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Tungsten in PDB 1n7d: Extracellular Domain of the Ldl Receptor

Protein crystallography data

The structure of Extracellular Domain of the Ldl Receptor, PDB code: 1n7d was solved by G.Rudenko, L.Henry, K.Henderson, K.Ichtchenko, M.S.Brown, J.L.Goldstein, J.Deisenhofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.30 / 3.70
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 185.290, 185.290, 85.186, 90.00, 90.00, 120.00
R / Rfree (%) 38.1 / 38.2

Other elements in 1n7d:

The structure of Extracellular Domain of the Ldl Receptor also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Tungsten Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 31;

Binding sites:

The binding sites of Tungsten atom in the Extracellular Domain of the Ldl Receptor (pdb code 1n7d). This binding sites where shown within 5.0 Angstroms radius around Tungsten atom.
In total 31 binding sites of Tungsten where determined in the Extracellular Domain of the Ldl Receptor, PDB code: 1n7d:
Jump to Tungsten binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Tungsten binding site 1 out of 31 in 1n7d

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Tungsten binding site 1 out of 31 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 1 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W6001

b:0.7
occ:1.00
W1 A:KEG6001 0.0 0.7 1.0
O29 A:KEG6001 1.6 0.7 1.0
O1 A:KEG6001 1.6 0.7 1.0
O23 A:KEG6001 1.7 0.7 1.0
O25 A:KEG6001 1.8 0.7 1.0
O27 A:KEG6001 2.0 0.7 1.0
O17 A:KEG6001 2.2 0.7 1.0
W7 A:KEG6001 3.0 0.7 1.0
W5 A:KEG6001 3.1 0.7 1.0
P1 A:KEG6001 3.2 0.7 1.0
O35 A:KEG6001 3.3 0.7 1.0
W3 A:KEG6001 3.4 0.7 1.0
O33 A:KEG6001 3.4 0.7 1.0
O21 A:KEG6001 3.5 0.7 1.0
O19 A:KEG6001 3.5 0.7 1.0
W9 A:KEG6001 3.6 0.7 1.0
O37 A:KEG6001 3.8 0.7 1.0
O39 A:KEG6001 3.9 0.7 1.0
O45 A:KEG6001 3.9 0.7 1.0
O43 A:KEG6001 4.0 0.7 1.0
O9 A:KEG6001 4.1 0.7 1.0
O7 A:KEG6001 4.2 0.7 1.0
O18 A:KEG6001 4.3 0.7 1.0
O5 A:KEG6001 4.6 0.7 1.0
O32 A:KEG6001 4.6 0.7 1.0
W12 A:KEG6001 4.6 0.7 1.0
O41 A:KEG6001 4.7 0.7 1.0
O11 A:KEG6001 4.7 0.7 1.0
O42 A:KEG6001 4.8 0.7 1.0
W11 A:KEG6001 4.9 0.7 1.0
O31 A:KEG6001 4.9 0.7 1.0

Tungsten binding site 2 out of 31 in 1n7d

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Tungsten binding site 2 out of 31 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 2 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W6001

b:0.7
occ:1.00
W2 A:KEG6001 0.0 0.7 1.0
O28 A:KEG6001 1.6 0.7 1.0
O2 A:KEG6001 1.6 0.7 1.0
O24 A:KEG6001 1.8 0.7 1.0
O26 A:KEG6001 1.8 0.7 1.0
O30 A:KEG6001 1.9 0.7 1.0
O18 A:KEG6001 2.2 0.7 1.0
W10 A:KEG6001 3.0 0.7 1.0
P1 A:KEG6001 3.1 0.7 1.0
O36 A:KEG6001 3.2 0.7 1.0
W6 A:KEG6001 3.3 0.7 1.0
W4 A:KEG6001 3.4 0.7 1.0
W8 A:KEG6001 3.4 0.7 1.0
O34 A:KEG6001 3.4 0.7 1.0
O19 A:KEG6001 3.4 0.7 1.0
O21 A:KEG6001 3.5 0.7 1.0
O46 A:KEG6001 3.7 0.7 1.0
O44 A:KEG6001 3.8 0.7 1.0
O38 A:KEG6001 3.9 0.7 1.0
O12 A:KEG6001 3.9 0.7 1.0
O40 A:KEG6001 4.0 0.7 1.0
O17 A:KEG6001 4.4 0.7 1.0
O8 A:KEG6001 4.4 0.7 1.0
O6 A:KEG6001 4.5 0.7 1.0
O10 A:KEG6001 4.6 0.7 1.0
O42 A:KEG6001 4.7 0.7 1.0
W12 A:KEG6001 4.7 0.7 1.0
O41 A:KEG6001 4.8 0.7 1.0
W11 A:KEG6001 4.8 0.7 1.0
CB A:ASN76 4.9 0.7 1.0
O31 A:KEG6001 4.9 0.7 1.0
O32 A:KEG6001 5.0 0.7 1.0

