Palladium in PDB 3np0: Crystal Structure of Pd(Allyl)/Apo-E45C/H49A/R52H-Rhlfr

The structure of Crystal Structure of Pd(Allyl)/Apo-E45C/H49A/R52H-Rhlfr, PDB code: 3np0 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)	19.29 / 1.48
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.959, 180.959, 180.959, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 21

The structure of Crystal Structure of Pd(Allyl)/Apo-E45C/H49A/R52H-Rhlfr also contains other interesting chemical elements:

Cadmium

(Cd)

1 atom

The binding sites of Palladium atom in the Crystal Structure of Pd(Allyl)/Apo-E45C/H49A/R52H-Rhlfr (pdb code 3np0). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 6 binding sites of Palladium where determined in the Crystal Structure of Pd(Allyl)/Apo-E45C/H49A/R52H-Rhlfr, PDB code: 3np0:
Jump to Palladium binding site number: 1; 2; 3; 4; 5; 6;

Palladium binding site 1 out of 6 in the Crystal Structure of Pd(Allyl)/Apo-E45C/H49A/R52H-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/H49A/R52H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd180 b:27.8 occ:1.00 PD X:PLL180 0.0 27.8 1.0 NE2 X:HIS114 2.2 23.3 1.0 SG X:CYS126 2.2 28.2 1.0 C20 X:PLL180 2.3 45.1 1.0 C21 X:PLL180 2.3 45.4 1.0 C19 X:PLL180 2.4 44.6 1.0 O X:CYS126 3.1 26.9 1.0 CD2 X:HIS114 3.1 21.6 1.0 CE1 X:HIS114 3.2 22.8 1.0 CB X:CYS126 3.3 25.5 1.0 C X:CYS126 3.5 26.1 1.0 CA X:CYS126 3.7 25.6 1.0 PD X:PLL181 3.7 45.5 1.0 O X:HOH353 3.8 13.1 0.3 ND1 X:HIS114 4.3 22.4 1.0 CG X:HIS114 4.3 20.5 1.0 N X:ASP127 4.5 27.0 1.0 C21 X:PLL181 4.7 67.7 1.0 C19 X:PLL181 4.9 67.5 1.0

Palladium binding site 2 out of 6 in the Crystal Structure of Pd(Allyl)/Apo-E45C/H49A/R52H-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/H49A/R52H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd181 b:45.5 occ:1.00 PD X:PLL181 0.0 45.5 1.0 C19 X:PLL181 2.3 67.5 1.0 C21 X:PLL181 2.3 67.7 1.0 C20 X:PLL181 2.3 67.6 1.0 O X:HOH353 2.3 13.1 0.3 SG X:CYS126 2.4 28.2 1.0 CB X:CYS126 3.4 25.5 1.0 PD X:PLL180 3.7 27.8 1.0 CE1 X:HIS114 4.3 22.8 1.0 NE2 X:HIS114 4.3 23.3 1.0 OG X:SER118 4.8 25.3 1.0 C19 X:PLL180 4.9 44.6 1.0 CA X:CYS126 4.9 25.6 1.0

Palladium binding site 3 out of 6 in the Crystal Structure of Pd(Allyl)/Apo-E45C/H49A/R52H-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/H49A/R52H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd182 b:14.0 occ:1.00 PD X:PLL182 0.0 14.0 1.0 C21 X:PLL182 2.3 16.9 1.0 C19 X:PLL182 2.3 16.8 1.0 C20 X:PLL182 2.3 13.0 1.0 O X:HOH337 2.4 9.4 1.0 SG X:CYS48 2.4 11.8 1.0 PD X:PLL183 3.2 12.6 1.0 CB X:CYS48 3.5 9.3 1.0 C19 X:PLL183 3.5 13.2 1.0 CB X:ASP38 3.6 9.6 1.0 CG X:ASP38 3.7 10.6 1.0 OD1 X:ASP38 3.7 12.2 1.0 C21 X:PLL183 3.9 17.4 1.0 O X:HOH202 4.0 29.8 1.0 OD2 X:ASP38 4.2 13.0 1.0 O X:HOH356 4.3 27.1 1.0 ND1 X:HIS52 4.6 11.7 1.0 C20 X:PLL183 4.7 17.9 1.0 CE1 X:HIS52 4.8 11.8 1.0 CA X:ASP38 4.8 9.3 1.0 CA X:CYS48 4.9 9.5 1.0

