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Copper in PDB 3fu9: Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol

Enzymatic activity of Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol

All present enzymatic activity of Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol:
1.10.3.2;

Protein crystallography data

The structure of Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol, PDB code: 3fu9 was solved by J.P.Kallio, N.Hakulinen, J.Rouvinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.61 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.120, 60.230, 117.130, 90.00, 98.36, 90.00
R / Rfree (%) 23 / 33

Other elements in 3fu9:

The structure of Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol (pdb code 3fu9). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol, PDB code: 3fu9:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 3fu9

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Copper binding site 1 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:15.6
occ:1.00
 ND1 A:HIS431 1.8 9.7 1.0
SG A:CYS503 2.1 11.5 1.0
ND1 A:HIS508 2.4 12.0 1.0
CE1 A:HIS431 2.8 15.0 1.0
CG A:HIS431 2.8 12.4 1.0
CG A:HIS508 3.1 8.3 1.0
CB A:CYS503 3.2 8.5 1.0
CB A:HIS508 3.2 9.0 1.0
CB A:HIS431 3.2 7.3 1.0
CE1 A:HIS508 3.5 12.3 1.0
CA A:HIS431 3.6 10.3 1.0
CD1 A:ILE505 3.7 6.3 1.0
CD1 A:LEU513 3.8 9.8 1.0
NE2 A:HIS431 3.9 13.5 1.0
CD2 A:HIS431 3.9 9.6 1.0
CB A:ILE505 4.0 4.8 1.0
CD A:PRO432 4.2 8.6 1.0
CG1 A:ILE505 4.2 2.9 1.0
O A:PRO430 4.3 11.4 1.0
CD2 A:HIS508 4.4 14.3 1.0
NE2 A:HIS508 4.5 8.9 1.0
C A:HIS431 4.5 9.3 1.0
CA A:CYS503 4.6 9.4 1.0
N A:PRO432 4.6 9.5 1.0
N A:HIS431 4.7 11.3 1.0
CA A:HIS508 4.7 10.0 1.0
N A:ILE505 4.8 2.5 1.0
CG A:LEU513 4.9 6.4 1.0
C A:PRO430 4.9 11.3 1.0
CG A:PRO432 4.9 6.2 1.0
CA A:ILE505 5.0 2.1 1.0
C A:CYS503 5.0 9.2 1.0

Copper binding site 2 out of 8 in 3fu9

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Copper binding site 2 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:22.2
occ:1.00
 NE2 A:HIS140 1.9 2.0 1.0
NE2 A:HIS436 1.9 7.8 1.0
NE2 A:HIS502 2.1 11.8 1.0
CE1 A:HIS140 2.5 15.6 1.0
CE1 A:HIS436 2.5 7.0 1.0
O A:HOH568 2.5 2.0 1.0
CD2 A:HIS502 2.9 10.5 1.0
CD2 A:HIS140 3.0 16.0 1.0
CD2 A:HIS436 3.2 8.9 1.0
CE1 A:HIS502 3.3 10.7 1.0
ND1 A:HIS140 3.6 10.3 1.0
ND1 A:HIS436 3.7 11.0 1.0
CG A:HIS140 3.9 13.9 1.0
NE2 A:HIS434 4.1 2.0 1.0
CD1 A:LEU500 4.1 10.5 1.0
CG A:HIS436 4.1 7.0 1.0
CG A:HIS502 4.1 13.6 1.0
CU A:CU604 4.1 14.8 1.0
CD2 A:HIS434 4.2 3.1 1.0
CD2 A:HIS93 4.2 10.3 1.0
ND1 A:HIS502 4.3 10.3 1.0
NE2 A:HIS93 4.4 4.2 1.0
CG A:HIS93 4.7 5.7 1.0
CU A:CU603 4.8 11.1 1.0
CB A:LEU500 4.9 11.0 1.0
CE1 A:HIS93 5.0 5.8 1.0
CD2 A:HIS504 5.0 2.0 1.0
NE2 A:HIS504 5.0 2.0 1.0