Tungsten binding site 3 out of 31 in 1n7d

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Tungsten binding site 3 out of 31 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 3 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W6001

b:0.7
occ:1.00
W3 A:KEG6001 0.0 0.7 1.0
O33 A:KEG6001 1.6 0.7 1.0
O5 A:KEG6001 1.7 0.7 1.0
O25 A:KEG6001 1.8 0.7 1.0
O31 A:KEG6001 2.0 0.7 1.0
O37 A:KEG6001 2.1 0.7 1.0
O21 A:KEG6001 2.6 0.7 1.0
W7 A:KEG6001 3.1 0.7 1.0
W1 A:KEG6001 3.4 0.7 1.0
O29 A:KEG6001 3.4 0.7 1.0
P1 A:KEG6001 3.7 0.7 1.0
W4 A:KEG6001 3.8 0.7 1.0
W12 A:KEG6001 3.8 0.7 1.0
O38 A:KEG6001 3.8 0.7 1.0
O41 A:KEG6001 3.9 0.7 1.0
O19 A:KEG6001 3.9 0.7 1.0
O9 A:KEG6001 4.0 0.7 1.0
O17 A:KEG6001 4.1 0.7 1.0
O34 A:KEG6001 4.1 0.7 1.0
O1 A:KEG6001 4.2 0.7 1.0
O27 A:KEG6001 4.3 0.7 1.0
O45 A:KEG6001 4.6 0.7 1.0
O6 A:KEG6001 4.8 0.7 1.0
O14 A:KEG6001 4.8 0.7 1.0
O18 A:KEG6001 4.9 0.7 1.0
O23 A:KEG6001 4.9 0.7 1.0
O43 A:KEG6001 4.9 0.7 1.0
W8 A:KEG6001 5.0 0.7 1.0

Tungsten binding site 4 out of 31 in 1n7d

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Tungsten binding site 4 out of 31 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 4 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W6001

b:0.7
occ:1.00
W4 A:KEG6001 0.0 0.7 1.0
O6 A:KEG6001 1.6 0.7 1.0
O26 A:KEG6001 1.8 0.7 1.0
O34 A:KEG6001 1.9 0.7 1.0
O38 A:KEG6001 1.9 0.7 1.0
O31 A:KEG6001 2.0 0.7 1.0
O21 A:KEG6001 2.6 0.7 1.0
W2 A:KEG6001 3.4 0.7 1.0
O30 A:KEG6001 3.5 0.7 1.0
W8 A:KEG6001 3.6 0.7 1.0
P1 A:KEG6001 3.7 0.7 1.0
W12 A:KEG6001 3.7 0.7 1.0
O37 A:KEG6001 3.8 0.7 1.0
W3 A:KEG6001 3.8 0.7 1.0
O28 A:KEG6001 3.8 0.7 1.0
O18 A:KEG6001 3.9 0.7 1.0
O19 A:KEG6001 3.9 0.7 1.0
O46 A:KEG6001 4.0 0.7 1.0
O33 A:KEG6001 4.1 0.7 1.0
O41 A:KEG6001 4.1 0.7 1.0
O2 A:KEG6001 4.3 0.7 1.0
O14 A:KEG6001 4.6 0.7 1.0
O10 A:KEG6001 4.7 0.7 1.0
W10 A:KEG6001 4.9 0.7 1.0
O5 A:KEG6001 4.9 0.7 1.0
W7 A:KEG6001 4.9 0.7 1.0
O24 A:KEG6001 4.9 0.7 1.0
O17 A:KEG6001 4.9 0.7 1.0

