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Copper in PDB 3x1b: Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution

Enzymatic activity of Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution

All present enzymatic activity of Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution, PDB code: 3x1b was solved by W.Y.Jeng, L.F.Shyur, A.H.J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.266, 188.676, 65.414, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 19.7

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution (pdb code 3x1b). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution, PDB code: 3x1b:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 3x1b

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Copper binding site 1 out of 8 in the Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution


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 Laccase From Lentinus Sp. at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu614

b:28.1
occ:1.00
 NE2 A:HIS420 2.0 23.6 1.0
NE2 A:HIS85 2.0 22.8 1.0
O A:HOH746 2.8 21.1 1.0
CD2 A:HIS420 2.9 18.5 1.0
CD2 A:HIS85 2.9 20.7 1.0
CE1 A:HIS85 2.9 22.1 1.0
CE1 A:HIS420 3.0 21.3 1.0
O A:HOH713 3.3 23.8 1.0
NE2 A:HIS422 3.4 21.5 1.0
ND1 A:HIS87 3.5 19.8 1.0
CD2 A:HIS422 3.5 21.9 1.0
CG A:HIS87 3.6 20.1 1.0
CE1 A:HIS422 3.7 21.7 1.0
CG A:HIS422 3.8 21.4 1.0
CE1 A:HIS87 3.9 21.3 1.0
CU A:CU615 3.9 22.3 1.0
ND1 A:HIS422 3.9 21.0 1.0
CA A:HIS87 4.0 19.2 1.0
ND1 A:HIS85 4.0 20.9 1.0
CG A:HIS85 4.0 21.3 1.0
CG A:HIS420 4.0 20.8 1.0
ND1 A:HIS420 4.1 21.8 1.0
CB A:HIS87 4.1 18.5 1.0
CD2 A:HIS87 4.1 19.6 1.0
NE2 A:HIS87 4.2 20.4 1.0
CU A:CU616 4.3 24.8 1.0
N A:GLY88 4.3 19.9 1.0
C A:HIS87 4.7 19.5 1.0
CA A:HIS422 4.7 21.4 1.0
CB A:HIS422 4.7 21.4 1.0
O A:HOH734 4.7 23.6 1.0
O A:HOH821 4.8 26.6 1.0

Copper binding site 2 out of 8 in 3x1b

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Copper binding site 2 out of 8 in the Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution


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 Laccase From Lentinus Sp. at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu615

b:22.3
occ:1.00
 ND1 A:HIS87 2.0 19.8 1.0
NE2 A:HIS130 2.0 14.8 1.0
NE2 A:HIS476 2.0 20.7 1.0
O A:HOH713 2.6 23.8 1.0
CE1 A:HIS476 2.9 22.1 1.0
CE1 A:HIS130 2.9 16.2 1.0
CE1 A:HIS87 2.9 21.3 1.0
CD2 A:HIS130 3.0 15.3 1.0
CG A:HIS87 3.1 20.1 1.0
CD2 A:HIS476 3.2 19.8 1.0
CB A:HIS87 3.5 18.5 1.0
CZ2 A:TRP128 3.5 16.4 1.0
CD2 A:HIS85 3.8 20.7 1.0
CE2 A:TRP128 3.9 17.2 1.0
CU A:CU614 3.9 28.1 1.0
NE1 A:TRP128 4.0 16.9 1.0
ND1 A:HIS130 4.0 14.3 1.0
ND1 A:HIS476 4.1 20.4 1.0
NE2 A:HIS87 4.1 20.4 1.0
CG A:HIS130 4.1 15.2 1.0
CD2 A:HIS87 4.2 19.6 1.0
CG A:HIS476 4.2 20.0 1.0
CH2 A:TRP128 4.2 17.4 1.0
NE2 A:HIS85 4.3 22.8 1.0
CD2 A:HIS420 4.4 18.5 1.0
NE2 A:HIS420 4.5 23.6 1.0
CA A:HIS87 4.6 19.2 1.0
CD2 A:TRP128 4.9 16.3 1.0

Copper binding site 3 out of 8 in 3x1b

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Copper binding site 3 out of 8 in the Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution


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 Laccase From Lentinus Sp. at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu616

b:24.8
occ:1.00
 NE2 A:HIS474 2.0 23.1 1.0
NE2 A:HIS422 2.0 21.5 1.0
NE2 A:HIS132 2.0 22.0 1.0
O A:HOH713 2.5 23.8 1.0
CE1 A:HIS422 2.8 21.7 1.0
CD2 A:HIS474 2.9 21.3 1.0
CE1 A:HIS132 3.0 22.7 1.0
CE1 A:HIS474 3.0 21.3 1.0
CD2 A:HIS132 3.0 20.1 1.0
CD2 A:HIS422 3.2 21.9 1.0
ND1 A:HIS422 4.0 21.0 1.0
CD2 A:HIS420 4.0 18.5 1.0
ND1 A:HIS474 4.1 21.5 1.0
CG A:HIS474 4.1 19.4 1.0
ND1 A:HIS132 4.1 19.8 1.0
CG A:HIS132 4.2 19.8 1.0
CG A:HIS422 4.2 21.4 1.0
CU A:CU614 4.3 28.1 1.0
CB A:PHE472 4.3 20.2 1.0
CD2 A:PHE472 4.3 18.9 1.0
CG A:PHE472 4.5 20.7 1.0
CD2 A:HIS85 4.6 20.7 1.0
NE2 A:HIS420 4.6 23.6 1.0
NE2 A:HIS85 4.7 22.8 1.0
CD2 A:LEU481 5.0 22.1 1.0

