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Copper in PDB 5o3k: Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium

Enzymatic activity of Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium

All present enzymatic activity of Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium, PDB code: 5o3k was solved by A.G.Gabdulkhakov, T.V.Tishchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.59 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 77.027, 94.957, 116.456, 89.88, 90.07, 91.70
R / Rfree (%) 19.6 / 26.2

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium (pdb code 5o3k). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 40 binding sites of Copper where determined in the Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium, PDB code: 5o3k:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 40 in 5o3k

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Copper binding site 1 out of 40 in the Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium


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 Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:20.7
occ:1.00
SG A:CYS289 1.9 8.9 1.0
ND1 A:HIS294 2.2 17.3 1.0
ND1 A:HIS232 2.5 15.7 1.0
CG A:HIS294 3.0 12.5 1.0
CB A:CYS289 3.0 12.5 1.0
CB A:HIS232 3.0 12.3 1.0
CG A:HIS232 3.2 15.2 1.0
CB A:HIS294 3.2 14.8 1.0
CE1 A:HIS294 3.3 19.3 1.0
SD A:MET299 3.5 19.2 1.0
CA A:HIS232 3.6 12.3 1.0
CE1 A:HIS232 3.7 13.4 1.0
CB A:VAL291 4.1 9.2 1.0
CG2 A:VAL291 4.1 8.6 1.0
CE A:MET299 4.2 10.7 1.0
CD2 A:HIS294 4.2 14.6 1.0
O A:TYR231 4.2 17.6 1.0
NE2 A:HIS294 4.3 13.1 1.0
CA A:CYS289 4.4 16.4 1.0
CD2 A:HIS232 4.4 12.4 1.0
N A:THR233 4.5 13.3 1.0
C A:HIS232 4.6 12.0 1.0
N A:HIS232 4.6 12.2 1.0
NE2 A:HIS232 4.6 10.6 1.0
CA A:HIS294 4.7 16.3 1.0
CG A:MET299 4.8 17.1 1.0
C A:TYR231 4.9 14.5 1.0
C A:CYS289 4.9 18.1 1.0
CG1 A:VAL291 4.9 11.1 1.0
CD2 A:PHE196 4.9 11.5 1.0
N A:VAL291 5.0 15.6 1.0

Copper binding site 2 out of 40 in 5o3k

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Copper binding site 2 out of 40 in the Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium


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 Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:27.0
occ:1.00
O A:O403 1.9 15.2 1.0
NE2 A:HIS288 2.2 12.4 1.0
NE2 A:HIS237 2.3 15.9 1.0
NE2 C:HIS159 2.6 18.3 1.0
CE1 A:HIS288 2.9 10.6 1.0
CE1 A:HIS237 3.2 16.2 1.0
CD2 C:HIS159 3.3 15.3 1.0
CD2 A:HIS237 3.3 14.7 1.0
CD2 A:HIS288 3.3 16.4 1.0
CE1 C:HIS159 3.5 15.4 1.0
CE1 C:HIS103 3.8 13.2 1.0
CU C:CU401 3.9 20.6 1.0
CD2 A:HIS235 3.9 8.2 1.0
NE2 C:HIS103 4.1 12.5 1.0
ND1 A:HIS288 4.1 12.9 1.0
NE2 A:HIS235 4.3 8.7 1.0
ND1 A:HIS237 4.3 15.6 1.0
CG A:HIS288 4.4 15.1 1.0
CG A:HIS237 4.4 10.7 1.0
CG C:HIS159 4.4 12.5 1.0
NE2 A:HIS290 4.5 9.8 1.0
ND1 C:HIS103 4.5 20.1 1.0
ND1 C:HIS159 4.5 15.8 1.0
ND1 C:HIS165 4.6 19.3 1.0
SD A:MET286 4.7 37.0 1.0
O A:HOH503 4.7 14.4 1.0
CD2 A:HIS290 4.8 11.2 1.0
CD2 C:HIS103 4.8 13.7 1.0

Copper binding site 3 out of 40 in 5o3k

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Copper binding site 3 out of 40 in the Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium


