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Copper in PDB 5lhl: Crystal Structure of Two-Domain Laccase From Streptomyces Griseoflavus

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

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

Protein crystallography data

The structure of Crystal Structure of Two-Domain Laccase From Streptomyces Griseoflavus, PDB code: 5lhl was solved by A.G.Gabdulkhakov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.36 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.640, 94.720, 117.400, 90.00, 90.67, 90.00
R / Rfree (%) 16.7 / 21

Other elements in 5lhl:

The structure of Crystal Structure of Two-Domain Laccase From Streptomyces Griseoflavus also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 2 atoms

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 From Streptomyces Griseoflavus (pdb code 5lhl). 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 From Streptomyces Griseoflavus, PDB code: 5lhl:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 24 in 5lhl

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Copper binding site 1 out of 24 in the Crystal Structure of Two-Domain Laccase 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 From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:18.2
occ:0.93
ND1 A:HIS294 2.0 22.5 1.0
ND1 A:HIS232 2.0 17.8 1.0
SG A:CYS289 2.2 18.9 1.0
CE1 A:HIS294 3.0 16.2 1.0
CG A:HIS232 3.0 14.5 1.0
CG A:HIS294 3.0 18.7 1.0
CE1 A:HIS232 3.1 18.2 1.0
CB A:CYS289 3.2 16.8 1.0
CB A:HIS232 3.3 17.5 1.0
CB A:HIS294 3.4 20.2 1.0
SD A:MET299 3.5 29.1 1.0
CA A:HIS232 3.7 16.6 1.0
O A:TYR231 4.0 17.6 1.0
NE2 A:HIS294 4.1 19.0 1.0
CG2 A:VAL291 4.1 13.8 1.0
CB A:VAL291 4.1 13.9 1.0
CD2 A:HIS294 4.1 20.7 1.0
CD2 A:HIS232 4.1 18.6 1.0
NE2 A:HIS232 4.2 19.0 1.0
CE A:MET299 4.2 21.1 1.0
N A:THR233 4.6 17.1 1.0
CA A:CYS289 4.6 16.3 1.0
N A:HIS232 4.7 13.3 1.0
C A:HIS232 4.7 21.2 1.0
C A:TYR231 4.8 18.3 1.0
CA A:HIS294 4.9 21.6 1.0
CD2 A:PHE196 4.9 21.6 1.0
CG1 A:VAL291 4.9 17.0 1.0
N A:VAL291 5.0 16.5 1.0

Copper binding site 2 out of 24 in 5lhl

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Copper binding site 2 out of 24 in the Crystal Structure of Two-Domain Laccase 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 From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:23.5
occ:1.00
NE2 A:HIS237 2.1 18.4 1.0
NE2 A:HIS288 2.2 17.2 1.0
NE2 C:HIS159 2.2 16.4 1.0
O1 A:OXY407 2.5 22.6 1.0
O2 A:OXY407 2.6 20.6 1.0
CE1 A:HIS237 2.9 22.5 1.0
CE1 A:HIS288 3.1 16.0 1.0
CE1 C:HIS159 3.1 17.8 1.0
CD2 A:HIS288 3.2 20.4 1.0
CD2 C:HIS159 3.2 16.7 1.0
CD2 A:HIS237 3.3 20.2 1.0
O A:HOH513 3.8 24.0 1.0
CE A:MET286 4.1 34.9 1.0
ND1 A:HIS237 4.1 19.8 1.0
ND1 A:HIS288 4.2 17.9 1.0
ND1 C:HIS159 4.3 19.2 1.0
CD2 A:HIS235 4.3 22.0 1.0
CG A:HIS288 4.3 23.9 1.0
CD2 C:HIS165 4.3 23.7 1.0
CG A:HIS237 4.3 18.9 1.0
CG C:HIS159 4.4 19.3 1.0
NE2 C:HIS103 4.5 21.4 1.0
SD A:MET286 4.7 49.9 1.0
NE2 A:HIS235 4.8 26.1 1.0
CD2 C:HIS103 4.9 22.6 1.0
CE1 C:HIS103 4.9 26.2 1.0
CU A:CU403 5.0 30.8 0.2

