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Copper in PDB 2q9o: Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase

Enzymatic activity of Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase

All present enzymatic activity of Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase:
1.10.3.2;

Protein crystallography data

The structure of Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase, PDB code: 2q9o 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) 15.00 / 1.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 173.740, 61.900, 124.210, 90.00, 96.36, 90.00
R / Rfree (%) 16.7 / 21.2

Copper Binding Sites:

The binding sites of Copper atom in the Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase (pdb code 2q9o). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase, PDB code: 2q9o:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 2q9o

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Copper binding site 1 out of 8 in the Near-Atomic Resolution Structure of A 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 Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu2001

b:7.6
occ:1.00
 ND1 A:HIS431 1.9 6.1 1.0
ND1 A:HIS508 2.0 6.9 1.0
SG A:CYS503 2.2 7.1 1.0
CE1 A:HIS431 2.9 6.6 1.0
CG A:HIS431 3.0 6.3 1.0
CG A:HIS508 3.0 6.5 1.0
CE1 A:HIS508 3.0 7.5 1.0
CB A:CYS503 3.2 6.9 1.0
CB A:HIS508 3.3 6.2 1.0
CB A:HIS431 3.4 6.5 1.0
CD1 A:ILE505 3.6 6.5 1.0
CD1 A:LEU513 3.6 7.7 1.0
CA A:HIS431 3.9 5.4 1.0
NE2 A:HIS431 4.0 7.1 1.0
CD2 A:HIS431 4.1 6.2 1.0
NE2 A:HIS508 4.1 7.0 1.0
CB A:ILE505 4.1 4.9 1.0
CD2 A:HIS508 4.1 7.1 1.0
CG1 A:ILE505 4.3 5.4 1.0
CD A:PRO432 4.4 6.3 1.0
O A:PRO430 4.4 8.3 1.0
CA A:CYS503 4.6 6.4 1.0
C A:HIS431 4.8 5.7 1.0
CA A:HIS508 4.8 6.2 1.0
N A:ILE505 4.9 6.1 1.0
N A:PRO432 4.9 5.7 1.0
N A:HIS431 4.9 7.2 1.0
CG A:LEU513 4.9 6.6 1.0
CG2 A:ILE505 4.9 6.2 1.0

Copper binding site 2 out of 8 in 2q9o

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Copper binding site 2 out of 8 in the Near-Atomic Resolution Structure of A 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 Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu2002

b:11.9
occ:1.00
 NE2 A:HIS436 2.0 7.1 1.0
NE2 A:HIS502 2.0 7.7 1.0
NE2 A:HIS140 2.0 8.2 1.0
O1 A:OXY4006 2.0 24.4 1.0
O2 A:OXY4006 2.5 26.0 1.0
CE1 A:HIS436 2.8 6.9 1.0
CE1 A:HIS502 3.0 8.1 1.0
CE1 A:HIS140 3.0 8.6 1.0
CD2 A:HIS502 3.0 7.3 1.0
CD2 A:HIS436 3.1 6.7 1.0
CD2 A:HIS140 3.1 8.3 1.0
CD2 A:HIS434 4.0 6.4 1.0
ND1 A:HIS436 4.0 6.9 1.0
CU A:CU2004 4.0 10.1 1.0
CD2 A:HIS93 4.0 6.8 1.0
ND1 A:HIS502 4.1 7.3 1.0
CG A:HIS502 4.1 6.5 1.0
ND1 A:HIS140 4.1 9.2 1.0
CG A:HIS436 4.1 7.1 1.0
NE2 A:HIS93 4.1 7.2 1.0
CG A:HIS140 4.2 7.4 1.0
O A:HOH4289 4.2 16.6 1.0
CD1 A:LEU500 4.4 9.7 1.0
NE2 A:HIS434 4.4 6.6 1.0
CE1 A:HIS138 4.6 8.1 1.0
CU A:CU2003 4.7 11.7 1.0
CB A:LEU500 4.7 7.1 1.0
CG A:HIS93 4.7 6.0 1.0
CE1 A:HIS93 4.9 6.9 1.0
NE2 A:HIS504 4.9 7.5 1.0

