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Copper in PDB 6rhq: Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus

Enzymatic activity of Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus

All present enzymatic activity of Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus, PDB code: 6rhq was solved by A.G.Gabdulkhakov, T.V.Tishchenko, I.A.Kolyadenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.61 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.790, 94.690, 116.490, 90.00, 90.87, 90.00
R / Rfree (%) 17.4 / 21.5

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus (pdb code 6rhq). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 24 binding sites of Copper where determined in the Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus, PDB code: 6rhq:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 24 in 6rhq

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Copper binding site 1 out of 24 in the Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus


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 Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:24.7
occ:1.00
ND1 A:HIS294 2.0 20.9 1.0
ND1 A:HIS232 2.1 24.4 1.0
SG A:CYS289 2.2 25.3 1.0
CG A:HIS232 3.0 20.7 1.0
CG A:HIS294 3.0 23.1 1.0
CE1 A:HIS294 3.0 24.0 1.0
CB A:HIS232 3.2 23.2 1.0
CB A:CYS289 3.2 24.2 1.0
CE1 A:HIS232 3.2 20.4 1.0
CB A:HIS294 3.3 20.7 1.0
SD A:MET299 3.5 31.5 1.0
CA A:HIS232 3.7 25.4 1.0
CE A:MET299 3.8 28.0 1.0
O A:TYR231 4.1 21.8 1.0
NE2 A:HIS294 4.1 26.1 1.0
CG2 A:VAL291 4.1 24.8 1.0
CD2 A:HIS294 4.1 28.4 1.0
CB A:VAL291 4.2 22.6 1.0
CD2 A:HIS232 4.2 25.7 1.0
NE2 A:HIS232 4.3 25.0 1.0
N A:THR233 4.6 22.4 1.0
CA A:CYS289 4.6 24.6 1.0
N A:HIS232 4.7 23.9 1.0
C A:HIS232 4.7 23.0 1.0
C A:TYR231 4.8 22.7 1.0
CD2 A:PHE196 4.8 25.0 1.0
CA A:HIS294 4.8 23.9 1.0
CG A:MET299 5.0 27.9 1.0

Copper binding site 2 out of 24 in 6rhq

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Copper binding site 2 out of 24 in the Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus


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 Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:39.4
occ:0.71
NE2 A:HIS237 2.1 35.9 1.0
O A:HOH525 2.2 32.1 1.0
NE2 A:HIS288 2.3 27.0 1.0
NE2 C:HIS159 2.4 28.2 1.0
CE1 A:HIS237 2.9 31.9 1.0
CE1 A:HIS288 3.1 23.8 1.0
CD2 A:HIS237 3.3 30.6 1.0
CD2 C:HIS159 3.3 29.0 1.0
CD2 A:HIS288 3.4 28.7 1.0
CE1 C:HIS159 3.5 34.1 1.0
O C:HOH568 3.7 31.2 1.0
CU A:CU403 3.9 94.6 0.3
CD2 A:HIS235 3.9 23.4 1.0
NE2 C:HIS103 4.1 41.4 1.0
ND1 A:HIS237 4.1 29.7 1.0
CE1 C:HIS103 4.2 38.7 1.0
ND1 A:HIS288 4.3 24.3 1.0
CG A:HIS237 4.3 29.0 1.0
NE2 A:HIS235 4.4 35.5 1.0
CG A:HIS288 4.4 27.2 1.0
CG C:HIS159 4.5 30.0 1.0
NE2 A:HIS290 4.5 24.8 1.0
CU C:CU401 4.5 30.6 1.0
ND1 C:HIS159 4.5 30.8 1.0
CD2 C:HIS165 4.6 34.0 1.0
CD2 C:HIS103 4.6 39.2 1.0
SD A:MET286 4.7 49.0 1.0
ND1 C:HIS103 4.8 34.2 1.0
CD2 A:HIS290 4.9 23.0 1.0

Copper binding site 3 out of 24 in 6rhq

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Copper binding site 3 out of 24 in the Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus


