Palladium in PDB 5e2d: Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr

The structure of Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr, PDB code: 5e2d was solved by B.Maity, K.Fukumori, S.Abe, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.03 / 1.87
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.190, 181.190, 181.190, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.1

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

Cadmium	(Cd)	1 atom
Iridium	(Ir)	6 atoms

The binding sites of Palladium atom in the Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr (pdb code 5e2d). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 3 binding sites of Palladium where determined in the Crystal Structure of Ircp*/Pd(Allyl)-Apo-Fr, PDB code: 5e2d:
Jump to Palladium binding site number: 1; 2; 3;

Palladium binding site 1 out of 3 in the Crystal Structure of Ircp*/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 Ircp*/Pd(Allyl)-Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd209 b:30.5 occ:0.70 PD A:PLL209 0.0 30.5 0.7 C20 A:PLL209 1.9 30.6 0.7 C19 A:PLL209 1.9 31.4 0.7 C21 A:PLL209 2.0 28.9 0.7 OE1 A:GLU45 2.5 20.8 0.7 SG A:CYS48 2.8 26.1 1.0 PD A:PLL210 2.9 25.6 1.0 CD A:GLU45 3.4 25.7 0.7 CA A:HIS49 3.5 18.3 1.0 N A:HIS49 3.5 16.2 1.0 OE2 A:GLU45 3.6 22.2 0.7 C19 A:PLL210 3.6 28.2 1.0 C A:CYS48 3.8 18.1 1.0 CB A:HIS49 3.8 24.7 1.0 CB A:CYS48 3.8 20.5 1.0 O A:CYS48 4.0 16.1 1.0 C20 A:PLL210 4.1 28.5 1.0 ND1 A:HIS49 4.3 44.6 1.0 OE1 A:GLU45 4.4 23.5 0.3 C21 A:PLL210 4.4 28.4 1.0 CA A:CYS48 4.4 16.4 1.0 CG A:ARG52 4.5 24.9 1.0 O A:GLU45 4.5 13.9 1.0 CG A:HIS49 4.5 31.2 1.0 CB A:ARG52 4.7 19.2 1.0 O A:HOH357 4.8 32.8 1.0 C A:HIS49 4.8 15.5 1.0 CG A:GLU45 4.9 22.3 0.7 NH2 A:ARG52 5.0 40.5 1.0

Palladium binding site 2 out of 3 in the Crystal Structure of Ircp*/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 Ircp*/Pd(Allyl)-Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd210 b:25.6 occ:1.00 PD A:PLL210 0.0 25.6 1.0 C19 A:PLL210 2.0 28.2 1.0 C20 A:PLL210 2.0 28.5 1.0 C21 A:PLL210 2.1 28.4 1.0 OE1 A:GLU45 2.3 23.5 0.3 SG A:CYS48 2.3 26.1 1.0 OE2 A:GLU45 2.4 22.2 0.7 PD A:PLL209 2.9 30.5 0.7 CD A:GLU45 3.3 25.7 0.7 OE1 A:GLU45 3.4 20.8 0.7 CD A:GLU45 3.4 24.1 0.3 CB A:CYS48 3.4 20.5 1.0 OD1 A:ASP38 3.7 17.4 1.0 C19 A:PLL209 3.7 31.4 0.7 OE2 A:GLU45 3.8 24.6 0.3 CG A:ASP38 3.8 18.7 1.0 CB A:ASP38 3.9 15.7 1.0 C21 A:PLL209 4.0 28.9 0.7 OD2 A:ASP38 4.6 17.9 1.0 C20 A:PLL209 4.6 30.6 0.7 CG A:GLU45 4.7 28.1 0.3 CG A:GLU45 4.7 22.3 0.7 CA A:CYS48 4.8 16.4 1.0 CA A:ASP38 4.9 15.2 1.0 CB A:GLU45 4.9 21.8 0.3

Palladium binding site 3 out of 3 in the Crystal Structure of Ircp*/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 Ircp*/Pd(Allyl)-Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd211 b:54.5 occ:0.60 NE2 A:HIS114 2.4 53.9 0.5 NE2 A:HIS114 2.4 47.3 0.5 CE1 A:HIS114 2.5 46.1 0.5 SG A:CYS126 2.5 82.3 1.0 O A:CYS126 3.1 57.3 1.0 CE1 A:HIS114 3.2 54.3 0.5 CB A:CYS126 3.3 59.5 1.0 IR A:IR3204 3.4 58.3 0.4 C A:CYS126 3.4 56.1 1.0 CD2 A:HIS114 3.5 54.9 0.5 ND1 A:HIS114 3.8 42.0 0.5 CD2 A:HIS114 3.8 45.5 0.5 CA A:CYS126 3.8 50.5 1.0 N A:ASP127 4.2 52.5 1.0 ND1 A:HIS114 4.3 52.0 0.5 CG A:HIS114 4.4 45.5 0.5 CB A:GLU130 4.5 59.3 1.0 CG A:HIS114 4.5 52.6 0.5 CA A:ASP127 4.8 48.9 1.0

B.Maity, K.Fukumori, S.Abe, T.Ueno. Immobilization of Two Organometallic Complexes Into A Single Cage to Construct Protein-Based Microcompartments Chem.Commun.(Camb.) V. 52 5463 2016.
ISSN: ESSN 1364-548X
PubMed: 27021005
DOI: 10.1039/C6CC00679E