Cadmium in PDB 5qrr: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z31720228

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z31720228, PDB code: 5qrr 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)	59.92 / 1.69
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	59.924, 59.924, 109.985, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 27.2

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z31720228 (pdb code 5qrr). 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 Z31720228, PDB code: 5qrr:
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 Z31720228


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 Z31720228 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:24.5 occ:0.50 O A:HOH457 2.3 18.7 0.5 SG A:CYS186 2.5 19.6 0.2 OE1 A:GLU167 2.5 24.3 1.0 SG A:CYS186 2.6 26.6 0.2 CB A:CYS186 3.3 30.0 0.2 CB A:CYS186 3.4 23.5 0.2 CD A:CD302 3.6 25.9 1.0 CD A:GLU167 3.7 22.3 1.0 O A:HOH445 4.2 25.6 1.0 OE2 A:GLU167 4.4 20.5 1.0 CG A:GLU167 4.7 21.8 1.0 CA A:CYS186 4.7 27.8 0.2 CA A:CYS186 4.8 24.2 0.2

Cadmium binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z31720228


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 Z31720228 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:25.9 occ:1.00 OE2 A:GLU167 2.2 20.5 1.0 O A:HOH461 2.4 20.1 1.0 OE1 A:GLU167 2.7 24.3 1.0 CD A:GLU167 2.7 22.3 1.0 CD A:CD301 3.6 24.5 0.5 NE2 A:GLN191 3.9 35.3 1.0 CG A:GLU167 4.2 21.8 1.0 CG A:PRO188 4.3 36.6 1.0 O A:HOH457 4.6 18.7 0.5 CB A:PRO188 4.6 29.7 1.0 SG A:CYS186 4.9 19.6 0.2 CB A:GLU167 4.9 21.5 1.0 CA A:PRO188 4.9 29.2 1.0

Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z31720228


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 Z31720228 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:52.1 occ:1.00 O A:HOH458 2.4 28.7 1.0 O A:HOH446 2.6 50.6 1.0 O A:HOH467 2.7 48.1 1.0 SG A:CYS122 2.8 42.1 1.0 CB A:CYS122 3.3 36.5 1.0 CD A:CD305 3.9 47.0 1.0 O A:HOH464 4.2 53.0 0.9 CA A:CYS122 4.8 34.2 1.0 O A:HOH416 4.8 35.4 1.0 O A:GLN157 4.9 40.3 1.0

Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z31720228


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 Z31720228 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:35.6 occ:1.00 O A:HOH462 2.1 34.3 1.0 NE2 A:HIS100 2.2 41.5 1.0 O A:HOH459 2.3 28.1 1.0 O A:HOH463 2.4 26.1 1.0 O A:HOH454 3.1 35.1 1.0 CD2 A:HIS100 3.1 38.2 1.0 CE1 A:HIS100 3.2 49.9 1.0 CB A:PRO115 4.2 61.0 1.0 ND1 A:HIS100 4.3 40.0 1.0 CG A:HIS100 4.3 38.1 1.0 CG A:PRO115 4.4 62.7 1.0

Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z31720228


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 Z31720228 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:47.0 occ:1.00 O A:HOH464 2.2 53.0 0.9 SG A:CYS122 2.3 42.1 1.0 O1 A:NY1306 2.4 41.3 0.9 N1 A:NY1306 2.5 52.1 0.9 O A:HOH467 2.7 48.1 1.0 C5 A:NY1306 3.1 51.2 0.9 C2 A:NY1306 3.3 52.8 0.9 CB A:CYS122 3.3 36.5 1.0 C3 A:NY1306 3.4 53.4 0.9 C1 A:NY1306 3.5 51.2 0.9 C4 A:NY1306 3.6 51.4 0.9 CD A:CD303 3.9 52.1 1.0 CA A:CYS122 4.0 34.2 1.0 N2 A:NY1306 4.2 52.7 0.9 C6 A:NY1306 4.5 53.5 0.9 C10 A:NY1306 4.5 54.3 0.9 S1 A:NY1306 4.8 52.9 0.9 N A:VAL123 4.9 28.5 1.0 N A:CYS122 5.0 33.2 1.0 C A:CYS122 5.0 30.9 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.