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 Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:94.6
occ:0.26
NE2 A:HIS235 1.8 35.5 1.0
NE2 C:HIS103 2.0 41.4 1.0
CE1 C:HIS103 2.2 38.7 1.0
CE1 A:HIS235 2.7 28.5 1.0
CD2 A:HIS235 2.7 23.4 1.0
O C:HOH502 3.1 33.6 1.0
O A:HOH525 3.1 32.1 1.0
CD2 C:HIS103 3.4 39.2 1.0
CD2 A:HIS237 3.4 30.6 1.0
NE2 C:HIS105 3.4 26.6 1.0
NE2 A:HIS237 3.4 35.9 1.0
ND1 C:HIS103 3.5 34.2 1.0
CU C:CU401 3.6 30.6 1.0
CD2 C:HIS105 3.6 32.2 1.0
ND1 A:HIS235 3.8 26.2 1.0
CE1 C:HIS105 3.8 27.5 1.0
CG A:HIS235 3.8 26.3 1.0
CU A:CU402 3.9 39.4 0.7
CG A:HIS237 4.0 29.0 1.0
CE1 A:HIS237 4.1 31.9 1.0
CG C:HIS103 4.1 33.8 1.0
CG C:HIS105 4.2 28.7 1.0
ND1 C:HIS105 4.3 29.4 1.0
O C:VAL104 4.3 25.2 1.0
ND1 A:HIS237 4.4 29.7 1.0
OH C:TYR109 4.6 31.8 1.0
CA A:HIS237 4.7 25.8 1.0
O A:HOH510 4.8 25.9 1.0
NE2 A:HIS290 4.8 24.8 1.0
OD2 A:ASP260 4.8 26.6 1.0
CB A:HIS237 4.9 29.7 1.0
C C:VAL104 4.9 27.9 1.0
CA C:HIS105 4.9 29.3 1.0
N A:HIS237 5.0 26.0 1.0

Copper binding site 4 out of 24 in 6rhq

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Copper binding site 4 out of 24 in the Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus


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 Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:30.4
occ:0.93
NE2 A:HIS105 2.0 22.2 1.0
NE2 B:HIS290 2.0 23.0 1.0
NE2 A:HIS157 2.1 24.1 1.0
O B:HOH527 2.2 32.0 1.0
CE1 A:HIS157 2.9 27.1 1.0
CD2 A:HIS105 2.9 22.4 1.0
CE1 A:HIS105 3.0 21.7 1.0
CD2 B:HIS290 3.0 19.4 1.0
CE1 B:HIS290 3.0 20.3 1.0
CD2 A:HIS157 3.3 23.7 1.0
NE2 A:HIS103 3.5 24.0 1.0
CD2 A:HIS103 3.6 31.7 1.0
CU B:CU403 3.9 36.7 0.1
ND1 A:HIS105 4.1 21.9 1.0
ND1 B:HIS290 4.1 19.3 1.0
CB A:ALA267 4.1 22.6 1.0
CG A:HIS105 4.1 20.8 1.0
CG B:HIS290 4.1 20.2 1.0
ND1 A:HIS157 4.1 25.5 1.0
NE2 B:HIS235 4.2 25.3 1.0
CE1 A:HIS155 4.3 20.9 1.0
CG A:HIS157 4.3 21.2 1.0
CD2 B:HIS235 4.4 21.7 1.0
O A:HOH548 4.6 34.9 1.0
CU B:CU402 4.7 37.2 0.9
CE1 A:HIS103 4.8 30.3 1.0
CE1 B:HIS235 4.8 20.1 1.0
NE2 A:HIS155 4.9 21.2 1.0
CG A:HIS103 4.9 28.4 1.0

Copper binding site 5 out of 24 in 6rhq

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Copper binding site 5 out of 24 in the Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus


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 Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:23.3
occ:1.00
ND1 B:HIS232 2.0 19.3 1.0
ND1 B:HIS294 2.0 22.6 1.0
SG B:CYS289 2.2 20.9 1.0
CE1 B:HIS232 2.9 21.1 1.0
CG B:HIS232 3.0 23.2 1.0
CG B:HIS294 3.0 23.6 1.0
CE1 B:HIS294 3.0 22.5 1.0
CB B:CYS289 3.2 19.3 1.0
CB B:HIS294 3.3 20.1 1.0
CB B:HIS232 3.3 22.7 1.0
SD B:MET299 3.6 27.0 1.0
CA B:HIS232 3.7 20.5 1.0
O B:TYR231 4.0 21.4 1.0
NE2 B:HIS232 4.1 25.5 1.0
CB B:VAL291 4.1 23.6 1.0
CD2 B:HIS232 4.1 22.5 1.0
CE B:MET299 4.1 23.4 1.0
NE2 B:HIS294 4.1 26.2 1.0
CG2 B:VAL291 4.1 18.8 1.0
CD2 B:HIS294 4.2 23.9 1.0
CA B:CYS289 4.6 19.8 1.0
N B:THR233 4.6 20.9 1.0
N B:HIS232 4.6 22.0 1.0
C B:HIS232 4.7 22.5 1.0
C B:TYR231 4.7 21.3 1.0
CD2 B:PHE196 4.8 28.1 1.0
CA B:HIS294 4.8 21.4 1.0
CG1 B:VAL291 4.9 21.9 1.0
N B:VAL291 5.0 17.1 1.0
CE2 B:PHE196 5.0 24.2 1.0

