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Platinum 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:

Cadmium (Cd) 7 atoms
Chlorine (Cl) 4 atoms

Platinum Binding Sites:

The binding sites of Platinum 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 Platinum atom.
In total 5 binding sites of Platinum 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 Platinum binding site number: 1; 2; 3; 4; 5;

Platinum binding site 1 out of 5 in 6hjt

Go back to Platinum Binding Sites List in 6hjt
Platinum binding site 1 out of 5 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 Platinum with other atoms in the Pt 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:Pt210

b:48.8
occ:0.30
O A:HOH304 2.0 50.7 0.3
O A:HOH474 2.1 46.2 0.3
NE2 A:HIS49 2.1 42.2 1.0
O A:HOH527 2.1 54.7 0.3
CD2 A:HIS49 2.9 41.8 1.0
CE1 A:HIS49 3.3 30.4 1.0
O A:HOH525 4.0 79.4 1.0
CG A:HIS49 4.1 39.0 1.0
CG A:GLU53 4.2 19.9 0.5
ND1 A:HIS49 4.3 58.7 1.0
CD A:GLU53 4.6 27.6 0.5
OE1 A:GLU53 4.9 53.2 0.5

Platinum binding site 2 out of 5 in 6hjt

Go back to Platinum Binding Sites List in 6hjt
Platinum binding site 2 out of 5 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 Platinum with other atoms in the Pt 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:Pt211

b:34.9
occ:0.35
O A:HOH378 1.7 27.5 0.3
O A:HOH311 1.9 22.4 0.3
O A:HOH519 2.0 40.4 0.3
ND1 A:HIS132 2.0 38.7 1.0
CE1 A:HIS132 3.0 53.3 1.0
CG A:HIS132 3.1 32.6 1.0
CB A:HIS132 3.4 31.2 1.0
CA A:HIS132 3.6 23.1 1.0
O A:SER131 4.0 34.8 1.0
NE2 A:HIS132 4.1 60.7 1.0
CD2 A:HIS132 4.2 40.1 1.0
NE A:ARG64 4.2 45.4 0.5
O A:HIS132 4.5 25.6 1.0
CZ A:ARG64 4.5 56.9 0.5
N A:HIS132 4.5 23.5 1.0
C A:SER131 4.6 28.3 1.0
C A:HIS132 4.6 22.7 1.0
NH2 A:ARG64 4.7 75.5 0.5
CD A:ARG64 4.7 31.2 0.5
NE A:ARG64 4.8 48.7 0.6
CD A:ARG64 4.8 29.6 0.6

Platinum binding site 3 out of 5 in 6hjt

Go back to Platinum Binding Sites List in 6hjt
Platinum binding site 3 out of 5 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 Platinum with other atoms in the Pt 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:Pt212

b:59.2
occ:0.40
O A:HOH422 1.9 42.4 0.4
ND1 A:HIS49 2.0 58.7 1.0
O A:HOH334 2.5 56.3 0.4
CL A:CL218 2.7 67.1 0.4
CE1 A:HIS49 2.9 30.4 1.0
CG A:HIS49 3.0 39.0 1.0
CB A:HIS49 3.3 18.9 1.0
NE2 A:HIS49 4.0 42.2 1.0
CD2 A:HIS49 4.0 41.8 1.0
CA A:HIS49 4.1 14.8 1.0
CD A:CD205 4.3 35.9 0.3
O A:HOH524 4.5 51.0 1.0
CL A:CL218 4.6 41.5 0.3
N A:HIS49 4.9 14.0 1.0
OE2 A:GLU45 5.0 49.5 0.5

Platinum binding site 4 out of 5 in 6hjt

Go back to Platinum Binding Sites List in 6hjt
Platinum binding site 4 out of 5 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 Platinum with other atoms in the Pt 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:Pt213

b:61.8
occ:0.25
NE2 A:HIS132 2.0 60.7 1.0
O A:HOH438 2.0 36.7 0.2
C1 A:DMS217 2.0 32.9 0.2
S A:DMS217 2.2 20.5 0.2
CE1 A:HIS132 2.6 53.3 1.0
C2 A:DMS217 3.0 30.1 0.2
CD2 A:HIS132 3.3 40.1 1.0
O A:DMS217 3.6 35.4 0.2
ND1 A:HIS132 3.8 38.7 1.0
O A:HOH497 4.1 45.5 1.0
CG A:HIS132 4.2 32.6 1.0
CB A:SER131 4.7 33.8 1.0

Platinum binding site 5 out of 5 in 6hjt

Go back to Platinum Binding Sites List in 6hjt
Platinum binding site 5 out of 5 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 Platinum with other atoms in the Pt 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:Pt214

b:37.5
occ:0.20
NE2 A:HIS114 2.1 19.4 0.3
CE1 A:HIS114 2.3 28.1 0.7
CE1 A:HIS114 2.6 15.2 0.3
NE2 A:HIS114 2.7 29.9 0.7
O A:HOH363 2.9 29.1 0.4
OE2 A:GLU130 3.2 34.0 1.0
CB A:CYS126 3.3 25.2 1.0
SG A:CYS126 3.4 32.3 1.0
CD2 A:HIS114 3.4 19.5 0.3
ND1 A:HIS114 3.5 29.3 0.7
ND1 A:HIS114 3.8 19.6 0.3
CD2 A:HIS114 3.9 24.3 0.7
CG A:HIS114 4.2 18.4 0.3
CG A:HIS114 4.3 23.9 0.7
CD A:GLU130 4.5 40.6 1.0
CA A:CYS126 4.5 23.1 1.0
O A:HOH550 4.6 72.1 1.0
O A:HOH363 4.7 21.1 0.6
CB A:SER118 4.9 28.0 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: Thu Oct 10 11:45:00 2024

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