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Copper in PDB 3mzt: Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T

Protein crystallography data

The structure of Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T, PDB code: 3mzt was solved by L.S.Wolfe, M.F.Calabrese, A.Nath, D.V.Blaho, A.D.Miranker, Y.Xiong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.891, 116.592, 66.317, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 25.6

Copper Binding Sites:

The binding sites of Copper atom in the Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T (pdb code 3mzt). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T, PDB code: 3mzt:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3mzt

Go back to Copper Binding Sites List in 3mzt
Copper binding site 1 out of 6 in the Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:0.0
occ:1.00
 O A:ILE1 1.9 0.8 1.0
NE2 A:HIS31 2.0 0.8 1.0
N A:ILE1 2.2 0.3 1.0
N A:MET0 2.3 0.7 1.0
CE1 A:HIS31 2.7 93.0 1.0
C A:ILE1 2.7 0.7 1.0
C A:MET0 2.8 0.7 1.0
CA A:MET0 3.0 0.5 1.0
CA A:ILE1 3.0 0.3 1.0
CD2 A:HIS31 3.2 0.4 1.0
O A:MET0 3.9 0.4 1.0
ND1 A:HIS31 3.9 91.3 1.0
CG2 A:ILE1 3.9 0.4 1.0
N A:GLN2 3.9 0.4 1.0
CB A:ILE1 4.1 0.9 1.0
CG A:HIS31 4.2 0.2 1.0
CB A:MET0 4.4 0.8 1.0
OE1 A:GLN2 4.4 0.8 1.0
CA A:GLN2 4.6 0.5 1.0
CB A:PHE30 4.6 91.0 1.0
CD2 A:PHE30 4.7 0.6 1.0
CG A:MET0 4.8 0.6 1.0
O A:ASP59 4.8 0.6 1.0
CG A:PHE30 4.9 89.7 1.0

Copper binding site 2 out of 6 in 3mzt

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Copper binding site 2 out of 6 in the Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:0.6
occ:1.00
 O B:ILE1 1.9 0.4 1.0
NE2 B:HIS31 2.0 0.0 1.0
N B:ILE1 2.2 0.7 1.0
N B:MET0 2.2 0.8 1.0
CE1 B:HIS31 2.7 0.1 1.0
C B:ILE1 2.7 0.3 1.0
C B:MET0 2.8 0.4 1.0
CA B:MET0 3.0 0.4 1.0
CA B:ILE1 3.0 0.9 1.0
CD2 B:HIS31 3.2 0.5 1.0
O B:MET0 3.9 0.0 1.0
ND1 B:HIS31 3.9 0.5 1.0
CG2 B:ILE1 3.9 0.6 1.0
N B:GLN2 4.0 0.9 1.0
CB B:ILE1 4.1 0.6 1.0
CG B:HIS31 4.2 0.2 1.0
CB B:MET0 4.3 0.9 1.0
OE1 B:GLN2 4.5 0.4 1.0
CA B:GLN2 4.6 0.9 1.0
CB B:PHE30 4.6 97.4 1.0
CD2 B:PHE30 4.7 0.5 1.0
CG B:MET0 4.7 0.7 1.0
O B:ASP59 4.8 1.0 1.0
CG B:PHE30 4.9 96.6 1.0

Copper binding site 3 out of 6 in 3mzt

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Copper binding site 3 out of 6 in the Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:94.2
occ:1.00
 O C:ILE1 1.9 97.4 1.0
NE2 C:HIS31 2.1 81.6 1.0
N C:ILE1 2.1 0.4 1.0
N C:MET0 2.2 0.3 1.0
CE1 C:HIS31 2.7 68.2 1.0
C C:ILE1 2.7 0.2 1.0
C C:MET0 2.8 1.0 1.0
CA C:MET0 2.9 0.3 1.0
CA C:ILE1 3.0 0.4 1.0
CD2 C:HIS31 3.3 78.5 1.0
O C:MET0 3.8 0.5 1.0
CG2 C:ILE1 3.8 0.0 1.0
ND1 C:HIS31 3.9 67.5 1.0
N C:GLN2 4.0 95.0 1.0
CB C:ILE1 4.0 0.3 1.0
CG C:HIS31 4.2 83.2 1.0
CB C:MET0 4.3 0.8 1.0
OE1 C:GLN2 4.5 0.7 1.0
CB C:PHE30 4.6 68.2 1.0
CA C:GLN2 4.6 98.1 1.0
CG C:MET0 4.7 0.8 1.0
CD2 C:PHE30 4.7 89.7 1.0
O C:ASP59 4.8 84.2 1.0
CG C:PHE30 4.9 66.6 1.0

