Cadmium in PDB 6env: X-Ray Structure of AU2PHEN-Encapsulated Horse Spleen Apoferritin

The structure of X-Ray Structure of AU2PHEN-Encapsulated Horse Spleen Apoferritin, PDB code: 6env 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)	104.48 / 1.82
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.967, 180.967, 180.967, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 17.5

The structure of X-Ray Structure of AU2PHEN-Encapsulated Horse Spleen Apoferritin also contains other interesting chemical elements:

Gold	(Au)	2 atoms
Chlorine	(Cl)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cadmium atom in the X-Ray Structure of AU2PHEN-Encapsulated Horse Spleen Apoferritin (pdb code 6env). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the X-Ray Structure of AU2PHEN-Encapsulated Horse Spleen Apoferritin, PDB code: 6env:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:44.0 occ:0.35 O A:HOH378 2.1 17.6 0.4 OE1 A:GLU11 2.5 18.3 1.0 OE2 A:GLU11 2.8 23.2 1.0 O A:HOH592 2.8 64.3 1.0 O A:HOH432 2.9 22.5 1.0 O A:HOH475 3.0 55.1 1.0 CD A:GLU11 3.0 21.4 1.0 OG1 A:THR10 3.9 19.6 1.0 O A:HOH456 4.0 59.7 1.0 CB A:SER9 4.5 12.7 1.0 CG A:GLU11 4.6 17.7 1.0 OE1 A:GLN120 4.6 27.3 1.0 N A:THR10 4.7 13.4 1.0 NE2 A:GLN120 4.7 26.7 1.0

Cadmium binding site 2 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:54.0 occ:0.40 O A:HOH315 2.1 11.2 0.3 OE2 A:GLU53 2.6 48.5 1.0 OE1 A:GLU56 2.7 37.1 1.0 OE1 A:GLU53 2.9 52.6 1.0 CD A:GLU53 3.1 39.1 1.0 CD A:GLU56 3.4 34.3 1.0 OE2 A:GLU56 3.4 44.1 1.0 O A:HOH322 3.7 40.4 1.0 CG A:GLU53 4.7 27.7 1.0 CG A:GLU56 4.7 22.8 1.0 CD A:CD203 5.0 27.9 0.3

Cadmium binding site 3 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:31.1 occ:0.30 CD A:CD203 0.0 31.1 0.3 CD A:CD203 1.9 27.9 0.3 O A:HOH304 1.9 30.0 1.0 OE2 A:GLU57 2.2 46.5 1.0 OE1 A:GLU60 2.4 31.4 1.0 O A:HOH494 2.5 17.6 0.3 CD A:GLU57 3.0 36.0 1.0 CD A:GLU60 3.0 25.4 1.0 OE2 A:GLU60 3.1 33.5 1.0 OE1 A:GLU57 3.1 41.6 1.0 OE2 A:GLU56 3.8 44.1 1.0 O A:HOH322 4.0 40.4 1.0 O A:HOH490 4.0 60.3 1.0 O A:HOH560 4.4 67.7 1.0 CG A:GLU57 4.5 28.1 1.0 CG A:GLU60 4.5 20.4 1.0 CD A:GLU56 4.6 34.3 1.0 CG A:GLU56 4.7 22.8 1.0 O A:HOH479 4.7 52.9 1.0

Cadmium binding site 4 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:27.9 occ:0.30 CD A:CD203 0.0 27.9 0.3 CD A:CD203 1.9 31.1 0.3 OE2 A:GLU56 2.1 44.1 1.0 OE2 A:GLU60 2.2 33.5 1.0 O A:HOH494 2.7 17.6 0.3 CD A:GLU60 2.9 25.4 1.0 OE1 A:GLU60 3.0 31.4 1.0 CD A:GLU56 3.1 34.3 1.0 OE2 A:GLU57 3.1 46.5 1.0 CG A:GLU56 3.5 22.8 1.0 O A:HOH304 3.7 30.0 1.0 O A:HOH322 3.8 40.4 1.0 OE1 A:GLU56 4.2 37.1 1.0 CD A:GLU57 4.3 36.0 1.0 CG A:GLU60 4.3 20.4 1.0 O A:HOH315 4.4 11.2 0.3 O A:HOH490 4.5 60.3 1.0 OE1 A:GLU57 4.7 41.6 1.0 CB A:GLU56 4.9 17.8 1.0 CD A:CD202 5.0 54.0 0.4

Cadmium binding site 5 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:13.0 occ:0.50 OD2 A:ASP80 2.2 13.2 1.0 OD1 A:ASP80 2.4 12.5 1.0 CL A:CL211 2.5 19.9 1.0 CG A:ASP80 2.7 13.4 1.0 CB A:ASP80 4.1 12.6 1.0 O A:HOH369 4.3 14.3 1.0 O A:HOH387 4.7 20.9 1.0

