Cadmium in PDB 5qrg: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340, PDB code: 5qrg 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)	59.74 / 1.95
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	59.740, 59.740, 110.350, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 28.1

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340 (pdb code 5qrg). 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 Z275151340, PDB code: 5qrg:
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 Z275151340


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 Z275151340 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:29.0 occ:0.50 O A:HOH455 2.1 23.7 0.5 SG A:CYS186 2.4 20.1 0.2 SG A:CYS186 2.5 31.2 0.2 OE1 A:GLU167 2.6 29.1 1.0 CB A:CYS186 3.3 31.7 0.2 CB A:CYS186 3.3 25.8 0.2 CD A:CD302 3.7 30.7 1.0 CD A:GLU167 3.8 33.1 1.0 O A:HOH439 4.3 25.3 1.0 OE2 A:GLU167 4.5 29.0 1.0 CG A:GLU167 4.7 32.2 1.0 CA A:CYS186 4.7 31.8 0.2 CA A:CYS186 4.8 27.8 0.2 O A:HOH459 5.0 18.0 1.0

Cadmium binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340


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 Z275151340 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:30.7 occ:1.00 O A:HOH459 2.3 18.0 1.0 OE2 A:GLU167 2.4 29.0 1.0 OE1 A:GLU167 2.7 29.1 1.0 CD A:GLU167 2.9 33.1 1.0 CD A:CD301 3.7 29.0 0.5 NE2 A:GLN191 3.8 52.5 1.0 CG A:GLU167 4.4 32.2 1.0 CG A:PRO188 4.4 38.7 1.0 O A:HOH455 4.5 23.7 0.5 CB A:PRO188 4.6 33.8 1.0 CA A:PRO188 4.8 32.8 1.0 SG A:CYS186 4.8 20.1 0.2 CB A:GLU167 5.0 32.1 1.0

Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340


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 Z275151340 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:61.7 occ:1.00 O A:HOH449 2.5 32.8 1.0 O A:HOH469 2.6 41.9 1.0 SG A:CYS122 2.7 53.7 1.0 O A:HOH457 3.0 50.2 1.0 CB A:CYS122 3.3 42.6 1.0 CD A:CD305 3.7 60.5 1.0 O A:HOH470 3.9 52.9 1.0 O A:HOH418 4.7 40.0 1.0 CA A:CYS122 4.8 40.2 1.0 O A:GLN157 4.9 54.1 1.0

Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340


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 Z275151340 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:42.5 occ:1.00 O A:HOH456 2.1 34.8 1.0 NE2 A:HIS100 2.2 51.6 1.0 O A:HOH461 2.3 26.4 1.0 O A:HOH460 2.5 30.5 1.0 O A:HOH446 3.1 36.1 1.0 CD2 A:HIS100 3.1 46.5 1.0 CE1 A:HIS100 3.3 49.9 1.0 CG A:HIS100 4.3 47.6 1.0 ND1 A:HIS100 4.4 47.8 1.0 CB A:PRO115 4.6 68.4 1.0 CG A:PRO115 4.7 72.0 1.0

Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z275151340


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 Z275151340 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:60.5 occ:1.00 O A:HOH447 2.5 30.0 1.0 O A:HOH470 2.6 52.9 1.0 O A:HOH469 2.6 41.9 1.0 SG A:CYS122 2.7 53.7 1.0 CB A:CYS122 3.5 42.6 1.0 CD A:CD303 3.7 61.7 1.0 CA A:CYS122 4.1 40.2 1.0 N A:VAL123 5.0 36.7 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.