Copper binding site 3 out of 24 in 5lhl

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Copper binding site 3 out of 24 in the Crystal Structure of Two-Domain Laccase 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 From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:30.8
occ:0.21
NE2 C:HIS103 2.1 21.4 1.0
NE2 A:HIS235 2.1 26.1 1.0
CE1 C:HIS103 2.3 26.2 1.0
O C:HOH646 2.5 28.4 1.0
CE1 A:HIS235 2.7 19.9 1.0
CD2 A:HIS235 3.3 22.0 1.0
CD2 C:HIS103 3.4 22.6 1.0
O2 A:OXY407 3.5 20.6 1.0
ND1 C:HIS103 3.6 25.2 1.0
CD2 A:HIS237 3.8 20.2 1.0
NE2 A:HIS237 3.9 18.4 1.0
CG A:HIS237 3.9 18.9 1.0
O C:VAL104 3.9 18.2 1.0
NE2 C:HIS105 3.9 20.6 1.0
CD2 C:HIS105 4.0 20.0 1.0
ND1 A:HIS235 4.0 21.1 1.0
OH C:TYR109 4.1 28.6 1.0
CG C:HIS103 4.2 21.9 1.0
CE1 A:HIS237 4.2 22.5 1.0
ND1 A:HIS237 4.2 19.8 1.0
CA A:HIS237 4.2 20.1 1.0
O A:HOH509 4.2 23.8 1.0
CE1 C:HIS105 4.2 19.0 1.0
CG C:HIS105 4.3 20.9 1.0
CG A:HIS235 4.3 18.3 1.0
ND1 C:HIS105 4.4 18.8 1.0
CU A:CU410 4.5 22.8 1.0
O A:MET236 4.5 19.9 1.0
OD2 A:ASP260 4.6 19.7 1.0
CB A:HIS237 4.6 21.5 1.0
CA C:HIS105 4.6 20.3 1.0
C C:VAL104 4.6 23.4 1.0
O1 A:OXY407 4.7 22.6 1.0
N A:HIS237 4.7 17.4 1.0
N C:HIS105 4.8 17.6 1.0
C A:MET236 4.9 20.1 1.0
CU A:CU402 5.0 23.5 1.0

Copper binding site 4 out of 24 in 5lhl

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Copper binding site 4 out of 24 in the Crystal Structure of Two-Domain Laccase 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 From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:19.2
occ:1.00
NE2 A:HIS105 2.0 19.3 1.0
NE2 B:HIS290 2.0 18.5 1.0
O1 A:OXY406 2.1 25.4 1.0
NE2 A:HIS157 2.1 17.6 1.0
CE1 A:HIS105 2.9 17.0 1.0
CD2 B:HIS290 2.9 15.9 1.0
CD2 A:HIS105 3.0 18.9 1.0
CE1 B:HIS290 3.0 16.5 1.0
CE1 A:HIS157 3.1 20.5 1.0
CD2 A:HIS157 3.1 17.7 1.0
O2 A:OXY406 3.2 23.0 1.0
CD2 A:HIS103 3.8 24.3 1.0
NE2 A:HIS103 3.9 28.0 1.0
ND1 A:HIS105 4.0 18.4 1.0
ND1 B:HIS290 4.1 17.5 1.0
CG B:HIS290 4.1 17.3 1.0
CB A:ALA267 4.1 16.2 1.0
CG A:HIS105 4.1 18.8 1.0
CU A:CU409 4.1 30.3 0.3
ND1 A:HIS157 4.2 18.7 1.0
CE1 A:HIS155 4.2 19.5 1.0
CG A:HIS157 4.2 18.1 1.0
NE2 B:HIS235 4.3 21.4 1.0
CD2 B:HIS235 4.4 22.4 1.0
O A:HOH596 4.7 25.2 1.0
CE1 B:HIS235 4.9 20.2 1.0
NE2 A:HIS155 5.0 19.3 1.0

Copper binding site 5 out of 24 in 5lhl

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Copper binding site 5 out of 24 in the Crystal Structure of Two-Domain Laccase 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 From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu408

b:24.1
occ:1.00
O2 A:OXY406 2.1 23.0 1.0
NE2 B:HIS237 2.1 22.1 1.0
NE2 A:HIS159 2.2 22.7 1.0
NE2 B:HIS288 2.2 19.8 1.0
CE1 B:HIS237 2.9 21.0 1.0
CD2 B:HIS288 3.1 21.0 1.0
CE1 A:HIS159 3.1 23.8 1.0
CD2 A:HIS159 3.2 19.1 1.0
CE1 B:HIS288 3.2 19.0 1.0
CD2 B:HIS237 3.3 21.0 1.0
O1 A:OXY406 3.3 25.4 1.0
O A:HOH596 3.7 25.2 1.0
ND1 B:HIS237 4.1 24.4 1.0
CD2 A:HIS165 4.2 22.0 1.0
CG B:HIS288 4.3 19.8 1.0
ND1 A:HIS159 4.3 21.2 1.0
ND1 B:HIS288 4.3 17.9 1.0
CG B:HIS237 4.3 21.6 1.0
CG A:HIS159 4.3 20.9 1.0
CD2 B:HIS235 4.4 22.4 1.0
CU A:CU409 4.5 30.3 0.3
NE2 A:HIS103 4.6 28.0 1.0
CE B:MET286 4.8 31.6 1.0
SD B:MET286 4.8 48.3 1.0
NE2 A:HIS165 4.8 23.8 1.0
NE2 B:HIS235 4.9 21.4 1.0
CD2 A:HIS103 5.0 24.3 1.0
CE1 A:HIS103 5.0 25.9 1.0

