Cadmium in PDB 3af8: Crystal Structure of Pd(Ally)/Apo-C126AFR

The structure of Crystal Structure of Pd(Ally)/Apo-C126AFR, PDB code: 3af8 was solved by S.Abe, T.Hikage, Y.Watanabe, S.Kitagawa, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.76 / 1.66
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.984, 181.984, 181.984, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 19.5

The structure of Crystal Structure of Pd(Ally)/Apo-C126AFR also contains other interesting chemical elements:

Palladium

(Pd)

2 atoms

The binding sites of Cadmium atom in the Crystal Structure of Pd(Ally)/Apo-C126AFR (pdb code 3af8). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Pd(Ally)/Apo-C126AFR, PDB code: 3af8:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Crystal Structure of Pd(Ally)/Apo-C126AFR


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Pd(Ally)/Apo-C126AFR within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd175 b:99.6 occ:0.33 O X:HOH308 2.2 28.9 1.0 O X:HOH360 2.7 31.3 1.0 OD1 X:ASP127 3.6 16.7 1.0 CD X:CD176 3.9 34.2 0.3 OE2 X:GLU130 3.9 17.7 1.0 OG X:SER131 4.4 18.4 1.0 CG X:ASP127 4.7 13.4 1.0 CB X:GLU130 4.9 12.7 1.0

Cadmium binding site 2 out of 3 in the Crystal Structure of Pd(Ally)/Apo-C126AFR


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Pd(Ally)/Apo-C126AFR within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd176 b:34.2 occ:0.33 O X:HOH330 2.0 18.5 1.0 OE2 X:GLU130 2.4 17.7 1.0 CD X:GLU130 3.3 16.1 1.0 OE1 X:GLU130 3.5 15.5 1.0 O X:HOH308 3.7 28.9 1.0 CD X:CD175 3.9 99.6 0.3 O X:HOH315 4.3 24.1 1.0 CG X:GLU130 4.7 12.7 1.0

Cadmium binding site 3 out of 3 in the Crystal Structure of Pd(Ally)/Apo-C126AFR


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Pd(Ally)/Apo-C126AFR within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd177 b:23.0 occ:0.50 OD2 X:ASP80 2.6 20.4 1.0 OD1 X:ASP80 2.6 15.3 1.0 CG X:ASP80 3.0 15.1 1.0 CB X:ASP80 4.4 13.8 1.0 O X:HOH361 4.5 37.8 1.0 O X:HOH263 4.7 18.4 1.0

S.Abe, T.Hikage, Y.Watanabe, S.Kitagawa, T.Ueno. Mechanism of Accumulation and Incorporation of Organometallic Pd Complexes Into the Protein Nanocage of Apo-Ferritin. Inorg.Chem. V. 49 6967 2010.
ISSN: ISSN 0020-1669
PubMed: 20586408
DOI: 10.1021/IC1003758