Copper binding site 4 out of 6 in 3mzt

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Copper binding site 4 out of 6 in the Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu201

b:95.1
occ:1.00
 NE2 D:HIS31 1.9 81.8 1.0
O D:ILE1 2.0 98.3 1.0
N D:MET0 2.1 0.4 1.0
N D:ILE1 2.2 0.3 1.0
CE1 D:HIS31 2.5 68.8 1.0
C D:MET0 2.8 0.0 1.0
C D:ILE1 2.8 0.2 1.0
CA D:MET0 2.9 0.0 1.0
CA D:ILE1 3.1 0.5 1.0
CD2 D:HIS31 3.2 78.7 1.0
ND1 D:HIS31 3.8 67.2 1.0
O D:MET0 3.8 0.1 1.0
CG2 D:ILE1 4.0 0.3 1.0
N D:GLN2 4.1 98.2 1.0
CG D:HIS31 4.1 81.8 1.0
CB D:ILE1 4.2 0.7 1.0
CB D:MET0 4.3 0.8 1.0
OE1 D:GLN2 4.5 0.7 1.0
CA D:GLN2 4.7 0.2 1.0
CG D:MET0 4.7 0.9 1.0
CB D:PHE30 4.7 68.9 1.0
O D:ASP59 4.8 84.1 1.0
CD2 D:PHE30 4.9 90.2 1.0

Copper binding site 5 out of 6 in 3mzt

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Copper binding site 5 out of 6 in the Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu201

b:85.3
occ:1.00
 NE2 E:HIS31 1.9 72.5 1.0
O E:ILE1 1.9 88.7 1.0
N E:MET0 2.2 0.0 1.0
N E:ILE1 2.2 98.5 1.0
CE1 E:HIS31 2.5 60.2 1.0
C E:ILE1 2.8 93.9 1.0
C E:MET0 2.9 98.5 1.0
CA E:MET0 3.0 0.5 1.0
CA E:ILE1 3.1 0.1 1.0
CD2 E:HIS31 3.1 70.0 1.0
ND1 E:HIS31 3.7 59.9 1.0
O E:MET0 3.9 0.8 1.0
CG2 E:ILE1 4.0 0.9 1.0
N E:GLN2 4.0 86.7 1.0
CG E:HIS31 4.1 73.6 1.0
CB E:ILE1 4.1 0.6 1.0
CB E:MET0 4.4 0.0 1.0
OE1 E:GLN2 4.5 0.2 1.0
CA E:GLN2 4.6 89.8 1.0
CB E:PHE30 4.6 60.5 1.0
O E:ASP59 4.7 77.5 1.0
CG E:MET0 4.8 0.8 1.0
CD2 E:PHE30 4.8 80.9 1.0
CG E:PHE30 5.0 59.4 1.0

Copper binding site 6 out of 6 in 3mzt

Go back to Copper Binding Sites List in 3mzt
Copper binding site 6 out of 6 in the Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Protein-Induced Photophysical Changes to the Amyloid Indicator Dye, Thioflavin T within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu201

b:91.6
occ:1.00
 O F:ILE1 1.9 93.8 1.0
NE2 F:HIS31 2.0 80.0 1.0
N F:ILE1 2.1 0.2 1.0
N F:MET0 2.2 0.6 1.0
C F:ILE1 2.7 0.3 1.0
C F:MET0 2.7 0.9 1.0
CE1 F:HIS31 2.7 65.7 1.0
CA F:MET0 2.9 0.9 1.0
CA F:ILE1 2.9 0.7 1.0
CD2 F:HIS31 3.2 75.4 1.0
O F:MET0 3.8 0.9 1.0
N F:GLN2 3.9 94.3 1.0
ND1 F:HIS31 4.0 62.2 1.0
CG2 F:ILE1 4.0 0.8 1.0
CB F:ILE1 4.1 0.5 1.0
CG F:HIS31 4.2 78.8 1.0
CB F:MET0 4.3 0.8 1.0
OE1 F:GLN2 4.4 0.2 1.0
CA F:GLN2 4.6 96.6 1.0
CG F:MET0 4.7 0.8 1.0
CB F:PHE30 4.8 66.0 1.0
CD2 F:PHE30 4.9 89.0 1.0
O F:ASP59 4.9 81.7 1.0

Reference:

L.S.Wolfe, M.F.Calabrese, A.Nath, D.V.Blaho, A.D.Miranker, Y.Xiong. Protein-Induced Photophysical Changes to the Amyloid Indicator Dye Thioflavin T. Proc.Natl.Acad.Sci.Usa V. 107 16863 2010.
ISSN: ISSN 0027-8424
PubMed: 20826442
DOI: 10.1073/PNAS.1002867107
Page generated: Mon Jul 14 02:26:27 2025

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