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Cadmium in PDB 6hjt: The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage

Protein crystallography data

The structure of The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage, PDB code: 6hjt was solved by A.Pica, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.30 / 1.33
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.156, 181.156, 181.156, 90.00, 90.00, 90.00
R / Rfree (%) 12.7 / 15.7

Other elements in 6hjt:

The structure of The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage also contains other interesting chemical elements:

Platinum (Pt) 5 atoms
Chlorine (Cl) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage (pdb code 6hjt). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage, PDB code: 6hjt:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 6hjt

Go back to Cadmium Binding Sites List in 6hjt
Cadmium binding site 1 out of 7 in the The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:36.2
occ:0.35
O A:HOH329 2.2 27.8 0.3
OE1 A:GLU11 2.4 21.9 1.0
OE2 A:GLU11 2.5 33.2 1.0
CL A:CL209 2.8 26.4 0.3
CD A:GLU11 2.8 24.6 1.0
O A:HOH517 3.8 61.7 1.0
OG1 A:THR10 3.9 23.7 1.0
O A:HOH457 3.9 86.7 1.0
CG A:GLU11 4.4 20.2 1.0
CB A:SER9 4.5 15.4 1.0
OE1 A:GLN120 4.6 30.6 1.0
N A:THR10 4.6 14.5 1.0
NE2 A:GLN120 4.9 30.3 1.0
N A:GLU11 4.9 14.4 1.0

Cadmium binding site 2 out of 7 in 6hjt

Go back to Cadmium Binding Sites List in 6hjt
Cadmium binding site 2 out of 7 in the The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:56.8
occ:0.35
O A:HOH309 2.2 35.5 0.3
OE1 A:GLU56 2.3 83.6 1.0
OE1 A:GLU53 2.3 53.2 0.5
OE2 A:GLU53 2.3 52.5 0.5
OE2 A:GLU53 2.6 54.2 0.5
CD A:GLU53 2.7 27.6 0.5
CD A:GLU56 3.4 42.4 1.0
OE2 A:GLU56 3.7 72.6 1.0
CD A:GLU53 3.8 81.5 0.5
CG A:GLU53 4.2 19.9 0.5
OE1 A:GLU53 4.3 38.8 0.5
O A:HOH304 4.6 50.7 0.3
CG A:GLU56 4.8 25.6 1.0
CG A:GLU53 4.9 29.4 0.5
CB A:GLU56 5.0 17.2 1.0

Cadmium binding site 3 out of 7 in 6hjt

Go back to Cadmium Binding Sites List in 6hjt
Cadmium binding site 3 out of 7 in the The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:51.3
occ:0.35
OE2 A:GLU60 2.3 50.0 1.0
O A:HOH307 2.3 31.6 0.3
OE1 A:GLU60 2.4 48.3 1.0
OE2 A:GLU56 2.5 72.6 1.0
CD A:GLU60 2.7 33.9 1.0
CD A:GLU56 3.3 42.4 1.0
CG A:GLU56 3.8 25.6 1.0
OE1 A:GLU53 4.2 38.8 0.5
CG A:GLU60 4.2 22.8 1.0
OE1 A:GLU56 4.3 83.6 1.0
O A:HOH309 4.8 35.5 0.3
CB A:GLU56 4.9 17.2 1.0

Cadmium binding site 4 out of 7 in 6hjt

Go back to Cadmium Binding Sites List in 6hjt
Cadmium binding site 4 out of 7 in the The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:14.3
occ:0.50
OD1 A:ASP80 2.3 13.7 1.0
OD2 A:ASP80 2.4 14.6 1.0
CL A:CL208 2.5 20.8 1.0
CG A:ASP80 2.7 12.8 1.0
CB A:ASP80 4.2 13.4 1.0
O A:HOH433 4.3 18.1 1.0
O A:HOH349 4.6 24.6 1.0
O A:HOH475 4.9 48.0 0.5

Cadmium binding site 5 out of 7 in 6hjt

Go back to Cadmium Binding Sites List in 6hjt
Cadmium binding site 5 out of 7 in the The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:35.9
occ:0.30
SG A:CYS48 2.1 19.5 1.0
CL A:CL218 2.6 41.5 0.3
CB A:CYS48 3.1 15.1 1.0
C A:CYS48 3.5 13.4 1.0
N A:HIS49 3.5 14.0 1.0
CD A:ARG52 3.7 34.5 1.0
O A:CYS48 3.8 15.0 1.0
CA A:HIS49 3.9 14.8 1.0
CA A:CYS48 3.9 13.2 1.0
NH1 A:ARG52 4.0 44.4 1.0
O A:HOH334 4.0 56.3 0.4
CG A:ARG52 4.2 26.4 1.0
PT A:PT212 4.3 59.2 0.4
O A:GLU45 4.4 14.5 0.5
O A:GLU45 4.4 14.1 0.5
CL A:CL218 4.4 67.1 0.4
CB A:HIS49 4.5 18.9 1.0
O A:HOH367 4.5 37.6 0.6
NE A:ARG52 4.7 31.9 1.0
CB A:ARG52 4.8 17.2 1.0
CZ A:ARG52 4.8 42.5 1.0
N A:CYS48 5.0 12.6 1.0

Cadmium binding site 6 out of 7 in 6hjt

Go back to Cadmium Binding Sites List in 6hjt
Cadmium binding site 6 out of 7 in the The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:49.9
occ:0.20
O A:HOH363 2.0 21.1 0.6
OE1 A:GLU130 2.3 38.5 1.0
O A:HOH318 3.1 46.9 0.6
CD A:GLU130 3.2 40.6 1.0
O A:HOH363 3.3 29.1 0.4
OE2 A:GLU130 3.6 34.0 1.0
CD A:CD207 4.1 44.7 0.2
CG A:GLU130 4.6 28.7 1.0
CB A:GLU130 5.0 29.2 1.0

Cadmium binding site 7 out of 7 in 6hjt

Go back to Cadmium Binding Sites List in 6hjt
Cadmium binding site 7 out of 7 in the The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of The X-Ray Structure of the Horse Spleen Ferritin Nanocage Containing Pt, Obtained Upon Encapsulation of A Pt(II) Terpyridine Compound Within the Protein Cage within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:44.7
occ:0.20
O A:HOH496 1.9 55.4 0.6
O A:HOH318 2.3 46.9 0.6
OD1 A:ASP127 3.7 33.9 1.0
CD A:CD206 4.1 49.9 0.2
OE1 A:GLU130 4.1 38.5 1.0
OG A:SER131 4.2 44.5 1.0
CG A:ASP127 4.8 27.7 1.0
CB A:GLU130 5.0 29.2 1.0

Reference:

G.Ferraro, A.Pica, G.Petruk, F.Pane, A.Amoresano, A.Cilibrizzi, R.Vilar, D.M.Monti, A.Merlino. Preparation, Structure, Cytotoxicity and Mechanism of Action of Ferritin-Pt(II) Terpyridine Compound Nanocomposites. Nanomedicine (Lond) V. 13 2995 2018.
ISSN: ISSN 1748-6963
PubMed: 30501559
DOI: 10.2217/NNM-2018-0259
Page generated: Sat Dec 12 08:28:39 2020

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