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Copper in PDB 5or4: Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form

Protein crystallography data

The structure of Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form, PDB code: 5or4 was solved by N.Hakulinen, L.Penttinen, C.Rutanen, J.Rouvinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.79 / 2.45
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.856, 81.879, 82.705, 87.15, 89.04, 73.86
R / Rfree (%) 20.3 / 26.1

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form (pdb code 5or4). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form, PDB code: 5or4:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 5or4

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Copper binding site 1 out of 8 in the Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu2001

b:25.3
occ:1.00
NE2 A:HIS119 2.1 12.5 1.0
NE2 A:HIS102 2.1 14.6 1.0
NE2 A:HIS110 2.2 17.2 1.0
CE1 A:HIS110 2.8 18.5 1.0
CE1 A:HIS119 2.9 12.2 1.0
CE1 A:HIS102 3.1 15.0 1.0
CD2 A:HIS102 3.1 15.2 1.0
CD2 A:HIS119 3.2 14.5 1.0
CD2 A:HIS110 3.3 13.0 1.0
CD1 A:ILE109 3.7 17.6 1.0
ND1 A:HIS110 4.0 19.0 1.0
ND1 A:HIS119 4.1 12.5 1.0
ND1 A:HIS102 4.2 14.9 1.0
CG A:HIS102 4.2 13.9 1.0
CG A:HIS110 4.3 17.0 1.0
CG A:HIS119 4.3 14.6 1.0
CG1 A:ILE109 4.3 18.2 1.0
CZ3 A:TRP118 4.5 13.8 1.0
CE2 A:PHE308 4.7 15.8 1.0
CZ A:PHE308 4.7 15.4 1.0
CU A:CU2002 4.7 30.9 1.0
NE2 A:HIS312 4.7 15.3 1.0
CE3 A:TRP118 4.9 13.4 1.0

Copper binding site 2 out of 8 in 5or4

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Copper binding site 2 out of 8 in the Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu2002

b:30.9
occ:1.00
NE2 A:HIS288 2.0 21.4 1.0
NE2 A:HIS312 2.0 15.3 1.0
NE2 A:HIS284 2.1 18.1 1.0
CE1 A:HIS288 2.9 22.3 1.0
CE1 A:HIS312 2.9 12.9 1.0
CD2 A:HIS284 2.9 16.5 1.0
CD2 A:HIS312 3.0 13.1 1.0
CD2 A:HIS288 3.1 18.1 1.0
CE1 A:HIS284 3.2 17.3 1.0
ND1 A:HIS312 4.0 12.2 1.0
ND1 A:HIS288 4.0 22.1 1.0
CE2 A:PHE308 4.0 15.8 1.0
CG A:HIS284 4.1 14.2 1.0
CG A:HIS312 4.1 13.2 1.0
CG A:HIS288 4.1 21.5 1.0
ND1 A:HIS284 4.2 11.5 1.0
CD2 A:HIS311 4.2 17.6 1.0
NE2 A:HIS311 4.3 16.8 1.0
CD2 A:PHE308 4.7 14.7 1.0
NE2 A:HIS119 4.7 12.5 1.0
CU A:CU2001 4.7 25.3 1.0
CD2 A:HIS119 4.8 14.5 1.0
CZ A:PHE308 4.8 15.4 1.0

Copper binding site 3 out of 8 in 5or4

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Copper binding site 3 out of 8 in the Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2001

b:32.2
occ:1.00
NE2 B:HIS102 2.1 16.7 1.0
NE2 B:HIS119 2.2 20.4 1.0
NE2 B:HIS110 2.2 22.3 1.0
CE1 B:HIS110 2.7 19.9 1.0
CD2 B:HIS102 3.1 18.0 1.0
CE1 B:HIS119 3.1 17.9 1.0
CD2 B:HIS119 3.1 20.3 1.0
CE1 B:HIS102 3.2 17.7 1.0
CD2 B:HIS110 3.4 21.4 1.0
CD1 B:ILE109 3.8 19.1 1.0
ND1 B:HIS110 3.9 21.7 1.0
CG B:HIS102 4.2 15.9 1.0
ND1 B:HIS119 4.2 16.0 1.0
CG B:HIS110 4.2 20.5 1.0
ND1 B:HIS102 4.2 19.2 1.0
CG B:HIS119 4.3 19.4 1.0
CG1 B:ILE109 4.3 22.9 1.0
CZ B:PHE308 4.5 16.8 1.0
NE2 B:HIS312 4.6 20.5 1.0
CZ3 B:TRP118 4.6 16.1 1.0
CE2 B:PHE308 4.6 17.0 1.0
CU B:CU2002 4.7 32.3 1.0
CE3 B:TRP118 5.0 16.6 1.0

