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Copper in PDB 2ih8: A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase

Enzymatic activity of A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase

All present enzymatic activity of A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase:
1.10.3.2;

Protein crystallography data

The structure of A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase, PDB code: 2ih8 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) 25.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 173.060, 61.810, 123.910, 90.00, 96.36, 90.00
R / Rfree (%) 18.3 / 21.3

Copper Binding Sites:

The binding sites of Copper atom in the A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase (pdb code 2ih8). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase, PDB code: 2ih8:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 2ih8

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Copper binding site 1 out of 8 in the A Low-Dose Crystal Structure of A Recombinant 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 A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:15.8
occ:1.00
ND1 A:HIS508 1.9 10.2 1.0
ND1 A:HIS431 1.9 11.8 1.0
SG A:CYS503 2.2 12.0 1.0
CE1 A:HIS431 2.8 11.8 1.0
CG A:HIS508 2.9 10.0 1.0
CE1 A:HIS508 3.0 11.7 1.0
CG A:HIS431 3.1 11.0 1.0
CB A:HIS508 3.2 9.7 1.0
CB A:CYS503 3.2 9.5 1.0
CB A:HIS431 3.6 9.6 1.0
CD1 A:LEU513 3.7 8.5 1.0
CD1 A:ILE505 3.8 8.4 1.0
NE2 A:HIS431 3.9 14.8 1.0
CA A:HIS431 4.0 10.1 1.0
CB A:ILE505 4.0 9.6 1.0
CD2 A:HIS508 4.0 11.9 1.0
NE2 A:HIS508 4.1 10.7 1.0
CD2 A:HIS431 4.1 11.8 1.0
CG1 A:ILE505 4.3 8.7 1.0
O A:PRO430 4.4 10.4 1.0
CD A:PRO432 4.4 8.0 1.0
CA A:CYS503 4.6 9.8 1.0
CA A:HIS508 4.7 10.8 1.0
CG2 A:ILE505 4.8 6.0 1.0
N A:ILE505 4.9 9.3 1.0
C A:HIS431 4.9 9.7 1.0
N A:PRO432 4.9 9.2 1.0
CG A:LEU513 5.0 9.4 1.0

Copper binding site 2 out of 8 in 2ih8

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Copper binding site 2 out of 8 in the A Low-Dose Crystal Structure of A Recombinant 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 A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:18.6
occ:1.00
NE2 A:HIS436 1.9 12.6 1.0
NE2 A:HIS502 1.9 13.5 1.0
NE2 A:HIS140 2.0 14.8 1.0
O1 A:OXY620 2.2 33.2 1.0
O2 A:OXY620 2.4 32.0 1.0
CE1 A:HIS436 2.7 11.0 1.0
CE1 A:HIS502 2.8 12.4 1.0
CE1 A:HIS140 2.9 13.7 1.0
CD2 A:HIS502 3.0 13.0 1.0
CD2 A:HIS140 3.0 12.9 1.0
CD2 A:HIS436 3.1 10.2 1.0
CU A:CU604 3.9 15.6 1.0
ND1 A:HIS502 3.9 13.9 1.0
ND1 A:HIS436 3.9 12.6 1.0
CD2 A:HIS93 4.0 7.5 1.0
CD2 A:HIS434 4.0 8.0 1.0
ND1 A:HIS140 4.0 13.2 1.0
CG A:HIS502 4.1 12.7 1.0
CG A:HIS140 4.1 13.7 1.0
CG A:HIS436 4.1 11.7 1.0
NE2 A:HIS93 4.2 9.2 1.0
O A:HOH1053 4.2 23.6 1.0
NE2 A:HIS434 4.5 11.8 1.0
CD1 A:LEU500 4.5 11.9 1.0
CE1 A:HIS138 4.6 11.3 1.0
CU A:CU603 4.7 15.9 1.0
CG A:HIS93 4.7 7.8 1.0
CB A:LEU500 4.8 7.6 1.0
NE2 A:HIS504 4.8 13.3 1.0
NE2 A:HIS138 4.9 12.3 1.0
CE1 A:HIS93 5.0 8.4 1.0
CD2 A:HIS504 5.0 10.1 1.0

