Palladium in PDB 2zg8: Crystal Structure of Pd(Allyl)/Apo-H49AFR

The structure of Crystal Structure of Pd(Allyl)/Apo-H49AFR, PDB code: 2zg8 was solved by S.Abe, J.Niemeyer, M.Abe, T.Ueno, T.Hikage, G.Erker, Y.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.15 / 1.60
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.339, 181.339, 181.339, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.1

The structure of Crystal Structure of Pd(Allyl)/Apo-H49AFR also contains other interesting chemical elements:

Cadmium

(Cd)

1 atom

The binding sites of Palladium atom in the Crystal Structure of Pd(Allyl)/Apo-H49AFR (pdb code 2zg8). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 4 binding sites of Palladium where determined in the Crystal Structure of Pd(Allyl)/Apo-H49AFR, PDB code: 2zg8:
Jump to Palladium binding site number: 1; 2; 3; 4;

Palladium binding site 1 out of 4 in the Crystal Structure of Pd(Allyl)/Apo-H49AFR


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-H49AFR within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd175 b:51.2 occ:1.00 SG X:CYS126 2.3 26.8 1.0 O X:HOH302 2.4 44.7 1.0 CB X:CYS126 3.3 26.6 1.0 PD X:PLL182 3.6 25.2 1.0 CE1 X:HIS114 4.1 23.3 1.0 OG X:SER118 4.3 22.7 0.5 NE2 X:HIS114 4.3 24.2 1.0 CA X:PRO123 4.7 20.0 1.0 CA X:CYS126 4.7 26.0 1.0 C19 X:PLL182 4.8 26.2 1.0

Palladium binding site 2 out of 4 in the Crystal Structure of Pd(Allyl)/Apo-H49AFR


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-H49AFR within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd181 b:16.7 occ:1.00 PD X:PLL181 0.0 16.7 1.0 C21 X:PLL181 2.3 20.0 1.0 OE2 X:GLU45 2.3 15.3 1.0 C19 X:PLL181 2.3 20.4 1.0 C20 X:PLL181 2.3 20.1 1.0 SG X:CYS48 2.4 15.6 1.0 PD X:PLL183 2.8 25.0 1.0 CD X:GLU45 3.0 16.9 1.0 OE1 X:GLU45 3.1 17.8 1.0 CB X:CYS48 3.4 12.5 1.0 OD1 X:ASP38 3.7 12.9 1.0 CG X:ASP38 3.8 11.6 1.0 CB X:ASP38 3.9 10.7 1.0 O X:HOH249 3.9 25.0 1.0 C20 X:PLL183 4.2 24.4 1.0 O X:HOH382 4.2 30.6 1.0 C21 X:PLL183 4.5 25.9 1.0 CG X:GLU45 4.5 14.0 1.0 OD2 X:ASP38 4.5 11.6 1.0 O X:HOH345 4.8 26.1 1.0 CA X:CYS48 4.8 11.6 1.0 CA X:ASP38 4.9 10.0 1.0 C19 X:PLL183 4.9 26.5 1.0

Palladium binding site 3 out of 4 in the Crystal Structure of Pd(Allyl)/Apo-H49AFR


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 3 of Crystal Structure of Pd(Allyl)/Apo-H49AFR within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd182 b:25.2 occ:1.00 PD X:PLL182 0.0 25.2 1.0 NE2 X:HIS114 2.1 24.2 1.0 C21 X:PLL182 2.2 26.8 1.0 C19 X:PLL182 2.3 26.2 1.0 C20 X:PLL182 2.3 26.1 1.0 SG X:CYS126 2.5 26.8 1.0 CE1 X:HIS114 3.0 23.3 1.0 O X:CYS126 3.2 27.3 1.0 CD2 X:HIS114 3.2 22.7 1.0 C X:CYS126 3.4 26.7 1.0 CB X:CYS126 3.4 26.6 1.0 PD X:PD175 3.6 51.2 1.0 CA X:CYS126 3.9 26.0 1.0 N X:ASP127 3.9 26.9 1.0 O X:HOH302 4.1 44.7 1.0 ND1 X:HIS114 4.2 23.4 1.0 CG X:HIS114 4.3 21.3 1.0 CA X:ASP127 4.3 27.4 1.0 CB X:GLU130 4.7 29.6 1.0

Palladium binding site 4 out of 4 in the Crystal Structure of Pd(Allyl)/Apo-H49AFR


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 4 of Crystal Structure of Pd(Allyl)/Apo-H49AFR within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd183 b:25.0 occ:1.00 PD X:PLL183 0.0 25.0 1.0 C21 X:PLL183 2.2 25.9 1.0 C20 X:PLL183 2.2 24.4 1.0 C19 X:PLL183 2.3 26.5 1.0 OE1 X:GLU45 2.3 17.8 1.0 SG X:CYS48 2.7 15.6 1.0 PD X:PLL181 2.8 16.7 1.0 CD X:GLU45 3.3 16.9 1.0 N X:ALA49 3.5 10.1 1.0 OE2 X:GLU45 3.6 15.3 1.0 CA X:ALA49 3.6 10.7 1.0 CB X:CYS48 3.8 12.5 1.0 C X:CYS48 3.8 11.0 1.0 CB X:ALA49 3.9 11.1 1.0 O X:CYS48 4.2 11.6 1.0 C20 X:PLL181 4.2 20.1 1.0 O X:HOH237 4.2 24.3 1.0 C21 X:PLL181 4.3 20.0 1.0 O X:GLU45 4.4 11.9 1.0 CA X:CYS48 4.4 11.6 1.0 C19 X:PLL181 4.5 20.4 1.0 CG X:ARG52 4.6 12.9 0.5 CG X:GLU45 4.6 14.0 1.0 O X:HOH382 4.7 30.6 1.0 CB X:ARG52 4.8 12.8 0.5 O X:HOH352 4.8 26.5 1.0 CB X:ARG52 4.9 12.2 0.5 CD X:ARG52 4.9 20.7 0.5 NH2 X:ARG52 5.0 17.7 0.5 C X:ALA49 5.0 10.8 1.0

S.Abe, J.Niemeyer, M.Abe, Y.Takezawa, T.Ueno, T.Hikage, G.Erker, Y.Watanabe. Control of the Coordination Structure of Organometallic Palladium Complexes in An Apo-Ferritin Cage. J.Am.Chem.Soc. V. 130 10512 2008.
ISSN: ISSN 0002-7863
PubMed: 18636721
DOI: 10.1021/JA802463A