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Copper in PDB 2yxw: The Deletion Mutant of Multicopper Oxidase Cueo

Protein crystallography data

The structure of The Deletion Mutant of Multicopper Oxidase Cueo, PDB code: 2yxw was solved by Y.Higuchi, H.Komori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.90 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.326, 51.573, 86.698, 83.77, 90.38, 67.14
R / Rfree (%) 17.7 / 20.7

Copper Binding Sites:

The binding sites of Copper atom in the The Deletion Mutant of Multicopper Oxidase Cueo (pdb code 2yxw). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 10 binding sites of Copper where determined in the The Deletion Mutant of Multicopper Oxidase Cueo, PDB code: 2yxw:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 10 in 2yxw

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Copper binding site 1 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:22.4
occ:1.00
ND1 A:HIS505 2.0 23.5 1.0
ND1 A:HIS443 2.1 20.2 1.0
SG A:CYS500 2.2 21.8 1.0
CE1 A:HIS443 3.0 22.1 1.0
CG A:HIS505 3.0 20.7 1.0
CE1 A:HIS505 3.0 22.9 1.0
CG A:HIS443 3.1 21.2 1.0
CB A:CYS500 3.2 21.1 1.0
SD A:MET510 3.3 23.1 1.0
CB A:HIS505 3.3 22.3 1.0
CB A:HIS443 3.5 21.7 1.0
CA A:HIS443 3.7 21.3 1.0
O A:LEU442 3.7 23.6 1.0
CB A:LEU502 4.0 21.0 1.0
NE2 A:HIS443 4.1 22.2 1.0
CE A:MET510 4.1 22.1 1.0
NE2 A:HIS505 4.1 22.4 1.0
CD2 A:HIS505 4.1 22.7 1.0
CD2 A:HIS443 4.2 21.7 1.0
C A:LEU442 4.4 22.3 1.0
N A:HIS443 4.4 21.1 1.0
CD1 A:LEU502 4.6 23.2 1.0
CA A:CYS500 4.6 21.1 1.0
CG A:MET510 4.8 21.5 1.0
CG A:LEU502 4.8 22.4 1.0
CA A:HIS505 4.9 21.9 1.0
O A:LEU502 4.9 21.0 1.0
C A:HIS443 4.9 21.7 1.0
N A:LEU502 5.0 21.5 1.0

Copper binding site 2 out of 10 in 2yxw

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Copper binding site 2 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu703

b:33.4
occ:1.00
NE2 A:HIS446 1.9 24.9 1.0
NE2 A:HIS101 2.0 24.6 1.0
O A:HOH755 2.7 14.6 1.0
O1 A:C2O702 2.7 36.7 1.0
CE1 A:HIS101 2.9 26.9 1.0
CE1 A:HIS446 2.9 23.5 1.0
CD2 A:HIS446 2.9 22.9 1.0
CD2 A:HIS101 3.0 24.5 1.0
CD2 A:HIS448 3.1 25.4 1.0
NE2 A:HIS448 3.2 24.0 1.0
CA A:HIS103 3.5 21.9 1.0
CG A:HIS103 3.5 22.5 1.0
ND1 A:HIS103 3.5 22.5 1.0
CU2 A:C2O702 3.6 29.2 1.0
CG A:HIS448 3.7 23.2 1.0
CB A:HIS103 3.7 21.6 1.0
CE1 A:HIS448 3.8 25.6 1.0
CU3 A:C2O702 3.9 25.4 1.0
ND1 A:HIS446 4.0 25.0 1.0
ND1 A:HIS101 4.0 25.9 1.0
CG A:HIS446 4.0 22.0 1.0
ND1 A:HIS448 4.0 24.8 1.0
CD2 A:HIS103 4.1 24.3 1.0
CG A:HIS101 4.1 24.3 1.0
CE1 A:HIS103 4.2 21.9 1.0
N A:GLY104 4.2 23.0 1.0
C A:HIS103 4.4 23.1 1.0
N A:HIS103 4.4 23.2 1.0
NE2 A:HIS103 4.5 22.5 1.0
CA A:HIS448 4.5 22.8 1.0
CB A:HIS448 4.6 24.1 1.0
O A:HOH740 4.6 14.3 1.0
O A:HOH720 4.7 11.4 1.0
O A:TRP102 4.8 23.5 1.0
C A:TRP102 4.9 23.4 1.0
N A:HIS448 4.9 22.3 1.0

