Palladium in PDB 5hqo: Crystal Structure of Ircp*/I-Pd(Allyl)-Apo-Rhlfr

The structure of Crystal Structure of Ircp*/I-Pd(Allyl)-Apo-Rhlfr, PDB code: 5hqo 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)	21.93 / 1.81
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.877, 180.877, 180.877, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.1

The structure of Crystal Structure of Ircp*/I-Pd(Allyl)-Apo-Rhlfr 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*/I-Pd(Allyl)-Apo-Rhlfr (pdb code 5hqo). 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*/I-Pd(Allyl)-Apo-Rhlfr, PDB code: 5hqo:
Jump to Palladium binding site number: 1; 2; 3;

Palladium binding site 1 out of 3 in the Crystal Structure of Ircp*/I-Pd(Allyl)-Apo-Rhlfr


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*/I-Pd(Allyl)-Apo-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd201 b:40.0 occ:0.20 SG A:CYS126 1.5 62.8 1.0 CE1 A:HIS114 2.7 49.1 1.0 NE2 A:HIS114 2.7 48.6 1.0 CB A:CYS126 3.1 52.9 1.0 O A:CYS126 3.5 48.3 1.0 IR A:IR204 3.6 43.7 0.3 C A:CYS126 3.6 50.2 1.0 CA A:CYS126 3.8 48.9 1.0 ND1 A:HIS114 4.0 51.5 1.0 CD2 A:HIS114 4.1 50.6 1.0 N A:ASP127 4.2 52.3 1.0 CB A:GLU130 4.3 59.1 1.0 CG A:HIS114 4.7 52.8 1.0 CA A:ASP127 4.8 52.8 1.0

Palladium binding site 2 out of 3 in the Crystal Structure of Ircp*/I-Pd(Allyl)-Apo-Rhlfr


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*/I-Pd(Allyl)-Apo-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd202 b:20.3 occ:0.20 PD A:PLL203 2.9 29.4 0.8 SG A:CYS48 3.1 26.9 1.0 CA A:HIS49 3.4 17.5 1.0 CD A:ARG52 3.4 36.2 1.0 N A:HIS49 3.5 12.6 1.0 CB A:HIS49 3.7 20.5 1.0 C A:CYS48 3.8 15.8 1.0 C19 A:PLL203 3.9 23.8 0.8 CB A:CYS48 4.1 20.1 1.0 O A:CYS48 4.1 14.9 1.0 NE A:ARG52 4.2 43.5 1.0 C21 A:PLL203 4.2 25.4 0.8 ND1 A:HIS49 4.2 38.9 1.0 CG A:ARG52 4.3 26.2 1.0 CG A:HIS49 4.4 28.6 1.0 CB A:ARG52 4.6 19.6 1.0 O A:GLU45 4.6 14.8 1.0 CA A:CYS48 4.6 15.6 1.0 C20 A:PLL203 4.6 24.7 0.8 OE2 A:GLU45 4.7 23.0 1.0 C A:HIS49 4.8 13.7 1.0

Palladium binding site 3 out of 3 in the Crystal Structure of Ircp*/I-Pd(Allyl)-Apo-Rhlfr


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*/I-Pd(Allyl)-Apo-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd203 b:29.4 occ:0.80 PD A:PLL203 0.0 29.4 0.8 C19 A:PLL203 2.3 23.8 0.8 SG A:CYS48 2.3 26.9 1.0 C20 A:PLL203 2.3 24.7 0.8 C21 A:PLL203 2.4 25.4 0.8 OE2 A:GLU45 2.5 23.0 1.0 PD A:PD202 2.9 20.3 0.2 CB A:CYS48 3.5 20.1 1.0 OD1 A:ASP38 3.7 17.6 1.0 CD A:GLU45 3.7 34.1 1.0 CG A:ASP38 3.9 18.1 1.0 CB A:ASP38 3.9 14.7 1.0 OE1 A:GLU45 4.3 38.1 1.0 CD A:ARG52 4.4 36.2 1.0 OD2 A:ASP38 4.6 16.7 1.0 CA A:CYS48 4.8 15.6 1.0 CA A:ASP38 4.9 13.1 1.0 CG A:GLU45 4.9 27.8 1.0 C A:CYS48 4.9 15.8 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