Copper binding site 6 out of 24 in 5lhl

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Copper binding site 6 out of 24 in the Crystal Structure of Two-Domain Laccase 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 From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu409

b:30.3
occ:0.33
NE2 A:HIS103 1.8 28.0 1.0
NE2 B:HIS235 2.1 21.4 1.0
CE1 A:HIS103 2.3 25.9 1.0
O A:HOH515 2.8 29.1 1.0
CE1 B:HIS235 3.0 20.2 1.0
O1 A:OXY406 3.1 25.4 1.0
CD2 B:HIS235 3.1 22.4 1.0
CD2 A:HIS103 3.2 24.3 1.0
O2 A:OXY406 3.4 23.0 1.0
NE2 B:HIS237 3.4 22.1 1.0
CD2 B:HIS237 3.5 21.0 1.0
ND1 A:HIS103 3.6 24.2 1.0
CE1 B:HIS237 3.8 21.0 1.0
CG B:HIS237 3.8 21.6 1.0
NE2 A:HIS105 3.9 19.3 1.0
ND1 B:HIS237 4.0 24.4 1.0
CG A:HIS103 4.0 22.4 1.0
CD2 A:HIS105 4.1 18.9 1.0
CU A:CU404 4.1 19.2 1.0
ND1 B:HIS235 4.1 16.5 1.0
CE1 A:HIS105 4.2 17.0 1.0
CG B:HIS235 4.2 17.9 1.0
O A:VAL104 4.4 20.1 1.0
OH A:TYR109 4.4 28.0 1.0
CA B:HIS237 4.4 19.5 1.0
CG A:HIS105 4.4 18.8 1.0
CU A:CU408 4.5 24.1 1.0
ND1 A:HIS105 4.5 18.4 1.0
CB B:HIS237 4.6 19.9 1.0
N B:HIS237 4.8 19.1 1.0
O B:HOH520 4.8 21.0 1.0
OD2 B:ASP260 4.9 19.4 1.0
CA A:HIS105 4.9 15.4 1.0
C A:VAL104 4.9 18.8 1.0

Copper binding site 7 out of 24 in 5lhl

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Copper binding site 7 out of 24 in the Crystal Structure of Two-Domain Laccase 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 From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu410

b:22.8
occ:1.00
NE2 C:HIS105 2.0 20.6 1.0
NE2 A:HIS290 2.0 18.6 1.0
NE2 C:HIS157 2.1 22.1 1.0
O2 A:OXY407 2.7 20.6 1.0
O1 A:OXY407 2.9 22.6 1.0
CE1 C:HIS105 2.9 19.0 1.0
CE1 A:HIS290 3.0 15.8 1.0
CD2 A:HIS290 3.0 16.2 1.0
CE1 C:HIS157 3.1 16.4 1.0
CD2 C:HIS105 3.1 20.0 1.0
CD2 C:HIS157 3.1 17.6 1.0
CD2 C:HIS103 3.7 22.6 1.0
NE2 C:HIS103 3.8 21.4 1.0
ND1 A:HIS290 4.1 16.2 1.0
ND1 C:HIS105 4.1 18.8 1.0
CB C:ALA267 4.1 15.4 1.0
CG A:HIS290 4.1 17.4 1.0
CG C:HIS105 4.2 20.9 1.0
ND1 C:HIS157 4.2 16.8 1.0
CG C:HIS157 4.2 16.5 1.0
NE2 A:HIS235 4.3 26.1 1.0
CE1 C:HIS155 4.3 20.0 1.0
CD2 A:HIS235 4.4 22.0 1.0
CU A:CU403 4.5 30.8 0.2
O A:HOH513 4.6 24.0 1.0
CE1 A:HIS235 4.9 19.9 1.0

Copper binding site 8 out of 24 in 5lhl

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Copper binding site 8 out of 24 in the Crystal Structure of Two-Domain Laccase 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 From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:18.1
occ:0.88
ND1 B:HIS232 2.0 17.2 1.0
ND1 B:HIS294 2.1 20.2 1.0
SG B:CYS289 2.2 20.8 1.0
CE1 B:HIS232 3.0 19.2 1.0
CG B:HIS232 3.0 20.4 1.0
CE1 B:HIS294 3.1 20.4 1.0
CG B:HIS294 3.1 16.9 1.0
CB B:CYS289 3.2 18.7 1.0
CB B:HIS232 3.4 14.1 1.0
CB B:HIS294 3.4 19.8 1.0
SD B:MET299 3.5 25.9 1.0
CA B:HIS232 3.7 15.3 1.0
CG2 B:VAL291 4.1 14.4 1.0
O B:TYR231 4.1 16.8 1.0
CE B:MET299 4.1 21.7 1.0
NE2 B:HIS232 4.1 20.2 1.0
CB B:VAL291 4.1 16.7 1.0
CD2 B:HIS232 4.2 17.8 1.0
NE2 B:HIS294 4.2 22.4 1.0
CD2 B:HIS294 4.2 24.3 1.0
CA B:CYS289 4.6 20.0 1.0
N B:THR233 4.6 14.0 1.0
N B:HIS232 4.7 15.3 1.0
C B:HIS232 4.7 16.2 1.0
C B:TYR231 4.8 18.7 1.0
CA B:HIS294 4.9 18.8 1.0
CG B:MET299 5.0 25.7 1.0
CG1 B:VAL291 5.0 17.9 1.0

