.0
CD2 C:HIS104 4.0 25.9 1.0
ND1 A:HIS236 4.4 27.6 1.0
ND1 C:HIS104 4.5 24.2 1.0
CG C:HIS104 4.5 25.2 1.0
CA A:HIS236 4.6 27.0 1.0
OH C:TYR108 4.6 36.2 1.0
O C:VAL103 4.7 28.5 1.0
CB A:HIS236 4.7 27.2 1.0
NE2 A:HIS289 4.8 22.3 1.0
N A:HIS236 4.8 27.7 1.0
NE2 A:HIS287 5.0 33.5 1.0

Copper binding site 5 out of 12 in 3cg8

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Copper binding site 5 out of 12 in the 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 Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu411

b:28.9
occ:1.00
ND1 B:HIS293 2.0 27.8 1.0
ND1 B:HIS231 2.0 27.3 1.0
SG B:CYS288 2.2 29.4 1.0
CE1 B:HIS231 2.9 26.4 1.0
CG B:HIS293 3.0 28.2 1.0
CE1 B:HIS293 3.0 29.2 1.0
CG B:HIS231 3.0 24.2 1.0
CB B:CYS288 3.2 28.1 1.0
CB B:HIS293 3.3 29.3 1.0
CB B:HIS231 3.4 25.6 1.0
SD B:MET298 3.4 32.4 1.0
CA B:HIS231 3.7 25.7 1.0
NE2 B:HIS231 4.0 24.6 1.0
NE2 B:HIS293 4.1 25.9 1.0
CD2 B:HIS293 4.1 28.4 1.0
CD2 B:HIS231 4.1 23.4 1.0
CG2 B:VAL290 4.1 19.9 1.0
CE B:MET298 4.1 29.4 1.0
O B:TYR230 4.1 24.4 1.0
CB B:VAL290 4.2 23.8 1.0
N B:THR232 4.5 27.4 1.0
CA B:CYS288 4.7 27.6 1.0
N B:HIS231 4.7 25.2 1.0
C B:HIS231 4.7 26.2 1.0
CA B:HIS293 4.8 30.0 1.0
C B:TYR230 4.8 25.4 1.0
CG B:MET298 4.9 31.9 1.0
CG1 B:VAL290 5.0 17.1 1.0
CD2 B:PHE195 5.0 29.6 1.0

Copper binding site 6 out of 12 in 3cg8

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Copper binding site 6 out of 12 in the 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 Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu412

b:28.1
occ:1.00
NE2 A:HIS104 1.9 21.4 1.0
NE2 A:HIS156 2.0 21.5 1.0
NE2 B:HIS289 2.0 24.5 1.0
O B:O501 2.4 8.2 0.4
CE1 A:HIS104 2.9 25.0 1.0
CE1 A:HIS156 2.9 23.7 1.0
CD2 A:HIS104 3.0 23.4 1.0
CD2 B:HIS289 3.0 23.4 1.0
CE1 B:HIS289 3.0 25.1 1.0
CD2 A:HIS156 3.0 22.9 1.0
CD2 A:HIS102 3.9 25.1 1.0
CU B:CU414 3.9 57.2 0.4
CB A:ALA266 4.0 22.0 1.0
ND1 A:HIS104 4.0 23.8 1.0
ND1 B:HIS289 4.1 24.4 1.0
CG B:HIS289 4.1 23.5 1.0
ND1 A:HIS156 4.1 22.4 1.0
CG A:HIS104 4.1 24.1 1.0
CG A:HIS156 4.1 23.6 1.0
CE1 A:HIS154 4.2 25.4 1.0
NE2 A:HIS102 4.2 27.8 1.0
NE2 B:HIS234 4.2 29.3 1.0
CD2 B:HIS234 4.3 28.6 1.0
O A:HOH708 4.7 51.6 1.0
NE2 A:HIS154 4.8 26.8 1.0
CE1 A:HIS226 4.9 25.8 1.0
CE1 B:HIS234 4.9 28.3 1.0
CU B:CU413 5.0 55.4 1.0

Copper binding site 7 out of 12 in 3cg8

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Copper binding site 7 out of 12 in the 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 Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu413

b:55.4
occ:1.00
NE2 B:HIS236 2.1 24.8 1.0
NE2 A:HIS158 2.3 29.8 1.0
NE2 B:HIS287 2.4 35.0 1.0
O B:O501 2.7 8.2 0.4
CE1 B:HIS236 2.9 25.6 1.0
CD2 A:HIS158 3.2 29.6 1.0
CD2 B:HIS236 3.3 25.1 1.0
CE1 A:HIS158 3.3 28.6 1.0
CE1 B:HIS287 3.4 33.1 1.0
CD2 B:HIS287 3.4 34.5 1.0
O A:HOH708 3.8 51.6 1.0
CD2 B:HIS234 3.9 28.6 1.0
CU B:CU414 4.0 57.2 0.4
NE2 A:HIS102 4.1 27.8 1.0
ND1 B:HIS236 4.1 25.6 1.0
NE2 B:HIS234 4.2 29.3 1.0
CG B:HIS236 4.3 24.1 1.0
CG A:HIS158 4.4 29.2 1.0
ND1 A:HIS158 4.4 29.8 1.0
CD2 A:HIS102 4.4 25.1 1.0
ND1 B:HIS287 4.5 33.1 1.0
CG B:HIS287 4.5 32.8 1.0
CD2 A:HIS164 4.5 35.9 1.0
CE1 A:HIS102 4.6 27.2 1.0
SD B:MET285 4.7 44.0 1.0
NE2 B:HIS289 4.7 24.5 1.0
CD2 B:HIS289 5.0 23.4 1.0
CU B:CU412 5.0 28.1 1.0

