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Copper in PDB 3dkh: L559A Mutant of Melanocarpus Albomyces Laccase

Enzymatic activity of L559A Mutant of Melanocarpus Albomyces Laccase

All present enzymatic activity of L559A Mutant of Melanocarpus Albomyces Laccase:
1.10.3.2;

Protein crystallography data

The structure of L559A Mutant of Melanocarpus Albomyces Laccase, PDB code: 3dkh was solved by N.Hakulinen, J.Rouvinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.82 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 173.510, 62.020, 125.670, 90.00, 99.92, 90.00
R / Rfree (%) 22.4 / 28.2

Other elements in 3dkh:

The structure of L559A Mutant of Melanocarpus Albomyces Laccase also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the L559A Mutant of Melanocarpus Albomyces Laccase (pdb code 3dkh). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the L559A Mutant of Melanocarpus Albomyces Laccase, PDB code: 3dkh:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 3dkh

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Copper binding site 1 out of 8 in the L559A Mutant of Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of L559A Mutant of Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:16.9
occ:1.00
ND1 A:HIS431 2.2 9.4 1.0
SG A:CYS503 2.2 13.3 1.0
ND1 A:HIS508 2.3 11.8 1.0
CE1 A:HIS431 2.9 8.8 1.0
CG A:HIS508 3.1 14.9 1.0
CG A:HIS431 3.1 10.2 1.0
CB A:HIS508 3.2 16.7 1.0
CB A:CYS503 3.3 6.1 1.0
CE1 A:HIS508 3.4 12.9 1.0
CB A:HIS431 3.6 8.3 1.0
CD1 A:LEU513 3.7 13.9 1.0
CD1 A:ILE505 3.8 1.0 1.0
NE2 A:HIS431 3.9 11.2 1.0
CA A:HIS431 4.0 8.9 1.0
CD2 A:HIS431 4.1 11.5 1.0
CB A:ILE505 4.2 4.7 1.0
O A:PRO430 4.3 9.1 1.0
CD2 A:HIS508 4.3 14.7 1.0
CG1 A:ILE505 4.4 2.4 1.0
NE2 A:HIS508 4.4 13.0 1.0
CD A:PRO432 4.5 8.4 1.0
CA A:CYS503 4.7 6.7 1.0
CA A:HIS508 4.7 17.0 1.0
CG A:LEU513 4.9 15.9 1.0
CG2 A:ILE505 4.9 1.3 1.0
C A:HIS431 4.9 8.6 1.0
N A:HIS431 5.0 6.4 1.0
N A:PRO432 5.0 7.4 1.0

Copper binding site 2 out of 8 in 3dkh

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Copper binding site 2 out of 8 in the L559A Mutant of Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of L559A Mutant of Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:26.0
occ:1.00
NE2 A:HIS436 2.1 1.0 1.0
NE2 A:HIS502 2.2 13.5 1.0
NE2 A:HIS140 2.2 17.2 1.0
O1 A:OXY900 2.6 1.0 1.0
O2 A:OXY900 2.7 1.1 1.0
CE1 A:HIS436 2.7 1.0 1.0
CD2 A:HIS502 3.0 13.1 1.0
CE1 A:HIS140 3.0 20.1 1.0
CE1 A:HIS502 3.1 14.5 1.0
CD2 A:HIS140 3.2 17.7 1.0
CD2 A:HIS436 3.3 3.9 1.0
ND1 A:HIS436 4.0 1.0 1.0
CU A:CU604 4.1 48.0 1.0
CG A:HIS502 4.1 14.2 1.0
ND1 A:HIS502 4.1 14.2 1.0
ND1 A:HIS140 4.1 16.2 1.0
CG A:HIS436 4.3 4.0 1.0
CG A:HIS140 4.3 17.3 1.0
CD2 A:HIS434 4.4 13.2 1.0
CD1 A:LEU500 4.4 9.1 1.0
CD2 A:HIS93 4.4 18.6 1.0
CB A:LEU500 4.7 7.5 1.0
NE2 A:HIS93 4.7 19.0 1.0
NE2 A:HIS434 4.8 13.4 1.0
CG A:HIS93 4.9 17.5 1.0
O A:HOH954 5.0 19.4 1.0