Palladium binding site 4 out of 6 in the Crystal Structure of Pd(Allyl)/Apo-E45C/H49A/R52H-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/H49A/R52H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd183 b:12.6 occ:1.00 PD X:PLL183 0.0 12.6 1.0 ND1 X:HIS52 2.2 11.7 1.0 C21 X:PLL183 2.3 17.4 1.0 C19 X:PLL183 2.3 13.2 1.0 C20 X:PLL183 2.3 17.9 1.0 SG X:CYS48 2.4 11.8 1.0 CE1 X:HIS52 3.2 11.8 1.0 CG X:HIS52 3.2 10.7 1.0 PD X:PLL182 3.2 14.0 1.0 O X:CYS48 3.3 9.6 1.0 C X:CYS48 3.5 9.0 1.0 CB X:HIS52 3.5 9.4 1.0 CB X:CYS48 3.6 9.3 1.0 C20 X:PLL182 3.6 13.0 1.0 N X:ALA49 3.9 8.8 1.0 CA X:CYS48 4.1 9.5 1.0 CA X:ALA49 4.1 8.9 1.0 NE2 X:HIS52 4.3 11.6 1.0 C21 X:PLL182 4.3 16.9 1.0 CD2 X:HIS52 4.3 12.6 1.0 O1 X:EDO188 4.5 35.3 1.0 O X:HOH337 4.6 9.4 1.0 CA X:HIS52 4.9 9.3 1.0 C19 X:PLL182 4.9 16.8 1.0 C2 X:EDO188 5.0 34.6 1.0

Palladium binding site 5 out of 6 in the Crystal Structure of Pd(Allyl)/Apo-E45C/H49A/R52H-Rhlfr


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 5 of Crystal Structure of Pd(Allyl)/Apo-E45C/H49A/R52H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd184 b:21.8 occ:1.00 PD X:PLL184 0.0 21.8 1.0 C21 X:PLL184 2.3 0.7 1.0 C20 X:PLL184 2.3 0.3 1.0 C19 X:PLL184 2.3 0.5 1.0 SG X:CYS45 2.3 16.4 1.0 O X:HOH216 2.3 13.7 1.0 O X:HOH291 3.4 25.9 1.0 PD X:PLL185 3.4 19.5 1.0 CB X:CYS45 3.5 11.5 1.0 C20 X:PLL185 3.9 63.5 1.0 NH2 X:ARG168 4.3 13.3 1.0 C21 X:PLL185 4.5 63.8 1.0 O X:HOH231 4.5 12.6 1.0 ND1 X:HIS173 4.5 22.3 1.0 C1 X:EDO187 4.6 30.7 1.0 C2 X:EDO187 4.6 31.6 1.0 CA X:CYS45 4.9 11.0 1.0

Palladium binding site 6 out of 6 in the Crystal Structure of Pd(Allyl)/Apo-E45C/H49A/R52H-Rhlfr


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 6 of Crystal Structure of Pd(Allyl)/Apo-E45C/H49A/R52H-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd185 b:19.5 occ:1.00 PD X:PLL185 0.0 19.5 1.0 C21 X:PLL185 2.3 63.8 1.0 C20 X:PLL185 2.3 63.5 1.0 ND1 X:HIS173 2.3 22.3 1.0 C19 X:PLL185 2.3 63.7 1.0 SG X:CYS45 2.4 16.4 1.0 CE1 X:HIS173 3.2 22.2 1.0 CG X:HIS173 3.3 24.2 1.0 PD X:PLL184 3.4 21.8 1.0 CB X:CYS45 3.5 11.5 1.0 C X:CYS45 3.6 9.8 1.0 CB X:HIS173 3.7 25.2 1.0 O X:CYS45 3.7 10.4 1.0 N X:GLY46 3.8 9.7 1.0 O X:HOH216 3.9 13.7 1.0 CA X:GLY46 4.1 9.5 1.0 CA X:CYS45 4.2 11.0 1.0 CA X:HIS173 4.2 25.5 1.0 NE2 X:HIS173 4.3 22.2 1.0 CD2 X:HIS173 4.4 23.7 1.0 C19 X:PLL184 4.8 0.5 1.0 O X:LYS172 4.9 23.5 1.0 OE2 X:GLU167 4.9 10.4 1.0 NH2 X:ARG168 4.9 13.3 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