Platinum in PDB 5mik: X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)

The structure of X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data), PDB code: 5mik was solved by N.Pontillo, G.Ferraro, J.R.Helliwell, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	104.30 / 1.96
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.654, 180.654, 180.654, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 19.2

The structure of X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) also contains other interesting chemical elements:

Cadmium	(Cd)	13 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Platinum atom in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) (pdb code 5mik). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 4 binding sites of Platinum where determined in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data), PDB code: 5mik:
Jump to Platinum binding site number: 1; 2; 3; 4;

Platinum binding site 1 out of 4 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt218 b:71.3 occ:0.30 NE2 A:HIS49 2.3 19.9 0.5 OE2 A:GLU45 2.5 40.6 1.0 CE1 A:HIS49 3.1 20.4 0.5 CD A:GLU45 3.2 33.3 1.0 CD A:CD211 3.4 43.0 0.3 CD2 A:HIS49 3.4 20.2 0.5 CG A:GLU45 3.8 25.2 1.0 OE1 A:GLU45 4.1 28.2 1.0 ND1 A:HIS49 4.3 20.9 0.5 CG A:HIS49 4.5 19.6 0.5 O A:HOH450 4.6 48.0 1.0 O A:HOH468 4.6 10.9 0.5 O A:HIS173 4.9 55.1 1.0

Platinum binding site 2 out of 4 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt218 b:94.3 occ:0.30 OE2 A:GLU53 2.5 39.1 0.5 NE2 A:HIS49 2.5 25.7 0.5 CD A:GLU53 3.1 29.5 0.5 CD2 A:HIS49 3.1 25.7 0.5 OE1 A:GLU53 3.5 31.1 0.5 CE1 A:HIS49 3.7 25.2 0.5 CG A:GLU53 4.0 25.1 0.5 CG A:GLU53 4.1 20.9 0.5 CG A:LYS172 4.1 60.4 1.0 CG A:HIS49 4.4 23.6 0.5 CB A:LYS172 4.4 54.5 1.0 CD A:GLU53 4.4 21.9 0.5 ND1 A:HIS49 4.6 26.3 0.5 OE2 A:GLU53 4.8 24.3 0.5 OE1 A:GLU53 4.9 25.3 0.5

Platinum binding site 3 out of 4 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt219 b:46.9 occ:0.30 PT A:PT219 0.0 46.9 0.3 PT A:PT219 2.2 63.9 0.3 NE2 A:HIS132 2.9 43.3 1.0 CD2 A:HIS132 3.8 41.5 1.0 CE1 A:HIS132 3.8 45.1 1.0 OD2 A:ASP127 4.4 36.3 1.0 O A:HOH359 4.4 30.6 1.0 CB A:SER131 4.7 36.2 1.0 ND1 A:HIS132 4.9 45.3 1.0 CG A:HIS132 4.9 36.7 1.0

Platinum binding site 4 out of 4 in the X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of X-Ray Structure of Carboplatin-Encapsulated Horse Spleen Apoferritin (Rotating Anode Data) within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt219 b:63.9 occ:0.30 PT A:PT219 0.0 63.9 0.3 PT A:PT219 2.2 46.9 0.3 NE2 A:HIS132 2.6 43.3 1.0 CE1 A:HIS132 3.1 45.1 1.0 CD2 A:HIS132 3.8 41.5 1.0 ND1 A:HIS132 4.3 45.3 1.0 NH1 A:ARG64 4.3 32.8 0.5 CG A:HIS132 4.6 36.7 1.0

N.Pontillo, G.Ferraro, J.R.Helliwell, A.Amoresano, A.Merlino. X-Ray Structure of the Carboplatin-Loaded Apo-Ferritin Nanocage. Acs Med Chem Lett V. 8 433 2017.
ISSN: ISSN 1948-5875
PubMed: 28435532
DOI: 10.1021/ACSMEDCHEMLETT.7B00025