Copper binding site 3 out of 8 in 3dkh

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Copper binding site 3 out of 8 in the L559A Mutant of Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of L559A Mutant of Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:15.5
occ:1.00
NE2 A:HIS504 2.2 7.7 1.0
ND1 A:HIS95 2.2 23.6 1.0
NE2 A:HIS138 2.3 20.9 1.0
O2 A:OXY900 2.5 1.1 1.0
O1 A:OXY900 2.7 1.0 1.0
CD2 A:HIS138 3.0 18.6 1.0
CE1 A:HIS95 3.0 24.1 1.0
CD2 A:HIS504 3.1 2.7 1.0
CE1 A:HIS504 3.2 2.1 1.0
CG A:HIS95 3.2 22.2 1.0
CE1 A:HIS138 3.3 20.9 1.0
CZ2 A:TRP136 3.5 9.7 1.0
CB A:HIS95 3.6 21.4 1.0
CE2 A:TRP136 4.0 12.7 1.0
CH2 A:TRP136 4.0 9.9 1.0
CU A:CU604 4.0 48.0 1.0
CD2 A:HIS93 4.1 18.6 1.0
CG A:HIS138 4.2 20.7 1.0
NE2 A:HIS95 4.2 22.2 1.0
ND1 A:HIS504 4.2 1.9 1.0
CG A:HIS504 4.2 1.1 1.0
CD2 A:HIS95 4.3 21.9 1.0
ND1 A:HIS138 4.3 20.8 1.0
NE1 A:TRP136 4.4 13.7 1.0
CD2 A:HIS434 4.4 13.2 1.0
NE2 A:HIS434 4.4 13.4 1.0
NE2 A:HIS93 4.7 19.0 1.0
CA A:HIS95 4.8 22.1 1.0
CZ3 A:TRP136 4.8 12.9 1.0
CD2 A:TRP136 4.8 12.4 1.0

Copper binding site 4 out of 8 in 3dkh

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Copper binding site 4 out of 8 in the L559A Mutant of Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of L559A Mutant of Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:48.0
occ:1.00
NE2 A:HIS93 2.0 19.0 1.0
NE2 A:HIS434 2.1 13.4 1.0
O2 A:OXY900 2.7 1.1 1.0
CD2 A:HIS93 2.8 18.6 1.0
CD2 A:HIS434 3.0 13.2 1.0
CL A:CL610 3.0 49.9 1.0
CE1 A:HIS434 3.1 13.7 1.0
CE1 A:HIS93 3.1 18.4 1.0
NE2 A:HIS436 3.3 1.0 1.0
CD2 A:HIS436 3.3 3.9 1.0
CE1 A:HIS436 3.6 1.0 1.0
CG A:HIS436 3.7 4.0 1.0
ND1 A:HIS436 3.8 1.0 1.0
O1 A:OXY900 3.9 1.0 1.0
CG A:HIS93 4.0 17.5 1.0
CU A:CU603 4.0 15.5 1.0
CG A:HIS95 4.0 22.2 1.0
ND1 A:HIS93 4.1 20.0 1.0
ND1 A:HIS95 4.1 23.6 1.0
CU A:CU602 4.1 26.0 1.0
CA A:HIS95 4.1 22.1 1.0
CG A:HIS434 4.2 12.5 1.0
ND1 A:HIS434 4.2 13.9 1.0
CB A:HIS95 4.3 21.4 1.0
O A:HOH1022 4.4 20.8 1.0
CA A:HIS436 4.5 8.9 1.0
CD2 A:HIS95 4.5 21.9 1.0
CE1 A:HIS95 4.5 24.1 1.0
CB A:HIS436 4.6 7.6 1.0
O A:LEU435 4.7 7.5 1.0
NE2 A:HIS95 4.8 22.2 1.0
N A:HIS95 4.8 21.9 1.0
N A:GLY96 4.9 21.2 1.0
N A:HIS436 4.9 8.7 1.0
C A:LEU435 4.9 9.2 1.0
O A:TRP94 5.0 20.7 1.0

