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Copper in PDB 3fu8: Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol

Enzymatic activity of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol

All present enzymatic activity of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol:
1.10.3.2;

Protein crystallography data

The structure of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) with 2,6- Dimethoxyphenol, PDB code: 3fu8 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) 19.78 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.710, 62.370, 125.140, 90.00, 96.36, 90.00
R / Rfree (%) 20.3 / 25.6

Other elements in 3fu8:

The structure of Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) 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 (10 Sec) with 2,6- Dimethoxyphenol (pdb code 3fu8). 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 (10 Sec) with 2,6- Dimethoxyphenol, PDB code: 3fu8:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 3fu8

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Copper binding site 1 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) 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 (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:14.2
occ:1.00
 ND1 A:HIS508 2.0 14.7 1.0
ND1 A:HIS431 2.0 11.5 1.0
SG A:CYS503 2.1 13.0 1.0
CE1 A:HIS431 3.0 15.1 1.0
CG A:HIS508 3.0 12.2 1.0
CE1 A:HIS508 3.0 15.0 1.0
CG A:HIS431 3.1 10.3 1.0
CB A:CYS503 3.2 10.8 1.0
CB A:HIS508 3.3 10.5 1.0
CB A:HIS431 3.5 10.3 1.0
CD1 A:LEU513 3.6 12.5 1.0
CD1 A:ILE505 3.8 9.2 1.0
CA A:HIS431 4.0 9.1 1.0
NE2 A:HIS508 4.1 14.7 1.0
NE2 A:HIS431 4.1 13.1 1.0
CD2 A:HIS508 4.1 12.8 1.0
CB A:ILE505 4.1 9.0 1.0
CD2 A:HIS431 4.2 10.7 1.0
CD A:PRO432 4.3 9.2 1.0
CG1 A:ILE505 4.4 9.5 1.0
O A:PRO430 4.4 11.1 1.0
CA A:CYS503 4.6 9.9 1.0
CA A:HIS508 4.8 11.7 1.0
N A:ILE505 4.9 9.2 1.0
CG A:LEU513 4.9 13.3 1.0
C A:HIS431 5.0 9.2 1.0
N A:PRO432 5.0 9.0 1.0
CG2 A:ILE505 5.0 8.7 1.0

Copper binding site 2 out of 8 in 3fu8

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Copper binding site 2 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) 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 (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:16.9
occ:1.00
 NE2 A:HIS436 2.0 16.2 1.0
NE2 A:HIS502 2.0 14.0 1.0
NE2 A:HIS140 2.2 13.7 1.0
O A:HOH1176 2.3 19.6 1.0
CE1 A:HIS436 2.8 10.7 1.0
CD2 A:HIS502 3.0 12.8 1.0
CE1 A:HIS502 3.0 15.0 1.0
CE1 A:HIS140 3.1 15.3 1.0
CD2 A:HIS436 3.2 10.6 1.0
CD2 A:HIS140 3.2 16.7 1.0
ND1 A:HIS436 4.0 12.8 1.0
CD2 A:HIS434 4.0 12.1 1.0
CU A:CU604 4.1 17.0 1.0
CD2 A:HIS93 4.1 11.9 1.0
ND1 A:HIS502 4.1 16.3 1.0
CG A:HIS502 4.1 12.4 1.0
O A:HOH1137 4.2 26.5 1.0
CG A:HIS436 4.2 11.1 1.0
ND1 A:HIS140 4.2 17.8 1.0
NE2 A:HIS93 4.2 14.2 1.0
CG A:HIS140 4.3 14.2 1.0
CD1 A:LEU500 4.4 12.5 1.0
O A:HOH1118 4.6 68.3 1.0
CB A:LEU500 4.6 10.4 1.0
NE2 A:HIS434 4.6 14.7 1.0
CG A:HIS93 4.8 10.7 1.0
O A:HOH1161 4.8 56.9 1.0
CU A:CU603 4.9 13.9 1.0
CE1 A:HIS93 5.0 14.9 1.0
CE1 A:HIS138 5.0 11.2 1.0

Copper binding site 3 out of 8 in 3fu8

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Copper binding site 3 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) 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 (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:13.9
occ:1.00
 ND1 A:HIS95 2.0 8.2 1.0
NE2 A:HIS138 2.1 12.6 1.0
NE2 A:HIS504 2.1 12.6 1.0
O A:HOH1176 2.6 19.6 1.0
CE1 A:HIS95 3.0 12.7 1.0
CD2 A:HIS138 3.0 9.6 1.0
CG A:HIS95 3.0 10.3 1.0
CD2 A:HIS504 3.1 7.7 1.0
CE1 A:HIS504 3.1 9.9 1.0
CE1 A:HIS138 3.1 11.2 1.0
CB A:HIS95 3.4 11.3 1.0
CZ2 A:TRP136 3.5 5.8 1.0
CE2 A:TRP136 3.9 11.7 1.0
CD2 A:HIS93 4.0 11.9 1.0
CU A:CU604 4.0 17.0 1.0
NE2 A:HIS95 4.1 11.2 1.0
CD2 A:HIS95 4.2 13.7 1.0
NE1 A:TRP136 4.2 10.7 1.0
CG A:HIS138 4.2 8.4 1.0
CH2 A:TRP136 4.2 12.7 1.0
ND1 A:HIS138 4.2 10.2 1.0
ND1 A:HIS504 4.2 7.6 1.0
CG A:HIS504 4.3 8.8 1.0
NE2 A:HIS434 4.3 14.7 1.0
CD2 A:HIS434 4.3 12.1 1.0
NE2 A:HIS93 4.5 14.2 1.0
O A:HOH1137 4.6 26.5 1.0
CA A:HIS95 4.7 11.6 1.0
CD2 A:TRP136 4.9 9.0 1.0
CU A:CU602 4.9 16.9 1.0

