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Copper in PDB 5mkm: Crystal Structure of Two-Domain Laccase Mutant H165F From Streptomyces Griseoflavus

Enzymatic activity of Crystal Structure of Two-Domain Laccase Mutant H165F From Streptomyces Griseoflavus

All present enzymatic activity of Crystal Structure of Two-Domain Laccase Mutant H165F From Streptomyces Griseoflavus:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of Two-Domain Laccase Mutant H165F From Streptomyces Griseoflavus, PDB code: 5mkm 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) 49.77 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.884, 95.075, 116.821, 90.00, 90.58, 90.00
R / Rfree (%) 20 / 23.3

Copper Binding Sites:

Pages:

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

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Two-Domain Laccase Mutant H165F From Streptomyces Griseoflavus (pdb code 5mkm). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Crystal Structure of Two-Domain Laccase Mutant H165F From Streptomyces Griseoflavus, PDB code: 5mkm:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in 5mkm

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Copper binding site 1 out of 12 in the Crystal Structure of Two-Domain Laccase Mutant H165F 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 H165F From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:23.2
occ:1.00
 ND1 A:HIS294 2.0 18.4 1.0
ND1 A:HIS232 2.0 17.0 1.0
SG A:CYS289 2.2 23.8 1.0
CG A:HIS294 2.9 19.8 1.0
CE1 A:HIS232 3.0 20.1 1.0
CE1 A:HIS294 3.0 24.5 1.0
CG A:HIS232 3.1 20.6 1.0
CB A:HIS294 3.2 20.2 1.0
CB A:CYS289 3.3 22.3 1.0
SD A:MET299 3.4 23.8 1.0
CB A:HIS232 3.5 16.9 1.0
CA A:HIS232 3.8 23.6 1.0
CE A:MET299 4.0 20.4 1.0
O A:TYR231 4.1 21.4 1.0
CG2 A:VAL291 4.1 15.9 1.0
CD2 A:HIS294 4.1 26.8 1.0
NE2 A:HIS294 4.1 20.1 1.0
NE2 A:HIS232 4.1 16.7 1.0
CB A:VAL291 4.2 20.2 1.0
CD2 A:HIS232 4.2 18.2 1.0
CA A:CYS289 4.7 20.1 1.0
N A:THR233 4.7 26.1 1.0
CA A:HIS294 4.7 22.0 1.0
N A:HIS232 4.7 21.4 1.0
C A:TYR231 4.8 20.4 1.0
C A:HIS232 4.8 24.9 1.0
CG A:MET299 4.9 21.0 1.0
N A:VAL291 5.0 19.1 1.0

Copper binding site 2 out of 12 in 5mkm

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Copper binding site 2 out of 12 in the Crystal Structure of Two-Domain Laccase Mutant H165F 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 H165F From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:30.4
occ:1.00
 NE2 A:HIS105 2.0 23.5 1.0
NE2 A:HIS157 2.0 25.0 1.0
NE2 B:HIS290 2.2 28.6 1.0
CD2 A:HIS105 2.9 22.7 1.0
CE1 A:HIS157 3.0 20.9 1.0
CE1 A:HIS105 3.0 24.7 1.0
CE1 B:HIS290 3.0 27.2 1.0
O2 A:OXY403 3.0 38.0 1.0
NE2 A:HIS103 3.1 29.2 1.0
CD2 A:HIS157 3.1 19.4 1.0
CD2 B:HIS290 3.2 20.4 1.0
CD2 A:HIS103 3.4 21.3 1.0
O1 A:OXY403 3.9 36.5 1.0
ND1 A:HIS105 4.1 21.9 1.0
CG A:HIS105 4.1 21.3 1.0
ND1 A:HIS157 4.1 19.4 1.0
ND1 B:HIS290 4.2 26.4 1.0
CG A:HIS157 4.2 23.5 1.0
CG B:HIS290 4.3 26.6 1.0
CE1 A:HIS103 4.3 25.8 1.0
CB A:ALA267 4.3 22.2 1.0
NE2 B:HIS235 4.4 26.4 1.0
CE1 A:HIS155 4.4 25.4 1.0
CD2 B:HIS235 4.5 23.7 1.0
O A:HOH537 4.6 29.0 1.0
CG A:HIS103 4.7 30.0 1.0
CE1 B:HIS235 5.0 23.9 1.0