Copper binding site 3 out of 10 in 2yxw

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Copper binding site 3 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu704

b:21.3
occ:1.00
NE2 A:HIS494 2.0 26.1 1.0
OE1 A:GLU110 2.3 31.2 1.0
O A:HOH1035 2.4 31.7 1.0
CD2 A:HIS494 2.9 26.6 1.0
CE1 A:HIS494 3.0 26.6 1.0
CD A:GLU110 3.3 30.9 1.0
OE2 A:GLU110 3.8 39.1 1.0
CG A:HIS494 4.1 24.6 1.0
ND1 A:HIS494 4.1 26.6 1.0
OE1 A:GLU493 4.3 30.6 1.0
CG A:GLU110 4.4 27.9 1.0

Copper binding site 4 out of 10 in 2yxw

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Copper binding site 4 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:29.2
occ:1.00
CU2 A:C2O702 0.0 29.2 1.0
O1 A:C2O702 2.0 36.7 1.0
NE2 A:HIS143 2.0 27.6 1.0
NE2 A:HIS448 2.0 24.0 1.0
NE2 A:HIS499 2.1 23.1 1.0
CE1 A:HIS448 2.9 25.6 1.0
CE1 A:HIS143 3.0 25.6 1.0
CE1 A:HIS499 3.0 26.2 1.0
CD2 A:HIS143 3.0 28.3 1.0
CD2 A:HIS448 3.1 25.4 1.0
CD2 A:HIS499 3.1 24.3 1.0
O A:HOH816 3.3 28.3 1.0
CD2 A:HIS446 3.5 22.9 1.0
CU A:CU703 3.6 33.4 1.0
CU3 A:C2O702 3.9 25.4 1.0
NE2 A:HIS101 3.9 24.6 1.0
CD2 A:HIS101 3.9 24.5 1.0
NE2 A:HIS446 4.0 24.9 1.0
ND1 A:HIS448 4.1 24.8 1.0
ND1 A:HIS143 4.1 29.7 1.0
ND1 A:HIS499 4.1 24.6 1.0
CG A:HIS143 4.2 27.9 1.0
CG A:HIS448 4.2 23.2 1.0
CG A:HIS499 4.2 21.8 1.0
CE1 A:HIS141 4.5 24.7 1.0
CE1 A:HIS101 4.6 26.9 1.0
CD2 A:HIS501 4.6 24.1 1.0
CG A:HIS101 4.7 24.3 1.0
NE2 A:HIS501 4.7 22.2 1.0
NE2 A:HIS141 4.7 20.5 1.0
CG A:HIS446 4.7 22.0 1.0
OE1 A:GLU506 4.8 35.5 1.0
CB A:MET497 4.9 23.3 1.0

Copper binding site 5 out of 10 in 2yxw

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Copper binding site 5 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:25.4
occ:1.00
CU3 A:C2O702 0.0 25.4 1.0
O1 A:C2O702 2.0 36.7 1.0
ND1 A:HIS103 2.0 22.5 1.0
NE2 A:HIS141 2.0 20.5 1.0
NE2 A:HIS501 2.1 22.2 1.0
CE1 A:HIS141 2.9 24.7 1.0
CE1 A:HIS103 2.9 21.9 1.0
CD2 A:HIS501 3.0 24.1 1.0
CE1 A:HIS501 3.1 24.1 1.0
CG A:HIS103 3.1 22.5 1.0
CD2 A:HIS141 3.1 23.4 1.0
CB A:HIS103 3.5 21.6 1.0
CU2 A:C2O702 3.9 29.2 1.0
CU A:CU703 3.9 33.4 1.0
CD2 A:HIS101 4.1 24.5 1.0
NE2 A:HIS103 4.1 22.5 1.0
ND1 A:HIS141 4.1 24.4 1.0
CZ2 A:TRP139 4.1 21.9 1.0
O A:HOH816 4.1 28.3 1.0
CD2 A:HIS446 4.1 22.9 1.0
CD2 A:HIS103 4.2 24.3 1.0
NE2 A:HIS446 4.2 24.9 1.0
ND1 A:HIS501 4.2 22.8 1.0
CG A:HIS501 4.2 23.3 1.0
CG A:HIS141 4.2 22.8 1.0
NE2 A:HIS101 4.4 24.6 1.0
CE2 A:TRP139 4.4 21.3 1.0
NE1 A:TRP139 4.5 21.6 1.0
CA A:HIS103 4.7 21.9 1.0
CE1 A:HIS499 4.8 26.2 1.0
CH2 A:TRP139 4.8 22.9 1.0
NE2 A:HIS143 4.9 27.6 1.0
NE2 A:HIS499 4.9 23.1 1.0
CG A:HIS446 4.9 22.0 1.0
CE1 A:HIS446 5.0 23.5 1.0

