Cadmium in PDB 5qrv: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198194396

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198194396, PDB code: 5qrv 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)	40.59 / 1.67
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	60.020, 60.020, 110.050, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 25.2

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198194396 (pdb code 5qrv). 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 Z198194396, PDB code: 5qrv:
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 Z198194396


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 Z198194396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:27.3 occ:0.50 O A:HOH457 2.3 26.6 0.5 SG A:CYS186 2.4 28.0 0.2 SG A:CYS186 2.5 22.1 0.2 OE1 A:GLU167 2.5 28.0 1.0 CB A:CYS186 3.3 31.3 0.2 CB A:CYS186 3.4 26.3 0.2 CD A:CD302 3.6 29.0 1.0 CD A:GLU167 3.7 25.8 1.0 O A:HOH443 4.3 26.6 1.0 OE2 A:GLU167 4.3 23.5 1.0 CA A:CYS186 4.7 29.1 0.2 CG A:GLU167 4.7 26.2 1.0 CA A:CYS186 4.8 25.8 0.2

Cadmium binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198194396


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 Z198194396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:29.0 occ:1.00 OE2 A:GLU167 2.3 23.5 1.0 O A:HOH462 2.3 23.4 1.0 OE1 A:GLU167 2.7 28.0 1.0 CD A:GLU167 2.8 25.8 1.0 CD A:CD301 3.6 27.3 0.5 NE2 A:GLN191 4.1 40.8 1.0 CG A:GLU167 4.3 26.2 1.0 CG A:PRO188 4.4 33.7 1.0 CB A:PRO188 4.6 30.7 1.0 SG A:CYS186 4.9 22.1 0.2 CB A:GLU167 4.9 25.0 1.0 CA A:PRO188 5.0 28.8 1.0

Cadmium binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198194396


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 Z198194396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:62.6 occ:1.00 O A:HOH455 2.4 37.6 1.0 SG A:CYS122 2.6 51.0 1.0 O A:HOH469 2.7 43.1 1.0 O A:HOH451 2.9 50.7 1.0 CB A:CYS122 3.4 44.7 1.0 CD A:CD305 3.8 62.3 1.0 O A:HOH470 4.1 49.9 1.0 O A:HOH420 4.7 45.3 1.0 O A:GLN157 4.8 43.1 1.0 CA A:CYS122 4.9 39.5 1.0

Cadmium binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198194396


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 Z198194396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:36.0 occ:1.00 O A:HOH463 2.2 30.2 1.0 NE2 A:HIS100 2.3 40.2 1.0 O A:HOH459 2.4 27.1 1.0 O A:HOH460 2.4 23.4 1.0 CD2 A:HIS100 3.2 37.8 1.0 CE1 A:HIS100 3.3 46.5 1.0 O A:HOH440 3.7 36.1 1.0 CG A:PRO115 4.1 58.9 1.0 CB A:PRO115 4.3 54.1 1.0 ND1 A:HIS100 4.4 40.1 1.0 CG A:HIS100 4.4 40.1 1.0

Cadmium binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z198194396


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 Z198194396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:62.3 occ:1.00 SG A:CYS122 2.5 51.0 1.0 O A:HOH446 2.6 34.3 1.0 O A:HOH470 2.6 49.9 1.0 O A:HOH469 2.7 43.1 1.0 CB A:CYS122 3.6 44.7 1.0 CD A:CD303 3.8 62.6 1.0 CA A:CYS122 4.1 39.5 1.0 N A:VAL123 4.9 33.4 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.