Tungsten binding site 5 out of 31 in 1n7d

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Tungsten binding site 5 out of 31 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 5 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W6001

b:0.7
occ:1.00
W5 A:KEG6001 0.0 0.7 1.0
O7 A:KEG6001 1.6 0.7 1.0
O23 A:KEG6001 1.7 0.7 1.0
O39 A:KEG6001 1.9 0.7 1.0
O35 A:KEG6001 1.9 0.7 1.0
O32 A:KEG6001 2.0 0.7 1.0
O17 A:KEG6001 2.5 0.7 1.0
W1 A:KEG6001 3.1 0.7 1.0
O29 A:KEG6001 3.4 0.7 1.0
O27 A:KEG6001 3.5 0.7 1.0
W11 A:KEG6001 3.5 0.7 1.0
P1 A:KEG6001 3.6 0.7 1.0
W9 A:KEG6001 3.7 0.7 1.0
O19 A:KEG6001 3.7 0.7 1.0
O40 A:KEG6001 3.7 0.7 1.0
W6 A:KEG6001 3.8 0.7 1.0
O43 A:KEG6001 3.8 0.7 1.0
O1 A:KEG6001 4.0 0.7 1.0
O18 A:KEG6001 4.0 0.7 1.0
O36 A:KEG6001 4.2 0.7 1.0
O42 A:KEG6001 4.4 0.7 1.0
W7 A:KEG6001 4.4 0.7 1.0
O13 A:KEG6001 4.5 0.7 1.0
O11 A:KEG6001 4.7 0.7 1.0
O8 A:KEG6001 4.8 0.7 1.0
O25 A:KEG6001 4.8 0.7 1.0
O21 A:KEG6001 5.0 0.7 1.0
O44 A:KEG6001 5.0 0.7 1.0

Tungsten binding site 6 out of 31 in 1n7d

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Tungsten binding site 6 out of 31 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 6 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W6001

b:0.7
occ:1.00
W6 A:KEG6001 0.0 0.7 1.0
O36 A:KEG6001 1.6 0.7 1.0
O8 A:KEG6001 1.6 0.7 1.0
O24 A:KEG6001 1.8 0.7 1.0
O40 A:KEG6001 1.9 0.7 1.0
O32 A:KEG6001 2.0 0.7 1.0
O18 A:KEG6001 2.3 0.7 1.0
W10 A:KEG6001 3.1 0.7 1.0
P1 A:KEG6001 3.3 0.7 1.0
W2 A:KEG6001 3.3 0.7 1.0
W11 A:KEG6001 3.4 0.7 1.0
O28 A:KEG6001 3.4 0.7 1.0
O19 A:KEG6001 3.4 0.7 1.0
O17 A:KEG6001 3.5 0.7 1.0
O39 A:KEG6001 3.7 0.7 1.0
O44 A:KEG6001 3.7 0.7 1.0
O42 A:KEG6001 3.8 0.7 1.0
W5 A:KEG6001 3.8 0.7 1.0
O30 A:KEG6001 3.9 0.7 1.0
O35 A:KEG6001 4.0 0.7 1.0
O12 A:KEG6001 4.1 0.7 1.0
O2 A:KEG6001 4.3 0.7 1.0
O13 A:KEG6001 4.5 0.7 1.0
O A:GLY56 4.6 0.7 1.0
W9 A:KEG6001 4.6 0.7 1.0
W8 A:KEG6001 4.7 0.7 1.0
O21 A:KEG6001 4.7 0.7 1.0
O43 A:KEG6001 4.8 0.7 1.0
O46 A:KEG6001 4.8 0.7 1.0
O26 A:KEG6001 4.9 0.7 1.0
O A:GLY55 4.9 0.7 1.0
O7 A:KEG6001 5.0 0.7 1.0
O23 A:KEG6001 5.0 0.7 1.0