Copper binding site 3 out of 8 in 3fu9

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Copper binding site 3 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:11.1
occ:1.00
 NE2 A:HIS138 2.0 8.9 1.0
NE2 A:HIS504 2.1 2.0 1.0
ND1 A:HIS95 2.3 6.4 1.0
O A:HOH568 2.4 2.0 1.0
CE1 A:HIS138 2.5 6.5 1.0
CE1 A:HIS504 3.1 3.5 1.0
CE1 A:HIS95 3.1 11.2 1.0
CD2 A:HIS504 3.1 2.0 1.0
CD2 A:HIS138 3.3 2.4 1.0
CG A:HIS95 3.3 9.2 1.0
ND1 A:HIS138 3.7 5.7 1.0
CB A:HIS95 3.8 8.1 1.0
CZ2 A:TRP136 4.0 8.0 1.0
CD2 A:HIS93 4.0 10.3 1.0
CU A:CU604 4.0 14.8 1.0
NE2 A:HIS434 4.0 2.0 1.0
CD2 A:HIS434 4.1 3.1 1.0
CG A:HIS138 4.1 7.0 1.0
ND1 A:HIS504 4.2 2.0 1.0
NE2 A:HIS95 4.2 4.4 1.0
CG A:HIS504 4.2 2.0 1.0
CE2 A:TRP136 4.2 7.0 1.0
CD2 A:HIS95 4.4 2.0 1.0
NE1 A:TRP136 4.4 4.5 1.0
NE2 A:HIS93 4.5 4.2 1.0
CH2 A:TRP136 4.5 7.0 1.0
NE2 A:HIS140 4.8 2.0 1.0
CU A:CU602 4.8 22.2 1.0
CA A:HIS95 4.8 9.0 1.0
O A:HOH856 4.9 19.9 1.0
CD2 A:TRP136 5.0 5.5 1.0
CE1 A:HIS434 5.0 4.9 1.0

Copper binding site 4 out of 8 in 3fu9

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Copper binding site 4 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:14.8
occ:1.00
 NE2 A:HIS93 1.9 4.2 1.0
NE2 A:HIS434 2.0 2.0 1.0
CE1 A:HIS434 2.5 4.9 1.0
CD2 A:HIS93 2.8 10.3 1.0
CE1 A:HIS93 2.9 5.8 1.0
CL A:CL610 3.0 41.1 1.0
NE2 A:HIS436 3.1 7.8 1.0
CD2 A:HIS436 3.2 8.9 1.0
CD2 A:HIS434 3.3 3.1 1.0
CE1 A:HIS436 3.6 7.0 1.0
O A:HOH568 3.6 2.0 1.0
CG A:HIS436 3.7 7.0 1.0
ND1 A:HIS434 3.8 9.5 1.0
ND1 A:HIS436 3.9 11.0 1.0
CA A:HIS95 3.9 9.0 1.0
ND1 A:HIS93 4.0 4.9 1.0
CG A:HIS93 4.0 5.7 1.0
CU A:CU603 4.0 11.1 1.0
CG A:HIS95 4.0 9.2 1.0
CU A:CU602 4.1 22.2 1.0
CG A:HIS434 4.2 3.8 1.0
CB A:HIS95 4.2 8.1 1.0
ND1 A:HIS95 4.2 6.4 1.0
CD2 A:HIS95 4.4 2.0 1.0
O A:LEU435 4.5 8.9 1.0
CA A:HIS436 4.6 7.0 1.0
CB A:HIS436 4.6 7.8 1.0
CE1 A:HIS95 4.6 11.2 1.0
N A:GLY96 4.7 7.6 1.0
N A:HIS95 4.7 9.8 1.0
O A:HOH563 4.7 5.0 1.0
NE2 A:HIS95 4.8 4.4 1.0
C A:HIS95 4.8 9.3 1.0
O A:TRP94 4.8 10.0 1.0
OD1 A:ASP477 4.9 6.5 1.0
N A:HIS436 4.9 8.3 1.0
C A:LEU435 4.9 9.1 1.0