Copper binding site 3 out of 8 in 2ih8

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Copper binding site 3 out of 8 in the A Low-Dose Crystal Structure of A Recombinant 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 A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:15.9
occ:1.00
ND1 A:HIS95 1.9 12.4 1.0
NE2 A:HIS138 2.0 12.3 1.0
NE2 A:HIS504 2.0 13.3 1.0
O2 A:OXY620 2.3 32.0 1.0
O1 A:OXY620 2.6 33.2 1.0
CD2 A:HIS138 2.8 9.5 1.0
CE1 A:HIS95 2.9 15.0 1.0
CE1 A:HIS504 2.9 11.2 1.0
CD2 A:HIS504 3.0 10.1 1.0
CE1 A:HIS138 3.0 11.3 1.0
CG A:HIS95 3.0 11.8 1.0
CB A:HIS95 3.4 11.1 1.0
CZ2 A:TRP136 3.7 5.4 1.0
CU A:CU604 3.9 15.6 1.0
CG A:HIS138 4.0 10.4 1.0
ND1 A:HIS504 4.0 9.9 1.0
NE2 A:HIS95 4.0 12.9 1.0
CD2 A:HIS93 4.0 7.5 1.0
ND1 A:HIS138 4.0 11.1 1.0
CE2 A:TRP136 4.1 9.4 1.0
CG A:HIS504 4.1 11.4 1.0
CD2 A:HIS95 4.1 11.3 1.0
CH2 A:TRP136 4.2 8.8 1.0
CD2 A:HIS434 4.3 8.0 1.0
NE2 A:HIS434 4.3 11.8 1.0
NE1 A:TRP136 4.4 9.7 1.0
NE2 A:HIS93 4.6 9.2 1.0
CA A:HIS95 4.6 12.4 1.0
O A:HOH1053 4.6 23.6 1.0
CU A:CU602 4.7 18.6 1.0
CD2 A:TRP136 4.9 8.1 1.0

Copper binding site 4 out of 8 in 2ih8

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Copper binding site 4 out of 8 in the A Low-Dose Crystal Structure of A Recombinant 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 A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:15.6
occ:1.00
NE2 A:HIS93 1.9 9.2 1.0
NE2 A:HIS434 1.9 11.8 1.0
CL A:CL610 2.5 22.7 1.0
O2 A:OXY620 2.6 32.0 1.0
CD2 A:HIS93 2.8 7.5 1.0
CD2 A:HIS434 2.8 8.0 1.0
CE1 A:HIS93 3.0 8.4 1.0
CE1 A:HIS434 3.0 8.3 1.0
CD2 A:HIS436 3.2 10.2 1.0
NE2 A:HIS436 3.3 12.6 1.0
ND1 A:HIS95 3.7 12.4 1.0
CG A:HIS95 3.7 11.8 1.0
CA A:HIS95 3.7 12.4 1.0
CG A:HIS436 3.8 11.7 1.0
O1 A:OXY620 3.9 33.2 1.0
CU A:CU602 3.9 18.6 1.0
CE1 A:HIS436 3.9 11.0 1.0
CU A:CU603 3.9 15.9 1.0
CB A:HIS95 4.0 11.1 1.0
CG A:HIS93 4.0 7.8 1.0
ND1 A:HIS93 4.0 8.2 1.0
CG A:HIS434 4.0 8.7 1.0
ND1 A:HIS434 4.1 8.4 1.0
ND1 A:HIS436 4.2 12.6 1.0
CE1 A:HIS95 4.2 15.0 1.0
CD2 A:HIS95 4.3 11.3 1.0
N A:GLY96 4.5 11.4 1.0
CA A:HIS436 4.5 10.6 1.0
N A:HIS95 4.6 12.1 1.0
NE2 A:HIS95 4.6 12.9 1.0
CB A:HIS436 4.7 10.7 1.0
C A:HIS95 4.7 12.2 1.0
O A:LEU435 4.8 8.6 1.0
N A:HIS436 4.9 9.0 1.0
NE2 A:HIS138 4.9 12.3 1.0
NE2 A:HIS502 5.0 13.5 1.0
O A:HOH856 5.0 18.4 1.0

