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Copper in PDB 3k7r: Crystal Structure of [Tm][CUATX1]3

Protein crystallography data

The structure of Crystal Structure of [Tm][CUATX1]3, PDB code: 3k7r was solved by Y.Xue, H.M.Alvarez, C.D.Robinson, A.Mondragon, T.V.O'halloran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.42 / 2.28
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 109.887, 182.242, 52.722, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 25.6

Other elements in 3k7r:

The structure of Crystal Structure of [Tm][CUATX1]3 also contains other interesting chemical elements:

Molybdenum (Mo) 4 atoms

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of [Tm][CUATX1]3 (pdb code 3k7r). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 16 binding sites of Copper where determined in the Crystal Structure of [Tm][CUATX1]3, PDB code: 3k7r:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 16 in 3k7r

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Copper binding site 1 out of 16 in the Crystal Structure of [Tm][CUATX1]3


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 [Tm][CUATX1]3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu74

b:29.8
occ:1.00
 SG A:CYS15 2.2 22.2 1.0
S2 C:4SM75 2.3 27.4 1.0
S1 C:4SM75 2.3 28.3 1.0
SG A:CYS18 2.3 24.8 1.0
MO1 C:4SM75 2.8 30.1 1.0
CU A:CU75 3.1 31.2 1.0
CB A:CYS15 3.4 21.8 1.0
N A:CYS15 3.5 23.0 1.0
N A:CYS18 3.8 19.9 1.0
CB A:CYS18 3.8 20.1 1.0
CU C:CU74 3.8 29.7 1.0
CU B:CU74 3.9 26.7 1.0
CA A:CYS15 3.9 21.8 1.0
NZ A:LYS65 4.2 24.9 1.0
O A:CYS15 4.2 21.6 1.0
CA A:CYS18 4.3 20.0 1.0
C A:CYS15 4.3 21.9 1.0
S3 C:4SM75 4.3 30.7 1.0
SG B:CYS15 4.5 22.1 1.0
SG C:CYS15 4.5 23.7 1.0
S4 C:4SM75 4.5 32.1 1.0
C A:THR14 4.6 23.3 1.0
CB A:THR14 4.6 23.6 1.0
C A:GLY17 4.6 20.8 1.0
N A:THR14 4.7 22.5 1.0
CA A:GLY17 4.8 21.1 1.0
N A:GLY17 4.8 20.6 1.0
CB B:CYS15 4.8 20.9 1.0
CA A:THR14 4.8 23.3 1.0
CG2 B:THR14 4.8 23.0 1.0

Copper binding site 2 out of 16 in 3k7r

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Copper binding site 2 out of 16 in the Crystal Structure of [Tm][CUATX1]3


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 [Tm][CUATX1]3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu75

b:31.2
occ:1.00
 SG C:CYS15 2.2 23.7 1.0
SG B:CYS15 2.3 22.1 1.0
SG A:CYS15 2.3 22.2 1.0
CU A:CU74 3.1 29.8 1.0
CB A:CYS15 3.2 21.8 1.0
CU C:CU74 3.2 29.7 1.0
CU B:CU74 3.2 26.7 1.0
CB C:CYS15 3.2 21.9 1.0
CB B:CYS15 3.2 20.9 1.0
S2 C:4SM75 3.6 27.4 1.0
S1 C:4SM75 3.7 28.3 1.0
S3 C:4SM75 3.7 30.7 1.0
MO1 C:4SM75 3.9 30.1 1.0
C2 D:MLT77 4.2 46.5 1.0
O2 D:MLT77 4.4 48.6 1.0
O4 D:MLT77 4.5 41.1 1.0
C1 D:MLT77 4.5 47.0 1.0
C4 D:MLT77 4.6 46.1 1.0
CA A:CYS15 4.6 21.8 1.0
CA C:CYS15 4.6 23.2 1.0
CA B:CYS15 4.7 21.8 1.0
C3 D:MLT77 4.8 43.8 1.0
N A:CYS15 5.0 23.0 1.0

Copper binding site 3 out of 16 in 3k7r

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Copper binding site 3 out of 16 in the Crystal Structure of [Tm][CUATX1]3