Copper binding site 9 out of 24 in 5lhl

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Copper binding site 9 out of 24 in the Crystal Structure of Two-Domain Laccase 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 From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:21.4
occ:1.00
NE2 B:HIS105 2.1 15.7 1.0
NE2 B:HIS157 2.1 16.3 1.0
O1 B:OXY405 2.1 23.0 1.0
NE2 C:HIS290 2.1 20.1 1.0
CE1 B:HIS157 3.0 18.2 1.0
CD2 B:HIS105 3.0 17.0 1.0
CE1 B:HIS105 3.1 14.4 1.0
CE1 C:HIS290 3.1 16.0 1.0
CD2 C:HIS290 3.1 17.4 1.0
CD2 B:HIS157 3.1 17.8 1.0
O2 B:OXY405 3.3 19.4 1.0
CU B:CU403 4.0 29.4 0.3
CD2 B:HIS103 4.0 23.9 1.0
ND1 B:HIS157 4.1 14.8 1.0
CB B:ALA267 4.1 17.6 1.0
ND1 B:HIS105 4.2 16.7 1.0
CG B:HIS105 4.2 18.1 1.0
ND1 C:HIS290 4.2 16.3 1.0
CE1 B:HIS155 4.2 16.4 1.0
CG B:HIS157 4.2 16.1 1.0
CG C:HIS290 4.2 17.4 1.0
NE2 C:HIS235 4.3 18.8 1.0
CD2 C:HIS235 4.4 17.2 1.0
NE2 B:HIS103 4.5 26.3 1.0
O B:HOH577 4.7 23.4 1.0
CE1 C:HIS235 4.8 21.4 1.0
NE2 B:HIS155 5.0 19.4 1.0

Copper binding site 10 out of 24 in 5lhl

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Copper binding site 10 out of 24 in the Crystal Structure of Two-Domain Laccase 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 From Streptomyces Griseoflavus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu403

b:29.4
occ:0.28
NE2 B:HIS103 1.8 26.3 1.0
NE2 C:HIS235 1.9 18.8 1.0
CE1 C:HIS235 2.7 21.4 1.0
CE1 B:HIS103 2.8 27.8 1.0
CD2 B:HIS103 2.8 23.9 1.0
O B:HOH515 2.9 21.9 1.0
CD2 C:HIS235 3.0 17.2 1.0
O1 B:OXY405 3.1 23.0 1.0
O2 B:OXY405 3.4 19.4 1.0
NE2 B:HIS105 3.6 15.7 1.0
CD2 B:HIS105 3.7 17.0 1.0
CD2 C:HIS237 3.7 19.0 1.0
NE2 C:HIS237 3.7 17.8 1.0
ND1 C:HIS235 3.9 15.7 1.0
ND1 B:HIS103 3.9 28.4 1.0
CG B:HIS103 3.9 23.0 1.0
CU B:CU402 4.0 21.4 1.0
CE1 B:HIS105 4.0 14.4 1.0
CE1 C:HIS237 4.0 22.8 1.0
CG C:HIS237 4.0 20.8 1.0
CG C:HIS235 4.0 20.3 1.0
ND1 C:HIS237 4.2 25.8 1.0
CG B:HIS105 4.2 18.1 1.0
O B:VAL104 4.3 16.2 1.0
CU B:CU407 4.4 23.6 1.0
OH B:TYR109 4.4 27.8 1.0
ND1 B:HIS105 4.4 16.7 1.0
CA C:HIS237 4.6 17.8 1.0
CB C:HIS237 4.8 23.4 1.0
C B:VAL104 4.8 18.9 1.0
O C:HOH604 4.9 22.3 1.0
CA B:HIS105 4.9 17.3 1.0
OD2 C:ASP260 4.9 19.6 1.0

Reference:

A.Gabdulkhakov, S.Tischenko, A.Lisov, A.Leontievsky. Crystal Structure of Two-Domain Laccase From Streptomyces Griseoflavus To Be Published.
Page generated: Sun Dec 13 11:18:21 2020

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