Copper binding site 6 out of 10 in 2yxw

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Copper binding site 6 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:18.6
occ:1.00
ND1 B:HIS443 2.0 13.4 1.0
ND1 B:HIS505 2.0 17.4 1.0
SG B:CYS500 2.3 18.9 1.0
CE1 B:HIS443 2.9 17.4 1.0
CE1 B:HIS505 3.0 14.8 1.0
CG B:HIS443 3.0 18.6 1.0
CG B:HIS505 3.0 16.5 1.0
CB B:CYS500 3.1 18.7 1.0
SD B:MET510 3.3 20.2 1.0
CB B:HIS505 3.4 17.3 1.0
CB B:HIS443 3.4 18.9 1.0
CA B:HIS443 3.7 19.6 1.0
O B:LEU442 3.9 21.3 1.0
CB B:LEU502 4.1 16.6 1.0
NE2 B:HIS443 4.1 18.5 1.0
NE2 B:HIS505 4.1 16.3 1.0
CD2 B:HIS443 4.1 18.3 1.0
CD2 B:HIS505 4.1 17.2 1.0
CE B:MET510 4.1 21.5 1.0
N B:HIS443 4.5 19.5 1.0
C B:LEU442 4.5 20.9 1.0
CA B:CYS500 4.6 18.4 1.0
CD1 B:LEU502 4.7 16.6 1.0
CG B:MET510 4.8 20.0 1.0
CG B:LEU502 4.9 16.6 1.0
CA B:HIS505 4.9 17.6 1.0
O B:LEU502 4.9 16.2 1.0
C B:HIS443 4.9 19.3 1.0

Copper binding site 7 out of 10 in 2yxw

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Copper binding site 7 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu703

b:29.7
occ:1.00
NE2 B:HIS446 2.0 19.6 1.0
NE2 B:HIS101 2.0 20.2 1.0
O B:HOH803 2.6 19.4 1.0
CE1 B:HIS101 2.8 21.1 1.0
O1 B:C2O702 2.9 24.9 1.0
CD2 B:HIS446 2.9 20.4 1.0
CE1 B:HIS446 3.0 21.1 1.0
NE2 B:HIS448 3.0 21.6 1.0
CD2 B:HIS448 3.1 22.8 1.0
CD2 B:HIS101 3.1 21.7 1.0
CU2 B:C2O702 3.5 24.3 1.0
CA B:HIS103 3.6 18.5 1.0
CE1 B:HIS448 3.6 20.9 1.0
CG B:HIS103 3.6 18.1 1.0
ND1 B:HIS103 3.6 18.3 1.0
CG B:HIS448 3.6 20.4 1.0
CB B:HIS103 3.8 19.1 1.0
ND1 B:HIS448 3.9 21.7 1.0
ND1 B:HIS101 4.0 20.8 1.0
CU3 B:C2O702 4.0 20.4 1.0
CG B:HIS446 4.0 19.0 1.0
ND1 B:HIS446 4.1 20.0 1.0
CG B:HIS101 4.1 19.8 1.0
CD2 B:HIS103 4.2 19.1 1.0
CE1 B:HIS103 4.2 19.4 1.0
N B:GLY104 4.3 18.6 1.0
C B:HIS103 4.5 19.0 1.0
O B:HOH715 4.5 18.0 1.0
CA B:HIS448 4.5 20.4 1.0
NE2 B:HIS103 4.5 18.3 1.0
N B:HIS103 4.5 18.3 1.0
CB B:HIS448 4.5 20.1 1.0
O B:HOH719 4.7 15.9 1.0
O B:TRP102 4.8 18.9 1.0
N B:HIS448 5.0 19.7 1.0
C B:TRP102 5.0 18.8 1.0
NE2 B:HIS499 5.0 19.4 1.0

Copper binding site 8 out of 10 in 2yxw

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Copper binding site 8 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu705

b:30.2
occ:1.00
NE2 B:HIS518 2.0 24.1 1.0
NE2 B:HIS520 2.0 26.5 1.0
O B:HOH955 2.7 38.6 1.0
CD2 B:HIS518 3.0 22.7 1.0
CD2 B:HIS520 3.0 26.5 1.0
CE1 B:HIS520 3.0 26.2 1.0
CE1 B:HIS518 3.0 23.6 1.0
ND1 B:HIS520 4.1 27.4 1.0
CG B:HIS520 4.1 26.2 1.0
ND1 B:HIS518 4.1 22.0 1.0
CG B:HIS518 4.1 22.5 1.0
O B:HOH1003 4.6 32.3 1.0

