Cadmium in PDB 5qrn: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z54226006

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z54226006, PDB code: 5qrn 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)	52.67 / 1.62
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	59.823, 59.823, 110.552, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 25.3

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z54226006 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z54226006 (pdb code 5qrn). 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 Z54226006, PDB code: 5qrn:
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 Z54226006


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 Z54226006 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:23.7 occ:0.50 O A:HOH445 2.1 17.7 0.5 OE1 A:GLU167 2.4 25.5 1.0 SG A:CYS186 2.5 29.1 0.2 SG A:CYS186 2.5 18.6 0.2 CB A:CYS186 3.3 32.6 0.2 CB A:CYS186 3.4 22.0 0.2 CD A:GLU167 3.6 20.2 1.0 CD A:CD302 3.6 25.6 1.0 O A:HOH442 4.3 25.5 1.0 OE2 A:GLU167 4.3 19.6 1.0 CG A:GLU167 4.6 22.3 1.0 CA A:CYS186 4.7 26.9 0.2 CA A:CYS186 4.8 22.1 0.2

Cadmium binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z54226006


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 Z54226006 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:25.6 occ:1.00 OE2 A:GLU167 2.2 19.6 1.0 O A:HOH460 2.4 19.3 1.0 OE1 A:GLU167 2.7 25.5 1.0 CD A:GLU167 2.7 20.2 1.0 CD A:CD301 3.6 23.7 0.5 NE2 A:GLN191 4.0 35.7 1.0 CG A:GLU167 4.2 22.3 1.0 CG A:PRO188 4.3 31.4 1.0 O A:HOH445 4.4 17.7 0.5 CB A:PRO188 4.6 27.5 1.0 CB A:GLU167 4.9 21.6 1.0 CA A:PRO188 4.9 24.9 1.0

Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z54226006


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 Z54226006 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:53.8 occ:1.00 O A:HOH454 2.4 34.4 1.0 O A:HOH450 2.6 49.0 1.0 O A:HOH470 2.7 42.0 1.0 SG A:CYS122 2.7 48.0 1.0 CB A:CYS122 3.3 41.1 1.0 CD A:CD305 3.8 54.4 1.0 O A:HOH471 4.0 47.0 1.0 O A:HOH420 4.6 42.0 1.0 CA A:CYS122 4.8 35.8 1.0 O A:GLN157 4.9 41.4 1.0

Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z54226006


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 Z54226006 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:34.6 occ:1.00 NE2 A:HIS100 2.2 34.5 1.0 O A:HOH463 2.3 32.6 1.0 O A:HOH458 2.4 23.9 1.0 O A:HOH459 2.4 27.5 1.0 CD2 A:HIS100 3.2 36.9 1.0 CE1 A:HIS100 3.2 45.8 1.0 O A:HOH444 3.4 34.4 1.0 CG A:PRO115 4.2 59.1 1.0 CB A:PRO115 4.3 55.4 1.0 ND1 A:HIS100 4.3 39.1 1.0 CG A:HIS100 4.3 39.0 1.0

Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z54226006


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 Z54226006 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:54.4 occ:1.00 O A:HOH471 2.4 47.0 1.0 SG A:CYS122 2.4 48.0 1.0 O A:HOH449 2.5 34.0 1.0 O A:HOH470 2.8 42.0 1.0 CB A:CYS122 3.4 41.1 1.0 CD A:CD303 3.8 53.8 1.0 CA A:CYS122 4.1 35.8 1.0 N A:VAL123 4.9 28.7 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.