Copper binding site 3 out of 8 in 2q9o

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Copper binding site 3 out of 8 in the Near-Atomic Resolution Structure of A 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 Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu2003

b:11.7
occ:1.00
 NE2 A:HIS138 2.0 8.2 1.0
ND1 A:HIS95 2.0 7.8 1.0
NE2 A:HIS504 2.1 7.5 1.0
O2 A:OXY4006 2.5 26.0 1.0
O1 A:OXY4006 2.6 24.4 1.0
CE1 A:HIS95 2.9 7.6 1.0
CE1 A:HIS138 3.0 8.1 1.0
CD2 A:HIS138 3.0 7.1 1.0
CE1 A:HIS504 3.0 6.9 1.0
CG A:HIS95 3.1 8.2 1.0
CD2 A:HIS504 3.1 6.3 1.0
CB A:HIS95 3.4 8.2 1.0
CZ2 A:TRP136 3.6 5.7 1.0
CU A:CU2004 4.0 10.1 1.0
CD2 A:HIS93 4.0 6.8 1.0
CE2 A:TRP136 4.0 5.8 1.0
ND1 A:HIS138 4.1 7.6 1.0
NE2 A:HIS95 4.1 8.1 1.0
CD2 A:HIS95 4.1 8.9 1.0
CG A:HIS138 4.1 6.4 1.0
CH2 A:TRP136 4.2 6.5 1.0
NE2 A:HIS434 4.2 6.6 1.0
ND1 A:HIS504 4.2 6.4 1.0
CG A:HIS504 4.2 5.9 1.0
CD2 A:HIS434 4.3 6.4 1.0
NE1 A:TRP136 4.3 6.7 1.0
NE2 A:HIS93 4.4 7.2 1.0
O A:HOH4289 4.6 16.6 1.0
CA A:HIS95 4.6 7.3 1.0
CU A:CU2002 4.7 11.9 1.0
CE1 A:HIS434 4.9 7.6 1.0
CD2 A:TRP136 4.9 5.5 1.0
O A:HOH4059 5.0 12.2 1.0

Copper binding site 4 out of 8 in 2q9o

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Copper binding site 4 out of 8 in the Near-Atomic Resolution Structure of A 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 Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu2004

b:10.1
occ:1.00
 NE2 A:HIS93 1.9 7.2 1.0
NE2 A:HIS434 1.9 6.6 1.0
O2 A:OXY4006 2.3 26.0 1.0
CL A:CL2010 2.5 15.2 1.0
CE1 A:HIS434 2.8 7.6 1.0
CE1 A:HIS93 2.8 6.9 1.0
CD2 A:HIS93 2.9 6.8 1.0
CD2 A:HIS434 3.0 6.4 1.0
CD2 A:HIS436 3.3 6.7 1.0
NE2 A:HIS436 3.4 7.1 1.0
O1 A:OXY4006 3.4 24.4 1.0
ND1 A:HIS95 3.6 7.8 1.0
CG A:HIS436 3.7 7.1 1.0
CG A:HIS95 3.7 8.2 1.0
CA A:HIS95 3.8 7.3 1.0
CE1 A:HIS436 3.9 6.9 1.0
CB A:HIS95 3.9 8.2 1.0
CU A:CU2003 4.0 11.7 1.0
CU A:CU2002 4.0 11.9 1.0
ND1 A:HIS93 4.0 6.9 1.0
ND1 A:HIS434 4.0 7.3 1.0
CG A:HIS93 4.0 6.0 1.0
CG A:HIS434 4.1 7.1 1.0
ND1 A:HIS436 4.1 6.9 1.0
CE1 A:HIS95 4.2 7.6 1.0
CD2 A:HIS95 4.4 8.9 1.0
CA A:HIS436 4.5 5.3 1.0
N A:GLY96 4.5 9.3 1.0
CB A:HIS436 4.6 6.2 1.0
NE2 A:HIS95 4.6 8.1 1.0
C A:HIS95 4.7 7.9 1.0
N A:HIS95 4.8 6.9 1.0
O A:LEU435 4.8 5.8 1.0
N A:HIS436 4.8 4.9 1.0
O A:TRP94 4.9 7.5 1.0

