Cadmium in PDB 5qs5: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z32400357

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z32400357, PDB code: 5qs5 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)	26.87 / 1.81
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	60.040, 60.040, 110.460, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.6

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z32400357 (pdb code 5qs5). 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 Z32400357, PDB code: 5qs5:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z32400357


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 Z32400357 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:30.4 occ:0.50 O A:HOH457 2.2 20.0 0.5 SG A:CYS186 2.4 28.9 0.2 SG A:CYS186 2.4 23.1 0.2 OE1 A:GLU167 2.5 31.8 1.0 CB A:CYS186 3.3 33.6 0.2 CB A:CYS186 3.3 28.9 0.2 CD A:CD302 3.6 31.8 1.0 CD A:GLU167 3.7 30.0 1.0 O A:HOH439 4.3 27.9 1.0 OE2 A:GLU167 4.5 27.8 1.0 CA A:CYS186 4.7 32.6 0.2 CG A:GLU167 4.7 30.8 1.0 CA A:CYS186 4.8 29.1 0.2

Cadmium binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z32400357


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 Z32400357 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:31.8 occ:1.00 OE2 A:GLU167 2.3 27.8 1.0 O A:HOH462 2.4 24.3 1.0 OE1 A:GLU167 2.6 31.8 1.0 CD A:GLU167 2.8 30.0 1.0 CD A:CD301 3.6 30.4 0.5 NE2 A:GLN191 3.8 52.8 1.0 CG A:GLU167 4.3 30.8 1.0 CG A:PRO188 4.3 37.4 1.0 O A:HOH457 4.4 20.0 0.5 CB A:PRO188 4.8 34.8 1.0 SG A:CYS186 4.8 23.1 0.2 CB A:GLU167 4.9 29.9 1.0 CD A:PRO188 5.0 35.8 1.0 CA A:PRO188 5.0 32.8 1.0

Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z32400357


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 Z32400357 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:85.4 occ:1.00 O A:HOH452 2.5 46.0 1.0 SG A:CYS122 2.6 56.1 1.0 O A:HOH472 3.0 53.9 1.0 O A:HOH447 3.0 52.8 1.0 CB A:CYS122 3.3 48.4 1.0 CD A:CD305 3.8 82.0 1.0 O A:HOH473 4.1 65.2 1.0 O A:HOH422 4.6 52.6 1.0 O A:GLN157 4.7 48.6 1.0 CA A:CYS122 4.8 42.0 1.0

Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z32400357


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 Z32400357 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:40.5 occ:1.00 O A:HOH460 2.1 37.8 1.0 NE2 A:HIS100 2.2 51.0 1.0 O A:HOH459 2.2 27.2 1.0 O A:HOH461 2.5 28.5 1.0 CD2 A:HIS100 3.1 44.4 1.0 CE1 A:HIS100 3.2 57.2 1.0 CG A:PRO115 4.2 69.8 1.0 CG A:HIS100 4.3 48.2 1.0 ND1 A:HIS100 4.3 48.6 1.0 CB A:PRO115 4.4 65.1 1.0

Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z32400357


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 Z32400357 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:82.0 occ:1.00 SG A:CYS122 2.5 56.1 1.0 O A:HOH454 2.6 43.6 1.0 O A:HOH473 2.8 65.2 1.0 O A:HOH472 3.0 53.9 1.0 CB A:CYS122 3.6 48.4 1.0 CD A:CD303 3.8 85.4 1.0 CA A:CYS122 4.2 42.0 1.0

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.