Cadmium in PDB 5erj: X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin

The structure of X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin, PDB code: 5erj was solved by N.Pontillo, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	104.44 / 1.45
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.899, 180.899, 180.899, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 17.3

The structure of X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin also contains other interesting chemical elements:

Platinum	(Pt)	1 atom
Chlorine	(Cl)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Cadmium atom in the X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin (pdb code 5erj). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 15 binding sites of Cadmium where determined in the X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin, PDB code: 5erj:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 15 in the X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:22.9 occ:0.40 O A:HOH386 2.2 41.0 1.0 OE1 A:GLU11 2.3 20.9 1.0 O A:HOH484 2.3 29.0 0.4 OE2 A:GLU11 2.6 30.8 1.0 CL A:CL203 2.6 19.2 0.4 CD A:GLU11 2.8 27.2 1.0 OG1 A:THR10 3.8 21.8 1.0 CG A:GLU11 4.3 20.8 1.0 CB A:SER9 4.5 14.7 1.0 N A:THR10 4.6 14.2 1.0 OE1 A:GLN120 4.6 31.2 1.0 NE2 A:GLN120 4.7 33.4 1.0 N A:GLU11 4.8 14.1 1.0 CD A:GLN120 5.0 28.8 1.0

Cadmium binding site 2 out of 15 in the X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:43.7 occ:0.40 OE1 A:GLU53 2.3 19.1 0.3 OE2 A:GLU53 2.4 36.0 0.7 O A:HOH331 2.5 60.1 1.0 OE1 A:GLU56 2.5 44.3 1.0 OE1 A:GLU53 2.9 48.4 0.7 CD A:GLU53 3.0 29.7 0.7 CD A:GLU56 3.3 40.5 1.0 OE2 A:GLU56 3.5 54.4 1.0 CD A:GLU53 3.5 19.8 0.3 OE2 A:GLU53 4.0 21.2 0.3 CG A:GLU53 4.5 22.4 0.7 CG A:GLU53 4.7 15.0 0.3 CG A:GLU56 4.7 24.7 1.0 CB A:GLU53 5.0 13.4 0.3

Cadmium binding site 3 out of 15 in the X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:44.0 occ:0.30 CD A:CD207 0.0 44.0 0.3 CD A:CD207 1.8 35.8 0.2 OE2 A:GLU60 2.2 36.5 1.0 OE2 A:GLU56 2.4 54.4 1.0 OE1 A:GLU60 2.7 34.1 1.0 CD A:GLU60 2.8 29.9 1.0 O A:HOH448 3.1 54.1 1.0 CD A:GLU56 3.4 40.5 1.0 CG A:GLU56 3.9 24.7 1.0 OE2 A:GLU53 4.1 21.2 0.3 CG A:GLU60 4.3 21.7 1.0 OE1 A:GLU56 4.4 44.3 1.0

Cadmium binding site 4 out of 15 in the X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:35.8 occ:0.20 CD A:CD207 0.0 35.8 0.2 CD A:CD207 1.8 44.0 0.3 O A:HOH448 2.2 54.1 1.0 OE1 A:GLU60 2.4 34.1 1.0 CD A:GLU60 3.2 29.9 1.0 OE2 A:GLU60 3.3 36.5 1.0 O A:HOH477 4.0 50.3 1.0 OE2 A:GLU56 4.1 54.4 1.0 OE2 A:GLU53 4.3 21.2 0.3 CG A:GLU57 4.4 17.2 0.6 CG A:GLU60 4.7 21.7 1.0 CD A:GLU56 4.9 40.5 1.0

Cadmium binding site 5 out of 15 in the X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:10.4 occ:0.40 CD A:CD208 0.0 10.4 0.4 CD A:CD208 0.7 19.5 0.1 OD1 A:ASP80 2.3 10.7 1.0 CL A:CL201 2.4 18.4 1.0 OD2 A:ASP80 2.5 12.8 1.0 CG A:ASP80 2.8 11.7 1.0 O A:HOH342 4.2 16.7 1.0 CB A:ASP80 4.2 10.8 1.0 O A:HOH330 4.6 25.8 1.0 O A:HOH426 4.6 27.4 0.2