Copper binding site 4 out of 8 in 3fu8

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Copper binding site 4 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) 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 (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:17.0
occ:1.00
 NE2 A:HIS93 1.9 14.2 1.0
NE2 A:HIS434 2.0 14.7 1.0
CD2 A:HIS93 2.8 11.9 1.0
CD2 A:HIS434 2.8 12.1 1.0
CL A:CL610 2.8 22.9 1.0
CE1 A:HIS93 2.9 14.9 1.0
CE1 A:HIS434 3.0 15.7 1.0
NE2 A:HIS436 3.3 16.2 1.0
O A:HOH1176 3.3 19.6 1.0
CD2 A:HIS436 3.3 10.6 1.0
ND1 A:HIS95 3.7 8.2 1.0
CG A:HIS95 3.7 10.3 1.0
CE1 A:HIS436 3.8 10.7 1.0
CG A:HIS436 3.9 11.1 1.0
CA A:HIS95 3.9 11.6 1.0
CB A:HIS95 3.9 11.3 1.0
CG A:HIS93 4.0 10.7 1.0
ND1 A:HIS93 4.0 11.7 1.0
CG A:HIS434 4.0 12.4 1.0
CU A:CU603 4.0 13.9 1.0
CU A:CU602 4.1 16.9 1.0
ND1 A:HIS434 4.1 11.9 1.0
ND1 A:HIS436 4.1 12.8 1.0
CE1 A:HIS95 4.2 12.7 1.0
CD2 A:HIS95 4.3 13.7 1.0
NE2 A:HIS95 4.6 11.2 1.0
N A:GLY96 4.6 14.1 1.0
CA A:HIS436 4.6 10.2 1.0
CB A:HIS436 4.8 10.6 1.0
C A:HIS95 4.8 12.6 1.0
N A:HIS95 4.8 11.6 1.0
O A:LEU435 4.8 9.4 1.0
N A:HIS436 5.0 10.8 1.0
O A:TRP94 5.0 12.4 1.0
O A:HOH672 5.0 16.6 1.0

Copper binding site 5 out of 8 in 3fu8

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Copper binding site 5 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) 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 (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu601

b:14.5
occ:1.00
 SG B:CYS503 2.1 12.1 1.0
ND1 B:HIS431 2.1 14.7 1.0
ND1 B:HIS508 2.1 10.5 1.0
CG B:HIS508 3.0 11.1 1.0
CE1 B:HIS431 3.1 15.9 1.0
CG B:HIS431 3.1 13.4 1.0
CE1 B:HIS508 3.1 11.5 1.0
CB B:CYS503 3.2 12.4 1.0
CB B:HIS508 3.2 9.2 1.0
CB B:HIS431 3.4 13.8 1.0
CD1 B:ILE505 3.7 9.2 1.0
CD1 B:LEU513 3.8 14.3 1.0
CA B:HIS431 4.0 12.4 1.0
CB B:ILE505 4.2 11.2 1.0
NE2 B:HIS431 4.2 15.0 1.0
CD2 B:HIS508 4.2 12.1 1.0
CD2 B:HIS431 4.2 13.9 1.0
NE2 B:HIS508 4.2 12.4 1.0
CD B:PRO432 4.3 12.3 1.0
CG1 B:ILE505 4.3 10.8 1.0
O B:PRO430 4.5 14.7 1.0
CA B:CYS503 4.5 12.2 1.0
CA B:HIS508 4.8 10.9 1.0
N B:ILE505 4.9 10.4 1.0
C B:HIS431 4.9 12.9 1.0
N B:PRO432 4.9 12.3 1.0
N B:HIS431 5.0 12.7 1.0

