Cadmium in PDB 5lg8: Human L-Type Ferritin Iron Loaded For 60 Minutes

The structure of Human L-Type Ferritin Iron Loaded For 60 Minutes, PDB code: 5lg8 was solved by C.Pozzi, F.Di Pisa, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.70 / 1.98
Space group	I 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	151.420, 151.420, 151.420, 90.00, 90.00, 90.00
R / Rfree (%)	14.2 / 17.7

The structure of Human L-Type Ferritin Iron Loaded For 60 Minutes also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Cadmium atom in the Human L-Type Ferritin Iron Loaded For 60 Minutes (pdb code 5lg8). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Human L-Type Ferritin Iron Loaded For 60 Minutes, PDB code: 5lg8:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in the Human L-Type Ferritin Iron Loaded For 60 Minutes


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Human L-Type Ferritin Iron Loaded For 60 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:20.4 occ:0.50 OD2 A:ASP15 2.3 28.7 1.0 OD1 A:ASP15 2.3 19.8 1.0 O A:HOH432 2.5 18.0 0.5 CG A:ASP15 2.6 26.8 1.0 O A:HOH445 2.7 30.0 0.5 CB A:ASP15 4.2 22.1 1.0 O4 A:SO4217 4.3 20.8 0.5 NH2 A:ARG124 4.6 25.9 1.0 OG1 A:THR14 4.6 30.5 1.0 O A:HOH415 4.8 47.6 1.0 N A:ASP15 5.0 17.6 1.0 CA A:ASP15 5.0 19.5 1.0

Cadmium binding site 2 out of 8 in the Human L-Type Ferritin Iron Loaded For 60 Minutes


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Human L-Type Ferritin Iron Loaded For 60 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:60.9 occ:0.30 OD1 A:ASP131 2.8 30.4 0.6 OD1 A:ASP131 3.8 22.2 0.4 CG A:ASP131 3.8 31.0 0.6 OD2 A:ASP131 4.1 29.9 0.6 OG1 A:THR135 4.2 28.9 1.0 OE1 A:GLU134 4.3 24.8 0.6 O A:HOH434 4.8 56.0 1.0 CG A:ASP131 5.0 22.6 0.4

Cadmium binding site 3 out of 8 in the Human L-Type Ferritin Iron Loaded For 60 Minutes


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Human L-Type Ferritin Iron Loaded For 60 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:56.7 occ:0.60 OE1 A:GLU134 2.1 23.0 0.4 OE2 A:GLU134 2.7 35.5 0.4 CD A:GLU134 2.7 30.3 0.4 OE1 A:GLU134 2.8 24.8 0.6 CD A:GLU134 2.9 23.4 0.6 OE2 A:GLU134 2.9 21.9 0.6 SG A:CYS130 3.9 27.1 0.4 CG A:GLU134 3.9 25.5 0.6 CG A:GLU134 4.2 26.1 0.4 CD A:CD204 4.4 55.1 0.4 O A:HOH484 4.5 43.2 1.0 CB A:GLU134 4.8 25.3 0.4 CB A:GLU134 4.9 22.7 0.6

Cadmium binding site 4 out of 8 in the Human L-Type Ferritin Iron Loaded For 60 Minutes


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Human L-Type Ferritin Iron Loaded For 60 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:55.1 occ:0.40 SG A:CYS130 2.5 27.1 0.4 NE2 A:HIS118 2.9 29.7 1.0 O A:HOH484 3.2 43.2 1.0 CB A:CYS130 3.4 23.0 0.4 CB A:CYS130 3.4 23.1 0.6 CE1 A:HIS118 3.5 27.4 1.0 OE2 A:GLU134 3.5 21.9 0.6 SG A:CYS130 3.8 22.4 0.6 OE2 A:GLU134 3.9 35.5 0.4 CD2 A:HIS118 4.1 23.1 1.0 CD A:CD203 4.4 56.7 0.6 ND1 A:HIS118 4.7 28.0 1.0 CA A:CYS130 4.7 24.7 0.4 CD A:GLU134 4.7 30.3 0.4 CD A:GLU134 4.7 23.4 0.6 CA A:CYS130 4.8 24.4 0.6

