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Cadmium in PDB 5qrx: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z364328788

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z364328788, PDB code: 5qrx 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) 40.47 / 1.87
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 59.620, 59.620, 110.050, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 27.2

Other elements in 5qrx:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z364328788 also contains other interesting chemical elements:

Fluorine (F) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z364328788 (pdb code 5qrx). 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 Z364328788, PDB code: 5qrx:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 5qrx

Go back to Cadmium Binding Sites List in 5qrx
Cadmium binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:33.7
occ:0.50
O A:HOH455 2.2 33.8 0.5
SG A:CYS186 2.5 26.2 0.2
OE1 A:GLU167 2.5 33.0 1.0
SG A:CYS186 2.5 31.8 0.2
CB A:CYS186 3.3 34.9 0.2
CB A:CYS186 3.4 31.9 0.2
CD A:CD302 3.6 35.9 1.0
CD A:GLU167 3.7 36.3 1.0
O A:HOH437 4.3 33.6 1.0
OE2 A:GLU167 4.5 32.5 1.0
CG A:GLU167 4.6 36.1 1.0
CA A:CYS186 4.8 35.3 0.2
CA A:CYS186 4.8 33.5 0.2

Cadmium binding site 2 out of 5 in 5qrx

Go back to Cadmium Binding Sites List in 5qrx
Cadmium binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:35.9
occ:1.00
O A:HOH457 2.4 25.0 1.0
OE2 A:GLU167 2.4 32.5 1.0
OE1 A:GLU167 2.6 33.0 1.0
CD A:GLU167 2.8 36.3 1.0
CD A:CD301 3.6 33.7 0.5
NE2 A:GLN191 3.8 56.9 1.0
CG A:PRO188 4.2 44.1 1.0
CG A:GLU167 4.3 36.1 1.0
CB A:PRO188 4.6 38.5 1.0
SG A:CYS186 4.8 26.2 0.2
CA A:PRO188 4.8 38.9 1.0
CB A:GLU167 4.9 35.2 1.0

Cadmium binding site 3 out of 5 in 5qrx

Go back to Cadmium Binding Sites List in 5qrx
Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:85.5
occ:1.00
O A:HOH445 2.5 43.7 1.0
SG A:CYS122 2.7 58.3 1.0
O A:HOH471 2.9 55.4 1.0
O A:HOH443 3.0 59.4 1.0
CB A:CYS122 3.3 48.3 1.0
CD A:CD305 3.8 76.2 1.0
O A:HOH472 3.9 63.2 1.0
O A:HOH419 4.6 48.5 1.0
CA A:CYS122 4.8 44.6 1.0
O A:GLN157 4.9 59.3 1.0

Cadmium binding site 4 out of 5 in 5qrx

Go back to Cadmium Binding Sites List in 5qrx
Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:45.1
occ:1.00
O A:HOH461 2.2 38.1 1.0
O A:HOH458 2.2 31.7 1.0
NE2 A:HIS100 2.3 54.4 1.0
O A:HOH460 2.5 30.4 1.0
CD2 A:HIS100 3.1 45.4 1.0
CE1 A:HIS100 3.4 58.0 1.0
CG A:HIS100 4.3 46.4 1.0
CB A:PRO115 4.4 74.3 1.0
ND1 A:HIS100 4.4 51.9 1.0
CG A:PRO115 4.6 78.0 1.0

Cadmium binding site 5 out of 5 in 5qrx

Go back to Cadmium Binding Sites List in 5qrx
Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:76.2
occ:1.00
SG A:CYS122 2.4 58.3 1.0
O A:HOH448 2.6 44.9 1.0
O A:HOH472 2.9 63.2 1.0
O A:HOH471 2.9 55.4 1.0
CB A:CYS122 3.5 48.3 1.0
CD A:CD303 3.8 85.5 1.0
CA A:CYS122 4.2 44.6 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 08:27:29 2020

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