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Copper in PDB 3qqx: Reduced Native Intermediate of the Multicopper Oxidase Cueo

Protein crystallography data

The structure of Reduced Native Intermediate of the Multicopper Oxidase Cueo, PDB code: 3qqx was solved by W.R.Montfort, S.A.Roberts, S.K.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.35 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.173, 91.375, 54.328, 90.00, 102.22, 90.00
R / Rfree (%) 20.6 / 24.2

Copper Binding Sites:

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

Copper binding site 1 out of 8 in 3qqx

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Copper binding site 1 out of 8 in the Reduced Native Intermediate of the 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 Reduced Native Intermediate of the Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:31.8
occ:0.80
O A:O701 2.0 31.6 1.0
NE2 A:HIS446 2.0 23.8 1.0
NE2 A:HIS101 2.0 26.6 1.0
O A:HOH1027 2.4 28.4 1.0
CE1 A:HIS101 2.8 29.7 1.0
CE1 A:HIS446 2.9 23.7 1.0
CD2 A:HIS446 3.1 22.4 1.0
CD2 A:HIS448 3.2 21.9 1.0
CD2 A:HIS101 3.2 23.6 1.0
NE2 A:HIS448 3.3 24.1 1.0
CG A:HIS103 3.6 22.3 1.0
CA A:HIS103 3.6 22.8 1.0
CU A:CU602 3.7 28.7 1.0
ND1 A:HIS103 3.7 23.0 1.0
CG A:HIS448 3.8 20.7 1.0
CB A:HIS103 3.8 22.4 1.0
ND1 A:HIS101 4.0 26.2 1.0
CE1 A:HIS448 4.0 25.8 1.0
ND1 A:HIS446 4.1 25.0 1.0
CD2 A:HIS103 4.1 19.9 1.0
N A:GLY104 4.2 24.5 1.0
CU A:CU1603 4.2 29.1 1.0
CG A:HIS446 4.2 22.0 1.0
CG A:HIS101 4.2 24.5 1.0
CE1 A:HIS103 4.2 21.3 1.0
ND1 A:HIS448 4.2 23.4 1.0
O A:O702 4.3 34.8 1.0
NE2 A:HIS103 4.4 20.4 1.0
C A:HIS103 4.4 23.7 1.0
CA A:HIS448 4.5 24.1 1.0
N A:HIS103 4.6 20.6 1.0
O A:HOH9 4.6 31.7 1.0
O A:HOH578 4.6 37.3 1.0
O A:TRP102 4.6 23.3 1.0
CB A:HIS448 4.7 23.1 1.0
C A:TRP102 4.9 21.8 1.0
N A:HIS448 5.0 23.2 1.0

Copper binding site 2 out of 8 in 3qqx

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Copper binding site 2 out of 8 in the Reduced Native Intermediate of the 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 Reduced Native Intermediate of the Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:28.7
occ:1.00
NE2 A:HIS143 2.1 27.9 1.0
O A:O702 2.1 34.8 1.0
NE2 A:HIS448 2.1 24.1 1.0
NE2 A:HIS499 2.1 22.6 1.0
O A:O701 2.2 31.6 1.0
CE1 A:HIS448 3.0 25.8 1.0
CD2 A:HIS143 3.0 26.6 1.0
CE1 A:HIS143 3.1 31.4 1.0
CE1 A:HIS499 3.1 25.9 1.0
CD2 A:HIS499 3.1 21.6 1.0
CD2 A:HIS448 3.1 21.9 1.0
CD2 A:HIS446 3.7 22.4 1.0
CU A:CU601 3.7 31.8 0.8
NE2 A:HIS101 3.9 26.6 1.0
CD2 A:HIS101 4.0 23.6 1.0
NE2 A:HIS446 4.0 23.8 1.0
ND1 A:HIS448 4.2 23.4 1.0
O A:HOH858 4.2 42.5 1.0
ND1 A:HIS143 4.2 26.2 1.0
ND1 A:HIS499 4.2 22.3 1.0
CG A:HIS143 4.2 24.8 1.0
CG A:HIS499 4.2 22.6 1.0
CG A:HIS448 4.2 20.7 1.0
CU A:CU1603 4.3 29.1 1.0
CE1 A:HIS101 4.5 29.7 1.0
CE1 A:HIS141 4.6 21.9 1.0
CG A:HIS101 4.7 24.5 1.0
NE2 A:HIS501 4.8 22.6 1.0
CB A:MET497 4.8 24.2 1.0
CD2 A:HIS501 4.8 23.3 1.0
NE2 A:HIS141 4.9 25.7 1.0
CG A:HIS446 5.0 22.0 1.0
ND1 A:HIS101 5.0 26.2 1.0

