Palladium in PDB 3np2: Crystal Structure of Pd(Allyl)/Apo-E45C/C48A-Rhlfr

The structure of Crystal Structure of Pd(Allyl)/Apo-E45C/C48A-Rhlfr, PDB code: 3np2 was solved by Z.Wang, T.Ueno, S.Abe, Y.Takezawa, H.Aoyagi, T.Hikage, Y.Watanabe, S.Kitagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.36 / 1.86
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	182.296, 182.296, 182.296, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 22.9

The structure of Crystal Structure of Pd(Allyl)/Apo-E45C/C48A-Rhlfr also contains other interesting chemical elements:

Cadmium

(Cd)

2 atoms

The binding sites of Palladium atom in the Crystal Structure of Pd(Allyl)/Apo-E45C/C48A-Rhlfr (pdb code 3np2). 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-E45C/C48A-Rhlfr, PDB code: 3np2:
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-E45C/C48A-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 Pd(Allyl)/Apo-E45C/C48A-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd176 b:34.1 occ:1.00 PD X:PLL176 0.0 34.1 1.0 NE2 X:HIS114 2.1 26.8 1.0 C19 X:PLL176 2.3 38.3 1.0 C21 X:PLL176 2.3 40.3 1.0 SG X:CYS126 2.4 33.8 1.0 C20 X:PLL176 2.5 39.1 1.0 O X:CYS126 2.9 35.6 1.0 CE1 X:HIS114 3.0 25.8 1.0 CD2 X:HIS114 3.1 24.5 1.0 CB X:CYS126 3.3 32.9 1.0 C X:CYS126 3.3 34.7 1.0 O X:HOH345 3.5 30.0 1.0 PD X:PLL177 3.6 54.0 1.0 CA X:CYS126 3.8 33.3 1.0 N X:ASP127 4.1 35.8 1.0 ND1 X:HIS114 4.2 26.0 1.0 CG X:HIS114 4.3 24.3 1.0 CB X:GLU130 4.6 40.5 1.0 CA X:ASP127 4.6 36.8 1.0

Palladium binding site 2 out of 4 in the Crystal Structure of Pd(Allyl)/Apo-E45C/C48A-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 Pd(Allyl)/Apo-E45C/C48A-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd177 b:54.0 occ:1.00 PD X:PLL177 0.0 54.0 1.0 O X:HOH345 2.1 30.0 1.0 C21 X:PLL177 2.3 64.1 1.0 C19 X:PLL177 2.3 64.5 1.0 C20 X:PLL177 2.3 63.5 1.0 SG X:CYS126 2.4 33.8 1.0 CB X:CYS126 3.2 32.9 1.0 PD X:PLL176 3.6 34.1 1.0 CE1 X:HIS114 3.9 25.8 1.0 NE2 X:HIS114 4.1 26.8 1.0 OG X:SER118 4.3 27.3 0.5 CA X:CYS126 4.7 33.3 1.0 C19 X:PLL176 4.9 38.3 1.0 ND1 X:HIS114 5.0 26.0 1.0

Palladium binding site 3 out of 4 in the Crystal Structure of Pd(Allyl)/Apo-E45C/C48A-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 Pd(Allyl)/Apo-E45C/C48A-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd178 b:32.9 occ:1.00 NE2 X:HIS49 1.9 22.8 1.0 SG X:CYS45 2.3 19.7 1.0 CE1 X:HIS49 2.9 24.1 1.0 CD2 X:HIS49 2.9 23.9 1.0 PD X:PD179 3.2 34.8 1.0 CB X:CYS45 3.3 16.1 1.0 NE2 X:HIS173 3.8 46.4 1.0 CA X:CYS45 3.8 15.9 1.0 ND1 X:HIS49 4.0 24.1 1.0 CG X:HIS49 4.0 20.4 1.0 O X:CYS45 4.1 16.5 1.0 C X:CYS45 4.2 16.1 1.0 CE1 X:HIS173 4.3 45.9 1.0 CD2 X:HIS173 4.4 46.3 1.0 O X:HOH253 4.6 22.4 1.0

Palladium binding site 4 out of 4 in the Crystal Structure of Pd(Allyl)/Apo-E45C/C48A-Rhlfr


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-E45C/C48A-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd179 b:34.8 occ:1.00 SG X:CYS45 2.4 19.7 1.0 CD2 X:HIS173 2.9 46.3 1.0 NE2 X:HIS173 3.0 46.4 1.0 PD X:PD178 3.2 32.9 1.0 CB X:CYS45 3.4 16.1 1.0 CG X:HIS173 4.2 44.4 1.0 NE2 X:HIS49 4.2 22.8 1.0 CE1 X:HIS173 4.2 45.9 1.0 O X:HOH322 4.4 41.7 1.0 CD2 X:HIS49 4.7 23.9 1.0 CA X:CYS45 4.8 15.9 1.0 ND1 X:HIS173 4.8 46.0 1.0 O2 X:EDO187 4.9 43.6 1.0 C1 X:EDO187 4.9 42.7 1.0

Z.Wang, Y.Takezawa, H.Aoyagi, S.Abe, T.Hikage, Y.Watanabe, S.Kitagawa, T.Ueno. Definite Coordination Arrangement of Organometallic Palladium Complexes Accumulated on the Designed Interior Surface of Apo-Ferritin. Chem.Commun.(Camb.) V. 47 170 2011.
ISSN: ISSN 1359-7345
PubMed: 20730233
DOI: 10.1039/C0CC02221G