Copper binding site 5 out of 8 in 2ih8

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Copper binding site 5 out of 8 in the A Low-Dose Crystal Structure of A Recombinant 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 A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu601

b:15.6
occ:1.00
ND1 B:HIS431 1.9 12.5 1.0
ND1 B:HIS508 1.9 13.2 1.0
SG B:CYS503 2.2 14.4 1.0
CE1 B:HIS431 2.8 12.3 1.0
CG B:HIS508 2.9 13.8 1.0
CE1 B:HIS508 3.0 14.8 1.0
CG B:HIS431 3.0 12.4 1.0
CB B:HIS508 3.2 11.7 1.0
CB B:CYS503 3.2 11.2 1.0
CB B:HIS431 3.5 12.1 1.0
CD1 B:LEU513 3.7 9.1 1.0
CD1 B:ILE505 3.9 10.5 1.0
NE2 B:HIS431 3.9 13.8 1.0
CA B:HIS431 4.0 11.9 1.0
CD2 B:HIS508 4.0 13.8 1.0
CD2 B:HIS431 4.0 13.7 1.0
NE2 B:HIS508 4.1 13.5 1.0
CB B:ILE505 4.1 11.1 1.0
CG1 B:ILE505 4.3 9.5 1.0
O B:PRO430 4.4 12.2 1.0
CD B:PRO432 4.5 10.5 1.0
CA B:CYS503 4.6 12.1 1.0
CA B:HIS508 4.7 12.6 1.0
C B:HIS431 4.9 11.6 1.0
N B:ILE505 4.9 10.7 1.0
CG2 B:ILE505 4.9 8.0 1.0
CG B:LEU513 4.9 9.1 1.0
N B:HIS431 4.9 11.8 1.0
N B:PRO432 5.0 11.8 1.0

Copper binding site 6 out of 8 in 2ih8

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Copper binding site 6 out of 8 in the A Low-Dose Crystal Structure of A Recombinant 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 A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:22.5
occ:1.00
NE2 B:HIS436 1.9 15.6 1.0
NE2 B:HIS502 1.9 17.6 1.0
NE2 B:HIS140 2.0 17.0 1.0
O1 B:OXY620 2.3 28.2 1.0
O2 B:OXY620 2.5 27.8 1.0
CE1 B:HIS436 2.7 11.7 1.0
CE1 B:HIS140 2.9 16.9 1.0
CE1 B:HIS502 2.9 16.8 1.0
CD2 B:HIS502 2.9 16.4 1.0
CD2 B:HIS140 3.0 16.8 1.0
CD2 B:HIS436 3.1 10.9 1.0
ND1 B:HIS436 3.9 12.7 1.0
CD2 B:HIS93 3.9 14.6 1.0
CU B:CU604 4.0 20.1 1.0
ND1 B:HIS502 4.0 15.8 1.0
ND1 B:HIS140 4.0 16.3 1.0
CG B:HIS502 4.0 14.7 1.0
CD2 B:HIS434 4.0 12.0 1.0
CG B:HIS436 4.1 12.9 1.0
CG B:HIS140 4.1 15.0 1.0
NE2 B:HIS93 4.2 15.4 1.0
O B:HOH970 4.2 27.5 1.0
CD1 B:LEU500 4.4 12.9 1.0
NE2 B:HIS434 4.5 13.9 1.0
CE1 B:HIS138 4.7 12.5 1.0
CU B:CU603 4.7 17.0 1.0
CG B:HIS93 4.7 14.0 1.0
CB B:LEU500 4.7 10.9 1.0
NE2 B:HIS504 4.9 12.1 1.0