Copper binding site 3 out of 12 in 5mkm

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Copper binding site 3 out of 12 in the Crystal Structure of Two-Domain Laccase Mutant H165F 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 H165F From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:22.3
occ:1.00
 ND1 B:HIS294 2.0 16.2 1.0
ND1 B:HIS232 2.1 23.3 1.0
SG B:CYS289 2.2 23.2 1.0
CE1 B:HIS232 2.9 22.1 1.0
CG B:HIS294 3.0 25.0 1.0
CE1 B:HIS294 3.1 16.9 1.0
CG B:HIS232 3.1 23.2 1.0
CB B:CYS289 3.1 25.3 1.0
CB B:HIS294 3.3 17.3 1.0
CB B:HIS232 3.5 15.8 1.0
SD B:MET299 3.6 24.8 1.0
CA B:HIS232 3.7 19.5 1.0
O B:TYR231 4.0 21.1 1.0
NE2 B:HIS232 4.1 22.3 1.0
CG2 B:VAL291 4.1 18.9 1.0
CB B:VAL291 4.1 23.1 1.0
CE B:MET299 4.1 23.5 1.0
CD2 B:HIS232 4.1 23.1 1.0
CD2 B:HIS294 4.1 24.3 1.0
NE2 B:HIS294 4.2 22.9 1.0
CA B:CYS289 4.6 28.2 1.0
N B:THR233 4.6 17.4 1.0
N B:HIS232 4.7 17.8 1.0
C B:TYR231 4.8 23.3 1.0
C B:HIS232 4.8 23.0 1.0
CA B:HIS294 4.8 22.6 1.0
N B:VAL291 5.0 22.1 1.0
CD2 B:PHE196 5.0 15.6 1.0

Copper binding site 4 out of 12 in 5mkm

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Copper binding site 4 out of 12 in the Crystal Structure of Two-Domain Laccase Mutant H165F 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 H165F From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:23.7
occ:0.74
 NE2 B:HIS157 2.0 24.1 1.0
NE2 C:HIS290 2.1 17.2 1.0
NE2 B:HIS105 2.2 23.5 1.0
O C:HOH626 2.4 25.7 1.0
CD2 B:HIS157 2.9 25.3 1.0
CE1 C:HIS290 2.9 21.3 1.0
CE1 B:HIS157 3.0 25.6 1.0
CD2 B:HIS105 3.1 15.5 1.0
CE1 B:HIS105 3.1 23.8 1.0
CD2 C:HIS290 3.2 17.6 1.0
CE1 B:HIS103 3.3 31.1 1.0
ND1 B:HIS103 3.5 30.9 1.0
CG B:HIS157 4.1 25.1 1.0
ND1 B:HIS157 4.1 26.0 1.0
ND1 C:HIS290 4.1 23.8 1.0
ND1 B:HIS105 4.2 29.0 1.0
NE2 C:HIS235 4.2 20.6 1.0
CG B:HIS105 4.2 25.6 1.0
CG C:HIS290 4.3 20.3 1.0
CB B:ALA267 4.3 20.0 1.0
CD2 C:HIS235 4.3 21.6 1.0
O B:HOH541 4.5 24.5 1.0
CE1 B:HIS155 4.5 20.6 1.0
NE2 B:HIS103 4.5 35.3 1.0
CG B:HIS103 4.8 30.4 1.0
CE1 C:HIS235 4.9 23.4 1.0

Copper binding site 5 out of 12 in 5mkm

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Copper binding site 5 out of 12 in the Crystal Structure of Two-Domain Laccase Mutant H165F 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 H165F From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:30.4
occ:0.85
 NE2 C:HIS105 1.9 22.2 1.0
NE2 C:HIS157 1.9 22.3 1.0
NE2 A:HIS290 2.1 25.7 1.0
CE1 C:HIS157 2.8 21.6 1.0
CE1 A:HIS290 2.9 18.1 1.0
O C:O501 2.9 28.3 1.0
CE1 C:HIS105 2.9 15.4 1.0
CD2 C:HIS105 3.0 20.0 1.0
CD2 C:HIS157 3.0 21.3 1.0
CD2 A:HIS290 3.2 17.0 1.0
NE2 C:HIS103 3.4 27.2 1.0
CD2 C:HIS103 3.4 29.7 1.0
ND1 C:HIS157 4.0 23.4 1.0
ND1 C:HIS105 4.0 21.9 1.0
ND1 A:HIS290 4.0 21.1 1.0
CG C:HIS105 4.1 27.6 1.0
CG C:HIS157 4.1 20.7 1.0
CB C:ALA267 4.2 18.7 1.0
CG A:HIS290 4.2 18.2 1.0
CE1 C:HIS155 4.3 17.8 1.0
NE2 A:HIS235 4.3 25.9 1.0
CD2 A:HIS235 4.4 22.3 1.0
CE1 C:HIS103 4.7 28.9 1.0
CG C:HIS103 4.7 25.8 1.0
NE2 C:HIS155 5.0 22.0 1.0