Copper binding site 4 out of 8 in 3x1b

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Copper binding site 4 out of 8 in the Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution


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 Laccase From Lentinus Sp. at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu617

b:25.8
occ:1.00
 ND1 A:HIS417 2.0 20.1 1.0
ND1 A:HIS480 2.0 20.5 1.0
SG A:CYS475 2.3 21.2 1.0
CE1 A:HIS417 2.9 18.9 1.0
CE1 A:HIS480 3.0 20.6 1.0
CG A:HIS480 3.1 18.6 1.0
CG A:HIS417 3.1 19.3 1.0
CB A:CYS475 3.3 19.3 1.0
CB A:HIS480 3.4 18.5 1.0
CB A:HIS417 3.5 18.4 1.0
CD2 A:PHE485 3.7 18.8 1.0
CD1 A:ILE477 3.8 21.1 1.0
CB A:ILE477 3.9 17.3 1.0
CE2 A:PHE485 3.9 20.0 1.0
NE2 A:HIS417 4.0 19.4 1.0
CA A:HIS417 4.1 19.2 1.0
NE2 A:HIS480 4.1 18.6 1.0
CD2 A:HIS417 4.2 19.1 1.0
CD2 A:HIS480 4.2 19.7 1.0
CG1 A:ILE477 4.2 18.3 1.0
CA A:CYS475 4.7 18.8 1.0
O A:GLY414 4.7 20.1 1.0
CG2 A:ILE477 4.7 17.2 1.0
CD A:PRO418 4.8 16.3 1.0
N A:ILE477 4.9 18.6 1.0
CA A:HIS480 4.9 18.5 1.0
CA A:ILE477 5.0 17.9 1.0
CG A:PHE485 5.0 18.6 1.0
O A:ILE477 5.0 18.3 1.0

Copper binding site 5 out of 8 in 3x1b

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Copper binding site 5 out of 8 in the Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution


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 Laccase From Lentinus Sp. at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu615

b:31.1
occ:1.00
 NE2 B:HIS420 2.0 27.1 1.0
NE2 B:HIS85 2.0 25.4 1.0
CD2 B:HIS420 2.8 24.9 1.0
O B:HOH704 2.8 22.1 1.0
CE1 B:HIS85 3.0 24.2 1.0
CD2 B:HIS85 3.0 23.0 1.0
CE1 B:HIS420 3.1 26.9 1.0
O B:HOH718 3.3 21.0 1.0
NE2 B:HIS422 3.4 25.5 1.0
ND1 B:HIS87 3.5 23.2 1.0
CD2 B:HIS422 3.5 24.8 1.0
CG B:HIS87 3.7 23.0 1.0
CE1 B:HIS422 3.7 24.8 1.0
CE1 B:HIS87 3.8 23.3 1.0
CG B:HIS422 3.8 24.5 1.0
CU B:CU616 3.9 25.7 1.0
CA B:HIS87 3.9 23.1 1.0
ND1 B:HIS422 3.9 23.4 1.0
CG B:HIS420 4.0 23.9 1.0
ND1 B:HIS85 4.0 23.6 1.0
CG B:HIS85 4.1 22.5 1.0
ND1 B:HIS420 4.1 26.0 1.0
CB B:HIS87 4.1 22.6 1.0
CD2 B:HIS87 4.1 22.1 1.0
NE2 B:HIS87 4.2 23.4 1.0
CU B:CU617 4.2 27.6 1.0
N B:GLY88 4.3 24.4 1.0
C B:HIS87 4.6 23.6 1.0
CA B:HIS422 4.6 24.4 1.0
CB B:HIS422 4.7 24.3 1.0
O B:HOH763 4.8 24.8 1.0
O B:HOH1044 4.8 30.6 1.0
N B:HIS87 5.0 22.5 1.0

Copper binding site 6 out of 8 in 3x1b

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Copper binding site 6 out of 8 in the Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution


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 Laccase From Lentinus Sp. at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu616

b:25.7
occ:1.00
 ND1 B:HIS87 2.0 23.2 1.0
NE2 B:HIS130 2.0 18.9 1.0
NE2 B:HIS476 2.0 22.3 1.0
O B:HOH718 2.6 21.0 1.0
CE1 B:HIS476 2.9 22.8 1.0
CE1 B:HIS87 2.9 23.3 1.0
CE1 B:HIS130 2.9 17.0 1.0
CD2 B:HIS130 3.0 16.3 1.0
CG B:HIS87 3.1 23.0 1.0
CD2 B:HIS476 3.1 22.1 1.0
CB B:HIS87 3.5 22.6 1.0
CZ2 B:TRP128 3.5 19.6 1.0
CD2 B:HIS85 3.8 23.0 1.0
CE2 B:TRP128 3.9 19.3 1.0
CU B:CU615 3.9 31.1 1.0
ND1 B:HIS130 4.0 15.6 1.0
NE2 B:HIS87 4.1 23.4 1.0
NE1 B:TRP128 4.1 19.7 1.0
ND1 B:HIS476 4.1 23.2 1.0
CG B:HIS130 4.1 17.6 1.0
CD2 B:HIS87 4.2 22.1 1.0
CH2 B:TRP128 4.2 17.9 1.0
CG B:HIS476 4.2 21.8 1.0
NE2 B:HIS85 4.3 25.4 1.0
CD2 B:HIS420 4.4 24.9 1.0
O B:HOH908 4.4 31.9 1.0
NE2 B:HIS420 4.5 27.1 1.0
CA B:HIS87 4.6 23.1 1.0
CD2 B:TRP128 4.8 19.0 1.0

Copper binding site 7 out of 8 in 3x1b

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Copper binding site 7 out of 8 in the Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution


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 Laccase From Lentinus Sp. at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu617

b:27.6
occ:1.00
 NE2 B:HIS422 2.0 25.5 1.0
NE2 B:HIS474 2.0 24.3 1.0
NE2 B:HIS132 2.0 24.1 1.0
O B:HOH718 2.4 21.0 1.0
CE1 B:HIS422 2.8 24.8 1.0
CD2 B:HIS474 2.9 23.0 1.0
CD2 B:HIS132 3.0 21.9 1.0
CE1 B:HIS132 3.0 23.8 1.0
CE1 B:HIS474 3.0 20.6 1.0
CD2 B:HIS422 3.2 24.8 1.0
O B:HOH908 3.7 31.9 1.0
ND1 B:HIS422 4.0 23.4 1.0
ND1 B:HIS474 4.1 21.6 1.0
CD2 B:HIS420 4.1 24.9 1.0
CG B:HIS474 4.1 21.7 1.0
ND1 B:HIS132 4.1 22.7 1.0
CG B:HIS132 4.1 22.5 1.0
CG B:HIS422 4.2 24.5 1.0
CB B:PHE472 4.2 23.0 1.0
CU B:CU615 4.2 31.1 1.0
CD2 B:PHE472 4.3 22.6 1.0
CD2 B:HIS85 4.4 23.0 1.0
CG B:PHE472 4.5 22.5 1.0
NE2 B:HIS85 4.6 25.4 1.0
NE2 B:HIS420 4.8 27.1 1.0

Copper binding site 8 out of 8 in 3x1b

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Copper binding site 8 out of 8 in the Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution


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 Laccase From Lentinus Sp. at 1.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu618

b:27.1
occ:1.00
 ND1 B:HIS480 2.0 23.5 1.0
ND1 B:HIS417 2.0 21.5 1.0
SG B:CYS475 2.3 24.1 1.0
CE1 B:HIS417 2.9 20.6 1.0
CE1 B:HIS480 3.0 22.4 1.0
CG B:HIS480 3.0 21.0 1.0
CG B:HIS417 3.1 20.0 1.0
CB B:CYS475 3.3 20.2 1.0
CB B:HIS480 3.3 21.0 1.0
CB B:HIS417 3.6 19.8 1.0
CD1 B:ILE477 3.6 21.4 1.0
CD2 B:PHE485 3.7 21.6 1.0
CB B:ILE477 3.9 18.7 1.0
CE2 B:PHE485 4.0 21.8 1.0
NE2 B:HIS417 4.0 20.4 1.0
CA B:HIS417 4.1 20.4 1.0
NE2 B:HIS480 4.1 21.3 1.0
CD2 B:HIS480 4.1 22.1 1.0
CG1 B:ILE477 4.1 19.1 1.0
CD2 B:HIS417 4.2 20.5 1.0
CG2 B:ILE477 4.6 16.9 1.0
CA B:CYS475 4.7 20.1 1.0
O B:GLY414 4.7 23.6 1.0
CD B:PRO418 4.8 20.1 1.0
N B:ILE477 4.9 19.8 1.0
CA B:HIS480 4.9 20.8 1.0
CA B:ILE477 4.9 19.4 1.0
O B:ILE477 5.0 19.5 1.0
CG B:PHE485 5.0 22.0 1.0

Reference:

W.C.Liu, M.Maestre-Reyna, W.Y.Jeng, C.C.Lee, C.A.Hsu, T.N.Wen, A.H.J.Wang, L.F.Shyur. Crystal Structure of Laccase From Lentinus Sp. at 1.8 A Resolution To Be Published.
Page generated: Wed Jul 31 02:24:46 2024

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