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Copper in PDB 3nt0: C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I)

Protein crystallography data

The structure of C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I), PDB code: 3nt0 was solved by S.A.Roberts, W.R.Montfort, S.K.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.50 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.861, 92.507, 54.330, 90.00, 102.47, 90.00
R / Rfree (%) 20.7 / 26.1

Copper Binding Sites:

The binding sites of Copper atom in the C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I) (pdb code 3nt0). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I), PDB code: 3nt0:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 3nt0

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Copper binding site 1 out of 9 in the C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:17.4
occ:1.00
NE2 A:HIS101 2.0 12.4 1.0
NE2 A:HIS446 2.0 10.6 1.0
O A:ACT610 2.3 19.4 1.0
CE1 A:HIS101 2.9 14.3 1.0
CE1 A:HIS446 3.0 8.9 1.0
CD2 A:HIS101 3.0 15.8 1.0
CD2 A:HIS446 3.1 14.1 1.0
CD2 A:HIS448 3.2 16.0 1.0
NE2 A:HIS448 3.3 12.9 1.0
C A:ACT610 3.3 20.9 1.0
O A:HOH901 3.5 29.1 1.0
CA A:HIS103 3.6 12.9 1.0
OXT A:ACT610 3.6 21.4 1.0
CG A:HIS103 3.6 10.5 1.0
ND1 A:HIS103 3.8 10.1 1.0
CB A:HIS103 3.8 13.5 1.0
CG A:HIS448 3.9 14.1 1.0
CU A:CU1603 3.9 19.2 1.0
CE1 A:HIS448 4.0 17.6 1.0
ND1 A:HIS101 4.1 13.4 1.0
ND1 A:HIS446 4.1 10.8 1.0
CD2 A:HIS103 4.1 8.1 1.0
CG A:HIS101 4.1 13.8 1.0
CG A:HIS446 4.2 9.0 1.0
CU A:CU1602 4.3 18.9 1.0
CE1 A:HIS103 4.3 10.2 1.0
ND1 A:HIS448 4.3 13.2 1.0
N A:GLY104 4.4 14.0 1.0
N A:HIS103 4.5 13.2 1.0
C A:HIS103 4.5 13.8 1.0
NE2 A:HIS103 4.5 8.6 1.0
CA A:HIS448 4.6 14.7 1.0
CH3 A:ACT610 4.6 21.3 1.0
CB A:HIS448 4.7 15.1 1.0
O A:TRP102 4.8 13.6 1.0
C A:TRP102 4.9 13.8 1.0

Copper binding site 2 out of 9 in 3nt0

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Copper binding site 2 out of 9 in the C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:18.9
occ:1.00
ND1 A:HIS103 2.0 10.1 1.0
NE2 A:HIS141 2.1 10.8 1.0
NE2 A:HIS501 2.2 11.7 1.0
O A:HOH901 2.8 29.1 1.0
CE1 A:HIS103 2.9 10.2 1.0
CE1 A:HIS141 3.0 14.2 1.0
CG A:HIS103 3.0 10.5 1.0
CD2 A:HIS501 3.1 12.4 1.0
CD2 A:HIS141 3.1 13.7 1.0
CE1 A:HIS501 3.2 14.7 1.0
CB A:HIS103 3.4 13.5 1.0
CZ2 A:TRP139 3.8 9.8 1.0
NE2 A:HIS103 4.1 8.6 1.0
CD2 A:HIS103 4.1 8.1 1.0
ND1 A:HIS141 4.2 14.9 1.0
CE2 A:TRP139 4.2 10.8 1.0
O A:HOH873 4.2 26.4 1.0
CG A:HIS141 4.2 11.7 1.0
NE1 A:TRP139 4.3 14.0 1.0
CU A:CU1601 4.3 17.4 1.0
CG A:HIS501 4.3 13.1 1.0
CD2 A:HIS101 4.3 15.8 1.0
ND1 A:HIS501 4.3 12.5 1.0
CD2 A:HIS446 4.5 14.1 1.0
NE2 A:HIS446 4.5 10.6 1.0
CH2 A:TRP139 4.6 11.2 1.0
CU A:CU1603 4.7 19.2 1.0
CA A:HIS103 4.7 12.9 1.0
NE2 A:HIS101 4.8 12.4 1.0