Copper binding site 4 out of 8 in 5or4

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Copper binding site 4 out of 8 in the Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2002

b:32.3
occ:1.00
NE2 B:HIS312 2.1 20.5 1.0
NE2 B:HIS288 2.1 23.5 1.0
NE2 B:HIS284 2.1 21.4 1.0
CD2 B:HIS284 2.9 18.0 1.0
CD2 B:HIS312 2.9 16.2 1.0
CD2 B:HIS288 3.0 22.5 1.0
CE1 B:HIS312 3.0 16.7 1.0
CE1 B:HIS288 3.1 23.2 1.0
CE1 B:HIS284 3.1 22.3 1.0
CE2 B:PHE308 3.9 17.0 1.0
CD2 B:HIS311 3.9 18.8 1.0
CG B:HIS312 4.0 15.7 1.0
ND1 B:HIS312 4.0 12.5 1.0
NE2 B:HIS311 4.0 19.3 1.0
CG B:HIS284 4.0 16.9 1.0
ND1 B:HIS284 4.1 20.4 1.0
ND1 B:HIS288 4.2 26.2 1.0
CG B:HIS288 4.2 22.6 1.0
CZ B:PHE308 4.5 16.8 1.0
CD2 B:PHE308 4.6 17.8 1.0
CU B:CU2001 4.7 32.2 1.0
CD2 B:HIS119 4.8 20.3 1.0
NE2 B:HIS119 4.8 20.4 1.0

Copper binding site 5 out of 8 in 5or4

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Copper binding site 5 out of 8 in the Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu2001

b:36.0
occ:1.00
NE2 C:HIS119 1.8 34.5 1.0
NE2 C:HIS102 2.1 28.9 1.0
NE2 C:HIS110 2.2 29.3 1.0
CE1 C:HIS119 2.2 30.6 1.0
CE1 C:HIS110 2.5 33.4 1.0
CE1 C:HIS102 3.0 29.0 1.0
CD2 C:HIS119 3.1 32.7 1.0
CD2 C:HIS102 3.1 28.8 1.0
CD2 C:HIS110 3.4 29.1 1.0
ND1 C:HIS119 3.5 27.2 1.0
ND1 C:HIS110 3.7 31.2 1.0
CD1 C:ILE109 3.7 28.5 1.0
CG C:HIS119 3.9 31.1 1.0
CG C:HIS110 4.1 31.7 1.0
ND1 C:HIS102 4.2 26.9 1.0
CG1 C:ILE109 4.2 28.1 1.0
CG C:HIS102 4.2 28.2 1.0
CZ3 C:TRP118 4.3 28.6 1.0
CZ C:PHE308 4.5 27.9 1.0
NE2 C:HIS312 4.6 31.0 1.0
CE3 C:TRP118 4.7 27.1 1.0
CE2 C:PHE308 4.7 30.4 1.0
CU C:CU2002 4.8 39.9 1.0
CE1 C:HIS312 5.0 28.5 1.0

Copper binding site 6 out of 8 in 5or4

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Copper binding site 6 out of 8 in the Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu2002

b:39.9
occ:1.00
NE2 C:HIS284 2.1 31.4 1.0
NE2 C:HIS312 2.1 31.0 1.0
NE2 C:HIS288 2.1 27.4 1.0
CD2 C:HIS284 2.9 30.0 1.0
CE1 C:HIS312 3.0 28.5 1.0
CD2 C:HIS312 3.0 31.0 1.0
CE1 C:HIS284 3.1 27.9 1.0
CD2 C:HIS288 3.1 27.6 1.0
CE1 C:HIS288 3.2 29.6 1.0
CD2 C:HIS311 3.9 29.8 1.0
NE2 C:HIS311 3.9 29.1 1.0
CE2 C:PHE308 4.0 30.4 1.0
CG C:HIS284 4.0 30.1 1.0
ND1 C:HIS312 4.0 28.6 1.0
CG C:HIS312 4.1 31.3 1.0
ND1 C:HIS284 4.1 29.3 1.0
CG C:HIS288 4.3 29.0 1.0
ND1 C:HIS288 4.3 27.3 1.0
CZ C:PHE308 4.6 27.9 1.0
NE2 C:HIS119 4.6 34.5 1.0
CD2 C:PHE308 4.7 27.5 1.0
CU C:CU2001 4.8 36.0 1.0
O C:HIS284 4.8 28.4 1.0
CD2 C:HIS119 4.8 32.7 1.0
NE2 C:HIS110 5.0 29.3 1.0