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 Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:28.7
occ:1.00
O B:HOH504 1.9 15.4 1.0
NE2 A:HIS105 1.9 11.6 1.0
NE2 B:HIS290 2.0 18.4 1.0
NE2 A:HIS157 2.5 16.5 1.0
CE1 A:HIS105 2.6 14.6 1.0
CE1 A:HIS103 2.6 21.2 1.0
CE1 B:HIS290 2.8 17.4 1.0
CD2 A:HIS105 3.1 18.8 1.0
CD2 B:HIS290 3.1 15.7 1.0
ND1 A:HIS103 3.4 22.0 1.0
CD2 A:HIS157 3.4 14.8 1.0
CE1 A:HIS157 3.4 17.3 1.0
NE2 A:HIS103 3.7 23.1 1.0
ND1 A:HIS105 3.8 16.8 1.0
O B:HOH501 3.8 20.6 1.0
NE2 B:HIS235 3.9 13.5 1.0
ND1 B:HIS290 4.0 15.8 1.0
CU B:CU402 4.0 34.1 1.0
CG A:HIS105 4.0 15.2 1.0
CG B:HIS290 4.1 13.4 1.0
CD2 B:HIS235 4.3 12.7 1.0
CE1 B:HIS235 4.3 13.6 1.0
CE1 A:HIS155 4.4 10.5 1.0
CB A:ALA267 4.5 13.8 1.0
ND1 A:HIS157 4.6 19.0 1.0
CG A:HIS157 4.6 17.9 1.0
CG A:HIS103 4.6 20.3 1.0
CD2 A:HIS103 4.8 22.2 1.0
CE1 B:HIS288 4.9 12.2 1.0
ND1 B:HIS235 4.9 15.4 1.0
CG B:HIS235 4.9 12.9 1.0

Copper binding site 4 out of 40 in 5o3k

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Copper binding site 4 out of 40 in the Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium


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 Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:18.3
occ:1.00
ND1 B:HIS232 1.8 13.7 1.0
SG B:CYS289 2.0 15.6 1.0
ND1 B:HIS294 2.1 13.4 1.0
CE1 B:HIS232 2.8 13.7 1.0
CG B:HIS232 2.9 15.8 1.0
CG B:HIS294 3.0 16.6 1.0
CB B:CYS289 3.0 17.0 1.0
CE1 B:HIS294 3.1 16.8 1.0
CB B:HIS294 3.3 15.7 1.0
CB B:HIS232 3.3 11.4 1.0
SD B:MET299 3.4 23.7 1.0
CE B:MET299 3.7 18.6 1.0
CA B:HIS232 3.7 16.5 1.0
NE2 B:HIS232 3.9 12.9 1.0
CD2 B:HIS232 4.0 14.1 1.0
CB B:VAL291 4.0 14.5 1.0
CG2 B:VAL291 4.0 14.3 1.0
CD2 B:HIS294 4.2 15.9 1.0
NE2 B:HIS294 4.2 19.7 1.0
O B:TYR231 4.3 15.7 1.0
CA B:CYS289 4.4 15.7 1.0
N B:THR233 4.5 15.6 1.0
C B:HIS232 4.7 15.1 1.0
CA B:HIS294 4.8 18.8 1.0
N B:HIS232 4.8 19.9 1.0
CG1 B:VAL291 4.8 15.1 1.0
N B:VAL291 4.9 22.5 1.0
C B:CYS289 4.9 17.4 1.0
C B:TYR231 5.0 15.9 1.0
CA B:VAL291 5.0 16.4 1.0

Copper binding site 5 out of 40 in 5o3k

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Copper binding site 5 out of 40 in the Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium


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 Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:34.1
occ:1.00
NE2 A:HIS159 2.0 16.0 1.0
NE2 B:HIS237 2.3 19.7 1.0
NE2 B:HIS288 2.4 13.4 1.0
O B:HOH504 2.5 15.4 1.0
CD2 A:HIS159 2.9 18.7 1.0
CE1 B:HIS237 3.0 17.7 1.0
CE1 B:HIS288 3.1 12.2 1.0
CE1 A:HIS159 3.1 13.2 1.0
CD2 B:HIS237 3.5 18.3 1.0
CD2 B:HIS288 3.5 14.0 1.0
CU A:CU404 4.0 28.7 1.0
CE1 A:HIS103 4.0 21.2 1.0
O B:HOH501 4.0 20.6 1.0
CD2 B:HIS235 4.1 12.7 1.0
CG A:HIS159 4.1 19.7 1.0
NE2 A:HIS103 4.1 23.1 1.0
NE2 B:HIS290 4.2 18.4 1.0
ND1 A:HIS159 4.2 17.4 1.0
ND1 B:HIS237 4.2 19.8 1.0
NE2 B:HIS235 4.2 13.5 1.0
ND1 B:HIS288 4.3 16.1 1.0
CG B:HIS237 4.5 15.7 1.0
ND1 A:HIS103 4.5 22.0 1.0
CG B:HIS288 4.5 13.9 1.0
CD2 B:HIS290 4.6 15.7 1.0
CD2 A:HIS165 4.7 18.3 1.0
CD2 A:HIS103 4.7 22.2 1.0
CG A:HIS103 4.9 20.3 1.0
CE B:MET286 5.0 25.6 1.0