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 [Tm][CUATX1]3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu74

b:26.7
occ:1.00
 S2 C:4SM75 2.2 27.4 1.0
S3 C:4SM75 2.3 30.7 1.0
SG B:CYS15 2.3 22.1 1.0
SG B:CYS18 2.4 25.0 1.0
MO1 C:4SM75 2.8 30.1 1.0
CU A:CU75 3.2 31.2 1.0
CB B:CYS15 3.5 20.9 1.0
N B:CYS15 3.6 21.5 1.0
N B:CYS18 3.7 22.2 1.0
CB B:CYS18 3.8 21.5 1.0
CU C:CU74 3.9 29.7 1.0
CU A:CU74 3.9 29.8 1.0
CA B:CYS15 4.0 21.8 1.0
CA B:CYS18 4.2 21.9 1.0
O B:CYS15 4.3 20.6 1.0
C B:CYS15 4.3 21.1 1.0
S1 C:4SM75 4.4 28.3 1.0
NZ B:LYS65 4.4 24.4 1.0
SG C:CYS15 4.4 23.7 1.0
S4 C:4SM75 4.4 32.1 1.0
C B:THR14 4.5 23.0 1.0
SG A:CYS15 4.5 22.2 1.0
CB B:THR14 4.5 24.5 1.0
C B:GLY17 4.5 21.5 1.0
CA B:GLY17 4.6 21.8 1.0
N B:GLY17 4.7 21.7 1.0
CB C:CYS15 4.7 21.9 1.0
N B:THR14 4.8 24.0 1.0
CA B:THR14 4.8 23.6 1.0

Copper binding site 4 out of 16 in 3k7r

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Copper binding site 4 out of 16 in the Crystal Structure of [Tm][CUATX1]3


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 [Tm][CUATX1]3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu74

b:29.7
occ:1.00
 S1 C:4SM75 2.2 28.3 1.0
SG C:CYS15 2.3 23.7 1.0
S3 C:4SM75 2.3 30.7 1.0
SG C:CYS18 2.3 25.2 1.0
MO1 C:4SM75 2.8 30.1 1.0
CU A:CU75 3.2 31.2 1.0
CB C:CYS15 3.4 21.9 1.0
N C:CYS15 3.4 23.5 1.0
N C:CYS18 3.6 21.7 1.0
CB C:CYS18 3.7 20.4 1.0
CU A:CU74 3.8 29.8 1.0
CA C:CYS15 3.9 23.2 1.0
CU B:CU74 3.9 26.7 1.0
NZ C:LYS65 4.1 29.9 1.0
CA C:CYS18 4.1 22.1 1.0
S2 C:4SM75 4.3 27.4 1.0
C C:CYS15 4.3 22.4 1.0
O C:CYS15 4.3 24.0 1.0
C C:THR14 4.5 24.2 1.0
S4 C:4SM75 4.5 32.1 1.0
SG B:CYS15 4.5 22.1 1.0
SG A:CYS15 4.5 22.2 1.0
C C:GLY17 4.6 21.9 1.0
N C:THR14 4.6 23.6 1.0
CB C:THR14 4.6 24.1 1.0
N C:GLY17 4.7 21.5 1.0
CA C:GLY17 4.7 21.5 1.0
CA C:THR14 4.8 23.8 1.0
CB A:CYS15 4.9 21.8 1.0

Copper binding site 5 out of 16 in 3k7r

Go back to Copper Binding Sites List in 3k7r
Copper binding site 5 out of 16 in the Crystal Structure of [Tm][CUATX1]3


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 [Tm][CUATX1]3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu74

b:27.9
occ:1.00
 S2 D:4SM76 2.3 30.7 1.0
SG D:CYS15 2.3 18.3 1.0
S1 D:4SM76 2.3 28.6 1.0
SG D:CYS18 2.4 22.1 1.0
MO1 D:4SM76 2.8 27.6 1.0
CU D:CU75 3.2 27.6 1.0
N D:CYS15 3.4 23.3 1.0
CB D:CYS15 3.5 21.7 1.0
N D:CYS18 3.5 19.7 1.0
CB D:CYS18 3.7 19.3 1.0
CU F:CU74 3.9 28.0 1.0
CU E:CU74 3.9 27.9 1.0
CA D:CYS15 3.9 21.7 1.0
CA D:CYS18 4.1 19.9 1.0
NZ D:LYS65 4.3 24.5 1.0
S3 D:4SM76 4.4 25.2 1.0
C D:CYS15 4.4 21.9 1.0
O D:CYS15 4.4 19.9 1.0
C D:THR14 4.4 24.4 1.0
S4 D:4SM76 4.4 31.2 1.0
CB D:THR14 4.5 24.8 1.0
C D:GLY17 4.5 20.4 1.0
SG F:CYS15 4.5 22.9 1.0
SG E:CYS15 4.6 20.6 1.0
CA D:GLY17 4.7 20.2 1.0
N D:GLY17 4.7 22.3 1.0
N D:THR14 4.7 24.1 1.0
CA D:THR14 4.8 24.3 1.0
CB E:CYS15 4.9 21.0 1.0

