Palladium in PDB 2zg7: Crystal Structure of Pd(Allyl)/Apo-Fr

The structure of Crystal Structure of Pd(Allyl)/Apo-Fr, PDB code: 2zg7 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)	22.01 / 1.70
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.450, 181.450, 181.450, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.2

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

Cadmium

(Cd)

1 atom

The binding sites of Palladium atom in the Crystal Structure of Pd(Allyl)/Apo-Fr (pdb code 2zg7). 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-Fr, PDB code: 2zg7:
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-Fr


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-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd180 b:24.8 occ:1.00 PD X:PLL180 0.0 24.8 1.0 NE2 X:HIS114 2.1 22.1 1.0 C19 X:PLL180 2.2 25.4 1.0 C21 X:PLL180 2.3 26.0 1.0 C20 X:PLL180 2.3 26.9 1.0 SG X:CYS126 2.5 23.0 1.0 CE1 X:HIS114 3.0 21.2 1.0 CD2 X:HIS114 3.2 20.8 1.0 O X:CYS126 3.2 23.4 1.0 CB X:CYS126 3.3 23.0 1.0 C X:CYS126 3.4 23.0 1.0 PD X:PLL181 3.7 42.2 1.0 N X:ASP127 3.8 23.2 1.0 CA X:CYS126 3.9 22.2 1.0 ND1 X:HIS114 4.2 21.8 1.0 O X:HOH404 4.2 31.4 1.0 CA X:ASP127 4.3 23.6 1.0 CG X:HIS114 4.3 19.7 1.0 CB X:GLU130 4.5 27.1 1.0 OE1 X:GLU130 5.0 32.2 1.0

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


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-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd181 b:42.2 occ:1.00 PD X:PLL181 0.0 42.2 1.0 C21 X:PLL181 2.3 42.7 1.0 C20 X:PLL181 2.3 42.2 1.0 C19 X:PLL181 2.3 42.8 1.0 O X:HOH404 2.3 31.4 1.0 SG X:CYS126 2.4 23.0 1.0 CB X:CYS126 3.3 23.0 1.0 PD X:PLL180 3.7 24.8 1.0 CE1 X:HIS114 4.1 21.2 1.0 NE2 X:HIS114 4.3 22.1 1.0 CA X:PRO123 4.7 17.6 1.0 CA X:CYS126 4.7 22.2 1.0 C19 X:PLL180 4.9 25.4 1.0

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


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-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd182 b:19.9 occ:1.00 PD X:PLL182 0.0 19.9 1.0 C21 X:PLL182 2.3 22.5 1.0 C20 X:PLL182 2.3 23.6 1.0 C19 X:PLL182 2.3 23.0 1.0 OE2 X:GLU45 2.3 18.4 1.0 SG X:CYS48 2.3 16.4 1.0 PD X:PLL183 3.1 22.5 1.0 CD X:GLU45 3.4 21.0 1.0 CB X:CYS48 3.4 13.3 1.0 OD1 X:ASP38 3.6 13.6 1.0 O X:HOH266 3.7 29.7 1.0 OE1 X:GLU45 3.7 24.8 1.0 CG X:ASP38 3.8 11.3 1.0 CB X:ASP38 3.9 10.3 1.0 CE1 X:HIS49 4.0 20.9 1.0 C20 X:PLL183 4.0 23.6 1.0 ND1 X:HIS49 4.1 19.7 1.0 O X:HOH396 4.1 24.9 1.0 OD2 X:ASP38 4.6 11.5 1.0 CG X:GLU45 4.7 16.7 1.0 CA X:CYS48 4.8 12.0 1.0 C21 X:PLL183 4.8 23.2 1.0 CA X:ASP38 4.8 9.8 1.0 C19 X:PLL183 4.9 22.6 1.0

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


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-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd183 b:22.5 occ:1.00 PD X:PLL183 0.0 22.5 1.0 ND1 X:HIS49 2.2 19.7 1.0 C20 X:PLL183 2.3 23.6 1.0 C21 X:PLL183 2.3 23.2 1.0 C19 X:PLL183 2.3 22.6 1.0 SG X:CYS48 2.6 16.4 1.0 CE1 X:HIS49 3.0 20.9 1.0 PD X:PLL182 3.1 19.9 1.0 CG X:HIS49 3.3 16.8 1.0 CA X:HIS49 3.4 12.5 1.0 N X:HIS49 3.4 11.2 1.0 C X:CYS48 3.7 12.4 1.0 CB X:HIS49 3.7 13.4 1.0 CB X:CYS48 3.8 13.3 1.0 O X:CYS48 4.0 11.6 1.0 O X:HOH266 4.1 29.7 1.0 NE2 X:HIS49 4.2 22.0 1.0 CD2 X:HIS49 4.3 20.2 1.0 CG X:ARG52 4.3 12.8 0.5 OE2 X:GLU45 4.3 18.4 1.0 C20 X:PLL182 4.4 23.6 1.0 C21 X:PLL182 4.4 22.5 1.0 CA X:CYS48 4.4 12.0 1.0 CB X:ARG52 4.5 13.1 0.5 CB X:ARG52 4.5 12.6 0.5 O X:GLU45 4.6 11.6 1.0 O X:HOH396 4.7 24.9 1.0 C X:HIS49 4.7 11.7 1.0 O X:HOH261 4.7 24.2 1.0 C19 X:PLL182 4.7 23.0 1.0 CG X:ARG52 5.0 14.8 0.5

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