Cadmium in PDB 5qrl: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z437516460

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z437516460, PDB code: 5qrl 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)	52.83 / 1.76
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	60.104, 60.104, 110.242, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 26.1

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z437516460 (pdb code 5qrl). 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 Z437516460, PDB code: 5qrl:
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 Z437516460


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 Z437516460 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:29.4 occ:0.50 O A:HOH437 2.2 29.7 0.5 SG A:CYS186 2.4 27.5 0.2 SG A:CYS186 2.5 22.2 0.2 OE1 A:GLU167 2.5 28.4 1.0 CB A:CYS186 3.3 33.0 0.2 CB A:CYS186 3.4 26.7 0.2 CD A:CD302 3.6 30.7 1.0 CD A:GLU167 3.7 27.7 1.0 O A:HOH446 4.2 29.4 1.0 OE2 A:GLU167 4.4 25.7 1.0 CG A:GLU167 4.7 29.4 1.0 CA A:CYS186 4.7 30.3 0.2 CA A:CYS186 4.8 26.2 0.2

Cadmium binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z437516460


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 Z437516460 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:30.7 occ:1.00 OE2 A:GLU167 2.3 25.7 1.0 O A:HOH462 2.4 24.6 1.0 OE1 A:GLU167 2.7 28.4 1.0 CD A:GLU167 2.8 27.7 1.0 CD A:CD301 3.6 29.4 0.5 NE2 A:GLN191 3.9 46.6 1.0 O A:HOH437 4.1 29.7 0.5 CG A:GLU167 4.3 29.4 1.0 CG A:PRO188 4.3 36.1 1.0 CB A:PRO188 4.7 32.4 1.0 SG A:CYS186 4.8 22.2 0.2 CB A:GLU167 4.9 28.3 1.0 CA A:PRO188 5.0 31.3 1.0

Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z437516460


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 Z437516460 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:61.3 occ:1.00 O A:HOH457 2.4 39.1 1.0 O A:HOH470 2.6 47.8 1.0 SG A:CYS122 2.7 52.5 1.0 O A:HOH450 2.8 51.7 1.0 CB A:CYS122 3.3 43.4 1.0 CD A:CD305 3.7 63.3 1.0 O A:HOH471 4.2 51.9 1.0 O A:HOH419 4.7 44.8 1.0 CA A:CYS122 4.8 37.5 1.0 O A:GLN157 4.9 40.4 1.0

Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z437516460


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 Z437516460 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:39.1 occ:1.00 NE2 A:HIS100 2.2 45.5 1.0 O A:HOH463 2.3 33.5 1.0 O A:HOH459 2.3 27.5 1.0 O A:HOH460 2.4 27.1 1.0 CD2 A:HIS100 3.2 39.4 1.0 CE1 A:HIS100 3.2 53.2 1.0 O A:HOH440 3.5 43.4 1.0 CG A:PRO115 4.3 67.8 1.0 CB A:PRO115 4.3 62.4 1.0 CG A:HIS100 4.3 46.5 1.0 ND1 A:HIS100 4.3 45.4 1.0

Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z437516460


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 Z437516460 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:63.3 occ:1.00 SG A:CYS122 2.4 52.5 1.0 O A:HOH453 2.5 32.9 1.0 O A:HOH471 2.6 51.9 1.0 O A:HOH470 2.7 47.8 1.0 CB A:CYS122 3.5 43.4 1.0 CD A:CD303 3.7 61.3 1.0 CA A:CYS122 4.1 37.5 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.