Copper binding site 3 out of 9 in 3nt0

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Copper binding site 3 out of 9 in the C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:19.2
occ:1.00
O A:HOH901 1.9 29.1 1.0
NE2 A:HIS448 2.0 12.9 1.0
NE2 A:HIS143 2.1 17.6 1.0
NE2 A:HIS499 2.2 15.2 1.0
CE1 A:HIS448 2.9 17.6 1.0
CE1 A:HIS143 3.0 19.1 1.0
CD2 A:HIS499 3.1 14.0 1.0
CD2 A:HIS143 3.1 18.8 1.0
CD2 A:HIS448 3.1 16.0 1.0
CE1 A:HIS499 3.2 16.8 1.0
CD2 A:HIS446 3.8 14.1 1.0
CU A:CU1601 3.9 17.4 1.0
O A:HOH873 3.9 26.4 1.0
ND1 A:HIS448 4.1 13.2 1.0
NE2 A:HIS101 4.1 12.4 1.0
CD2 A:HIS101 4.1 15.8 1.0
ND1 A:HIS143 4.2 17.6 1.0
CG A:HIS448 4.2 14.1 1.0
CG A:HIS143 4.2 16.5 1.0
CG A:HIS499 4.2 13.1 1.0
ND1 A:HIS499 4.2 12.4 1.0
NE2 A:HIS446 4.3 10.6 1.0
CB A:MET497 4.4 14.9 1.0
CU A:CU1602 4.7 18.9 1.0
OE2 A:GLU506 4.7 30.5 1.0
CE1 A:HIS101 4.8 14.3 1.0
CG A:HIS101 4.9 13.8 1.0
CG A:MET497 5.0 15.3 1.0

Copper binding site 4 out of 9 in 3nt0

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Copper binding site 4 out of 9 in the C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:24.4
occ:1.00
OD2 A:ASP439 2.2 19.3 1.0
SD A:MET355 2.2 24.9 1.0
SD A:MET441 2.3 23.5 1.0
OD1 A:ASP360 2.3 29.0 1.0
OD2 A:ASP360 2.6 30.3 1.0
CG A:ASP360 2.8 28.8 1.0
CG A:ASP439 3.0 22.0 1.0
OD1 A:ASP439 3.1 20.3 1.0
CE A:MET441 3.2 21.9 1.0
CG A:MET441 3.3 20.2 1.0
CG A:MET355 3.3 21.0 1.0
CE A:MET355 3.5 26.9 1.0
CB A:MET355 3.5 20.2 1.0
O A:HOH731 3.6 25.2 1.0
CB A:MET441 3.7 19.4 1.0
N A:MET441 4.2 21.1 1.0
CB A:ASP360 4.4 28.1 1.0
O A:HOH694 4.4 34.8 1.0
CB A:ASP439 4.4 22.0 1.0
N A:MET440 4.6 24.0 1.0
CA A:MET441 4.6 19.8 1.0
CA A:MET355 5.0 20.1 1.0

Copper binding site 5 out of 9 in 3nt0

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Copper binding site 5 out of 9 in the C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu605

b:44.9
occ:1.00
SD A:MET358 2.2 38.2 1.0
SD A:MET362 2.7 35.6 1.0
O A:HOH872 3.0 45.3 1.0
CG A:MET358 3.3 32.4 1.0
CE A:MET362 3.4 38.2 1.0
CG A:MET362 3.4 30.8 1.0
CE A:MET358 3.5 36.5 1.0
CB A:MET358 4.8 29.9 1.0
O A:MET358 4.8 27.4 1.0
CB A:MET362 4.9 27.2 1.0

