Cadmium in PDB 3rd0: Horse Spleen Apo-Ferritin with Bound Thiopental

The structure of Horse Spleen Apo-Ferritin with Bound Thiopental, PDB code: 3rd0 was solved by S.H.Oakley, L.S.Vedula, J.Xi, R.Liu, R.G.Eckenhoff, P.J.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.79 / 2.00
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	182.175, 182.175, 182.175, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 20.5

The binding sites of Cadmium atom in the Horse Spleen Apo-Ferritin with Bound Thiopental (pdb code 3rd0). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Horse Spleen Apo-Ferritin with Bound Thiopental, PDB code: 3rd0:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Horse Spleen Apo-Ferritin with Bound Thiopental


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Horse Spleen Apo-Ferritin with Bound Thiopental within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd176 b:55.5 occ:1.00 OD2 A:ASP80 2.6 41.9 1.0 OD1 A:ASP80 3.0 25.3 1.0 CG A:ASP80 3.2 27.6 1.0 CB A:ASP80 4.6 29.7 1.0

Cadmium binding site 2 out of 5 in the Horse Spleen Apo-Ferritin with Bound Thiopental


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Horse Spleen Apo-Ferritin with Bound Thiopental within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd177 b:54.6 occ:0.33 O A:HOH276 2.2 49.4 0.9 OE1 A:GLU130 2.6 45.7 1.0 OE2 A:GLU130 3.2 35.9 1.0 CD A:GLU130 3.2 39.5 1.0 CG A:GLU130 4.6 38.4 1.0 O A:HOH337 4.7 43.7 1.0 CD A:CD178 4.8 50.3 0.3

Cadmium binding site 3 out of 5 in the Horse Spleen Apo-Ferritin with Bound Thiopental


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Horse Spleen Apo-Ferritin with Bound Thiopental within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd178 b:50.3 occ:0.28 OD1 A:ASP127 3.7 49.4 1.0 OE1 A:GLU130 4.4 45.7 1.0 OG A:SER131 4.5 49.1 1.0 CD A:CD177 4.8 54.6 0.3 CG A:ASP127 5.0 45.0 1.0

Cadmium binding site 4 out of 5 in the Horse Spleen Apo-Ferritin with Bound Thiopental


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Horse Spleen Apo-Ferritin with Bound Thiopental within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd179 b:59.8 occ:0.39 O A:HOH300 2.4 58.6 1.0 OE1 A:GLU53 2.5 39.7 0.5 OE1 A:GLU56 2.6 47.5 1.0 OE1 A:GLU53 2.6 39.9 0.5 OE2 A:GLU53 2.9 36.4 0.5 CD A:GLU53 3.2 34.6 0.5 CD A:GLU56 3.6 48.4 1.0 CD A:GLU53 3.6 37.3 0.5 OE2 A:GLU56 3.8 57.7 1.0 OE2 A:GLU53 4.1 36.6 0.5 CG A:GLU53 4.7 31.3 0.5 CG A:GLU53 4.9 31.7 0.5 CG A:GLU56 4.9 37.5 1.0

Cadmium binding site 5 out of 5 in the Horse Spleen Apo-Ferritin with Bound Thiopental


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Horse Spleen Apo-Ferritin with Bound Thiopental within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd180 b:59.4 occ:0.43 O A:HOH264 2.2 44.2 1.0 O A:HOH265 2.3 55.3 1.0 OE2 A:GLU60 2.6 47.8 1.0 OE2 A:GLU57 2.7 49.8 1.0 OE1 A:GLU60 2.8 42.7 1.0 CD A:GLU60 3.0 43.1 1.0 CD A:GLU56 3.5 48.4 1.0 OE1 A:GLU56 3.7 47.5 1.0 OE2 A:GLU56 3.7 57.7 1.0 CD A:GLU57 3.8 47.3 1.0 CG A:GLU56 3.9 37.5 1.0 OE2 A:GLU53 4.0 36.6 0.5 OE1 A:GLU57 4.2 53.4 1.0 CG A:GLU60 4.5 32.0 1.0 O A:HOH300 4.9 58.6 1.0

S.H.Oakley, L.S.Vedula, J.Xi, R.Liu, R.G.Eckenhoff, P.J.Loll. High Resolution View of Barbiturate Recognition By A Protein Binding Site To Be Published.