Tungsten binding site 7 out of 31 in 1n7d

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Tungsten binding site 7 out of 31 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 7 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W6001

b:0.7
occ:1.00
W7 A:KEG6001 0.0 0.7 1.0
O9 A:KEG6001 1.7 0.7 1.0
O29 A:KEG6001 1.7 0.7 1.0
O33 A:KEG6001 1.8 0.7 1.0
O43 A:KEG6001 1.9 0.7 1.0
O41 A:KEG6001 1.9 0.7 1.0
O19 A:KEG6001 2.4 0.7 1.0
W1 A:KEG6001 3.0 0.7 1.0
O25 A:KEG6001 3.1 0.7 1.0
W3 A:KEG6001 3.1 0.7 1.0
P1 A:KEG6001 3.2 0.7 1.0
O23 A:KEG6001 3.4 0.7 1.0
W8 A:KEG6001 3.5 0.7 1.0
O17 A:KEG6001 3.5 0.7 1.0
O21 A:KEG6001 3.5 0.7 1.0
W11 A:KEG6001 3.5 0.7 1.0
O44 A:KEG6001 3.7 0.7 1.0
O39 A:KEG6001 3.7 0.7 1.0
O31 A:KEG6001 3.9 0.7 1.0
O34 A:KEG6001 4.0 0.7 1.0
O1 A:KEG6001 4.1 0.7 1.0
O5 A:KEG6001 4.3 0.7 1.0
O18 A:KEG6001 4.3 0.7 1.0
W5 A:KEG6001 4.4 0.7 1.0
O10 A:KEG6001 4.5 0.7 1.0
O13 A:KEG6001 4.6 0.7 1.0
O37 A:KEG6001 4.7 0.7 1.0
O27 A:KEG6001 4.8 0.7 1.0
O40 A:KEG6001 4.9 0.7 1.0
W4 A:KEG6001 4.9 0.7 1.0
O30 A:KEG6001 4.9 0.7 1.0

Tungsten binding site 8 out of 31 in 1n7d

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Tungsten binding site 8 out of 31 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 8 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W6001

b:0.7
occ:1.00
W8 A:KEG6001 0.0 0.7 1.0
O10 A:KEG6001 1.6 0.7 1.0
O44 A:KEG6001 1.8 0.7 1.0
O41 A:KEG6001 1.8 0.7 1.0
O30 A:KEG6001 1.9 0.7 1.0
O34 A:KEG6001 2.0 0.7 1.0
O19 A:KEG6001 2.4 0.7 1.0
O43 A:KEG6001 3.3 0.7 1.0
W11 A:KEG6001 3.4 0.7 1.0
W2 A:KEG6001 3.4 0.7 1.0
P1 A:KEG6001 3.4 0.7 1.0
W7 A:KEG6001 3.5 0.7 1.0
W4 A:KEG6001 3.6 0.7 1.0
O18 A:KEG6001 3.6 0.7 1.0
O26 A:KEG6001 3.6 0.7 1.0
O24 A:KEG6001 3.8 0.7 1.0
O21 A:KEG6001 3.8 0.7 1.0
O40 A:KEG6001 3.9 0.7 1.0
O33 A:KEG6001 4.1 0.7 1.0
O31 A:KEG6001 4.1 0.7 1.0
O13 A:KEG6001 4.3 0.7 1.0
O2 A:KEG6001 4.5 0.7 1.0
O9 A:KEG6001 4.5 0.7 1.0
W6 A:KEG6001 4.7 0.7 1.0
O28 A:KEG6001 4.7 0.7 1.0
O6 A:KEG6001 4.7 0.7 1.0
O17 A:KEG6001 4.7 0.7 1.0
O39 A:KEG6001 4.9 0.7 1.0
O29 A:KEG6001 4.9 0.7 1.0
W3 A:KEG6001 5.0 0.7 1.0