Copper binding site 6 out of 24 in 6rhq

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Copper binding site 6 out of 24 in the Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus


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 Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:37.2
occ:0.89
NE2 B:HIS237 2.1 25.6 1.0
NE2 A:HIS159 2.3 20.0 1.0
NE2 B:HIS288 2.3 27.8 1.0
O B:HOH527 2.5 32.0 1.0
CE1 B:HIS237 2.9 26.0 1.0
CE1 B:HIS288 3.1 24.4 1.0
CD2 B:HIS237 3.2 25.9 1.0
CE1 A:HIS159 3.2 26.7 1.0
CD2 A:HIS159 3.2 26.9 1.0
CD2 B:HIS288 3.3 25.7 1.0
CU B:CU403 3.6 36.7 0.1
CD2 B:HIS235 3.9 21.7 1.0
O A:HOH548 3.9 34.9 1.0
NE2 A:HIS103 4.1 24.0 1.0
ND1 B:HIS237 4.1 29.5 1.0
NE2 B:HIS235 4.1 25.3 1.0
CG B:HIS237 4.3 24.2 1.0
CE1 A:HIS103 4.3 30.3 1.0
ND1 B:HIS288 4.3 27.5 1.0
ND1 A:HIS159 4.3 26.8 1.0
CG A:HIS159 4.4 26.4 1.0
CG B:HIS288 4.4 26.9 1.0
NE2 B:HIS290 4.5 23.0 1.0
CD2 A:HIS165 4.6 29.2 1.0
CD2 A:HIS103 4.6 31.7 1.0
CU A:CU404 4.7 30.4 0.9
CE B:MET286 4.7 29.1 1.0
CD2 B:HIS290 4.8 19.4 1.0
ND1 A:HIS103 4.9 27.3 1.0
SD B:MET286 4.9 54.9 1.0

Copper binding site 7 out of 24 in 6rhq

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Copper binding site 7 out of 24 in the Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus


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 Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu403

b:36.7
occ:0.15
NE2 B:HIS235 1.9 25.3 1.0
NE2 A:HIS103 1.9 24.0 1.0
CE1 A:HIS103 2.2 30.3 1.0
CE1 B:HIS235 2.7 20.1 1.0
O B:HOH527 2.8 32.0 1.0
CD2 B:HIS235 3.0 21.7 1.0
O A:HOH528 3.0 27.8 1.0
CD2 B:HIS237 3.1 25.9 1.0
NE2 B:HIS237 3.1 25.6 1.0
CD2 A:HIS103 3.3 31.7 1.0
ND1 A:HIS103 3.5 27.3 1.0
CU B:CU402 3.6 37.2 0.9
CG B:HIS237 3.7 24.2 1.0
CE1 B:HIS237 3.7 26.0 1.0
NE2 A:HIS105 3.8 22.2 1.0
CU A:CU404 3.9 30.4 0.9
ND1 B:HIS235 3.9 24.0 1.0
CG A:HIS103 4.0 28.4 1.0
ND1 B:HIS237 4.0 29.5 1.0
CG B:HIS235 4.0 24.4 1.0
CD2 A:HIS105 4.1 22.4 1.0
CE1 A:HIS105 4.1 21.7 1.0
CA B:HIS237 4.5 24.5 1.0
OH A:TYR109 4.6 32.9 1.0
ND1 A:HIS105 4.6 21.9 1.0
CG A:HIS105 4.6 20.8 1.0
CB B:HIS237 4.6 25.7 1.0
O A:VAL104 4.6 17.9 1.0
N B:HIS237 4.8 20.2 1.0
NE2 B:HIS288 4.9 27.8 1.0
NE2 B:HIS290 4.9 23.0 1.0
O B:MET236 4.9 23.8 1.0

Copper binding site 8 out of 24 in 6rhq

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Copper binding site 8 out of 24 in the Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus


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 Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu404

b:35.0
occ:1.00
NE2 B:HIS157 2.0 25.9 1.0
NE2 B:HIS105 2.1 26.7 1.0
O C:HOH523 2.1 35.6 1.0
NE2 C:HIS290 2.1 28.2 1.0
CE1 B:HIS157 2.9 26.0 1.0
CD2 B:HIS105 3.0 25.4 1.0
CE1 C:HIS290 3.0 29.0 1.0
CD2 B:HIS157 3.1 28.2 1.0
CE1 B:HIS105 3.1 24.5 1.0
CD2 C:HIS290 3.2 24.4 1.0
CD2 B:HIS103 3.5 30.3 1.0
NE2 B:HIS103 3.7 37.0 1.0
CU C:CU404 3.9 42.1 0.2
ND1 B:HIS157 4.1 26.9 1.0
NE2 C:HIS235 4.1 26.7 1.0
ND1 C:HIS290 4.2 27.1 1.0
CG B:HIS157 4.2 24.4 1.0
CG B:HIS105 4.2 25.7 1.0
CB B:ALA267 4.2 22.0 1.0
ND1 B:HIS105 4.2 24.4 1.0
CG C:HIS290 4.2 26.7 1.0
CE1 B:HIS155 4.3 29.4 1.0
CD2 C:HIS235 4.3 28.1 1.0
CU C:CU403 4.5 42.2 0.6
O B:HOH570 4.7 32.2 1.0
CE1 C:HIS235 4.8 24.3 1.0
CG B:HIS103 4.8 33.2 1.0
NE2 B:HIS155 5.0 28.8 1.0

