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Copper in PDB 2ih9: A High-Dose Crystal Structure of A Recombinant Melanocarbus Albomyces Laccase

Enzymatic activity of A High-Dose Crystal Structure of A Recombinant Melanocarbus Albomyces Laccase

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

Protein crystallography data

The structure of A High-Dose Crystal Structure of A Recombinant Melanocarbus Albomyces Laccase, PDB code: 2ih9 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 (°) 174.490, 62.330, 125.100, 90.00, 96.25, 90.00
R / Rfree (%) 26.3 / 29.9

Other elements in 2ih9:

The structure of A High-Dose Crystal Structure of A Recombinant Melanocarbus Albomyces Laccase also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the A High-Dose Crystal Structure of A Recombinant Melanocarbus Albomyces Laccase (pdb code 2ih9). 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 High-Dose Crystal Structure of A Recombinant Melanocarbus Albomyces Laccase, PDB code: 2ih9:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 2ih9

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

b:16.1
occ:1.00
ND1 A:HIS508 1.9 13.9 1.0
ND1 A:HIS431 1.9 15.0 1.0
SG A:CYS503 2.2 11.4 1.0
CE1 A:HIS431 2.8 13.6 1.0
CE1 A:HIS508 2.9 14.1 1.0
CG A:HIS508 2.9 14.5 1.0
CG A:HIS431 3.0 14.1 1.0
CB A:HIS508 3.3 11.9 1.0
CB A:CYS503 3.4 14.1 1.0
CB A:HIS431 3.5 11.1 1.0
CD1 A:ILE505 3.8 13.6 1.0
CD1 A:LEU513 3.9 12.5 1.0
CA A:HIS431 3.9 12.9 1.0
NE2 A:HIS431 4.0 13.5 1.0
NE2 A:HIS508 4.0 13.4 1.0
CD2 A:HIS508 4.0 12.6 1.0
CD2 A:HIS431 4.1 13.6 1.0
CB A:ILE505 4.1 13.5 1.0
CG1 A:ILE505 4.2 13.4 1.0
O A:PRO430 4.3 7.5 1.0
CD A:PRO432 4.5 15.5 1.0
CA A:CYS503 4.7 12.3 1.0
CA A:HIS508 4.8 15.2 1.0
N A:HIS431 4.9 9.4 1.0
C A:HIS431 4.9 13.6 1.0
CG2 A:ILE505 4.9 12.6 1.0
N A:PRO432 4.9 15.0 1.0
N A:ILE505 5.0 8.2 1.0

Copper binding site 2 out of 8 in 2ih9

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

b:19.1
occ:1.00
NE2 A:HIS436 1.9 16.7 1.0
NE2 A:HIS502 1.9 15.3 1.0
NE2 A:HIS140 2.0 15.0 1.0
O A:HOH1160 2.6 11.2 1.0
CE1 A:HIS436 2.6 15.9 1.0
CE1 A:HIS502 2.8 14.3 1.0
CE1 A:HIS140 2.8 15.0 1.0
CD2 A:HIS502 3.0 12.8 1.0
CD2 A:HIS140 3.1 15.3 1.0
CD2 A:HIS436 3.1 14.5 1.0
ND1 A:HIS436 3.8 14.7 1.0
ND1 A:HIS502 3.9 15.6 1.0
ND1 A:HIS140 4.0 15.2 1.0
CD2 A:HIS93 4.1 10.0 1.0
CG A:HIS502 4.1 14.0 1.0
CU A:CU604 4.1 21.4 1.0
CD2 A:HIS434 4.1 18.2 1.0
CG A:HIS436 4.1 14.2 1.0
CG A:HIS140 4.2 14.0 1.0
NE2 A:HIS93 4.2 14.3 1.0
CD1 A:LEU500 4.5 17.9 1.0
NE2 A:HIS434 4.6 20.8 1.0
CB A:LEU500 4.8 11.9 1.0
CE1 A:HIS138 4.8 12.8 1.0
CG A:HIS93 4.8 11.3 1.0
CU A:CU603 4.9 16.4 1.0

Copper binding site 3 out of 8 in 2ih9

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

b:16.4
occ:1.00
NE2 A:HIS138 1.9 15.2 1.0
ND1 A:HIS95 1.9 17.6 1.0
NE2 A:HIS504 2.0 11.1 1.0
O A:HOH1160 2.3 11.2 1.0
CE1 A:HIS95 2.9 18.1 1.0
CE1 A:HIS504 2.9 9.8 1.0
CD2 A:HIS138 2.9 12.7 1.0
CE1 A:HIS138 2.9 12.8 1.0
CG A:HIS95 3.0 18.2 1.0
CD2 A:HIS504 3.1 6.4 1.0
CB A:HIS95 3.4 19.3 1.0
CZ2 A:TRP136 3.7 12.6 1.0
CU A:CU604 3.9 21.4 1.0
CD2 A:HIS93 4.0 10.0 1.0
NE2 A:HIS95 4.0 16.3 1.0
ND1 A:HIS138 4.0 15.3 1.0
ND1 A:HIS504 4.0 5.6 1.0
CG A:HIS138 4.0 14.9 1.0
CD2 A:HIS95 4.1 18.2 1.0
CE2 A:TRP136 4.1 14.3 1.0
CG A:HIS504 4.2 7.0 1.0
CH2 A:TRP136 4.3 12.2 1.0
CD2 A:HIS434 4.3 18.2 1.0
NE2 A:HIS434 4.4 20.8 1.0
NE1 A:TRP136 4.4 13.7 1.0
NE2 A:HIS93 4.5 14.3 1.0
CA A:HIS95 4.7 19.7 1.0
CU A:CU602 4.9 19.1 1.0