Copper binding site 5 out of 8 in 3fu9

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Copper binding site 5 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu601

b:12.8
occ:1.00
 SG B:CYS503 2.0 7.2 1.0
ND1 B:HIS431 2.1 9.0 1.0
ND1 B:HIS508 2.3 16.3 1.0
CG B:HIS508 3.0 12.4 1.0
CE1 B:HIS431 3.0 3.3 1.0
CG B:HIS431 3.1 4.1 1.0
CB B:HIS508 3.2 14.7 1.0
CB B:CYS503 3.2 7.7 1.0
CE1 B:HIS508 3.3 13.3 1.0
CB B:HIS431 3.4 5.9 1.0
CD1 B:LEU513 3.8 13.6 1.0
CA B:HIS431 3.9 6.6 1.0
CD1 B:ILE505 4.1 2.0 1.0
NE2 B:HIS431 4.1 2.8 1.0
CD2 B:HIS508 4.2 12.7 1.0
CD2 B:HIS431 4.2 10.5 1.0
CB B:ILE505 4.2 4.1 1.0
NE2 B:HIS508 4.3 6.6 1.0
O B:PRO430 4.5 7.5 1.0
CG1 B:ILE505 4.5 6.8 1.0
CA B:CYS503 4.5 6.0 1.0
CD B:PRO432 4.6 5.4 1.0
CA B:HIS508 4.7 13.5 1.0
C B:HIS431 4.8 5.3 1.0
CG B:LEU513 4.8 11.1 1.0
N B:PRO432 4.9 4.7 1.0
N B:ILE505 5.0 5.2 1.0
N B:HIS431 5.0 6.3 1.0
CB B:LEU513 5.0 8.5 1.0

Copper binding site 6 out of 8 in 3fu9

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Copper binding site 6 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:18.3
occ:1.00
 NE2 B:HIS502 2.0 2.0 1.0
NE2 B:HIS140 2.1 9.7 1.0
NE2 B:HIS436 2.2 2.0 1.0
O B:HOH617 2.8 9.4 1.0
CE1 B:HIS436 2.8 7.5 1.0
CE1 B:HIS502 2.8 2.0 1.0
CE1 B:HIS140 2.9 5.9 1.0
CD2 B:HIS502 3.1 2.0 1.0
CD2 B:HIS436 3.2 9.3 1.0
CD2 B:HIS140 3.3 8.6 1.0
CD1 B:LEU500 3.7 11.9 1.0
ND1 B:HIS436 3.9 13.8 1.0
CD2 B:HIS434 3.9 9.7 1.0
ND1 B:HIS502 4.0 2.0 1.0
CU B:CU604 4.0 15.3 1.0
ND1 B:HIS140 4.1 2.4 1.0
CG B:HIS502 4.1 6.6 1.0
CG B:HIS436 4.1 2.8 1.0
O B:HOH623 4.1 10.3 1.0
CG B:HIS140 4.3 9.2 1.0
CD2 B:HIS93 4.4 9.6 1.0
NE2 B:HIS434 4.4 11.0 1.0
O B:HOH609 4.4 19.2 1.0
NE2 B:HIS93 4.4 4.4 1.0
CB B:LEU500 4.6 6.3 1.0
NE2 B:HIS504 4.8 2.0 1.0
CG B:LEU500 4.8 9.0 1.0
CU B:CU603 4.9 10.2 1.0
CG B:HIS93 5.0 9.2 1.0