Copper binding site 6 out of 16 in 3k7r

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Copper binding site 6 out of 16 in the Crystal Structure of [Tm][CUATX1]3


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 [Tm][CUATX1]3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu75

b:27.6
occ:1.00
 SG E:CYS15 2.2 20.6 1.0
SG D:CYS15 2.3 18.3 1.0
SG F:CYS15 2.3 22.9 1.0
CU E:CU74 3.1 27.9 1.0
CU F:CU74 3.1 28.0 1.0
CB E:CYS15 3.2 21.0 1.0
CB D:CYS15 3.2 21.7 1.0
CU D:CU74 3.2 27.9 1.0
CB F:CYS15 3.3 23.6 1.0
S3 D:4SM76 3.6 25.2 1.0
S1 D:4SM76 3.6 28.6 1.0
S2 D:4SM76 3.6 30.7 1.0
MO1 D:4SM76 3.8 27.6 1.0
C3 D:MLT77 4.1 43.8 1.0
C1 D:MLT77 4.4 47.0 1.0
O2 D:MLT77 4.5 48.6 1.0
C4 D:MLT77 4.5 46.1 1.0
CA D:CYS15 4.6 21.7 1.0
CA E:CYS15 4.6 21.0 1.0
O4 D:MLT77 4.7 41.1 1.0
O1 D:MLT77 4.7 50.5 1.0
C2 D:MLT77 4.7 46.5 1.0
CA F:CYS15 4.7 23.6 1.0
N D:GLY17 4.9 22.3 1.0
N D:CYS15 5.0 23.3 1.0
O3 D:MLT77 5.0 39.5 1.0

Copper binding site 7 out of 16 in 3k7r

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Copper binding site 7 out of 16 in the Crystal Structure of [Tm][CUATX1]3


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 [Tm][CUATX1]3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu74

b:27.9
occ:1.00
 SG E:CYS15 2.2 20.6 1.0
S3 D:4SM76 2.3 25.2 1.0
S1 D:4SM76 2.3 28.6 1.0
SG E:CYS18 2.3 23.4 1.0
MO1 D:4SM76 2.8 27.6 1.0
CU D:CU75 3.1 27.6 1.0
CB E:CYS15 3.4 21.0 1.0
N E:CYS15 3.5 21.9 1.0
N E:CYS18 3.6 19.9 1.0
CB E:CYS18 3.7 20.8 1.0
CU F:CU74 3.8 28.0 1.0
CU D:CU74 3.9 27.9 1.0
CA E:CYS15 3.9 21.0 1.0
CA E:CYS18 4.1 20.4 1.0
S2 D:4SM76 4.3 30.7 1.0
C E:CYS15 4.4 21.1 1.0
NZ E:LYS65 4.4 23.9 1.0
O E:CYS15 4.4 20.9 1.0
S4 D:4SM76 4.4 31.2 1.0
C E:GLY17 4.4 20.8 1.0
SG F:CYS15 4.5 22.9 1.0
C E:THR14 4.5 23.0 1.0
SG D:CYS15 4.5 18.3 1.0
CB E:THR14 4.6 23.2 1.0
CA E:GLY17 4.6 20.8 1.0
N E:GLY17 4.7 20.6 1.0
N E:THR14 4.8 22.6 1.0
CB F:CYS15 4.8 23.6 1.0
CA E:THR14 4.9 23.3 1.0

Copper binding site 8 out of 16 in 3k7r

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Copper binding site 8 out of 16 in the Crystal Structure of [Tm][CUATX1]3


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 [Tm][CUATX1]3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu74

b:28.0
occ:1.00
 S3 D:4SM76 2.2 25.2 1.0
S2 D:4SM76 2.3 30.7 1.0
SG F:CYS15 2.3 22.9 1.0
SG F:CYS18 2.4 23.9 1.0
MO1 D:4SM76 2.8 27.6 1.0
CU D:CU75 3.1 27.6 1.0
CB F:CYS15 3.4 23.6 1.0
N F:CYS15 3.5 24.2 1.0
CB F:CYS18 3.8 20.1 1.0
CU E:CU74 3.8 27.9 1.0
N F:CYS18 3.8 21.0 1.0
CU D:CU74 3.9 27.9 1.0
CA F:CYS15 3.9 23.6 1.0
CA F:CYS18 4.2 21.8 1.0
O F:CYS15 4.3 22.7 1.0
C F:CYS15 4.3 23.1 1.0
S1 D:4SM76 4.3 28.6 1.0
SG D:CYS15 4.4 18.3 1.0
NZ F:LYS65 4.4 29.5 1.0
C F:THR14 4.4 24.3 1.0
SG E:CYS15 4.5 20.6 1.0
S4 D:4SM76 4.5 31.2 1.0
CB F:THR14 4.6 25.8 1.0
CB D:CYS15 4.6 21.7 1.0
N F:THR14 4.7 25.0 1.0
C F:GLY17 4.7 21.9 1.0
CA F:THR14 4.8 25.5 1.0
N F:GLY17 4.9 22.4 1.0
CA F:GLY17 4.9 21.8 1.0
CG2 D:THR14 5.0 24.7 1.0

