Palladium in PDB 3af9: Crystal Structure of Pd(Allyl)/Apo-C48AFR

The structure of Crystal Structure of Pd(Allyl)/Apo-C48AFR, PDB code: 3af9 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)	25.55 / 1.85
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	182.433, 182.433, 182.433, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.3

The structure of Crystal Structure of Pd(Allyl)/Apo-C48AFR also contains other interesting chemical elements:

Cadmium

(Cd)

3 atoms

The binding sites of Palladium atom in the Crystal Structure of Pd(Allyl)/Apo-C48AFR (pdb code 3af9). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 2 binding sites of Palladium where determined in the Crystal Structure of Pd(Allyl)/Apo-C48AFR, PDB code: 3af9:
Jump to Palladium binding site number: 1; 2;

Palladium binding site 1 out of 2 in the Crystal Structure of Pd(Allyl)/Apo-C48AFR


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 1 of Crystal Structure of Pd(Allyl)/Apo-C48AFR within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd179 b:28.2 occ:1.00 PD X:PLL179 0.0 28.2 1.0 NE2 X:HIS114 2.1 18.3 1.0 C19 X:PLL179 2.3 22.6 1.0 C21 X:PLL179 2.3 21.3 1.0 C20 X:PLL179 2.4 20.5 1.0 SG X:CYS126 2.4 21.8 1.0 CE1 X:HIS114 3.0 17.7 1.0 O X:HOH293 3.0 34.9 1.0 CD2 X:HIS114 3.2 17.9 1.0 CB X:CYS126 3.3 20.8 1.0 O X:CYS126 3.3 20.8 1.0 C X:CYS126 3.4 20.6 1.0 PD X:PD180 3.6 46.6 1.0 N X:ASP127 3.9 20.1 1.0 CA X:CYS126 3.9 19.8 1.0 ND1 X:HIS114 4.2 18.6 1.0 CA X:ASP127 4.3 20.4 1.0 CG X:HIS114 4.3 17.0 1.0 CB X:GLU130 4.6 22.5 1.0

Palladium binding site 2 out of 2 in the Crystal Structure of Pd(Allyl)/Apo-C48AFR


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 2 of Crystal Structure of Pd(Allyl)/Apo-C48AFR within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd180 b:46.6 occ:1.00 SG X:CYS126 2.4 21.8 1.0 O X:HOH293 3.1 34.9 1.0 CB X:CYS126 3.3 20.8 1.0 PD X:PLL179 3.6 28.2 1.0 CE1 X:HIS114 3.9 17.7 1.0 NE2 X:HIS114 4.2 18.3 1.0 C19 X:PLL179 4.7 22.6 1.0 CA X:PRO123 4.7 15.5 1.0 CA X:CYS126 4.7 19.8 1.0 ND1 X:HIS114 4.9 18.6 1.0 CB X:SER118 4.9 22.8 1.0 CA X:SER118 5.0 22.4 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