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Cadmium in PDB 5ix6: X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin

Protein crystallography data

The structure of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin, PDB code: 5ix6 was solved by G.Ferraro, N.Pontillo, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 104.30 / 1.85
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 180.645, 180.645, 180.645, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.6

Other elements in 5ix6:

The structure of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin also contains other interesting chemical elements:

Gold (Au) 7 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin (pdb code 5ix6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin, PDB code: 5ix6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 5ix6

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Cadmium binding site 1 out of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:40.5
occ:0.40
 O A:HOH325 2.2 11.0 0.4
O A:HOH311 2.2 53.6 1.0
OE1 A:GLU11 2.6 19.5 1.0
O A:HOH446 2.7 20.4 1.0
OE2 A:GLU11 2.8 27.9 1.0
O A:HOH547 2.8 41.3 1.0
CD A:GLU11 3.0 24.7 1.0
OG1 A:THR10 3.8 22.7 1.0
CB A:SER9 4.4 14.1 1.0
OE1 A:GLN120 4.5 35.6 1.0
CG A:GLU11 4.5 21.1 1.0
O A:HOH439 4.7 45.8 1.0
N A:THR10 4.7 13.8 1.0
NE2 A:GLN120 4.8 34.1 1.0
N A:GLU11 5.0 15.3 1.0
CD A:GLN120 5.0 32.3 1.0

Cadmium binding site 2 out of 9 in 5ix6

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Cadmium binding site 2 out of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:58.7
occ:0.45
 OE1 A:GLU53 2.4 18.3 0.3
OE1 A:GLU56 2.5 52.8 1.0
OE2 A:GLU53 2.7 19.5 0.3
CD A:GLU53 2.9 17.6 0.3
CD A:GLU56 3.3 38.8 1.0
OE2 A:GLU56 3.4 51.5 1.0
O A:HOH329 3.9 40.6 1.0
CG A:GLU53 4.4 17.0 0.3
CG A:GLU56 4.7 30.0 1.0
CG A:GLU53 4.7 27.3 0.7

Cadmium binding site 3 out of 9 in 5ix6

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Cadmium binding site 3 out of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd210

b:15.6
occ:0.50
 OD2 A:ASP80 2.2 13.8 1.0
O A:HOH495 2.4 5.4 1.0
OD1 A:ASP80 2.4 13.3 1.0
CG A:ASP80 2.7 14.1 1.0
CB A:ASP80 4.2 13.4 1.0
O A:HOH402 4.3 14.4 1.0
O A:HOH380 4.6 27.8 1.0

Cadmium binding site 4 out of 9 in 5ix6

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Cadmium binding site 4 out of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd211

b:43.6
occ:0.50
 O A:HOH415 2.1 13.9 0.5
NE2 A:HIS132 2.3 54.7 1.0
CE1 A:HIS132 2.8 52.1 1.0
CD2 A:HIS132 3.5 49.3 1.0
O A:HOH417 3.8 14.0 0.5
ND1 A:HIS132 4.0 54.4 1.0
CG A:HIS132 4.4 44.8 1.0
O A:HOH478 4.9 45.0 1.0

Cadmium binding site 5 out of 9 in 5ix6

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Cadmium binding site 5 out of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd212

b:28.2
occ:0.30
 OE1 A:GLU130 2.5 34.1 1.0
OE2 A:GLU130 2.5 36.1 1.0
CD A:GLU130 2.8 31.6 1.0
O A:HOH301 4.0 28.4 1.0
O A:HOH490 4.2 33.0 1.0
CG A:GLU130 4.4 29.6 1.0
O A:HOH307 4.4 40.4 1.0
CD A:CD214 5.0 37.4 0.2

Cadmium binding site 6 out of 9 in 5ix6

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Cadmium binding site 6 out of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd213

b:65.1
occ:0.35
 O A:HOH465 2.0 11.2 0.3
O A:HOH388 2.9 40.2 1.0
OE1 A:GLU45 2.9 28.7 1.0
O A:HOH349 3.2 32.4 1.0
O A:HOH345 3.3 29.5 1.0
CD A:GLU45 3.9 32.1 1.0
OE2 A:GLU45 4.2 43.1 1.0
CD2 A:HIS173 4.4 77.5 1.0
NH1 A:ARG168 4.5 14.9 1.0
NH2 A:ARG168 4.8 14.9 1.0
O A:HOH330 4.9 51.6 1.0

Cadmium binding site 7 out of 9 in 5ix6

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Cadmium binding site 7 out of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd214

b:37.4
occ:0.20
 O A:HOH301 2.3 28.4 1.0
O A:HOH427 2.4 37.8 1.0
OD1 A:ASP127 3.8 28.5 1.0
OE1 A:GLU130 4.0 34.1 1.0
OG A:SER131 4.5 44.4 1.0
O A:HOH350 4.7 27.2 0.4
CB A:GLU130 4.9 28.0 1.0
CD A:CD212 5.0 28.2 0.3

Cadmium binding site 8 out of 9 in 5ix6

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Cadmium binding site 8 out of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd215

b:41.9
occ:0.40
 OE2 A:GLU60 2.4 37.5 1.0
O A:HOH472 2.5 19.7 0.4
OE2 A:GLU56 2.7 51.5 1.0
OE2 A:GLU57 2.7 42.2 1.0
OE1 A:GLU60 2.8 34.0 1.0
CD A:GLU60 2.9 28.2 1.0
O A:HOH329 3.4 40.6 1.0
CD A:GLU56 3.5 38.8 1.0
CD A:GLU57 3.9 35.0 1.0
CG A:GLU56 3.9 30.0 1.0
O A:HOH456 4.2 70.1 1.0
O A:HOH303 4.2 39.3 1.0
OE1 A:GLU57 4.4 46.2 1.0
CG A:GLU60 4.4 23.2 1.0
OE1 A:GLU56 4.6 52.8 1.0

Cadmium binding site 9 out of 9 in 5ix6

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Cadmium binding site 9 out of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd216

b:42.0
occ:0.15
 OE2 A:GLU53 1.9 47.3 0.7
CD A:GLU53 3.1 35.5 0.7
O A:HOH316 3.3 52.6 1.0
O A:HOH462 3.4 38.5 0.7
OE1 A:GLU53 3.7 37.1 0.7
CB A:LYS172 4.1 57.7 1.0
CG A:GLU53 4.3 27.3 0.7
CG A:GLU53 4.5 17.0 0.3
OE1 A:GLU53 4.8 18.3 0.3
CD A:GLU53 4.9 17.6 0.3

Reference:

G.Ferraro, D.M.Monti, A.Amoresano, N.Pontillo, G.Petruk, F.Pane, M.A.Cinellu, A.Merlino. Gold-Based Drug Encapsulation Within A Ferritin Nanocage: X-Ray Structure and Biological Evaluation As A Potential Anticancer Agent of the AUOXO3-Loaded Protein. Chem.Commun.(Camb.) V. 52 9518 2016.
ISSN: ESSN 1364-548X
PubMed: 27326513
DOI: 10.1039/C6CC02516A
Page generated: Sat Dec 12 08:26:52 2020

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