Copper binding site 9 out of 16 in 3k7r

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Copper binding site 9 out of 16 in the Crystal Structure of [Tm][CUATX1]3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of [Tm][CUATX1]3 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu74

b:29.1
occ:1.00
 SG G:CYS15 2.2 22.8 1.0
S2 I:4SM75 2.3 31.4 1.0
SG G:CYS18 2.3 24.1 1.0
S1 I:4SM75 2.4 29.4 1.0
MO1 I:4SM75 2.8 31.8 1.0
CU G:CU75 3.2 27.8 1.0
CB G:CYS15 3.5 21.4 1.0
N G:CYS15 3.6 22.5 1.0
N G:CYS18 3.6 23.1 1.0
CB G:CYS18 3.7 22.2 1.0
CU H:CU74 3.8 30.5 1.0
CU I:CU74 3.9 28.6 1.0
CA G:CYS15 3.9 21.8 1.0
CA G:CYS18 4.1 22.9 1.0
S3 I:4SM75 4.3 31.6 1.0
C G:CYS15 4.4 21.0 1.0
O G:CYS15 4.4 19.5 1.0
C G:THR14 4.5 24.1 1.0
S4 I:4SM75 4.5 35.4 1.0
SG H:CYS15 4.5 19.3 1.0
SG I:CYS15 4.5 18.6 1.0
CB G:THR14 4.5 23.7 1.0
C G:GLY17 4.6 22.9 1.0
NZ G:LYS65 4.7 28.6 1.0
CA G:GLY17 4.7 21.7 1.0
CB H:CYS15 4.8 20.5 1.0
N G:GLY17 4.8 22.4 1.0
N G:THR14 4.9 24.8 1.0
CA G:THR14 4.9 23.6 1.0

Copper binding site 10 out of 16 in 3k7r

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Copper binding site 10 out of 16 in the Crystal Structure of [Tm][CUATX1]3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of [Tm][CUATX1]3 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu75

b:27.8
occ:1.00
 SG H:CYS15 2.2 19.3 1.0
SG G:CYS15 2.3 22.8 1.0
SG I:CYS15 2.3 18.6 1.0
CB H:CYS15 3.1 20.5 1.0
CU H:CU74 3.2 30.5 1.0
CU G:CU74 3.2 29.1 1.0
CU I:CU74 3.2 28.6 1.0
CB I:CYS15 3.3 19.6 1.0
CB G:CYS15 3.3 21.4 1.0
S3 I:4SM75 3.7 31.6 1.0
S1 I:4SM75 3.8 29.4 1.0
S2 I:4SM75 3.8 31.4 1.0
MO1 I:4SM75 3.9 31.8 1.0
O1 L:MLT75 4.2 47.5 1.0
C3 L:MLT75 4.3 41.9 1.0
C1 L:MLT75 4.3 47.5 1.0
O4 L:MLT75 4.3 43.5 1.0
C4 L:MLT75 4.4 47.8 1.0
CA H:CYS15 4.6 20.3 1.0
CA I:CYS15 4.7 20.7 1.0
CA G:CYS15 4.7 21.8 1.0
C2 L:MLT75 4.8 45.7 1.0
O2 L:MLT75 4.8 47.5 1.0
N H:CYS15 5.0 21.3 1.0

Reference:

H.M.Alvarez, Y.Xue, C.D.Robinson, M.A.Canalizo-Hernandez, R.G.Marvin, R.A.Kelly, A.Mondragon, J.E.Penner-Hahn, T.V.O'halloran. Tetrathiomolybdate Inhibits Copper Trafficking Proteins Through Metal Cluster Formation. Science V. 327 331 2010.
ISSN: ISSN 0036-8075
PubMed: 19965379
DOI: 10.1126/SCIENCE.1179907
Page generated: Wed Jul 31 01:13:45 2024

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