Copper binding site 6 out of 40 in 5o3k

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Copper binding site 6 out of 40 in the Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium


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 Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu403

b:26.1
occ:1.00
NE2 B:HIS157 2.1 10.6 1.0
NE2 C:HIS290 2.4 13.9 1.0
NE2 B:HIS105 2.6 16.6 1.0
CE1 B:HIS157 2.7 12.8 1.0
CE1 B:HIS103 2.8 13.1 1.0
CD2 C:HIS290 3.2 12.8 1.0
CD2 B:HIS105 3.3 14.8 1.0
CD2 B:HIS157 3.3 11.7 1.0
ND1 B:HIS103 3.4 16.1 1.0
CE1 C:HIS290 3.5 12.0 1.0
CE1 B:HIS105 3.6 13.2 1.0
NE2 C:HIS235 3.8 15.7 1.0
NE2 B:HIS103 3.9 16.3 1.0
ND1 B:HIS157 4.0 13.8 1.0
CD2 C:HIS235 4.1 12.1 1.0
CG B:HIS157 4.3 10.4 1.0
CU C:CU403 4.3 27.7 0.9
CG C:HIS290 4.4 13.2 1.0
CG B:HIS105 4.5 13.6 1.0
ND1 C:HIS290 4.5 10.2 1.0
CE1 C:HIS235 4.5 16.6 1.0
ND1 B:HIS105 4.6 14.5 1.0
CB B:ALA267 4.6 12.2 1.0
CG B:HIS103 4.7 12.5 1.0
O B:HOH505 4.7 14.7 1.0
CD2 B:HIS159 4.7 10.2 1.0
NE2 B:HIS159 4.8 11.4 1.0
CG C:HIS235 4.8 18.8 1.0
CD2 B:HIS103 4.9 13.0 1.0
NE2 C:HIS288 4.9 13.9 1.0
CE1 C:HIS288 5.0 11.5 1.0

Copper binding site 7 out of 40 in 5o3k

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Copper binding site 7 out of 40 in the Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium


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 Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu401

b:20.6
occ:1.00
O A:O403 2.0 15.2 1.0
NE2 A:HIS290 2.1 9.8 1.0
NE2 C:HIS105 2.2 15.7 1.0
NE2 C:HIS157 2.3 16.6 1.0
CE1 C:HIS103 2.8 13.2 1.0
CE1 A:HIS290 2.9 14.6 1.0
CE1 C:HIS157 3.1 16.1 1.0
CE1 C:HIS105 3.1 10.6 1.0
CD2 A:HIS290 3.2 11.2 1.0
CD2 C:HIS105 3.2 11.3 1.0
CD2 C:HIS157 3.4 16.4 1.0
ND1 C:HIS103 3.4 20.1 1.0
CU A:CU402 3.9 27.0 1.0
NE2 C:HIS103 4.0 12.5 1.0
ND1 A:HIS290 4.1 15.6 1.0
O A:HOH503 4.1 14.4 1.0
NE2 A:HIS235 4.2 8.7 1.0
ND1 C:HIS105 4.2 11.5 1.0
ND1 C:HIS157 4.2 20.6 1.0
CG A:HIS290 4.2 11.4 1.0
CG C:HIS105 4.3 10.6 1.0
CD2 A:HIS235 4.4 8.2 1.0
CG C:HIS157 4.4 16.7 1.0
CE1 A:HIS235 4.7 11.0 1.0
CG C:HIS103 4.7 17.1 1.0
CB C:ALA267 4.8 12.3 1.0
CE1 C:HIS155 4.8 13.4 1.0
CE1 A:HIS288 4.8 10.6 1.0
CD2 C:HIS159 4.9 15.3 1.0
CG A:HIS235 5.0 10.1 1.0

Copper binding site 8 out of 40 in 5o3k

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Copper binding site 8 out of 40 in the Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium


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 Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu402

b:20.1
occ:1.00
ND1 C:HIS294 1.9 7.8 1.0
ND1 C:HIS232 2.0 15.4 1.0
SG C:CYS289 2.2 13.1 1.0
CG C:HIS294 2.9 12.6 1.0
CE1 C:HIS232 2.9 11.4 1.0
CE1 C:HIS294 2.9 10.1 1.0
CG C:HIS232 3.1 16.7 1.0
CB C:HIS294 3.2 15.1 1.0
CB C:CYS289 3.2 12.1 1.0
SD C:MET299 3.4 11.5 1.0
CB C:HIS232 3.5 15.1 1.0
CA C:HIS232 4.0 16.7 1.0
CD2 C:HIS294 4.0 12.2 1.0
NE2 C:HIS294 4.0 11.7 1.0
NE2 C:HIS232 4.0 12.3 1.0
O C:TYR231 4.1 12.5 1.0
CD2 C:HIS232 4.1 11.9 1.0
CG2 C:VAL291 4.2 12.3 1.0
CB C:VAL291 4.4 11.1 1.0
CE C:MET299 4.5 13.4 1.0
CA C:HIS294 4.6 13.9 1.0
CA C:CYS289 4.6 13.3 1.0
CD2 C:PHE196 4.8 17.2 1.0
CG C:MET299 4.8 19.6 1.0
N C:THR233 4.8 20.2 1.0
C C:TYR231 4.9 14.9 1.0
N C:HIS232 4.9 17.5 1.0
CE2 C:PHE196 4.9 15.3 1.0
SD C:MET199 5.0 24.3 1.0
C C:HIS232 5.0 15.9 1.0