Copper binding site 6 out of 9 in 3nt0

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Copper binding site 6 out of 9 in the C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu606

b:45.6
occ:1.00
SD A:MET376 2.4 36.4 1.0
SD A:MET364 2.4 27.8 0.5
SD A:MET368 2.6 30.3 1.0
CE A:MET376 2.9 36.4 1.0
CG A:MET376 3.1 33.8 1.0
CG A:MET368 3.2 25.9 1.0
CE A:MET364 3.2 27.4 0.5
CG A:MET364 3.5 25.9 0.5
CE A:MET368 3.7 30.0 1.0
O A:MET364 4.4 24.4 0.5
CB A:MET376 4.5 32.1 1.0
CB A:MET368 4.6 23.1 1.0
O A:MET364 4.7 23.8 0.5
CB A:MET364 4.8 24.9 0.5
CB A:MET364 4.8 24.4 0.5

Copper binding site 7 out of 9 in 3nt0

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Copper binding site 7 out of 9 in the C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu607

b:38.6
occ:1.00
ND1 A:HIS488 2.1 24.1 1.0
O A:HOH892 2.3 34.7 1.0
CG A:HIS488 3.0 24.9 1.0
CE1 A:HIS488 3.1 24.8 1.0
CB A:HIS488 3.3 26.0 1.0
O A:HOH791 3.5 45.5 1.0
CA A:HIS488 3.8 26.3 1.0
O A:ASN487 4.0 27.1 1.0
CD2 A:HIS488 4.2 23.3 1.0
CG A:PRO108 4.2 19.9 1.0
NE2 A:HIS488 4.2 23.9 1.0
CD A:PRO108 4.5 19.4 1.0
N A:HIS488 4.6 26.4 1.0
C A:ASN487 4.6 26.7 1.0
O A:HOH581 4.9 24.0 1.0
N A:ASP489 4.9 26.5 1.0
C A:HIS488 4.9 26.4 1.0

Copper binding site 8 out of 9 in 3nt0

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Copper binding site 8 out of 9 in the C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu608

b:33.8
occ:1.00
ND1 A:HIS145 2.2 26.8 1.0
O A:HOH730 2.2 36.4 1.0
SD A:MET417 2.4 31.8 1.0
O A:HOH788 2.6 30.8 1.0
CE A:MET417 3.1 32.5 1.0
CE1 A:HIS145 3.1 25.7 1.0
CG A:HIS145 3.1 22.5 1.0
CB A:HIS145 3.4 21.0 1.0
CG A:MET417 3.5 28.6 1.0
CB A:MET417 3.5 27.3 1.0
NE2 A:HIS145 4.2 25.6 1.0
CD2 A:HIS145 4.3 25.3 1.0
O A:HOH549 4.5 21.7 1.0
O A:HOH745 4.9 33.5 1.0
CA A:HIS145 5.0 19.8 1.0

Copper binding site 9 out of 9 in 3nt0

Go back to Copper Binding Sites List in 3nt0
Copper binding site 9 out of 9 in the C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of C500S (T1D) Mutant of Cueo Soaked in and Bound to Cu(I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu609

b:35.5
occ:0.30
SD A:MET361 2.2 41.9 1.0
O A:HOH881 2.5 43.2 1.0
CG A:MET361 2.6 33.7 1.0
CE A:MET361 2.8 37.8 1.0
O A:HOH880 3.5 44.2 1.0
CB A:MET361 4.0 30.3 1.0
CE A:MET358 4.8 36.5 1.0

Reference:

S.K.Singh, S.A.Roberts, S.F.Mcdevitt, A.Weichsel, G.F.Wildner, G.B.Grass, C.Rensing, W.R.Montfort. Crystal Structures of Multicopper Oxidase Cueo Bound to Copper(I) and Silver(I): Functional Role of A Methionine-Rich Sequence. J. Biol. Chem. V. 286 37849 2011.
ISSN: ESSN 1083-351X
PubMed: 21903583
DOI: 10.1074/JBC.M111.293589
Page generated: Sun Dec 13 11:11:05 2020

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