Copper binding site 7 out of 8 in 5or4

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Copper binding site 7 out of 8 in the Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu2001

b:32.8
occ:1.00
NE2 D:HIS119 2.1 26.2 1.0
NE2 D:HIS102 2.1 25.8 1.0
NE2 D:HIS110 2.2 29.8 1.0
CE1 D:HIS110 2.8 27.1 1.0
CD2 D:HIS102 3.0 25.6 1.0
CE1 D:HIS119 3.1 23.6 1.0
CD2 D:HIS119 3.2 23.9 1.0
CE1 D:HIS102 3.2 24.0 1.0
O D:HOH2194 3.3 30.5 1.0
CD2 D:HIS110 3.3 23.6 1.0
CD1 D:ILE109 3.9 23.5 1.0
ND1 D:HIS110 4.0 30.1 1.0
CG D:HIS102 4.2 24.9 1.0
ND1 D:HIS119 4.2 21.3 1.0
CG D:HIS110 4.2 27.1 1.0
ND1 D:HIS102 4.3 25.0 1.0
CG D:HIS119 4.3 23.9 1.0
CG1 D:ILE109 4.4 24.6 1.0
CU D:CU2002 4.6 36.9 1.0
CZ3 D:TRP118 4.6 23.4 1.0
NE2 D:HIS312 4.6 27.3 1.0
CE2 D:PHE308 4.7 28.7 1.0
CZ D:PHE308 4.7 26.6 1.0

Copper binding site 8 out of 8 in 5or4

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Copper binding site 8 out of 8 in the Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Aspergillus Oryzae Catechol Oxidase in Deoxy-Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu2002

b:36.9
occ:1.00
NE2 D:HIS284 2.0 32.2 1.0
NE2 D:HIS312 2.1 27.3 1.0
NE2 D:HIS288 2.1 28.1 1.0
CD2 D:HIS284 2.7 27.3 1.0
CE1 D:HIS288 2.9 28.6 1.0
CE1 D:HIS312 3.0 23.0 1.0
CD2 D:HIS312 3.0 23.1 1.0
CD2 D:HIS288 3.2 28.2 1.0
CE1 D:HIS284 3.2 30.5 1.0
O D:HOH2194 3.3 30.5 1.0
CG D:HIS284 3.9 27.2 1.0
CE2 D:PHE308 3.9 28.7 1.0
ND1 D:HIS312 4.0 21.1 1.0
CG D:HIS312 4.1 21.5 1.0
CD2 D:HIS311 4.1 23.0 1.0
ND1 D:HIS288 4.1 30.9 1.0
ND1 D:HIS284 4.1 31.8 1.0
CG D:HIS288 4.2 29.8 1.0
NE2 D:HIS311 4.3 24.8 1.0
CD2 D:PHE308 4.6 26.6 1.0
CU D:CU2001 4.6 32.8 1.0
CZ D:PHE308 4.7 26.6 1.0
CD2 D:HIS119 4.8 23.9 1.0
NE2 D:HIS119 4.8 26.2 1.0

Reference:

L.Penttinen, C.Rutanen, M.Saloheimo, K.Kruus, J.Rouvinen, N.Hakulinen. A New Crystal Form of Aspergillus Oryzae Catechol Oxidase and Evaluation of Copper Site Structures in Coupled Binuclear Copper Enzymes. Plos One V. 13 96691 2018.
ISSN: ESSN 1932-6203
PubMed: 29715329
DOI: 10.1371/JOURNAL.PONE.0196691
Page generated: Sun Dec 13 11:19:37 2020

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