Cadmium binding site 6 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:54.2 occ:0.20 O A:HOH358 2.3 49.2 1.0 OE2 A:GLU88 2.5 36.7 1.0 OE1 A:GLU88 2.9 33.6 1.0 CD A:GLU88 3.0 31.9 1.0 O A:HOH471 3.3 53.0 1.0 CG A:GLU88 4.5 22.5 1.0 O A:HOH454 4.6 44.1 1.0 NH2 A:ARG39 4.6 23.9 1.0 O A:HOH590 4.8 46.7 1.0 NH1 A:ARG39 4.8 23.6 1.0

Cadmium binding site 7 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:62.6 occ:0.20 OD2 A:ASP127 2.4 15.7 0.5 CD A:CD207 2.4 29.0 0.2 OD2 A:ASP127 2.9 21.9 0.5 CG A:ASP127 3.2 14.8 0.5 OG A:SER131 3.2 32.1 1.0 OD1 A:ASP127 3.3 16.8 0.5 CB A:SER131 3.7 27.2 1.0 O A:HOH335 3.9 9.7 0.4 CG A:ASP127 4.0 19.7 0.5 O A:HOH325 4.2 20.4 1.0 O A:ASP127 4.2 15.9 0.5 CD A:CD207 4.2 38.1 0.4 O A:HOH329 4.4 32.9 1.0 O A:ASP127 4.5 15.2 0.5 O A:HOH535 4.6 27.1 0.4 CB A:ASP127 4.6 15.0 0.5 NE2 A:HIS132 4.7 38.9 1.0 C A:ASP127 4.7 15.8 0.5 C A:ASP127 4.8 14.8 0.5 OD1 A:ASP127 4.8 18.3 0.5 CB A:ASP127 4.8 17.7 0.5

Cadmium binding site 8 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:38.1 occ:0.40 CD A:CD207 0.0 38.1 0.4 O A:HOH458 1.9 18.6 0.4 CD A:CD207 2.0 29.0 0.2 NE2 A:HIS132 2.3 38.9 1.0 O A:HOH535 2.8 27.1 0.4 CE1 A:HIS132 3.1 39.3 1.0 CD2 A:HIS132 3.4 37.7 1.0 CD A:CD206 4.2 62.6 0.2 ND1 A:HIS132 4.3 37.5 1.0 CG A:HIS132 4.5 30.9 1.0 NH1 A:ARG64 4.9 48.5 1.0

Cadmium binding site 9 out of 12 in the X-Ray Structure of AU2PHEN-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 AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:29.0 occ:0.20 CD A:CD207 0.0 29.0 0.2 CD A:CD207 2.0 38.1 0.4 CD A:CD206 2.4 62.6 0.2 NE2 A:HIS132 3.1 38.9 1.0 O A:HOH535 3.6 27.1 0.4 O A:HOH458 3.7 18.6 0.4 CD2 A:HIS132 3.7 37.7 1.0 OD2 A:ASP127 3.8 15.7 0.5 CE1 A:HIS132 4.1 39.3 1.0 O A:HOH325 4.2 20.4 1.0 CB A:SER131 4.4 27.2 1.0 OG A:SER131 4.7 32.1 1.0 CG A:ASP127 4.9 14.8 0.5 CG A:HIS132 5.0 30.9 1.0

Cadmium binding site 10 out of 12 in the X-Ray Structure of AU2PHEN-Encapsulated Horse Spleen Apoferritin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of X-Ray Structure of AU2PHEN-Encapsulated Horse Spleen Apoferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:33.3 occ:0.20 OE1 A:GLU130 2.4 32.9 1.0 CD A:GLU130 3.3 26.6 1.0 O A:HOH515 3.4 44.2 1.0 OE2 A:GLU130 3.5 22.0 1.0 OD1 A:ASP127 4.0 18.3 0.5 CG A:GLU130 4.7 21.7 1.0 CG A:ASP127 4.9 19.7 0.5 CD A:CD210 4.9 30.0 0.3 CB A:ASP127 4.9 17.7 0.5

D.M.Monti, G.Ferraro, G.Petruk, L.Maiore, F.Pane, A.Amoresano, M.A.Cinellu, A.Merlino. Ferritin Nanocages Loaded with Gold Ions Induce Oxidative Stress and Apoptosis in Mcf-7 Human Breast Cancer Cells. Dalton Trans V. 46 15354 2017.
ISSN: ESSN 1477-9234
PubMed: 29072740
DOI: 10.1039/C7DT02370G