Copper binding site 5 out of 8 in 2q9o

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Copper binding site 5 out of 8 in the Near-Atomic Resolution Structure of A 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 Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2001

b:7.9
occ:1.00
 ND1 B:HIS431 2.0 7.3 1.0
ND1 B:HIS508 2.0 7.8 1.0
SG B:CYS503 2.2 7.2 1.0
CE1 B:HIS431 2.9 7.2 1.0
CG B:HIS508 3.0 7.4 1.0
CE1 B:HIS508 3.0 7.7 1.0
CG B:HIS431 3.0 7.2 1.0
CB B:CYS503 3.2 7.3 1.0
CB B:HIS508 3.3 6.8 1.0
CB B:HIS431 3.4 7.2 1.0
CD1 B:ILE505 3.6 7.4 1.0
CD1 B:LEU513 3.8 7.4 1.0
CA B:HIS431 3.9 6.8 1.0
NE2 B:HIS431 4.1 7.3 1.0
CB B:ILE505 4.1 6.3 1.0
CD2 B:HIS431 4.1 7.2 1.0
NE2 B:HIS508 4.1 7.8 1.0
CD2 B:HIS508 4.1 7.7 1.0
CG1 B:ILE505 4.2 6.9 1.0
CD B:PRO432 4.3 6.5 1.0
O B:PRO430 4.4 7.5 1.0
CA B:CYS503 4.6 6.3 1.0
CA B:HIS508 4.8 7.0 1.0
C B:HIS431 4.8 6.0 1.0
N B:ILE505 4.8 6.2 1.0
N B:PRO432 4.9 6.0 1.0
N B:HIS431 4.9 7.0 1.0
CG2 B:ILE505 4.9 7.0 1.0

Copper binding site 6 out of 8 in 2q9o

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Copper binding site 6 out of 8 in the Near-Atomic Resolution Structure of A 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 Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2002

b:12.3
occ:1.00
 NE2 B:HIS436 2.0 6.7 1.0
NE2 B:HIS502 2.0 7.6 1.0
NE2 B:HIS140 2.1 10.4 1.0
O1 B:OXY4005 2.2 23.9 1.0
O2 B:OXY4005 2.3 25.2 1.0
CE1 B:HIS436 2.8 6.9 1.0
CE1 B:HIS140 3.0 10.1 1.0
CD2 B:HIS502 3.0 7.9 1.0
CE1 B:HIS502 3.1 8.1 1.0
CD2 B:HIS436 3.1 6.8 1.0
CD2 B:HIS140 3.2 8.9 1.0
CD2 B:HIS434 4.0 6.9 1.0
CU B:CU2004 4.0 10.6 1.0
ND1 B:HIS436 4.0 6.5 1.0
CD2 B:HIS93 4.0 7.6 1.0
ND1 B:HIS140 4.1 8.7 1.0
CG B:HIS502 4.1 7.2 1.0
ND1 B:HIS502 4.1 7.3 1.0
CG B:HIS436 4.2 6.8 1.0
NE2 B:HIS93 4.2 7.6 1.0
O B:HOH4223 4.2 16.6 1.0
CG B:HIS140 4.2 8.1 1.0
CD1 B:LEU500 4.4 8.7 1.0
NE2 B:HIS434 4.5 6.8 1.0
CB B:LEU500 4.6 7.5 1.0
CE1 B:HIS138 4.6 8.3 1.0
CU B:CU2003 4.7 11.7 1.0
CG B:HIS93 4.8 7.8 1.0
NE2 B:HIS504 4.9 7.5 1.0
CE1 B:HIS93 4.9 7.6 1.0

