Cadmium in PDB 2z5p: Apo-Fr with Low Content of Pd Ions

The structure of Apo-Fr with Low Content of Pd Ions, PDB code: 2z5p 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)	34.79 / 1.65
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.790, 180.790, 180.790, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 18.8

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

Palladium

(Pd)

6 atoms

The binding sites of Cadmium atom in the Apo-Fr with Low Content of Pd Ions (pdb code 2z5p). 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 Low Content of Pd Ions, PDB code: 2z5p:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Apo-Fr with Low 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 Low Content of Pd Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:13.6 occ:0.50 OD1 A:ASP80 2.4 10.6 1.0 OD2 A:ASP80 2.4 12.9 1.0 CG A:ASP80 2.8 11.0 1.0 CB A:ASP80 4.3 11.1 1.0 O A:HOH1020 4.3 14.1 1.0 O A:HOH1028 4.6 20.1 1.0

Cadmium binding site 2 out of 2 in the Apo-Fr with Low 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 Low Content of Pd Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:0.6 occ:0.10 NE2 A:HIS132 2.7 27.0 0.5 CD2 A:HIS132 3.1 26.5 0.5 OG A:SER131 3.7 26.5 0.5 OD2 A:ASP127 3.9 27.3 0.3 CE1 A:HIS132 4.0 26.9 0.5 CG A:HIS132 4.4 25.0 0.5 CA A:PHE128 4.5 24.6 0.8 O A:ASP127 4.7 26.2 0.6 ND1 A:HIS132 4.8 26.6 0.5 CG A:ASP127 4.9 27.0 0.3 N A:PHE128 4.9 25.4 0.8 C A:ASP127 5.0 26.2 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