Copper binding site 9 out of 40 in 5o3k

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Copper binding site 9 out of 40 in the Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium


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 Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu403

b:27.7
occ:0.91
NE2 C:HIS237 1.9 15.3 1.0
NE2 B:HIS159 2.1 11.4 1.0
NE2 C:HIS288 2.4 13.9 1.0
CE1 C:HIS237 2.7 16.1 1.0
CE1 B:HIS159 2.8 13.9 1.0
CD2 C:HIS237 3.1 13.8 1.0
CD2 C:HIS288 3.1 17.8 1.0
CD2 B:HIS159 3.2 10.2 1.0
CE1 C:HIS288 3.4 11.5 1.0
ND1 C:HIS237 3.9 13.2 1.0
ND1 B:HIS159 4.0 16.3 1.0
CG C:HIS237 4.1 11.8 1.0
CD2 C:HIS235 4.2 12.1 1.0
CG B:HIS159 4.2 13.8 1.0
O B:HOH505 4.2 14.7 1.0
CU B:CU403 4.3 26.1 1.0
NE2 B:HIS103 4.3 16.3 1.0
CE1 B:HIS103 4.3 13.1 1.0
CG C:HIS288 4.4 17.6 1.0
NE2 C:HIS235 4.4 15.7 1.0
ND1 B:HIS165 4.5 11.4 1.0
ND1 C:HIS288 4.5 16.2 1.0
SD C:MET286 4.6 30.0 1.0
CE C:MET286 4.8 15.7 1.0
CD2 B:HIS103 4.9 13.0 1.0
NE2 C:HIS290 5.0 13.9 1.0
ND1 B:HIS103 5.0 16.1 1.0

Copper binding site 10 out of 40 in 5o3k

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Copper binding site 10 out of 40 in the Crystal Structure of Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium


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 Mutant M54L/M64L/M96L of Two-Domain Laccase From Streptomyces Griseoflavus with 1 Mm Copper Sulfate on Growth Medium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu401

b:15.6
occ:1.00
ND1 D:HIS294 2.0 14.9 1.0
SG D:CYS289 2.0 13.2 1.0
ND1 D:HIS232 2.2 19.1 1.0
CG D:HIS294 2.9 12.3 1.0
CE1 D:HIS294 3.1 14.1 1.0
CB D:HIS294 3.2 12.8 1.0
CE1 D:HIS232 3.2 14.8 1.0
CG D:HIS232 3.2 14.4 1.0
CB D:CYS289 3.4 9.5 1.0
CB D:HIS232 3.5 13.5 1.0
SD D:MET299 3.7 15.0 1.0
CE D:MET299 3.8 12.7 1.0
CA D:HIS232 3.8 12.8 1.0
CG2 D:VAL291 3.9 9.5 1.0
CD2 D:HIS294 4.1 13.4 1.0
NE2 D:HIS294 4.1 10.8 1.0
CB D:VAL291 4.1 9.8 1.0
O D:TYR231 4.2 12.3 1.0
NE2 D:HIS232 4.3 14.9 1.0
CD2 D:HIS232 4.3 15.5 1.0
CA D:HIS294 4.6 13.7 1.0
N D:THR233 4.7 11.4 1.0
CA D:CYS289 4.7 11.7 1.0
N D:HIS232 4.8 14.7 1.0
C D:HIS232 4.8 13.4 1.0
N D:VAL291 4.9 10.5 1.0
C D:TYR231 4.9 14.0 1.0

Reference:

A.G.Gabdulkhakov, O.S.Kostareva, I.A.Kolyadenko, A.O.Mikhaylina, L.I.Trubitsina, S.V.Tishchenko. Incorporation of Copper Ions Into T2/T3 Centers of Two-Domain Laccases. Mol.Biol.(Moscow) V. 52 29 2018.
ISSN: ISSN 0026-8984
PubMed: 29512633
DOI: 10.7868/S0026898418010056
Page generated: Sun Dec 13 11:19:12 2020

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