Cadmium binding site 5 out of 8 in the Human L-Type Ferritin Iron Loaded For 60 Minutes


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Human L-Type Ferritin Iron Loaded For 60 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:54.8 occ:0.50 NE2 A:HIS136 2.3 37.6 1.0 O A:HOH464 2.4 36.1 0.5 O A:HOH449 2.4 26.2 0.5 CE1 A:HIS136 3.1 36.3 1.0 CD2 A:HIS136 3.4 35.0 1.0 ND1 A:HIS136 4.2 32.0 1.0 O A:HOH400 4.4 55.5 1.0 CG A:HIS136 4.4 32.4 1.0 CG2 A:THR135 4.8 30.9 1.0

Cadmium binding site 6 out of 8 in the Human L-Type Ferritin Iron Loaded For 60 Minutes


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Human L-Type Ferritin Iron Loaded For 60 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:49.1 occ:0.40 OE2 A:GLU90 2.2 23.6 0.4 O A:HOH416 2.3 9.2 0.4 OE1 A:GLU90 2.4 31.7 0.4 CD A:GLU90 2.7 25.2 0.4 O A:HOH450 2.7 24.5 0.4 O A:HOH395 3.0 34.6 1.0 CG A:GLU90 4.2 23.9 0.4 CG A:GLU90 4.2 29.4 0.6 O A:ASP98 4.4 18.7 1.0 CB A:ASP98 4.5 24.3 1.0 O A:TRP93 4.5 21.9 1.0 CE3 A:TRP93 4.6 16.7 1.0 CD A:GLU90 4.7 33.0 0.6 OE1 A:GLU90 4.7 39.1 0.6 O A:HOH411 4.7 54.7 1.0 O A:HOH410 4.8 38.9 1.0 C A:ASP98 4.9 19.8 1.0 C A:TRP93 4.9 21.6 1.0 CB A:ALA102 4.9 17.9 1.0 CA A:TRP93 5.0 21.4 1.0

Cadmium binding site 7 out of 8 in the Human L-Type Ferritin Iron Loaded For 60 Minutes


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Human L-Type Ferritin Iron Loaded For 60 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:81.3 occ:0.50 OE2 A:GLU49 2.5 31.9 0.5 OE1 A:GLU49 2.9 43.3 0.5 OD2 A:ASP178 2.9 38.9 0.5 CD A:GLU49 2.9 34.5 0.5 CG A:ASP178 3.5 43.1 0.5 CA A:ASP178 4.1 55.9 0.5 CB A:ASP178 4.1 48.3 0.5 OD1 A:ASP178 4.2 45.8 0.5 CG A:GLU49 4.3 27.1 0.5 N A:ASP178 4.3 63.9 0.5

Cadmium binding site 8 out of 8 in the Human L-Type Ferritin Iron Loaded For 60 Minutes


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Human L-Type Ferritin Iron Loaded For 60 Minutes within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:57.4 occ:0.20 OE1 A:GLU90 2.2 39.1 0.6 OE2 A:GLU90 2.5 34.7 0.6 CD A:GLU90 2.7 33.0 0.6 CG A:GLU90 4.2 29.4 0.6 CG A:GLU90 4.6 23.9 0.4 OE1 A:GLU90 4.7 31.7 0.4 CD A:GLU90 4.8 25.2 0.4 O A:HOH355 5.0 37.5 1.0

C.Pozzi, S.Ciambellotti, C.Bernacchioni, F.Di Pisa, S.Mangani, P.Turano. Chemistry at the Protein-Mineral Interface in L-Ferritin Assists the Assembly of A Functional ( Mu (3)-Oxo)Tris[( Mu (2)-Peroxo)] Triiron(III) Cluster. Proc. Natl. Acad. Sci. V. 114 2580 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28202724
DOI: 10.1073/PNAS.1614302114