Cadmium binding site 6 out of 15 in the X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:19.5 occ:0.10 CD A:CD208 0.0 19.5 0.1 CD A:CD208 0.7 10.4 0.4 OD2 A:ASP80 1.8 12.8 1.0 OD1 A:ASP80 2.1 10.7 1.0 CG A:ASP80 2.3 11.7 1.0 CL A:CL201 2.8 18.4 1.0 CB A:ASP80 3.7 10.8 1.0 O A:HOH426 3.9 27.4 0.2 O A:HOH330 3.9 25.8 1.0 O A:HOH342 4.1 16.7 1.0 CA A:ASP80 4.7 10.1 1.0 N A:ASP80 5.0 10.5 1.0

Cadmium binding site 7 out of 15 in the X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd209 b:44.4 occ:0.30 O A:HOH305 1.9 36.8 1.0 O A:HOH432 2.2 44.5 1.0 OE2 A:GLU88 2.3 36.6 1.0 O A:HOH419 2.6 52.4 1.0 CD A:GLU88 3.0 34.0 1.0 OE1 A:GLU88 3.1 40.1 1.0 CG A:GLU88 4.3 20.9 1.0 O A:HOH495 4.4 57.5 1.0 NH2 A:ARG39 4.4 23.9 1.0 NH1 A:ARG39 4.6 20.4 1.0

Cadmium binding site 8 out of 15 in the X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd210 b:45.2 occ:0.40 O A:HOH463 2.5 32.8 1.0 O A:HOH465 2.5 39.4 0.9 OG A:SER131 2.7 41.8 1.0 OD1 A:ASP127 3.0 31.4 1.0 CG A:ASP127 3.3 35.3 1.0 CD A:CD211 3.4 42.0 0.5 OD2 A:ASP127 3.4 45.8 1.0 CB A:SER131 3.5 35.2 1.0 O A:HOH417 4.0 48.0 1.0 O A:ASP127 4.3 22.1 1.0 NE2 A:HIS132 4.6 38.2 1.0 CB A:ASP127 4.6 27.7 1.0 C A:ASP127 4.6 23.0 1.0 O A:HOH328 4.8 35.8 0.5

Cadmium binding site 9 out of 15 in the X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd211 b:42.0 occ:0.50 O A:HOH328 1.7 35.8 0.5 O A:HOH463 2.4 32.8 1.0 NE2 A:HIS132 2.5 38.2 1.0 O A:HOH465 2.5 39.4 0.9 CE1 A:HIS132 3.3 42.4 1.0 CD A:CD210 3.4 45.2 0.4 CD2 A:HIS132 3.6 34.6 1.0 ND1 A:HIS132 4.5 41.7 1.0 CB A:SER131 4.6 35.2 1.0 CG A:HIS132 4.7 34.6 1.0 O A:HOH417 4.9 48.0 1.0 OG A:SER131 4.9 41.8 1.0 CD1 A:PHE128 5.0 19.1 1.0

Cadmium binding site 10 out of 15 in the X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of X-Ray Structure of Cisplatin-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd212 b:42.0 occ:0.20 CL A:CL202 1.9 12.6 0.2 OE1 A:GLU130 2.4 39.5 1.0 O A:HOH337 2.5 31.7 0.8 CD A:GLU130 3.3 38.4 1.0 OE2 A:GLU130 3.6 38.2 1.0 CG A:GLU130 4.7 27.7 1.0

N.Pontillo, F.Pane, L.Messori, A.Amoresano, A.Merlino. Cisplatin Encapsulation Within A Ferritin Nanocage: A High-Resolution Crystallographic Study. Chem.Commun.(Camb.) V. 52 4136 2016.
ISSN: ESSN 1364-548X
PubMed: 26888424
DOI: 10.1039/C5CC10365G