Sodium in PDB 7bd7: X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin

Protein crystallography data

The structure of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin, PDB code: 7bd7 was solved by G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.54 / 1.50
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.91, 180.91, 180.91, 90, 90, 90
R / Rfree (%) 16.6 / 18.5

Other elements in 7bd7:

The structure of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin also contains other interesting chemical elements:

Arsenic (As) 1 atom
Chlorine (Cl) 1 atom
Cadmium (Cd) 15 atoms
Platinum (Pt) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin (pdb code 7bd7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin, PDB code: 7bd7:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7bd7

Go back to Sodium Binding Sites List in 7bd7
Sodium binding site 1 out of 3 in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:24.2
occ:1.00
O4 A:SO4221 2.5 61.2 1.0
N A:TYR8 3.0 11.3 1.0
O A:HOH442 3.2 47.7 1.0
O A:TYR8 3.3 12.4 1.0
N A:ASN7 3.3 11.0 1.0
CG A:ARG5 3.7 13.1 1.0
C A:TYR8 3.8 11.3 1.0
C A:GLN6 3.8 10.8 1.0
CA A:TYR8 3.8 11.5 1.0
S A:SO4221 3.8 65.5 1.0
C A:ASN7 3.9 11.0 1.0
CA A:ASN7 3.9 11.3 1.0
NE A:ARG5 3.9 15.2 1.0
N A:GLN6 4.0 10.5 1.0
CA A:GLN6 4.0 11.1 1.0
CD A:ARG5 4.1 14.8 1.0
CB A:TYR8 4.2 11.8 1.0
C A:ARG5 4.2 11.9 1.0
O1 A:SO4221 4.3 69.5 1.0
O A:ARG5 4.4 12.2 1.0
O3 A:SO4221 4.4 75.5 1.0
CB A:ARG5 4.6 11.8 1.0
O A:HOH477 4.6 38.6 1.0
O A:GLN6 4.6 10.3 1.0
N A:SER9 4.8 11.3 1.0
O2 A:SO4221 4.9 65.7 1.0
CA A:ARG5 5.0 11.9 1.0

Sodium binding site 2 out of 3 in 7bd7

Go back to Sodium Binding Sites List in 7bd7
Sodium binding site 2 out of 3 in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin within 5.0Å range:

Sodium binding site 3 out of 3 in 7bd7

Go back to Sodium Binding Sites List in 7bd7
Sodium binding site 3 out of 3 in the X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of Arsenoplatin-1-Encapsulated Horse Spleen Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:52.6
occ:1.00
OD2 A:ASP112 2.8 17.8 1.0
O A:HOH467 2.9 60.0 1.0
OD1 A:ASP112 3.4 18.0 1.0
CG A:ASP112 3.4 16.4 1.0
CG A:GLN108 3.8 15.1 1.0
OE1 A:GLN108 4.0 23.3 1.0
CD A:GLN108 4.2 19.1 1.0
O A:HOH325 4.9 30.6 1.0
CB A:ASP112 4.9 15.0 1.0

Reference:

G.Ferraro, A.Pratesi, D.Cirri, P.Imbimbo, D.Maria Monti, L.Messori, A.Merlino. Arsenoplatin-Ferritin Nanocage: Structure and Cytotoxicity. Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
PubMed: 33668605
DOI: 10.3390/IJMS22041874
Page generated: Sat Apr 3 17:52:46 2021

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