Copper binding site 8 out of 12 in 3cg8

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Copper binding site 8 out of 12 in the 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 Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu414

b:57.2
occ:0.40
NE2 A:HIS102 1.8 27.8 1.0
NE2 B:HIS234 1.9 29.3 1.0
O B:O501 2.6 8.2 0.4
CE1 A:HIS102 2.6 27.2 1.0
CE1 B:HIS234 2.7 28.3 1.0
O A:HOH612 2.8 38.4 1.0
CD2 A:HIS102 2.9 25.1 1.0
CD2 B:HIS234 3.0 28.6 1.0
CD2 B:HIS236 3.4 25.1 1.0
NE2 B:HIS236 3.5 24.8 1.0
NE2 A:HIS104 3.5 21.4 1.0
CD2 A:HIS104 3.8 23.4 1.0
ND1 A:HIS102 3.8 26.1 1.0
CE1 A:HIS104 3.9 25.0 1.0
ND1 B:HIS234 3.9 29.4 1.0
CU B:CU412 3.9 28.1 1.0
CG A:HIS102 4.0 25.3 1.0
CU B:CU413 4.0 55.4 1.0
CG B:HIS236 4.0 24.1 1.0
CG B:HIS234 4.1 28.0 1.0
CE1 B:HIS236 4.1 25.6 1.0
CG A:HIS104 4.2 24.1 1.0
ND1 A:HIS104 4.3 23.8 1.0
O A:VAL103 4.3 24.5 1.0
ND1 B:HIS236 4.4 25.6 1.0
OH A:TYR108 4.5 34.0 1.0
CA B:HIS236 4.6 26.6 1.0
C A:VAL103 4.9 24.3 1.0
O A:HOH738 4.9 31.5 1.0
CB B:HIS236 4.9 26.5 1.0
CA A:HIS104 4.9 24.9 1.0
N B:HIS236 4.9 27.1 1.0

Copper binding site 9 out of 12 in 3cg8

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Copper binding site 9 out of 12 in the 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 Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu411

b:29.6
occ:1.00
ND1 C:HIS293 1.9 29.0 1.0
ND1 C:HIS231 2.0 25.4 1.0
SG C:CYS288 2.2 27.9 1.0
CG C:HIS293 2.9 30.0 1.0
CE1 C:HIS293 2.9 29.0 1.0
CE1 C:HIS231 3.0 23.8 1.0
CG C:HIS231 3.0 25.0 1.0
CB C:CYS288 3.2 27.6 1.0
CB C:HIS293 3.2 30.2 1.0
CB C:HIS231 3.3 25.6 1.0
SD C:MET298 3.4 34.9 1.0
CA C:HIS231 3.7 26.0 1.0
NE2 C:HIS293 4.0 26.4 1.0
CD2 C:HIS293 4.0 28.8 1.0
O C:TYR230 4.1 25.8 1.0
NE2 C:HIS231 4.1 21.4 1.0
CG2 C:VAL290 4.1 23.5 1.0
CD2 C:HIS231 4.1 22.4 1.0
CB C:VAL290 4.1 25.2 1.0
CE C:MET298 4.1 34.6 1.0
CA C:CYS288 4.6 27.6 1.0
N C:THR232 4.6 25.7 1.0
N C:HIS231 4.7 26.3 1.0
C C:HIS231 4.7 25.6 1.0
CA C:HIS293 4.8 30.6 1.0
C C:TYR230 4.8 26.3 1.0
CG C:MET298 4.9 34.9 1.0
CG1 C:VAL290 4.9 20.5 1.0
CD2 C:PHE195 4.9 29.6 1.0

