Cadmium in PDB 5qry: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z2856434890

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z2856434890, PDB code: 5qry 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)	52.82 / 1.58
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	60.095, 60.095, 110.247, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 25.2

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z2856434890 (pdb code 5qry). 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 Z2856434890, PDB code: 5qry:
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 Z2856434890


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 Z2856434890 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:22.4 occ:0.50 O A:HOH438 1.9 20.6 0.5 OE1 A:GLU167 2.4 24.5 1.0 SG A:CYS186 2.5 24.8 0.2 SG A:CYS186 2.6 17.8 0.2 CB A:CYS186 3.3 29.2 0.2 CB A:CYS186 3.4 21.0 0.2 CD A:CD302 3.6 24.2 1.0 CD A:GLU167 3.6 19.8 1.0 O A:HOH439 4.3 25.5 1.0 OE2 A:GLU167 4.3 19.1 1.0 CG A:GLU167 4.7 21.3 1.0 CA A:CYS186 4.8 24.6 0.2 CA A:CYS186 4.8 21.1 0.2

Cadmium binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z2856434890


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 Z2856434890 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:24.2 occ:1.00 OE2 A:GLU167 2.2 19.1 1.0 O A:HOH463 2.5 18.6 1.0 CD A:GLU167 2.7 19.8 1.0 OE1 A:GLU167 2.7 24.5 1.0 CD A:CD301 3.6 22.4 0.5 NE2 A:GLN191 4.0 32.8 1.0 O A:HOH438 4.0 20.6 0.5 CG A:GLU167 4.2 21.3 1.0 CG A:PRO188 4.4 28.2 1.0 CB A:PRO188 4.5 25.7 1.0 CB A:GLU167 4.9 19.1 1.0 CA A:PRO188 5.0 24.4 1.0 SG A:CYS186 5.0 17.8 0.2

Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z2856434890


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 Z2856434890 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:50.9 occ:1.00 O A:HOH456 2.4 31.9 1.0 SG A:CYS122 2.6 45.4 1.0 O A:HOH472 2.6 38.9 1.0 O A:HOH455 2.7 46.8 1.0 CB A:CYS122 3.4 36.8 1.0 CD A:CD305 3.8 52.9 1.0 O A:HOH471 4.0 44.4 1.0 O A:HOH434 4.6 38.7 1.0 CA A:CYS122 4.8 33.1 1.0 O A:GLN157 4.9 39.8 1.0

Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z2856434890


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 Z2856434890 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:32.5 occ:1.00 NE2 A:HIS100 2.2 32.9 1.0 O A:HOH462 2.3 31.3 1.0 O A:HOH460 2.4 25.1 1.0 O A:HOH459 2.4 23.6 1.0 CD2 A:HIS100 3.2 35.1 1.0 CE1 A:HIS100 3.2 44.2 1.0 O A:HOH442 3.5 35.5 1.0 CG A:PRO115 4.0 52.8 1.0 CB A:PRO115 4.3 49.5 1.0 ND1 A:HIS100 4.3 39.3 1.0 CG A:HIS100 4.3 38.0 1.0

Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z2856434890


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 Z2856434890 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:52.9 occ:1.00 O A:HOH471 2.4 44.4 1.0 SG A:CYS122 2.4 45.4 1.0 O A:HOH452 2.5 32.9 1.0 O A:HOH472 2.7 38.9 1.0 CB A:CYS122 3.5 36.8 1.0 CD A:CD303 3.8 50.9 1.0 CA A:CYS122 4.1 33.1 1.0 N A:VAL123 5.0 29.3 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.