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Platinum in PDB 6hju: 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: 6hju 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) 90.30 / 1.58
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.530, 180.530, 180.530, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 18.2

Other elements in 6hju:

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 6hju). 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: 6hju:
Jump to Platinum binding site number: 1; 2; 3; 4; 5;

Platinum binding site 1 out of 5 in 6hju

Go back to Platinum Binding Sites List in 6hju
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:52.7
occ:0.30
OE2 A:GLU53 1.8 56.4 0.5
O A:HOH423 2.0 61.3 0.3
O A:HOH307 2.0 55.7 0.3
O A:HOH473 2.0 69.8 0.3
NE2 A:HIS49 2.0 64.6 1.0
CD2 A:HIS49 2.9 52.0 1.0
CD A:GLU53 2.9 41.9 0.5
CE1 A:HIS49 3.2 36.4 1.0
OE1 A:GLU53 3.6 49.1 0.5
CG A:GLU53 4.0 29.3 0.5
CG A:HIS49 4.1 41.8 1.0
ND1 A:HIS49 4.2 49.5 1.0
O A:HOH407 4.5 75.1 1.0

Platinum binding site 2 out of 5 in 6hju

Go back to Platinum Binding Sites List in 6hju
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:43.6
occ:0.35
O A:HOH425 1.9 36.6 0.3
O A:HOH330 2.0 31.6 0.3
ND1 A:HIS132 2.0 48.3 1.0
O A:HOH474 2.0 37.5 0.3
CE1 A:HIS132 2.9 54.5 1.0
CG A:HIS132 3.1 41.4 1.0
CB A:HIS132 3.4 38.9 1.0
CA A:HIS132 3.6 37.6 1.0
NE2 A:HIS132 4.1 68.0 1.0
O A:SER131 4.1 45.6 1.0
CD2 A:HIS132 4.2 49.6 1.0
OE2 A:GLU136 4.3 49.8 0.5
NH2 A:ARG64 4.3 70.0 0.6
CZ A:ARG64 4.4 59.7 0.6
NE A:ARG64 4.4 47.0 0.4
O A:HIS132 4.5 32.7 1.0
CD A:ARG64 4.5 39.7 0.4
NE A:ARG64 4.5 49.2 0.6
N A:HIS132 4.6 34.3 1.0
C A:HIS132 4.6 32.3 1.0
C A:SER131 4.7 35.0 1.0
CZ A:ARG64 4.7 51.5 0.4
CD A:ARG64 4.8 34.9 0.6
NH1 A:ARG64 4.9 68.9 0.6

Platinum binding site 3 out of 5 in 6hju

Go back to Platinum Binding Sites List in 6hju
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:72.9
occ:0.40
O A:HOH426 1.9 39.5 0.4
ND1 A:HIS49 2.2 49.5 1.0
O A:HOH385 2.8 41.8 0.4
CE1 A:HIS49 2.9 36.4 1.0
CG A:HIS49 3.0 41.8 1.0
CB A:HIS49 3.3 27.4 1.0
CL A:CL218 3.5 48.3 0.4
CA A:HIS49 4.1 22.4 1.0
NE2 A:HIS49 4.1 64.6 1.0
CD2 A:HIS49 4.1 52.0 1.0
CD A:CD205 4.4 41.7 0.3
OE2 A:GLU45 4.7 75.9 0.5
N A:HIS49 4.8 19.9 1.0
CL A:CL218 5.0 37.1 0.3

Platinum binding site 4 out of 5 in 6hju

Go back to Platinum Binding Sites List in 6hju
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:77.2
occ:0.20
NE2 A:HIS132 1.9 68.0 1.0
O A:HOH383 1.9 52.8 0.2
S A:DMS217 2.2 34.8 0.2
CE1 A:HIS132 2.6 54.5 1.0
C1 A:DMS217 2.7 44.2 0.2
C2 A:DMS217 3.2 42.5 0.2
CD2 A:HIS132 3.2 49.6 1.0
O A:DMS217 3.5 34.4 0.2
ND1 A:HIS132 3.8 48.3 1.0
CG A:HIS132 4.1 41.4 1.0
CB A:SER131 4.7 49.2 1.0

Platinum binding site 5 out of 5 in 6hju

Go back to Platinum Binding Sites List in 6hju
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:56.8
occ:0.20
NE2 A:HIS114 2.1 33.0 0.5
CE1 A:HIS114 2.5 27.9 0.5
NE2 A:HIS114 2.5 29.8 0.5
CE1 A:HIS114 2.8 29.1 0.5
OE2 A:GLU130 2.9 49.4 1.0
CB A:CYS126 3.2 32.8 1.0
CD2 A:HIS114 3.2 28.6 0.5
O A:HOH489 3.3 55.5 1.0
SG A:CYS126 3.3 44.3 1.0
ND1 A:HIS114 3.7 28.9 0.5
CD2 A:HIS114 3.7 32.5 0.5
O A:HOH404 3.8 48.7 1.0
ND1 A:HIS114 4.0 31.8 0.5
CD A:GLU130 4.2 38.3 1.0
CG A:HIS114 4.2 25.0 0.5
CG A:HIS114 4.3 30.4 0.5
CA A:CYS126 4.4 24.5 1.0
C A:CYS126 4.9 25.7 1.0
OE1 A:GLU130 5.0 46.1 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: Wed Dec 16 02:05:37 2020

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