Tungsten binding site 9 out of 31 in 1n7d

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Tungsten binding site 9 out of 31 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 9 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W6001

b:0.7
occ:1.00
W9 A:KEG6001 0.0 0.7 1.0
O11 A:KEG6001 1.6 0.7 1.0
O42 A:KEG6001 1.7 0.7 1.0
O27 A:KEG6001 1.9 0.7 1.0
O45 A:KEG6001 1.9 0.7 1.0
O35 A:KEG6001 2.0 0.7 1.0
O17 A:KEG6001 2.5 0.7 1.0
W10 A:KEG6001 3.3 0.7 1.0
O46 A:KEG6001 3.5 0.7 1.0
W1 A:KEG6001 3.6 0.7 1.0
P1 A:KEG6001 3.6 0.7 1.0
W12 A:KEG6001 3.7 0.7 1.0
O36 A:KEG6001 3.7 0.7 1.0
W5 A:KEG6001 3.7 0.7 1.0
O18 A:KEG6001 3.7 0.7 1.0
O23 A:KEG6001 3.9 0.7 1.0
O32 A:KEG6001 3.9 0.7 1.0
O21 A:KEG6001 4.0 0.7 1.0
O12 A:KEG6001 4.3 0.7 1.0
O37 A:KEG6001 4.4 0.7 1.0
O25 A:KEG6001 4.4 0.7 1.0
O1 A:KEG6001 4.5 0.7 1.0
W6 A:KEG6001 4.6 0.7 1.0
O14 A:KEG6001 4.7 0.7 1.0
O28 A:KEG6001 4.7 0.7 1.0
O7 A:KEG6001 4.7 0.7 1.0
O19 A:KEG6001 4.8 0.7 1.0
O29 A:KEG6001 4.9 0.7 1.0

Tungsten binding site 10 out of 31 in 1n7d

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Tungsten binding site 10 out of 31 in the Extracellular Domain of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 10 of Extracellular Domain of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W6001

b:0.7
occ:1.00
W10 A:KEG6001 0.0 0.7 1.0
O12 A:KEG6001 1.6 0.7 1.0
O28 A:KEG6001 1.7 0.7 1.0
O36 A:KEG6001 1.7 0.7 1.0
O42 A:KEG6001 1.9 0.7 1.0
O46 A:KEG6001 1.9 0.7 1.0
O18 A:KEG6001 2.2 0.7 1.0
W2 A:KEG6001 3.0 0.7 1.0
O24 A:KEG6001 3.1 0.7 1.0
P1 A:KEG6001 3.1 0.7 1.0
W6 A:KEG6001 3.1 0.7 1.0
W9 A:KEG6001 3.3 0.7 1.0
O17 A:KEG6001 3.4 0.7 1.0
O45 A:KEG6001 3.4 0.7 1.0
W12 A:KEG6001 3.5 0.7 1.0
O21 A:KEG6001 3.6 0.7 1.0
O26 A:KEG6001 3.7 0.7 1.0
O2 A:KEG6001 3.9 0.7 1.0
O32 A:KEG6001 4.0 0.7 1.0
O38 A:KEG6001 4.0 0.7 1.0
O8 A:KEG6001 4.1 0.7 1.0
O35 A:KEG6001 4.1 0.7 1.0
O19 A:KEG6001 4.2 0.7 1.0
O11 A:KEG6001 4.4 0.7 1.0
O30 A:KEG6001 4.6 0.7 1.0
O27 A:KEG6001 4.6 0.7 1.0
O14 A:KEG6001 4.7 0.7 1.0
O40 A:KEG6001 4.7 0.7 1.0
W4 A:KEG6001 4.9 0.7 1.0
CB A:ASN76 5.0 0.7 1.0

Reference:

G.Rudenko, L.Henry, K.Henderson, K.Ichtchenko, M.S.Brown, J.L.Goldstein, J.Deisenhofer. Structure of the Ldl Receptor Extracellular Domain at Endosomal pH Science V. 298 2353 2002.
ISSN: ISSN 0036-8075
PubMed: 12459547
DOI: 10.1126/SCIENCE.1078124
Page generated: Thu Oct 29 07:06:51 2020

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