Copper binding site 7 out of 8 in 3fu9

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Copper binding site 7 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu603

b:10.2
occ:1.00
 NE2 B:HIS504 1.9 2.0 1.0
NE2 B:HIS138 1.9 6.0 1.0
ND1 B:HIS95 2.2 3.5 1.0
O B:HOH617 2.6 9.4 1.0
CE1 B:HIS504 2.7 4.3 1.0
CE1 B:HIS138 2.8 2.7 1.0
CD2 B:HIS138 3.0 7.7 1.0
CG B:HIS95 3.0 11.0 1.0
CD2 B:HIS504 3.1 3.0 1.0
CE1 B:HIS95 3.2 5.2 1.0
CB B:HIS95 3.3 8.6 1.0
CZ2 B:TRP136 3.6 6.8 1.0
ND1 B:HIS504 3.8 2.0 1.0
ND1 B:HIS138 4.0 4.9 1.0
CE2 B:TRP136 4.0 8.0 1.0
CH2 B:TRP136 4.0 9.3 1.0
CD2 B:HIS93 4.1 9.6 1.0
CG B:HIS504 4.1 2.0 1.0
CU B:CU604 4.1 15.3 1.0
CG B:HIS138 4.1 6.4 1.0
CD2 B:HIS95 4.2 2.0 1.0
NE2 B:HIS95 4.2 2.0 1.0
NE1 B:TRP136 4.3 2.0 1.0
CD2 B:HIS434 4.3 9.7 1.0
NE2 B:HIS434 4.4 11.0 1.0
NE2 B:HIS93 4.5 4.4 1.0
CA B:HIS95 4.7 8.0 1.0
O B:HOH609 4.8 19.2 1.0
CD2 B:TRP136 4.8 5.3 1.0
CZ3 B:TRP136 4.9 8.4 1.0
CU B:CU602 4.9 18.3 1.0

Copper binding site 8 out of 8 in 3fu9

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Copper binding site 8 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Melanocarpus Albomyces Laccase Crystal Soaked (20 Min) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu604

b:15.3
occ:1.00
 NE2 B:HIS434 1.9 11.0 1.0
NE2 B:HIS93 2.1 4.4 1.0
CD2 B:HIS436 2.5 9.3 1.0
NE2 B:HIS436 2.7 2.0 1.0
CL B:CL610 2.7 26.3 1.0
CD2 B:HIS434 2.9 9.7 1.0
CE1 B:HIS434 2.9 13.1 1.0
CE1 B:HIS93 3.0 4.5 1.0
CD2 B:HIS93 3.0 9.6 1.0
ND1 B:HIS95 3.5 3.5 1.0
CG B:HIS95 3.7 11.0 1.0
CG B:HIS436 3.7 2.8 1.0
CB B:HIS95 3.8 8.6 1.0
CE1 B:HIS436 3.9 7.5 1.0
CA B:HIS95 4.0 8.0 1.0
ND1 B:HIS434 4.0 12.6 1.0
CG B:HIS434 4.0 5.2 1.0
CU B:CU602 4.0 18.3 1.0
O B:HOH617 4.0 9.4 1.0
CU B:CU603 4.1 10.2 1.0
ND1 B:HIS93 4.1 11.0 1.0
CE1 B:HIS95 4.1 5.2 1.0
CG B:HIS93 4.1 9.2 1.0
ND1 B:HIS436 4.3 13.8 1.0
CD2 B:HIS95 4.4 2.0 1.0
CA B:HIS436 4.5 3.8 1.0
N B:GLY96 4.5 7.8 1.0
O B:HOH844 4.6 6.6 1.0
O B:LEU435 4.6 4.3 1.0
CB B:HIS436 4.6 4.0 1.0
NE2 B:HIS95 4.7 2.0 1.0
C B:HIS95 4.8 7.9 1.0
N B:HIS436 5.0 2.0 1.0
N B:HIS95 5.0 8.3 1.0
O B:TRP94 5.0 6.0 1.0

Reference:

J.P.Kallio, S.Auer, J.Janis, M.Andberg, K.Kruus, J.Rouvinen, A.Koivula, N.Hakulinen. Structure-Function Studies of A Melanocarpus Albomyces Laccase Suggest A Pathway For Oxidation of Phenolic Compounds. J.Mol.Biol. V. 392 895 2009.
ISSN: ISSN 0022-2836
PubMed: 19563811
DOI: 10.1016/J.JMB.2009.06.053
Page generated: Wed Jul 31 00:56:10 2024

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