Palladium in PDB 3af7: Crystal Structure of 25PD(Allyl)/Apo-Fr

The structure of Crystal Structure of 25PD(Allyl)/Apo-Fr, PDB code: 3af7 was solved by S.Abe, T.Hikage, Y.Watanabe, S.Kitagawa, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.17 / 1.58
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.520, 181.520, 181.520, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 21.2

The structure of Crystal Structure of 25PD(Allyl)/Apo-Fr also contains other interesting chemical elements:

Cadmium

(Cd)

1 atom

The binding sites of Palladium atom in the Crystal Structure of 25PD(Allyl)/Apo-Fr (pdb code 3af7). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 5 binding sites of Palladium where determined in the Crystal Structure of 25PD(Allyl)/Apo-Fr, PDB code: 3af7:
Jump to Palladium binding site number: 1; 2; 3; 4; 5;

Palladium binding site 1 out of 5 in the Crystal Structure of 25PD(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 25PD(Allyl)/Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd177 b:27.1 occ:0.20 O X:HOH333 2.2 26.7 1.0 PD X:PLL179 2.4 26.1 0.5 OD1 X:ASP38 3.0 12.1 1.0 CG X:GLU45 3.7 16.2 1.0 CA X:GLU45 3.7 11.2 1.0 SG X:CYS48 3.8 12.9 1.0 CB X:CYS48 3.8 10.6 1.0 CB X:GLU45 3.8 12.0 1.0 CG X:ASP38 3.9 10.0 1.0 CB X:ASP38 4.0 8.4 1.0 O X:HOH352 4.1 27.1 1.0 CA X:ASP38 4.1 8.3 1.0 C20 X:PLL179 4.2 32.2 0.5 C21 X:PLL179 4.2 32.5 0.5 O X:HOH326 4.3 23.6 1.0 N X:GLU45 4.5 9.5 1.0 CE1 X:HIS49 4.5 14.6 0.5 O X:GLU45 4.6 9.3 1.0 C19 X:PLL179 4.7 32.6 0.5 C X:GLU45 4.7 9.5 1.0 O X:PHE37 4.7 8.6 1.0 CD X:GLU45 4.7 17.1 1.0 ND1 X:HIS49 4.9 14.8 0.5 N X:ASP38 4.9 7.8 1.0 PD X:PD178 4.9 30.0 0.3 OD2 X:ASP38 5.0 11.1 1.0

Palladium binding site 2 out of 5 in the Crystal Structure of 25PD(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 25PD(Allyl)/Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd178 b:30.0 occ:0.30 ND1 X:HIS49 1.9 14.8 0.5 CE1 X:HIS49 2.4 14.6 0.5 C19 X:PLL179 3.0 32.6 0.5 CG X:HIS49 3.0 12.4 0.5 SG X:CYS48 3.2 12.9 1.0 PD X:PLL179 3.2 26.1 0.5 CA X:HIS49 3.4 9.9 0.5 CA X:HIS49 3.4 9.8 0.5 N X:HIS49 3.5 9.5 1.0 NE2 X:HIS49 3.6 14.8 0.5 CD X:ARG52 3.7 18.5 1.0 CB X:HIS49 3.7 10.8 0.5 CB X:HIS49 3.8 10.6 0.5 C X:CYS48 3.8 9.4 1.0 CD2 X:HIS49 3.9 14.6 0.5 C21 X:PLL179 4.0 32.5 0.5 O X:CYS48 4.0 9.4 1.0 ND1 X:HIS49 4.1 15.9 0.5 CB X:CYS48 4.1 10.6 1.0 O X:HOH352 4.1 27.1 1.0 CG X:ARG52 4.3 14.0 1.0 CG X:HIS49 4.4 13.2 0.5 CB X:ARG52 4.5 11.4 1.0 NH1 X:ARG52 4.5 28.2 1.0 CA X:CYS48 4.6 10.2 1.0 O X:GLU45 4.7 9.3 1.0 C X:HIS49 4.7 9.6 1.0 NE X:ARG52 4.7 23.7 1.0 PD X:PD177 4.9 27.1 0.2 C20 X:PLL179 4.9 32.2 0.5