Copper binding site 5 out of 8 in 3dkh

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Copper binding site 5 out of 8 in the L559A Mutant of Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of L559A Mutant of Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu601

b:14.4
occ:1.00
ND1 B:HIS508 2.1 12.9 1.0
SG B:CYS503 2.1 14.2 1.0
ND1 B:HIS431 2.1 7.4 1.0
CE1 B:HIS431 2.9 8.8 1.0
CG B:HIS508 3.0 13.6 1.0
CG B:HIS431 3.1 8.6 1.0
CE1 B:HIS508 3.1 12.5 1.0
CB B:HIS508 3.2 15.7 1.0
CB B:CYS503 3.3 8.5 1.0
CB B:HIS431 3.6 7.3 1.0
CD1 B:LEU513 3.7 14.0 1.0
CD1 B:ILE505 3.8 3.1 1.0
CA B:HIS431 4.0 7.3 1.0
NE2 B:HIS431 4.0 11.0 1.0
CB B:ILE505 4.1 4.7 1.0
CD2 B:HIS508 4.1 14.5 1.0
CD2 B:HIS431 4.1 8.7 1.0
NE2 B:HIS508 4.2 14.6 1.0
CD B:PRO432 4.3 5.6 1.0
O B:PRO430 4.3 10.6 1.0
CG1 B:ILE505 4.4 3.4 1.0
CA B:CYS503 4.6 8.1 1.0
CA B:HIS508 4.7 13.6 1.0
N B:PRO432 4.9 6.7 1.0
N B:ILE505 4.9 3.5 1.0
CG2 B:ILE505 4.9 1.7 1.0
C B:HIS431 4.9 6.1 1.0
N B:HIS431 5.0 6.3 1.0
CG B:LEU513 5.0 12.8 1.0

Copper binding site 6 out of 8 in 3dkh

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Copper binding site 6 out of 8 in the L559A Mutant of Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of L559A Mutant of Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:22.9
occ:1.00
NE2 B:HIS436 2.1 10.1 1.0
NE2 B:HIS502 2.1 12.4 1.0
NE2 B:HIS140 2.3 28.7 1.0
O1 B:OXY901 2.5 9.9 1.0
O2 B:OXY901 2.6 8.3 1.0
CE1 B:HIS436 2.8 8.5 1.0
CE1 B:HIS502 3.0 14.0 1.0
CD2 B:HIS502 3.1 12.0 1.0
CD2 B:HIS140 3.2 28.4 1.0
CE1 B:HIS140 3.2 29.0 1.0
CD2 B:HIS436 3.3 12.8 1.0
ND1 B:HIS436 4.0 11.9 1.0
ND1 B:HIS502 4.1 13.6 1.0
CD2 B:HIS93 4.1 19.9 1.0
CG B:HIS502 4.1 12.1 1.0
O B:HOH1121 4.2 23.4 1.0
CG B:HIS436 4.3 12.8 1.0
ND1 B:HIS140 4.3 27.4 1.0
CG B:HIS140 4.4 26.9 1.0
CU B:CU604 4.4 58.1 1.0
NE2 B:HIS93 4.4 19.7 1.0
CD2 B:HIS434 4.4 16.6 1.0
CD1 B:LEU500 4.5 11.3 1.0
CB B:LEU500 4.8 8.3 1.0
CG B:HIS93 4.8 20.1 1.0
NE2 B:HIS434 5.0 16.3 1.0

