Cadmium in PDB 2z5r: Apo-Fr with High Content of Pd Ions

The structure of Apo-Fr with High Content of Pd Ions, PDB code: 2z5r was solved by T.Ueno, K.Hirata, M.Abe, M.Suzuki, S.Abe, N.Shimizu, M.Yamamoto, M.Takata, Y.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.41 / 2.50
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.594, 181.594, 181.594, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 28.7

The structure of Apo-Fr with High Content of Pd Ions also contains other interesting chemical elements:

Palladium

(Pd)

10 atoms

The binding sites of Cadmium atom in the Apo-Fr with High Content of Pd Ions (pdb code 2z5r). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Apo-Fr with High Content of Pd Ions, PDB code: 2z5r:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Apo-Fr with High Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Apo-Fr with High Content of Pd Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd211 b:27.3 occ:0.50 OD2 A:ASP80 2.1 2.3 0.5 OD1 A:ASP80 2.6 2.0 0.5 CG A:ASP80 2.6 9.2 1.0 CB A:ASP80 4.2 13.6 1.0 O A:HOH1023 4.5 29.1 1.0

Cadmium binding site 2 out of 2 in the Apo-Fr with High Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Apo-Fr with High Content of Pd Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd212 b:0.5 occ:0.10 OE1 A:GLU60 2.5 45.2 1.0 OE2 A:GLU60 3.2 46.4 1.0 CD A:GLU60 3.2 42.5 1.0 OE2 A:GLU57 3.6 54.0 1.0 O A:HOH1033 3.6 37.3 1.0 CG A:GLU60 4.7 31.1 1.0 CD A:GLU57 4.9 48.5 1.0

T.Ueno, M.Abe, K.Hirata, S.Abe, M.Suzuki, N.Shimizu, M.Yamamoto, M.Takata, Y.Watanabe. Process of Accumulation of Metal Ions on the Interior Surface of Apo-Ferritin: Crystal Structures of A Series of Apo-Ferritins Containing Variable Quantities of Pd(II) Ions. J.Am.Chem.Soc. V. 131 5094 2009.
ISSN: ISSN 0002-7863
PubMed: 19317403
DOI: 10.1021/JA806688S