Copper binding site 6 out of 12 in 5mkm

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Copper binding site 6 out of 12 in the Crystal Structure of Two-Domain Laccase Mutant H165F 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 H165F From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu503

b:22.5
occ:1.00
 ND1 C:HIS294 2.0 17.7 1.0
ND1 C:HIS232 2.0 21.5 1.0
SG C:CYS289 2.2 23.9 1.0
CG C:HIS294 2.9 20.4 1.0
CG C:HIS232 3.0 20.9 1.0
CE1 C:HIS294 3.0 19.0 1.0
CE1 C:HIS232 3.0 20.6 1.0
CB C:CYS289 3.1 18.9 1.0
CB C:HIS294 3.2 15.6 1.0
CB C:HIS232 3.3 17.4 1.0
SD C:MET299 3.6 25.3 1.0
CA C:HIS232 3.7 19.3 1.0
CE C:MET299 3.9 22.7 1.0
O C:TYR231 4.0 16.0 1.0
CD2 C:HIS294 4.1 21.4 1.0
NE2 C:HIS294 4.1 22.1 1.0
NE2 C:HIS232 4.1 22.1 1.0
CD2 C:HIS232 4.1 20.4 1.0
CB C:VAL291 4.1 20.4 1.0
CG2 C:VAL291 4.2 19.0 1.0
CA C:CYS289 4.5 19.9 1.0
N C:THR233 4.7 18.5 1.0
N C:HIS232 4.7 20.0 1.0
C C:TYR231 4.8 20.1 1.0
CA C:HIS294 4.8 20.6 1.0
C C:HIS232 4.8 19.9 1.0
CD2 C:PHE196 4.9 18.2 1.0
CG1 C:VAL291 5.0 20.3 1.0
N C:VAL291 5.0 21.1 1.0

Copper binding site 7 out of 12 in 5mkm

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Copper binding site 7 out of 12 in the Crystal Structure of Two-Domain Laccase Mutant H165F 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 H165F From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu502

b:21.6
occ:1.00
 ND1 D:HIS294 1.9 14.9 1.0
ND1 D:HIS232 2.0 24.3 1.0
SG D:CYS289 2.2 19.7 1.0
CG D:HIS294 2.9 14.9 1.0
CE1 D:HIS232 2.9 25.9 1.0
CE1 D:HIS294 2.9 19.8 1.0
CG D:HIS232 3.0 19.8 1.0
CB D:CYS289 3.2 18.3 1.0
CB D:HIS294 3.3 17.4 1.0
CB D:HIS232 3.3 20.6 1.0
SD D:MET299 3.6 23.4 1.0
CA D:HIS232 3.7 18.8 1.0
NE2 D:HIS294 4.0 26.1 1.0
NE2 D:HIS232 4.1 20.9 1.0
CD2 D:HIS294 4.1 22.4 1.0
O D:TYR231 4.1 19.0 1.0
CD2 D:HIS232 4.1 20.6 1.0
CB D:VAL291 4.1 13.1 1.0
CE D:MET299 4.1 12.4 1.0
CG2 D:VAL291 4.2 12.1 1.0
CA D:CYS289 4.6 19.9 1.0
N D:THR233 4.7 20.1 1.0
N D:HIS232 4.7 20.9 1.0
CA D:HIS294 4.8 16.8 1.0
C D:HIS232 4.8 21.4 1.0
C D:TYR231 4.8 24.6 1.0
CD2 D:PHE196 4.8 21.4 1.0
CG1 D:VAL291 4.9 14.9 1.0
N D:VAL291 5.0 15.1 1.0

Copper binding site 8 out of 12 in 5mkm

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Copper binding site 8 out of 12 in the Crystal Structure of Two-Domain Laccase Mutant H165F 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 H165F From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu503

