Cadmium in PDB 5qsl: Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153, PDB code: 5qsl 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)	52.63 / 2.20
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	59.902, 59.902, 109.696, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 30.5

The binding sites of Cadmium atom in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153 (pdb code 5qsl). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153, PDB code: 5qsl:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153


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 Z1273312153 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:34.7 occ:0.50 O A:HOH410 1.6 1.1 0.3 OE1 A:GLU167 2.4 31.6 1.0 SG A:CYS186 2.7 26.4 0.5 SG A:CYS186 2.8 22.1 0.5 CB A:CYS186 3.1 31.4 0.5 CB A:CYS186 3.1 28.6 0.5 CD A:GLU167 3.5 36.0 1.0 CD A:CD302 3.6 34.5 1.0 O A:HOH431 4.3 24.8 1.0 OE2 A:GLU167 4.3 31.4 1.0 CG A:GLU167 4.5 31.8 1.0 CA A:CYS186 4.6 31.1 0.5 CA A:CYS186 4.6 29.3 0.5 O A:HOH455 5.0 45.0 1.0

Cadmium binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153


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 Z1273312153 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:34.5 occ:1.00 OE2 A:GLU167 2.4 31.4 1.0 OE1 A:GLU167 2.6 31.6 1.0 CD A:GLU167 2.8 36.0 1.0 CD A:CD301 3.6 34.7 0.5 NE2 A:GLN191 3.8 31.5 1.0 O A:HOH410 4.3 1.1 0.3 CG A:GLU167 4.3 31.8 1.0 CB A:PRO188 4.5 35.0 1.0 CG A:PRO188 4.5 34.4 1.0 CA A:PRO188 4.8 36.4 1.0 CB A:GLU167 4.9 32.0 1.0

Cadmium binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153


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 Z1273312153 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:70.8 occ:1.00 O A:HOH471 2.5 40.6 1.0 O A:HOH445 2.6 33.5 1.0 SG A:CYS122 2.8 53.4 1.0 CB A:CYS122 3.3 46.1 1.0 O A:HOH451 3.6 40.1 1.0 CD A:CD305 4.0 64.7 1.0 O A:HOH409 4.5 61.9 1.0 CA A:CYS122 4.8 45.1 1.0 O A:GLN157 5.0 43.5 1.0

Cadmium binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153


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 Z1273312153 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:44.1 occ:1.00 O A:HOH453 2.0 18.0 1.0 NE2 A:HIS100 2.4 63.2 1.0 CD2 A:HIS100 3.0 63.0 1.0 O A:HOH434 3.3 40.5 1.0 CE1 A:HIS100 3.6 65.2 1.0 CG A:HIS100 4.3 53.4 1.0 ND1 A:HIS100 4.5 52.2 1.0 CB A:PRO115 4.9 58.9 1.0

Cadmium binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153


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 Z1273312153 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:64.7 occ:1.00 SG A:CYS122 2.5 53.4 1.0 O A:HOH447 2.6 30.7 1.0 O A:HOH471 2.9 40.6 1.0 CB A:CYS122 3.3 46.1 1.0 CD A:CD303 4.0 70.8 1.0 CA A:CYS122 4.0 45.1 1.0 N A:VAL123 4.9 41.9 1.0

Cadmium binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Pandda Analysis Group Deposition -- Crystal Structure of Human Brachyury in Complex with Z1273312153 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd306 b:0.1 occ:1.00 ND1 A:HIS135 2.7 44.2 1.0 CG A:HIS135 3.5 42.2 1.0 CB A:HIS135 3.6 40.5 1.0 CE A:LYS138 3.6 73.0 1.0 O A:HOH456 3.6 51.0 1.0 CE1 A:HIS135 3.7 43.0 1.0 NZ A:LYS138 4.0 71.7 1.0 OD1 A:ASN131 4.1 38.1 1.0 CA A:HIS135 4.3 40.8 1.0 CD A:LYS138 4.6 69.3 1.0 CD2 A:HIS135 4.7 48.5 1.0 NE2 A:HIS135 4.8 44.1 1.0 ND2 A:ASN131 4.8 35.0 1.0 CG A:ASN131 4.8 41.1 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.