Copper binding site 4 out of 8 in 2ih9

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

b:21.4
occ:1.00
NE2 A:HIS93 1.9 14.3 1.0
NE2 A:HIS434 1.9 20.8 1.0
CD2 A:HIS93 2.8 10.0 1.0
CD2 A:HIS434 2.9 18.2 1.0
CL A:CL610 2.9 31.9 1.0
CE1 A:HIS434 2.9 20.5 1.0
CE1 A:HIS93 2.9 10.7 1.0
CD2 A:HIS436 3.1 14.5 1.0
NE2 A:HIS436 3.2 16.7 1.0
O A:HOH1160 3.5 11.2 1.0
CG A:HIS95 3.7 18.2 1.0
CG A:HIS436 3.7 14.2 1.0
ND1 A:HIS95 3.8 17.6 1.0
CA A:HIS95 3.8 19.7 1.0
CE1 A:HIS436 3.8 15.9 1.0
CB A:HIS95 3.9 19.3 1.0
CU A:CU603 3.9 16.4 1.0
CG A:HIS93 4.0 11.3 1.0
CG A:HIS434 4.0 18.8 1.0
ND1 A:HIS434 4.0 20.6 1.0
ND1 A:HIS93 4.0 11.8 1.0
CU A:CU602 4.1 19.1 1.0
ND1 A:HIS436 4.1 14.7 1.0
CD2 A:HIS95 4.2 18.2 1.0
CE1 A:HIS95 4.3 18.1 1.0
CA A:HIS436 4.5 12.0 1.0
NE2 A:HIS95 4.6 16.3 1.0
N A:HIS95 4.6 19.4 1.0
CB A:HIS436 4.7 13.5 1.0
N A:GLY96 4.7 21.6 1.0
C A:HIS95 4.8 21.0 1.0
O A:LEU435 4.9 8.2 1.0
N A:HIS436 4.9 10.2 1.0
NE2 A:HIS138 5.0 15.2 1.0

Copper binding site 5 out of 8 in 2ih9

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

b:17.4
occ:1.00
ND1 B:HIS431 1.9 17.8 1.0
ND1 B:HIS508 1.9 15.2 1.0
SG B:CYS503 2.2 14.2 1.0
CE1 B:HIS431 2.8 18.4 1.0
CG B:HIS508 2.9 13.5 1.0
CE1 B:HIS508 2.9 16.3 1.0
CG B:HIS431 2.9 18.3 1.0
CB B:HIS508 3.3 13.6 1.0
CB B:CYS503 3.3 15.3 1.0
CB B:HIS431 3.4 14.1 1.0
CD1 B:LEU513 3.8 13.5 1.0
CA B:HIS431 3.9 14.0 1.0
NE2 B:HIS431 4.0 18.3 1.0
NE2 B:HIS508 4.0 11.4 1.0
CD1 B:ILE505 4.0 12.5 1.0
CD2 B:HIS508 4.0 15.2 1.0
CD2 B:HIS431 4.0 18.0 1.0
CB B:ILE505 4.2 8.6 1.0
CG1 B:ILE505 4.4 9.0 1.0
CD B:PRO432 4.4 15.4 1.0
O B:PRO430 4.5 11.6 1.0
CA B:CYS503 4.7 13.7 1.0
CA B:HIS508 4.8 14.3 1.0
C B:HIS431 4.9 13.2 1.0
N B:HIS431 4.9 12.3 1.0
N B:PRO432 4.9 14.0 1.0
CG2 B:ILE505 5.0 7.2 1.0
N B:ILE505 5.0 8.8 1.0