b:32.7
occ:1.00
 NE2 D:HIS105 2.0 27.5 1.0
NE2 E:HIS290 2.1 27.6 1.0
NE2 D:HIS157 2.1 32.0 1.0
O1 D:OXY505 2.8 36.2 1.0
CE1 D:HIS157 3.0 28.7 1.0
CE1 E:HIS290 3.0 20.9 1.0
CD2 D:HIS105 3.0 22.4 1.0
CE1 D:HIS105 3.0 28.7 1.0
CD2 E:HIS290 3.1 26.6 1.0
CD2 D:HIS157 3.2 34.2 1.0
CD2 D:HIS103 3.4 35.5 1.0
NE2 D:HIS103 3.5 33.3 1.0
O2 D:OXY505 4.0 36.4 1.0
ND1 E:HIS290 4.1 24.5 1.0
ND1 D:HIS157 4.1 30.8 1.0
ND1 D:HIS105 4.1 30.9 1.0
CG D:HIS105 4.2 26.2 1.0
CE1 D:HIS155 4.2 27.8 1.0
CG E:HIS290 4.2 24.1 1.0
CG D:HIS157 4.3 30.2 1.0
NE2 E:HIS235 4.3 31.3 1.0
CB D:ALA267 4.4 16.9 1.0
CD2 E:HIS235 4.5 24.6 1.0
CG D:HIS103 4.8 35.3 1.0
CE1 D:HIS103 4.8 34.4 1.0
NE2 D:HIS155 4.9 26.3 1.0
CE1 E:HIS235 5.0 24.9 1.0

Copper binding site 9 out of 12 in 5mkm

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Copper binding site 9 out of 12 in the Crystal Structure of Two-Domain Laccase Mutant H165F 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 H165F From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu401

b:24.6
occ:1.00
 SG E:CYS289 2.1 22.9 1.0
ND1 E:HIS294 2.2 18.6 1.0
ND1 E:HIS232 2.2 17.8 1.0
CB E:CYS289 3.0 22.2 1.0
CG E:HIS294 3.1 27.2 1.0
CG E:HIS232 3.1 16.7 1.0
CE1 E:HIS232 3.2 23.5 1.0
CE1 E:HIS294 3.2 17.9 1.0
CB E:HIS294 3.3 26.8 1.0
SD E:MET299 3.4 29.9 1.0
CB E:HIS232 3.4 16.9 1.0
CA E:HIS232 3.8 21.6 1.0
CB E:VAL291 4.1 27.0 1.0
CG2 E:VAL291 4.1 19.6 1.0
CE E:MET299 4.2 31.3 1.0
O E:TYR231 4.2 18.1 1.0
CD2 E:HIS294 4.2 21.9 1.0
NE2 E:HIS232 4.2 21.9 1.0
NE2 E:HIS294 4.3 27.1 1.0
CD2 E:HIS232 4.3 21.0 1.0
CA E:CYS289 4.5 22.9 1.0
N E:THR233 4.7 22.6 1.0
N E:HIS232 4.8 21.1 1.0
CA E:HIS294 4.8 25.3 1.0
C E:HIS232 4.8 22.6 1.0
CG1 E:VAL291 4.9 19.5 1.0
C E:TYR231 4.9 24.7 1.0
CG E:MET299 4.9 23.5 1.0
N E:VAL291 4.9 21.0 1.0
CE E:MET199 4.9 29.1 1.0

Copper binding site 10 out of 12 in 5mkm

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Copper binding site 10 out of 12 in the Crystal Structure of Two-Domain Laccase Mutant H165F 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 H165F From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu402

b:26.8
occ:1.00
 NE2 E:HIS105 2.0 22.7 0.6
NE2 E:HIS105 2.1 22.5 0.4
NE2 F:HIS290 2.1 19.0 1.0
NE2 E:HIS157 2.2 23.0 1.0
CE1 E:HIS105 2.4 23.0 0.4
CE1 E:HIS105 2.9 22.3 0.6
CE1 F:HIS290 2.9 20.6 1.0
CD2 E:HIS105 3.0 24.1 0.6
CE1 E:HIS103 3.0 25.9 1.0
CE1 E:HIS157 3.1 32.0 1.0
CD2 F:HIS290 3.2 18.5 1.0
CD2 E:HIS157 3.3 30.9 1.0
CD2 E:HIS105 3.3 22.7 0.4
O E:HOH515 3.5 23.4 1.0
ND1 E:HIS103 3.5 31.8 1.0
ND1 E:HIS105 3.6 25.5 0.4
ND1 E:HIS105 4.0 23.4 0.6
CG E:HIS105 4.1 25.1 0.4
NE2 F:HIS235 4.1 25.4 1.0
CG E:HIS105 4.1 25.5 0.6
ND1 F:HIS290 4.1 20.3 1.0
NE2 E:HIS103 4.2 29.6 1.0
CD2 F:HIS235 4.2 20.5 1.0
CG F:HIS290 4.2 19.9 1.0
ND1 E:HIS157 4.2 29.2 1.0
CB E:ALA267 4.4 18.6 1.0
CG E:HIS157 4.4 24.9 1.0
O E:HOH531 4.4 29.5 1.0
CE1 E:HIS155 4.8 25.3 1.0
CE1 F:HIS235 4.8 21.2 1.0
CG E:HIS103 4.9 26.6 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: Wed Jul 31 04:38:40 2024

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