Copper binding site 6 out of 8 in 3fu8

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Copper binding site 6 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) 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 (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:17.4
occ:1.00
 NE2 B:HIS436 2.0 11.4 1.0
NE2 B:HIS502 2.0 14.8 1.0
NE2 B:HIS140 2.2 16.0 1.0
O B:HOH717 2.2 16.9 1.0
CE1 B:HIS436 2.9 14.5 1.0
CD2 B:HIS502 2.9 13.1 1.0
CE1 B:HIS502 3.0 14.7 1.0
CD2 B:HIS436 3.1 10.5 1.0
CD2 B:HIS140 3.2 17.9 1.0
CE1 B:HIS140 3.2 18.2 1.0
CD2 B:HIS434 4.0 10.8 1.0
ND1 B:HIS436 4.0 11.2 1.0
CG B:HIS502 4.1 12.1 1.0
CU B:CU604 4.1 17.2 1.0
ND1 B:HIS502 4.1 13.5 1.0
CD2 B:HIS93 4.1 14.2 1.0
CG B:HIS436 4.2 10.5 1.0
NE2 B:HIS93 4.2 13.8 1.0
CD1 B:LEU500 4.3 9.7 1.0
ND1 B:HIS140 4.3 17.9 1.0
CG B:HIS140 4.3 15.5 1.0
O B:HOH1019 4.4 20.2 1.0
NE2 B:HIS434 4.5 9.9 1.0
CB B:LEU500 4.6 8.8 1.0
CG B:HIS93 4.9 12.6 1.0
CU B:CU603 4.9 13.5 1.0
CE1 B:HIS138 5.0 11.1 1.0
CE1 B:HIS93 5.0 13.7 1.0
O B:HOH1355 5.0 48.1 1.0

Copper binding site 7 out of 8 in 3fu8

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Copper binding site 7 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) 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 (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu603

b:13.5
occ:1.00
 NE2 B:HIS138 2.0 12.2 1.0
ND1 B:HIS95 2.0 14.6 1.0
NE2 B:HIS504 2.1 12.2 1.0
O B:HOH717 2.7 16.9 1.0
CD2 B:HIS138 3.0 11.3 1.0
CE1 B:HIS138 3.0 11.1 1.0
CE1 B:HIS504 3.0 12.6 1.0
CE1 B:HIS95 3.0 15.8 1.0
CG B:HIS95 3.0 12.4 1.0
CD2 B:HIS504 3.2 11.5 1.0
CB B:HIS95 3.4 11.2 1.0
CZ2 B:TRP136 3.5 7.1 1.0
CE2 B:TRP136 4.0 11.6 1.0
CD2 B:HIS93 4.0 14.2 1.0
ND1 B:HIS138 4.1 11.2 1.0
CU B:CU604 4.1 17.2 1.0
CG B:HIS138 4.1 11.3 1.0
CH2 B:TRP136 4.1 12.2 1.0
NE2 B:HIS95 4.1 13.7 1.0
ND1 B:HIS504 4.1 10.5 1.0
CD2 B:HIS95 4.2 15.9 1.0
CG B:HIS504 4.2 12.1 1.0
NE1 B:TRP136 4.3 13.1 1.0
CD2 B:HIS434 4.3 10.8 1.0
NE2 B:HIS434 4.4 9.9 1.0
NE2 B:HIS93 4.6 13.8 1.0
CA B:HIS95 4.6 12.4 1.0
O B:HOH1019 4.8 20.2 1.0
CD2 B:TRP136 4.9 11.4 1.0
CU B:CU602 4.9 17.4 1.0
CZ3 B:TRP136 5.0 11.9 1.0

Copper binding site 8 out of 8 in 3fu8

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Copper binding site 8 out of 8 in the Melanocarpus Albomyces Laccase Crystal Soaked (10 Sec) 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 (10 Sec) with 2,6- Dimethoxyphenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu604

b:17.2
occ:1.00
 NE2 B:HIS434 2.0 9.9 1.0
NE2 B:HIS93 2.0 13.8 1.0
CL B:CL610 2.9 24.2 1.0
CD2 B:HIS93 2.9 14.2 1.0
CD2 B:HIS434 2.9 10.8 1.0
CE1 B:HIS434 2.9 12.8 1.0
CE1 B:HIS93 3.0 13.7 1.0
O B:HOH717 3.3 16.9 1.0
CD2 B:HIS436 3.5 10.5 1.0
NE2 B:HIS436 3.5 11.4 1.0
ND1 B:HIS95 3.7 14.6 1.0
CG B:HIS95 3.8 12.4 1.0
CA B:HIS95 3.8 12.4 1.0
CG B:HIS436 3.9 10.5 1.0
CE1 B:HIS436 3.9 14.5 1.0
CB B:HIS95 4.0 11.2 1.0
ND1 B:HIS434 4.0 11.2 1.0
CG B:HIS434 4.1 13.1 1.0
CG B:HIS93 4.1 12.6 1.0
CU B:CU603 4.1 13.5 1.0
ND1 B:HIS93 4.1 11.6 1.0
CU B:CU602 4.1 17.4 1.0
ND1 B:HIS436 4.1 11.2 1.0
CE1 B:HIS95 4.3 15.8 1.0
CD2 B:HIS95 4.3 15.9 1.0
N B:GLY96 4.4 15.2 1.0
NE2 B:HIS95 4.6 13.7 1.0
CA B:HIS436 4.6 9.7 1.0
C B:HIS95 4.6 14.3 1.0
N B:HIS95 4.7 12.8 1.0
CB B:HIS436 4.8 10.4 1.0
O B:TRP94 4.8 12.7 1.0
O B:LEU435 4.9 9.1 1.0
N B:HIS436 5.0 10.5 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 00:56:06 2024

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