Copper binding site 7 out of 8 in 2ih8

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Copper binding site 7 out of 8 in the A Low-Dose Crystal Structure of A Recombinant 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 A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu603

b:17.0
occ:1.00
ND1 B:HIS95 1.9 14.4 1.0
NE2 B:HIS138 2.0 15.4 1.0
NE2 B:HIS504 2.0 12.1 1.0
O2 B:OXY620 2.3 27.8 1.0
O1 B:OXY620 2.7 28.2 1.0
CE1 B:HIS95 2.9 15.8 1.0
CD2 B:HIS138 2.9 12.0 1.0
CE1 B:HIS504 2.9 8.7 1.0
CE1 B:HIS138 3.0 12.5 1.0
CG B:HIS95 3.0 15.5 1.0
CD2 B:HIS504 3.0 10.0 1.0
CB B:HIS95 3.4 14.8 1.0
CZ2 B:TRP136 3.7 6.0 1.0
CU B:CU604 3.9 20.1 1.0
CD2 B:HIS93 4.0 14.6 1.0
NE2 B:HIS95 4.0 15.6 1.0
CG B:HIS138 4.0 11.7 1.0
ND1 B:HIS138 4.0 13.2 1.0
ND1 B:HIS504 4.0 10.1 1.0
CD2 B:HIS95 4.1 14.7 1.0
CG B:HIS504 4.1 10.4 1.0
CE2 B:TRP136 4.1 8.0 1.0
CD2 B:HIS434 4.2 12.0 1.0
NE2 B:HIS434 4.3 13.9 1.0
CH2 B:TRP136 4.3 9.7 1.0
NE1 B:TRP136 4.4 9.6 1.0
NE2 B:HIS93 4.5 15.4 1.0
CA B:HIS95 4.6 15.4 1.0
CU B:CU602 4.7 22.5 1.0
O B:HOH970 4.7 27.5 1.0
O B:HOH1070 5.0 20.9 1.0
CG B:HIS434 5.0 14.1 1.0

Copper binding site 8 out of 8 in 2ih8

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Copper binding site 8 out of 8 in the A Low-Dose Crystal Structure of A Recombinant 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 A Low-Dose Crystal Structure of A Recombinant Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu604

b:20.1
occ:1.00
NE2 B:HIS93 1.9 15.4 1.0
NE2 B:HIS434 1.9 13.9 1.0
CL B:CL610 2.6 27.0 1.0
O2 B:OXY620 2.7 27.8 1.0
CD2 B:HIS93 2.8 14.6 1.0
CD2 B:HIS434 2.8 12.0 1.0
CE1 B:HIS434 2.9 12.8 1.0
CE1 B:HIS93 3.0 13.3 1.0
CD2 B:HIS436 3.2 10.9 1.0
NE2 B:HIS436 3.3 15.6 1.0
CG B:HIS95 3.7 15.5 1.0
CA B:HIS95 3.7 15.4 1.0
ND1 B:HIS95 3.7 14.4 1.0
CG B:HIS436 3.8 12.9 1.0
CB B:HIS95 3.9 14.8 1.0
CU B:CU603 3.9 17.0 1.0
CE1 B:HIS436 3.9 11.7 1.0
O1 B:OXY620 3.9 28.2 1.0
CU B:CU602 4.0 22.5 1.0
CG B:HIS93 4.0 14.0 1.0
CG B:HIS434 4.0 14.1 1.0
ND1 B:HIS434 4.0 14.6 1.0
ND1 B:HIS93 4.0 14.0 1.0
ND1 B:HIS436 4.2 12.7 1.0
CD2 B:HIS95 4.3 14.7 1.0
CE1 B:HIS95 4.3 15.8 1.0
N B:GLY96 4.5 16.8 1.0
N B:HIS95 4.5 16.0 1.0
CA B:HIS436 4.5 11.5 1.0
NE2 B:HIS95 4.6 15.6 1.0
C B:HIS95 4.6 17.4 1.0
CB B:HIS436 4.7 11.0 1.0
O B:LEU435 4.8 9.7 1.0
NE2 B:HIS138 4.9 15.4 1.0
N B:HIS436 4.9 10.0 1.0
O B:HOH876 4.9 20.1 1.0
O B:TRP94 5.0 16.0 1.0

Reference:

N.Hakulinen, K.Kruus, A.Koivula, J.Rouvinen. A Crystallographic and Spectroscopic Study on the Effect of X-Ray Radiation on the Crystal Structure of Melanocarpus Albomyces Laccase. Biochem.Biophys.Res.Commun. V. 350 929 2006.
ISSN: ISSN 0006-291X
PubMed: 17045575
DOI: 10.1016/J.BBRC.2006.09.144
Page generated: Thu Sep 3 16:42:43 2020
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