Copper binding site 3 out of 8 in 3qqx

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Copper binding site 3 out of 8 in the Reduced Native Intermediate of the 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 Reduced Native Intermediate of the Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:29.1
occ:1.00
ND1 A:HIS103 2.0 23.0 1.0
NE2 A:HIS501 2.1 22.6 1.0
NE2 A:HIS141 2.1 25.7 1.0
O A:O702 2.7 34.8 1.0
O A:O701 2.8 31.6 1.0
CE1 A:HIS103 2.9 21.3 1.0
CE1 A:HIS501 3.0 24.1 1.0
CG A:HIS103 3.0 22.3 1.0
CD2 A:HIS501 3.1 23.3 1.0
CE1 A:HIS141 3.1 21.9 1.0
CD2 A:HIS141 3.1 22.5 1.0
CB A:HIS103 3.5 22.4 1.0
CZ2 A:TRP139 3.8 21.3 1.0
NE2 A:HIS103 4.0 20.4 1.0
CE2 A:TRP139 4.1 19.6 1.0
ND1 A:HIS501 4.1 20.0 1.0
CD2 A:HIS103 4.1 19.9 1.0
CD2 A:HIS101 4.1 23.6 1.0
CU A:CU601 4.2 31.8 0.8
ND1 A:HIS141 4.2 23.2 1.0
CG A:HIS501 4.2 22.1 1.0
NE1 A:TRP139 4.2 20.0 1.0
CG A:HIS141 4.2 23.1 1.0
CU A:CU602 4.3 28.7 1.0
NE2 A:HIS446 4.3 23.8 1.0
NE2 A:HIS101 4.4 26.6 1.0
CD2 A:HIS446 4.4 22.4 1.0
CH2 A:TRP139 4.6 21.2 1.0
CA A:HIS103 4.7 22.8 1.0

Copper binding site 4 out of 8 in 3qqx

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Copper binding site 4 out of 8 in the Reduced Native Intermediate of the 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 Reduced Native Intermediate of the Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:27.0
occ:1.00
ND1 A:HIS443 2.1 25.1 1.0
ND1 A:HIS505 2.1 23.7 1.0
SG A:CYS500 2.2 25.3 1.0
CE1 A:HIS443 3.1 22.1 1.0
CE1 A:HIS505 3.1 25.1 1.0
CG A:HIS505 3.1 23.0 1.0
CG A:HIS443 3.1 21.6 1.0
CB A:CYS500 3.3 23.2 1.0
SD A:MET510 3.3 25.2 1.0
CB A:HIS505 3.4 25.1 1.0
CB A:HIS443 3.5 23.6 1.0
CA A:HIS443 3.7 23.4 1.0
O A:LEU442 3.7 26.7 1.0
CB A:LEU502 4.0 21.9 1.0
CE A:MET510 4.0 28.6 1.0
NE2 A:HIS443 4.2 24.6 1.0
NE2 A:HIS505 4.2 24.8 1.0
CD2 A:HIS505 4.2 25.0 1.0
CD2 A:HIS443 4.3 24.5 1.0
C A:LEU442 4.4 25.4 1.0
N A:HIS443 4.4 24.7 1.0
CA A:CYS500 4.7 22.8 1.0
CD1 A:LEU502 4.7 20.9 1.0
CG A:MET510 4.9 23.5 1.0
CG A:LEU502 4.9 20.5 1.0
C A:HIS443 4.9 23.4 1.0
O A:LEU502 4.9 21.4 1.0
CA A:HIS505 4.9 23.8 1.0
N A:LEU502 5.0 21.9 1.0