Palladium binding site 3 out of 5 in the Crystal Structure of 25PD(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 25PD(Allyl)/Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd179 b:26.1 occ:0.50 PD X:PLL179 0.0 26.1 0.5 C21 X:PLL179 2.3 32.5 0.5 C19 X:PLL179 2.4 32.6 0.5 PD X:PD177 2.4 27.1 0.2 SG X:CYS48 2.4 12.9 1.0 C20 X:PLL179 2.5 32.2 0.5 PD X:PD178 3.2 30.0 0.3 OD1 X:ASP38 3.3 12.1 1.0 CB X:CYS48 3.6 10.6 1.0 CG X:ASP38 3.7 10.0 1.0 CB X:ASP38 3.8 8.4 1.0 O X:HOH352 3.8 27.1 1.0 CE1 X:HIS49 3.9 14.6 0.5 ND1 X:HIS49 4.1 14.8 0.5 O X:HOH333 4.3 26.7 1.0 OD2 X:ASP38 4.5 11.1 1.0 CA X:ASP38 4.7 8.3 1.0 CD X:ARG52 4.9 18.5 1.0 CA X:CYS48 4.9 10.2 1.0 CG X:GLU45 5.0 16.2 1.0

Palladium binding site 4 out of 5 in the Crystal Structure of 25PD(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 25PD(Allyl)/Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd180 b:23.2 occ:0.80 PD X:PLL180 0.0 23.2 0.8 NE2 X:HIS114 2.2 19.6 1.0 SG X:CYS126 2.3 21.1 0.8 C21 X:PLL180 2.3 20.0 0.8 C20 X:PLL180 2.3 19.2 0.8 C19 X:PLL180 2.4 18.4 0.8 CD2 X:HIS114 3.2 18.2 1.0 CE1 X:HIS114 3.2 19.6 1.0 O X:CYS126 3.2 23.8 1.0 CB X:CYS126 3.3 22.6 0.2 CB X:CYS126 3.4 22.3 0.8 C X:CYS126 3.5 23.1 1.0 CA X:CYS126 3.7 22.4 0.8 CA X:CYS126 3.7 22.7 0.2 PD X:PLL181 3.8 28.4 0.8 O X:HOH304 3.8 6.3 0.3 SG X:CYS126 4.2 23.4 0.2 ND1 X:HIS114 4.3 18.9 1.0 CG X:HIS114 4.3 17.4 1.0 N X:ASP127 4.4 23.8 1.0 C21 X:PLL181 4.9 37.4 0.8 C19 X:PLL181 5.0 37.4 0.8

Palladium binding site 5 out of 5 in the Crystal Structure of 25PD(Allyl)/Apo-Fr


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 25PD(Allyl)/Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ X:Pd181 b:28.4 occ:0.80 PD X:PLL181 0.0 28.4 0.8 O X:HOH304 2.3 6.3 0.3 C21 X:PLL181 2.3 37.4 0.8 C19 X:PLL181 2.3 37.4 0.8 C20 X:PLL181 2.3 37.7 0.8 SG X:CYS126 2.4 21.1 0.8 CB X:CYS126 3.4 22.3 0.8 CB X:CYS126 3.5 22.6 0.2 SG X:CYS126 3.7 23.4 0.2 PD X:PLL180 3.8 23.2 0.8 CE1 X:HIS114 4.3 19.6 1.0 NE2 X:HIS114 4.3 19.6 1.0 OG X:SER118 4.8 21.7 1.0 CA X:CYS126 4.9 22.4 0.8 CA X:CYS126 4.9 22.7 0.2 C19 X:PLL180 5.0 18.4 0.8

S.Abe, T.Hikage, Y.Watanabe, S.Kitagawa, T.Ueno. Mechanism of Accumulation and Incorporation of Organometallic Pd Complexes Into the Protein Nanocage of Apo-Ferritin. Inorg.Chem. V. 49 6967 2010.
ISSN: ISSN 0020-1669
PubMed: 20586408
DOI: 10.1021/IC1003758