Cadmium in PDB 5qri: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z2856434826

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z2856434826, PDB code: 5qri 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)	52.72 / 1.83
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	59.957, 59.957, 110.153, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26.9

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z2856434826 (pdb code 5qri). 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 Z2856434826, PDB code: 5qri:
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 Z2856434826


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 Z2856434826 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:28.1 occ:0.50 O A:HOH454 2.3 25.9 0.5 SG A:CYS186 2.4 21.4 0.2 SG A:CYS186 2.4 29.0 0.2 OE1 A:GLU167 2.5 28.2 1.0 CB A:CYS186 3.3 32.4 0.2 CB A:CYS186 3.3 25.6 0.2 CD A:CD302 3.6 29.7 1.0 CD A:GLU167 3.7 26.9 1.0 O A:HOH442 4.2 27.5 1.0 OE2 A:GLU167 4.4 26.0 1.0 CG A:GLU167 4.7 27.4 1.0 CA A:CYS186 4.7 30.4 0.2 CA A:CYS186 4.8 26.4 0.2

Cadmium binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z2856434826


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 Z2856434826 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:29.7 occ:1.00 O A:HOH463 2.3 22.2 1.0 OE2 A:GLU167 2.4 26.0 1.0 OE1 A:GLU167 2.6 28.2 1.0 CD A:GLU167 2.8 26.9 1.0 CD A:CD301 3.6 28.1 0.5 NE2 A:GLN191 3.9 47.5 1.0 CG A:GLU167 4.3 27.4 1.0 CG A:PRO188 4.4 36.9 1.0 O A:HOH454 4.4 25.9 0.5 CB A:PRO188 4.6 32.3 1.0 SG A:CYS186 4.8 21.4 0.2 CB A:GLU167 4.9 27.9 1.0 CA A:PRO188 4.9 30.5 1.0

Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z2856434826


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 Z2856434826 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:63.2 occ:1.00 O A:HOH455 2.5 36.7 1.0 O A:HOH471 2.7 46.1 1.0 SG A:CYS122 2.7 48.2 1.0 O A:HOH458 2.9 52.6 1.0 CB A:CYS122 3.3 40.8 1.0 CD A:CD305 3.7 62.3 1.0 O A:HOH470 3.9 55.8 1.0 O A:HOH417 4.7 43.2 1.0 CA A:CYS122 4.8 37.6 1.0 O A:GLN157 4.9 47.0 1.0

Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z2856434826


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 Z2856434826 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:38.4 occ:1.00 O A:HOH462 2.1 34.2 1.0 O A:HOH459 2.2 27.5 1.0 NE2 A:HIS100 2.2 45.7 1.0 O A:HOH461 2.5 28.5 1.0 CD2 A:HIS100 3.1 41.0 1.0 CE1 A:HIS100 3.3 52.3 1.0 O A:HOH449 3.3 41.5 1.0 CG A:HIS100 4.3 42.3 1.0 CG A:PRO115 4.3 66.8 1.0 ND1 A:HIS100 4.3 42.6 1.0 CB 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 Z2856434826


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 Z2856434826 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:62.3 occ:1.00 SG A:CYS122 2.3 48.2 1.0 O A:HOH448 2.5 32.4 1.0 O A:HOH470 2.6 55.8 1.0 O A:HOH471 2.8 46.1 1.0 CB A:CYS122 3.4 40.8 1.0 CD A:CD303 3.7 63.2 1.0 CA A:CYS122 4.1 37.6 1.0 N A:VAL123 4.9 35.2 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.