Copper binding site 5 out of 8 in 3qqx

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Copper binding site 5 out of 8 in the Reduced Native Intermediate of the 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 Reduced Native Intermediate of the Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu605

b:25.4
occ:0.75
OD1 A:ASP439 2.1 27.7 1.0
OD1 A:ASP360 2.2 30.2 1.0
SD A:MET355 2.2 27.8 1.0
SD A:MET441 2.3 27.8 1.0
CG A:ASP439 2.9 27.8 1.0
OD2 A:ASP439 3.0 26.9 1.0
CG A:ASP360 3.0 35.5 1.0
CE A:MET355 3.1 27.1 1.0
OD2 A:ASP360 3.2 38.3 1.0
CE A:MET441 3.2 28.8 1.0
CG A:MET441 3.3 25.8 1.0
CG A:MET355 3.3 27.1 1.0
CB A:MET441 3.6 26.0 1.0
CB A:MET355 3.6 25.9 1.0
O A:HOH573 4.0 35.0 1.0
N A:MET441 4.1 26.9 1.0
CB A:ASP439 4.3 27.5 1.0
N A:MET440 4.4 29.1 1.0
CB A:ASP360 4.5 34.5 1.0
CA A:MET441 4.5 26.1 1.0
CA A:ASP439 4.9 27.6 1.0
O A:ALA206 5.0 24.3 1.0
CA A:ASP360 5.0 33.8 1.0

Copper binding site 6 out of 8 in 3qqx

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Copper binding site 6 out of 8 in the Reduced Native Intermediate of the 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 Reduced Native Intermediate of the Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu606

b:47.9
occ:1.00
O A:HOH574 2.2 48.0 1.0
SD A:MET362 2.3 41.1 1.0
NE2 A:HIS398 2.4 46.0 1.0
SD A:MET358 2.5 43.2 1.0
CD2 A:HIS398 3.3 48.5 1.0
CE1 A:HIS398 3.3 48.8 1.0
CG A:MET358 3.3 38.1 1.0
CG A:MET362 3.3 35.5 1.0
CE A:MET358 3.5 45.0 1.0
CE A:MET362 3.6 43.5 1.0
ND1 A:HIS398 4.4 50.5 1.0
CG A:HIS398 4.4 50.8 1.0
CB A:MET362 4.8 33.6 1.0
CB A:MET358 4.8 36.5 1.0
CG A:PHE402 4.8 47.3 1.0
CD2 A:PHE402 4.8 47.5 1.0
CB A:PHE402 4.8 47.0 1.0
O A:MET358 5.0 34.9 1.0
CE A:MET361 5.0 37.8 0.5

Copper binding site 7 out of 8 in 3qqx

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Copper binding site 7 out of 8 in the Reduced Native Intermediate of the 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 Reduced Native Intermediate of the Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu607

b:74.2
occ:1.00
SD A:MET376 2.2 49.0 1.0
SD A:MET368 2.3 41.0 1.0
O A:HOH805 2.7 53.4 1.0
CE A:MET376 2.8 46.6 1.0
CG A:MET376 2.9 41.9 1.0
CE A:MET368 2.9 36.2 1.0
CG A:MET368 3.2 34.2 1.0
O A:HOH1004 3.3 48.5 1.0
CB A:MET376 4.2 39.0 1.0
CB A:MET368 4.5 31.0 1.0
O A:MET364 4.9 32.4 1.0

Copper binding site 8 out of 8 in 3qqx

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Copper binding site 8 out of 8 in the Reduced Native Intermediate of the 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 Reduced Native Intermediate of the Multicopper Oxidase Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu608

b:62.5
occ:1.00
O A:HOH534 2.0 47.3 1.0
OE1 A:GLU30 2.1 40.9 1.0
O A:HOH1074 2.1 34.2 1.0
CD A:GLU30 2.9 38.9 1.0
OE2 A:GLU30 3.2 42.7 1.0
CG A:GLU30 4.3 40.5 1.0

Reference:

S.K.Singh, S.A.Roberts, J.T.Hazzard, S.Franke-Mcdevitt, A.Weichsel, C.Rensing, W.R.Montfort. Cueo E506D Mutant: Crystal Structure of Reduced Native Intermediate, Kinetics, and Impairment of Product Release To Be Published.
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