Cadmium in PDB 5qs2: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z291279160

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z291279160, PDB code: 5qs2 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)	52.93 / 1.68
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	60.290, 60.290, 110.020, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 24.4

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z291279160 also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z291279160 (pdb code 5qs2). 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 Z291279160, PDB code: 5qs2:
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 Z291279160


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 Z291279160 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:24.9 occ:0.50 O A:HOH459 2.4 22.1 0.5 SG A:CYS186 2.4 22.0 0.2 SG A:CYS186 2.5 21.9 0.2 OE1 A:GLU167 2.5 23.2 1.0 CB A:CYS186 3.3 25.8 0.2 CB A:CYS186 3.3 25.0 0.2 CD A:CD302 3.6 26.3 1.0 CD A:GLU167 3.7 22.4 1.0 O A:HOH447 4.2 27.6 1.0 OE2 A:GLU167 4.3 21.9 1.0 CA A:CYS186 4.7 24.9 0.2 CG A:GLU167 4.8 22.2 1.0 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 Z291279160


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 Z291279160 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:26.3 occ:1.00 OE2 A:GLU167 2.3 21.9 1.0 O A:HOH463 2.3 21.6 1.0 OE1 A:GLU167 2.7 23.2 1.0 CD A:GLU167 2.8 22.4 1.0 CD A:CD301 3.6 24.9 0.5 NE2 A:GLN191 3.9 38.5 1.0 CG A:GLU167 4.3 22.2 1.0 CG A:PRO188 4.3 30.9 1.0 CB A:PRO188 4.6 26.8 1.0 SG A:CYS186 4.7 22.0 0.2 CB A:GLU167 4.9 22.2 1.0

Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z291279160


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 Z291279160 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:95.8 occ:1.00 O A:HOH453 2.5 42.4 1.0 SG A:CYS122 2.6 51.8 1.0 O A:HOH471 3.3 60.5 1.0 CB A:CYS122 3.4 44.6 1.0 CD A:CD305 3.9 84.4 1.0 O A:HOH472 4.5 56.4 1.0 O A:GLN157 4.7 40.8 1.0 O A:HOH428 4.7 46.4 1.0 CA A:CYS122 4.9 36.4 1.0

Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z291279160


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 Z291279160 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:31.1 occ:0.50 O A:HOH461 2.2 18.4 1.0 NE2 A:HIS100 2.3 31.9 0.5 CE1 A:HIS100 3.2 32.4 0.5 CD2 A:HIS100 3.3 32.7 0.5 O A:HOH438 3.8 31.5 1.0 ND1 A:HIS100 4.3 32.5 0.5 CG A:HIS100 4.4 33.5 0.5 CG A:PRO115 4.5 52.0 0.5 CB A:PRO115 4.7 52.5 0.5

Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z291279160


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 Z291279160 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:84.4 occ:1.00 SG A:CYS122 2.6 51.8 1.0 O A:HOH452 2.7 38.5 1.0 O A:HOH472 3.1 56.4 1.0 O A:HOH471 3.2 60.5 1.0 CB A:CYS122 3.6 44.6 1.0 CD A:CD303 3.9 95.8 1.0 CA A:CYS122 4.1 36.4 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.