Copper binding site 7 out of 8 in 2q9o

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Copper binding site 7 out of 8 in the Near-Atomic Resolution Structure of A 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 Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2003

b:11.7
occ:1.00
 ND1 B:HIS95 2.0 7.8 1.0
NE2 B:HIS138 2.0 8.1 1.0
NE2 B:HIS504 2.0 7.5 1.0
O2 B:OXY4005 2.5 25.2 1.0
O1 B:OXY4005 2.6 23.9 1.0
CE1 B:HIS95 2.9 7.4 1.0
CE1 B:HIS138 2.9 8.3 1.0
CD2 B:HIS138 2.9 8.2 1.0
CE1 B:HIS504 3.0 7.5 1.0
CG B:HIS95 3.1 7.5 1.0
CD2 B:HIS504 3.1 7.3 1.0
CB B:HIS95 3.4 8.4 1.0
CZ2 B:TRP136 3.6 5.3 1.0
CU B:CU2004 4.0 10.6 1.0
CD2 B:HIS93 4.0 7.6 1.0
ND1 B:HIS138 4.0 8.0 1.0
CE2 B:TRP136 4.1 5.7 1.0
NE2 B:HIS95 4.1 7.8 1.0
CG B:HIS138 4.1 7.4 1.0
CD2 B:HIS95 4.1 7.1 1.0
ND1 B:HIS504 4.1 7.0 1.0
CG B:HIS504 4.2 7.3 1.0
CD2 B:HIS434 4.2 6.9 1.0
CH2 B:TRP136 4.2 6.2 1.0
NE2 B:HIS434 4.2 6.8 1.0
NE1 B:TRP136 4.3 6.5 1.0
NE2 B:HIS93 4.5 7.6 1.0
O B:HOH4223 4.6 16.6 1.0
CA B:HIS95 4.6 7.9 1.0
CU B:CU2002 4.7 12.3 1.0
O B:HOH4098 5.0 15.7 1.0
CD2 B:TRP136 5.0 5.6 1.0

Copper binding site 8 out of 8 in 2q9o

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Copper binding site 8 out of 8 in the Near-Atomic Resolution Structure of A 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 Near-Atomic Resolution Structure of A Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2004

b:10.6
occ:1.00
 NE2 B:HIS93 1.9 7.6 1.0
NE2 B:HIS434 1.9 6.8 1.0
CL B:CL2010 2.5 15.4 1.0
O2 B:OXY4005 2.7 25.2 1.0
CD2 B:HIS93 2.9 7.6 1.0
CE1 B:HIS93 2.9 7.6 1.0
CD2 B:HIS434 2.9 6.9 1.0
CE1 B:HIS434 2.9 7.7 1.0
CD2 B:HIS436 3.3 6.8 1.0
NE2 B:HIS436 3.4 6.7 1.0
ND1 B:HIS95 3.6 7.8 1.0
CG B:HIS95 3.7 7.5 1.0
O1 B:OXY4005 3.8 23.9 1.0
CG B:HIS436 3.8 6.8 1.0
CA B:HIS95 3.8 7.9 1.0
CE1 B:HIS436 3.9 6.9 1.0
CB B:HIS95 3.9 8.4 1.0
CU B:CU2003 4.0 11.7 1.0
CU B:CU2002 4.0 12.3 1.0
ND1 B:HIS93 4.0 6.8 1.0
CG B:HIS93 4.1 7.8 1.0
ND1 B:HIS434 4.1 7.3 1.0
CG B:HIS434 4.1 7.0 1.0
ND1 B:HIS436 4.1 6.5 1.0
CE1 B:HIS95 4.2 7.4 1.0
CD2 B:HIS95 4.3 7.1 1.0
N B:GLY96 4.5 8.6 1.0
CA B:HIS436 4.5 6.3 1.0
NE2 B:HIS95 4.5 7.8 1.0
CB B:HIS436 4.6 6.5 1.0
C B:HIS95 4.7 8.4 1.0
N B:HIS95 4.7 7.1 1.0
N B:HIS436 4.8 6.2 1.0
O B:LEU435 4.9 6.2 1.0
O B:TRP94 4.9 7.8 1.0

Reference:

N.Hakulinen, M.Andberg, J.Kallio, A.Koivula, K.Kruus, J.Rouvinen. A Near Atomic Resolution Structure of A Melanocarpus Albomyces Laccase. J.Struct.Biol. V. 162 29 2008.
ISSN: ISSN 1047-8477
PubMed: 18249560
DOI: 10.1016/J.JSB.2007.12.003
Page generated: Thu Sep 3 16:49:04 2020
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