Copper binding site 10 out of 12 in 3cg8

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Copper binding site 10 out of 12 in the 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 Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu412

b:31.2
occ:1.00
NE2 B:HIS104 1.9 22.4 1.0
NE2 C:HIS289 2.1 24.8 1.0
NE2 B:HIS156 2.1 29.5 1.0
O C:O501 2.7 2.8 0.4
CE1 B:HIS104 2.8 27.1 1.0
CD2 B:HIS104 3.0 26.2 1.0
CD2 C:HIS289 3.0 24.3 1.0
CE1 C:HIS289 3.1 26.3 1.0
CE1 B:HIS156 3.1 29.6 1.0
CD2 B:HIS156 3.1 28.2 1.0
CU C:CU414 3.3 63.6 0.4
CD2 B:HIS102 3.9 33.3 1.0
ND1 B:HIS104 4.0 26.1 1.0
CB B:ALA266 4.0 24.8 1.0
CG B:HIS104 4.1 26.0 1.0
ND1 C:HIS289 4.1 23.6 1.0
CG C:HIS289 4.2 24.5 1.0
ND1 B:HIS156 4.2 27.0 1.0
CE1 B:HIS154 4.2 26.1 1.0
CG B:HIS156 4.2 27.8 1.0
NE2 C:HIS234 4.3 30.1 1.0
CD2 C:HIS234 4.4 28.0 1.0
NE2 B:HIS102 4.4 35.3 1.0
O B:HOH702 4.5 49.0 1.0
NE2 B:HIS154 4.9 26.0 1.0
CE1 C:HIS234 4.9 29.6 1.0
CE1 B:HIS226 5.0 25.1 1.0

Copper binding site 11 out of 12 in 3cg8

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Copper binding site 11 out of 12 in the Laccase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 11 of Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu413

b:56.3
occ:1.00
NE2 C:HIS236 2.1 26.6 1.0
NE2 B:HIS158 2.2 36.0 1.0
NE2 C:HIS287 2.4 35.4 1.0
O C:O501 2.4 2.8 0.4
CE1 C:HIS236 2.9 29.2 1.0
CD2 B:HIS158 3.2 34.4 1.0
CE1 B:HIS158 3.2 35.1 1.0
CD2 C:HIS236 3.3 26.7 1.0
CE1 C:HIS287 3.3 34.4 1.0
CD2 C:HIS287 3.3 33.2 1.0
O B:HOH702 3.5 49.0 1.0
CU C:CU414 3.6 63.6 0.4
CD2 C:HIS234 4.0 28.0 1.0
ND1 C:HIS236 4.1 27.1 1.0
NE2 B:HIS102 4.2 35.3 1.0
CG C:HIS236 4.3 25.5 1.0
NE2 C:HIS234 4.3 30.1 1.0
CG B:HIS158 4.3 32.8 1.0
ND1 B:HIS158 4.3 33.7 1.0
ND1 C:HIS287 4.4 34.1 1.0
CG C:HIS287 4.4 31.3 1.0
CD2 B:HIS102 4.5 33.3 1.0
SD C:MET285 4.5 44.9 1.0
ND1 B:HIS164 4.6 35.4 1.0
CE1 B:HIS102 4.7 33.2 1.0
NE2 C:HIS289 4.8 24.8 1.0

Copper binding site 12 out of 12 in 3cg8

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Copper binding site 12 out of 12 in the Laccase From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 12 of Laccase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu414

b:63.6
occ:0.40
NE2 B:HIS102 1.9 35.3 1.0
NE2 C:HIS234 2.0 30.1 1.0
CD2 B:HIS102 2.6 33.3 1.0
O C:O501 2.7 2.8 0.4
O B:HOH613 2.8 44.4 1.0
CD2 C:HIS234 2.9 28.0 1.0
CE1 C:HIS234 3.1 29.6 1.0
CE1 B:HIS102 3.1 33.2 1.0
NE2 B:HIS104 3.2 22.4 1.0
CU C:CU412 3.3 31.2 1.0
NE2 C:HIS236 3.5 26.6 1.0
CE1 B:HIS104 3.6 27.1 1.0
CD2 B:HIS104 3.6 26.2 1.0
CU C:CU413 3.6 56.3 1.0
CD2 C:HIS236 3.7 26.7 1.0
CG B:HIS102 3.9 30.7 1.0
CG C:HIS234 4.0 28.0 1.0
ND1 C:HIS234 4.1 29.6 1.0
ND1 B:HIS102 4.1 30.8 1.0
ND1 B:HIS104 4.2 26.1 1.0
CG B:HIS104 4.2 26.0 1.0
CE1 C:HIS236 4.3 29.2 1.0
NE2 C:HIS289 4.4 24.8 1.0
CG C:HIS236 4.5 25.5 1.0
NE2 B:HIS156 4.5 29.5 1.0
CD2 C:HIS289 4.6 24.3 1.0
ND1 C:HIS236 4.7 27.1 1.0
CD2 B:HIS158 4.8 34.4 1.0
O B:VAL103 4.9 28.2 1.0
NE2 C:HIS287 4.9 35.4 1.0
NE2 B:HIS158 4.9 36.0 1.0

Reference:

T.Skalova, J.Dohnalek, L.H.Ostergaard, P.R.Ostergaard, P.Kolenko, J.Duskova, A.Stepankova, J.Hasek. The Structure of the Small Laccase From Streptomyces Coelicolor Reveals A Link Between Laccases and Nitrite Reductases. J.Mol.Biol. V. 385 1165 2009.
ISSN: ISSN 0022-2836
PubMed: 19063896
DOI: 10.1016/J.JMB.2008.11.024
Page generated: Wed Oct 28 14:23:34 2020
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