Copper binding site 9 out of 24 in 6rhq

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Copper binding site 9 out of 24 in the Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus


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 Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu401

b:30.6
occ:0.96
NE2 C:HIS105 2.1 26.6 1.0
NE2 A:HIS290 2.1 24.8 1.0
NE2 C:HIS157 2.2 25.6 1.0
O A:HOH525 2.3 32.1 1.0
CD2 C:HIS105 3.0 32.2 1.0
CE1 A:HIS290 3.0 25.2 1.0
CE1 C:HIS105 3.0 27.5 1.0
CD2 A:HIS290 3.1 23.0 1.0
NE2 C:HIS103 3.2 41.4 1.0
CE1 C:HIS157 3.2 27.2 1.0
CD2 C:HIS157 3.2 21.5 1.0
CD2 C:HIS103 3.4 39.2 1.0
CU A:CU403 3.6 94.6 0.3
ND1 A:HIS290 4.1 26.4 1.0
ND1 C:HIS105 4.2 29.4 1.0
CG A:HIS290 4.2 23.8 1.0
CG C:HIS105 4.2 28.7 1.0
NE2 A:HIS235 4.3 35.5 1.0
CB C:ALA267 4.3 23.3 1.0
ND1 C:HIS157 4.3 24.8 1.0
CG C:HIS157 4.3 21.9 1.0
CD2 A:HIS235 4.4 23.4 1.0
CE1 C:HIS155 4.4 28.9 1.0
O C:HOH568 4.4 31.2 1.0
CE1 C:HIS103 4.4 38.7 1.0
CU A:CU402 4.5 39.4 0.7
CG C:HIS103 4.7 33.8 1.0
CE1 A:HIS235 4.9 28.5 1.0

Copper binding site 10 out of 24 in 6rhq

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Copper binding site 10 out of 24 in the Crystal Structure of Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus


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 Two-Domain Laccase Mutant I170A From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu402

b:25.4
occ:1.00
ND1 C:HIS232 2.0 24.0 1.0
SG C:CYS289 2.2 22.9 1.0
ND1 C:HIS294 2.2 24.2 1.0
CE1 C:HIS232 3.0 22.3 1.0
CG C:HIS232 3.0 23.1 1.0
CG C:HIS294 3.1 23.6 1.0
CB C:CYS289 3.1 22.7 1.0
CE1 C:HIS294 3.2 19.7 1.0
CB C:HIS232 3.3 22.3 1.0
CB C:HIS294 3.4 25.8 1.0
SD C:MET299 3.5 26.9 1.0
CA C:HIS232 3.7 20.8 1.0
CE C:MET299 4.0 22.8 1.0
NE2 C:HIS232 4.1 23.9 1.0
O C:TYR231 4.1 21.9 1.0
CD2 C:HIS232 4.1 21.3 1.0
CB C:VAL291 4.1 25.0 1.0
CG2 C:VAL291 4.2 21.6 1.0
CD2 C:HIS294 4.3 25.7 1.0
NE2 C:HIS294 4.3 23.9 1.0
CA C:CYS289 4.6 22.2 1.0
N C:THR233 4.7 23.3 1.0
N C:HIS232 4.7 21.1 1.0
C C:HIS232 4.8 25.0 1.0
C C:TYR231 4.8 20.5 1.0
CA C:HIS294 4.9 24.6 1.0
CG C:MET299 4.9 24.3 1.0
N C:VAL291 4.9 22.7 1.0
CG1 C:VAL291 5.0 22.0 1.0

Reference:

A.Gabdulkhakov, I.Kolyadenko, O.Kostareva, A.Mikhaylina, P.Oliveira, P.Tamagnini, A.Lisov, S.Tishchenko. Investigations of Accessibility of T2/T3 Copper Center of Two-Domain Laccase Fromstreptomyces Griseoflavusac-993. Int J Mol Sci V. 20 2019.
ISSN: ESSN 1422-0067
PubMed: 31261802
DOI: 10.3390/IJMS20133184
Page generated: Sun Dec 13 11:25:24 2020

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