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

Protein crystallography 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

Other elements in 5mik:

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

Platinum Binding Sites:

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 5mik

Go back to Platinum Binding Sites List in 5mik
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 5mik

Go back to Platinum Binding Sites List in 5mik
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 5mik

Go back to Platinum Binding Sites List in 5mik
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 5mik

Go back to Platinum Binding Sites List in 5mik
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

Reference:

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
Page generated: Wed Dec 16 02:05:22 2020

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