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Cadmium in PDB 5qrs: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393, PDB code: 5qrs was solved by J.A.Newman, A.E.Gavard, A.Fernandez-Cid, L.Sherestha, N.A.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.87 / 2.06
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 59.871, 59.871, 110.259, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 26.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393 (pdb code 5qrs). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393, PDB code: 5qrs:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5qrs

Go back to Cadmium Binding Sites List in 5qrs
Cadmium binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:24.6
occ:0.50
SG A:CYS186 2.4 27.7 0.2
SG A:CYS186 2.4 20.2 0.2
O A:HOH456 2.4 23.6 0.5
OE1 A:GLU167 2.6 24.7 1.0
CB A:CYS186 3.3 27.6 0.2
CB A:CYS186 3.3 23.0 0.2
CD A:CD302 3.7 27.1 1.0
CD A:GLU167 3.8 27.6 1.0
O A:HOH433 4.3 23.2 1.0
OE2 A:GLU167 4.5 24.6 1.0
CA A:CYS186 4.7 26.7 0.2
CG A:GLU167 4.7 27.4 1.0
CA A:CYS186 4.8 23.9 0.2

Cadmium binding site 2 out of 5 in 5qrs

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Cadmium binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:27.1
occ:1.00
O A:HOH460 2.4 14.6 1.0
OE2 A:GLU167 2.4 24.6 1.0
OE1 A:GLU167 2.7 24.7 1.0
CD A:GLU167 2.9 27.6 1.0
CD A:CD301 3.7 24.6 0.5
NE2 A:GLN191 3.7 43.9 1.0
CG A:GLU167 4.3 27.4 1.0
CG A:PRO188 4.4 29.2 1.0
CB A:PRO188 4.7 27.1 1.0
SG A:CYS186 4.8 20.2 0.2
CA A:PRO188 4.9 27.6 1.0
CB A:GLU167 4.9 27.1 1.0

Cadmium binding site 3 out of 5 in 5qrs

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Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:68.5
occ:1.00
O A:HOH450 2.5 37.9 1.0
SG A:CYS122 2.7 53.5 1.0
O A:HOH468 2.8 42.0 1.0
O A:HOH444 3.0 45.2 1.0
CB A:CYS122 3.3 43.6 1.0
CD A:CD305 3.8 61.3 1.0
O A:HOH469 4.1 44.0 1.0
O A:HOH430 4.5 50.5 1.0
CA A:CYS122 4.8 38.7 1.0
O A:GLN157 4.9 46.0 1.0

Cadmium binding site 4 out of 5 in 5qrs

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Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:35.5
occ:1.00
O A:HOH455 2.2 21.8 1.0
O A:HOH458 2.2 24.9 1.0
NE2 A:HIS100 2.3 48.5 1.0
O A:HOH457 2.5 20.6 1.0
CD2 A:HIS100 3.2 43.0 1.0
CE1 A:HIS100 3.3 47.5 1.0
O A:HOH442 3.4 37.6 1.0
CG A:PRO115 4.2 64.0 1.0
CB A:PRO115 4.4 61.8 1.0
ND1 A:HIS100 4.4 43.7 1.0
CG A:HIS100 4.4 43.0 1.0
CD A:PRO115 5.0 63.1 1.0

Cadmium binding site 5 out of 5 in 5qrs

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Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1891773393 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:61.3
occ:1.00
SG A:CYS122 2.5 53.5 1.0
O A:HOH469 2.5 44.0 1.0
O A:HOH445 2.6 34.7 1.0
O A:HOH468 2.9 42.0 1.0
CB A:CYS122 3.5 43.6 1.0
CD A:CD303 3.8 68.5 1.0
CA A:CYS122 4.1 38.7 1.0
N A:VAL123 5.0 32.6 1.0

Reference:

J.A.Newman, A.E.Gavard, A.Fernandez-Cid, L.Sherestha, N.A.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, O.Gileadi. Pandda Analysis Group Deposition To Be Published.
Page generated: Sat Dec 12 08:27:27 2020

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