Copper binding site 6 out of 8 in 2ih9

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

b:18.3
occ:1.00
NE2 B:HIS436 1.9 16.1 1.0
NE2 B:HIS502 1.9 20.7 1.0
NE2 B:HIS140 2.0 16.8 1.0
O B:HOH1141 2.3 13.8 1.0
CE1 B:HIS436 2.6 16.4 1.0
CE1 B:HIS502 2.9 21.3 1.0
CE1 B:HIS140 2.9 15.1 1.0
CD2 B:HIS502 2.9 19.7 1.0
CD2 B:HIS436 3.1 16.0 1.0
CD2 B:HIS140 3.1 16.4 1.0
ND1 B:HIS436 3.8 15.7 1.0
CD2 B:HIS93 4.0 12.7 1.0
ND1 B:HIS502 4.0 19.3 1.0
NE2 B:HIS93 4.0 16.0 1.0
ND1 B:HIS140 4.1 13.9 1.0
CG B:HIS502 4.1 18.5 1.0
CG B:HIS436 4.1 15.3 1.0
CD2 B:HIS434 4.1 17.4 1.0
CU B:CU604 4.1 22.1 1.0
CG B:HIS140 4.2 13.2 1.0
O B:HOH1087 4.4 33.8 1.0
CD1 B:LEU500 4.5 10.9 1.0
NE2 B:HIS434 4.5 18.8 1.0
CG B:HIS93 4.7 13.6 1.0
CB B:LEU500 4.8 9.1 1.0
CE1 B:HIS93 4.8 13.8 1.0
CU B:CU603 4.8 18.7 1.0
CE1 B:HIS138 4.9 13.7 1.0

Copper binding site 7 out of 8 in 2ih9

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

b:18.7
occ:1.00
NE2 B:HIS138 2.0 16.4 1.0
ND1 B:HIS95 2.0 19.8 1.0
NE2 B:HIS504 2.0 5.5 1.0
O B:HOH1141 2.5 13.8 1.0
CE1 B:HIS95 2.8 20.2 1.0
CE1 B:HIS504 2.8 2.2 1.0
CE1 B:HIS138 2.9 13.7 1.0
CD2 B:HIS138 3.0 13.8 1.0
CD2 B:HIS504 3.1 3.4 1.0
CG B:HIS95 3.1 18.8 1.0
CB B:HIS95 3.5 19.1 1.0
CZ2 B:TRP136 3.8 16.7 1.0
CD2 B:HIS93 3.8 12.7 1.0
ND1 B:HIS138 4.0 15.8 1.0
NE2 B:HIS95 4.0 20.4 1.0
ND1 B:HIS504 4.0 1.4 1.0
CG B:HIS138 4.1 15.4 1.0
CU B:CU604 4.1 22.1 1.0
CD2 B:HIS95 4.1 18.6 1.0
CG B:HIS504 4.1 2.2 1.0
CD2 B:HIS434 4.2 17.4 1.0
NE2 B:HIS93 4.2 16.0 1.0
NE2 B:HIS434 4.2 18.8 1.0
CE2 B:TRP136 4.2 19.1 1.0
CH2 B:TRP136 4.3 15.1 1.0
NE1 B:TRP136 4.6 21.1 1.0
O B:HOH1087 4.7 33.8 1.0
CA B:HIS95 4.7 19.6 1.0
CU B:CU602 4.8 18.3 1.0
CG B:HIS434 5.0 17.6 1.0

Copper binding site 8 out of 8 in 2ih9

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

b:22.1
occ:1.00
NE2 B:HIS93 1.9 16.0 1.0
NE2 B:HIS434 1.9 18.8 1.0
CL B:CL610 2.8 32.1 1.0
CE1 B:HIS93 2.8 13.8 1.0
CE1 B:HIS434 2.9 20.2 1.0
CD2 B:HIS434 2.9 17.4 1.0
CD2 B:HIS93 3.0 12.7 1.0
CD2 B:HIS436 3.2 16.0 1.0
NE2 B:HIS436 3.3 16.1 1.0
O B:HOH1141 3.4 13.8 1.0
CG B:HIS436 3.8 15.3 1.0
ND1 B:HIS95 3.8 19.8 1.0
CA B:HIS95 3.8 19.6 1.0
CG B:HIS95 3.9 18.8 1.0
ND1 B:HIS93 3.9 14.9 1.0
CE1 B:HIS436 3.9 16.4 1.0
ND1 B:HIS434 4.0 19.5 1.0
CG B:HIS434 4.0 17.6 1.0
CU B:CU603 4.1 18.7 1.0
CG B:HIS93 4.1 13.6 1.0
CU B:CU602 4.1 18.3 1.0
CB B:HIS95 4.1 19.1 1.0
ND1 B:HIS436 4.2 15.7 1.0
CE1 B:HIS95 4.3 20.2 1.0
CD2 B:HIS95 4.4 18.6 1.0
CA B:HIS436 4.4 12.7 1.0
N B:GLY96 4.5 22.0 1.0
CB B:HIS436 4.6 12.0 1.0
NE2 B:HIS95 4.6 20.4 1.0
N B:HIS95 4.7 19.2 1.0
O B:LEU435 4.7 11.7 1.0
C B:HIS95 4.7 21.0 1.0
N B:HIS436 4.8 11.0 1.0
O B:HOH821 4.9 20.8 1.0
C B:LEU435 4.9 13.5 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: Wed Oct 28 14:20:10 2020
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