Copper binding site 7 out of 8 in 3dkh

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Copper binding site 7 out of 8 in the L559A Mutant of Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of L559A Mutant of Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu603

b:25.9
occ:1.00
NE2 B:HIS504 2.1 11.2 1.0
ND1 B:HIS95 2.2 26.7 1.0
NE2 B:HIS138 2.2 14.6 1.0
O2 B:OXY901 2.7 8.3 1.0
O1 B:OXY901 2.9 9.9 1.0
CD2 B:HIS138 3.0 12.2 1.0
CE1 B:HIS504 3.0 7.1 1.0
CG B:HIS95 3.2 25.9 1.0
CD2 B:HIS504 3.2 8.9 1.0
CE1 B:HIS95 3.2 27.2 1.0
CE1 B:HIS138 3.3 15.9 1.0
CZ2 B:TRP136 3.4 8.2 1.0
CB B:HIS95 3.4 24.8 1.0
CE2 B:TRP136 3.8 7.8 1.0
CH2 B:TRP136 3.9 9.1 1.0
CD2 B:HIS93 4.1 19.9 1.0
CG B:HIS138 4.1 15.1 1.0
ND1 B:HIS504 4.2 7.8 1.0
NE1 B:TRP136 4.2 11.3 1.0
ND1 B:HIS138 4.2 16.4 1.0
CG B:HIS504 4.3 6.8 1.0
NE2 B:HIS95 4.3 26.8 1.0
CD2 B:HIS95 4.3 26.8 1.0
CU B:CU604 4.4 58.1 1.0
CD2 B:HIS434 4.5 16.6 1.0
NE2 B:HIS434 4.5 16.3 1.0
NE2 B:HIS93 4.6 19.7 1.0
CA B:HIS95 4.7 23.2 1.0
CD2 B:TRP136 4.7 8.4 1.0
CZ3 B:TRP136 4.8 9.9 1.0
O B:HOH1121 4.9 23.4 1.0

Copper binding site 8 out of 8 in 3dkh

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Copper binding site 8 out of 8 in the L559A Mutant of Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of L559A Mutant of Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu604

b:58.1
occ:1.00
NE2 B:HIS93 2.0 19.7 1.0
NE2 B:HIS434 2.1 16.3 1.0
CE1 B:HIS93 2.9 19.2 1.0
CD2 B:HIS434 3.0 16.6 1.0
CD2 B:HIS93 3.0 19.9 1.0
CE1 B:HIS434 3.1 16.4 1.0
O2 B:OXY901 3.1 8.3 1.0
CD2 B:HIS436 3.3 12.8 1.0
NE2 B:HIS436 3.5 10.1 1.0
CG B:HIS436 3.7 12.8 1.0
CA B:HIS95 3.8 23.2 1.0
CE1 B:HIS436 4.0 8.5 1.0
CG B:HIS95 4.0 25.9 1.0
ND1 B:HIS93 4.1 21.4 1.0
ND1 B:HIS95 4.1 26.7 1.0
CB B:HIS95 4.1 24.8 1.0
ND1 B:HIS436 4.1 11.9 1.0
CG B:HIS93 4.1 20.1 1.0
CG B:HIS434 4.2 16.5 1.0
ND1 B:HIS434 4.2 18.4 1.0
CA B:HIS436 4.2 11.2 1.0
O1 B:OXY901 4.2 9.9 1.0
O B:LEU435 4.3 10.8 1.0
CU B:CU602 4.4 22.9 1.0
CU B:CU603 4.4 25.9 1.0
CB B:HIS436 4.5 11.2 1.0
CD2 B:HIS95 4.5 26.8 1.0
N B:HIS95 4.6 23.4 1.0
N B:HIS436 4.7 10.8 1.0
CE1 B:HIS95 4.7 27.2 1.0
C B:LEU435 4.7 11.5 1.0
N B:GLY96 4.8 23.4 1.0
C B:HIS95 4.9 23.5 1.0
NE2 B:HIS95 4.9 26.8 1.0

Reference:

M.Andberg, N.Hakulinen, S.Auer, M.Saloheimo, A.Koivula, J.Rouvinen, K.Kruus. Essential Role of the C-Terminus in Melanocarpus Albomyces Laccase For Enzyme Production, Catalytic Properties and Structure Febs J. V. 276 6285 2009.
ISSN: ISSN 1742-464X
PubMed: 19780817
DOI: 10.1111/J.1742-4658.2009.07336.X
Page generated: Wed Oct 28 14:23:40 2020
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