Copper binding site 9 out of 10 in 2yxw

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Copper binding site 9 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:24.3
occ:1.00
CU2 B:C2O702 0.0 24.3 1.0
O1 B:C2O702 2.0 24.9 1.0
NE2 B:HIS143 2.0 20.6 1.0
NE2 B:HIS448 2.1 21.6 1.0
NE2 B:HIS499 2.1 19.4 1.0
CE1 B:HIS448 2.9 20.9 1.0
CE1 B:HIS499 3.0 20.2 1.0
CD2 B:HIS143 3.0 23.7 1.0
CE1 B:HIS143 3.0 21.4 1.0
CD2 B:HIS499 3.1 19.8 1.0
CD2 B:HIS448 3.2 22.8 1.0
O B:HOH982 3.5 35.9 1.0
CD2 B:HIS446 3.5 20.4 1.0
CU B:CU703 3.5 29.7 1.0
NE2 B:HIS101 3.8 20.2 1.0
CD2 B:HIS101 3.8 21.7 1.0
CU3 B:C2O702 3.8 20.4 1.0
NE2 B:HIS446 4.0 19.6 1.0
ND1 B:HIS448 4.1 21.7 1.0
ND1 B:HIS499 4.1 19.9 1.0
ND1 B:HIS143 4.1 22.6 1.0
CG B:HIS143 4.2 21.0 1.0
CG B:HIS499 4.2 18.6 1.0
CG B:HIS448 4.2 20.4 1.0
CE1 B:HIS141 4.5 21.2 1.0
NE2 B:HIS501 4.5 16.7 1.0
CD2 B:HIS501 4.6 18.5 1.0
CE1 B:HIS101 4.6 21.1 1.0
NE2 B:HIS141 4.7 15.8 1.0
CG B:HIS101 4.7 19.8 1.0
CG B:HIS446 4.7 19.0 1.0
OE1 B:GLU506 4.9 26.6 1.0
CB B:MET497 5.0 19.9 1.0
ND1 B:HIS103 5.0 18.3 1.0

Copper binding site 10 out of 10 in 2yxw

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Copper binding site 10 out of 10 in the The Deletion Mutant of Multicopper Oxidase Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of The Deletion Mutant of Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:20.4
occ:1.00
CU3 B:C2O702 0.0 20.4 1.0
O1 B:C2O702 1.9 24.9 1.0
NE2 B:HIS141 2.0 15.8 1.0
ND1 B:HIS103 2.0 18.3 1.0
NE2 B:HIS501 2.0 16.7 1.0
CE1 B:HIS103 2.9 19.4 1.0
CE1 B:HIS141 2.9 21.2 1.0
CE1 B:HIS501 3.0 17.5 1.0
CD2 B:HIS501 3.1 18.5 1.0
CD2 B:HIS141 3.1 21.0 1.0
CG B:HIS103 3.1 18.1 1.0
CB B:HIS103 3.6 19.1 1.0
CU2 B:C2O702 3.8 24.3 1.0
CU B:CU703 4.0 29.7 1.0
O B:HOH982 4.0 35.9 1.0
CD2 B:HIS101 4.0 21.7 1.0
NE2 B:HIS103 4.0 18.3 1.0
ND1 B:HIS141 4.1 18.6 1.0
CZ2 B:TRP139 4.1 19.5 1.0
ND1 B:HIS501 4.1 17.8 1.0
CG B:HIS141 4.2 18.1 1.0
CG B:HIS501 4.2 18.8 1.0
CD2 B:HIS446 4.2 20.4 1.0
CD2 B:HIS103 4.2 19.1 1.0
NE2 B:HIS446 4.2 19.6 1.0
NE2 B:HIS101 4.3 20.2 1.0
CE2 B:TRP139 4.5 18.7 1.0
NE1 B:TRP139 4.5 18.7 1.0
CA B:HIS103 4.7 18.5 1.0
CH2 B:TRP139 4.8 17.7 1.0
CE1 B:HIS499 4.8 20.2 1.0
NE2 B:HIS143 4.9 20.6 1.0
NE2 B:HIS499 4.9 19.4 1.0
CG B:HIS446 5.0 19.0 1.0

Reference:

K.Kataoka, H.Komori, Y.Ueki, Y.Konno, Y.Kamitaka, S.Kurose, S.Tsujimura, Y.Higuchi, K.Kano, D.Seo, T.Sakurai. Structure and Function of the Engineered Multicopper Oxidase Cueo From Escherichia Coli--Deletion of the Methionine-Rich Helical Region Covering the Substrate-Binding Site J.Mol.Biol. V. 373 141 2007.
ISSN: ISSN 0022-2836
PubMed: 17804014
DOI: 10.1016/J.JMB.2007.07.041
Page generated: Thu Sep 3 17:00:42 2020
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