Palladium in PDB 2z5p: Apo-Fr with Low Content of Pd Ions

The structure of Apo-Fr with Low Content of Pd Ions, PDB code: 2z5p was solved by T.Ueno, K.Hirata, M.Abe, M.Suzuki, S.Abe, N.Shimizu, M.Yamamoto, M.Takata, Y.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.79 / 1.65
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.790, 180.790, 180.790, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 18.8

The structure of Apo-Fr with Low Content of Pd Ions also contains other interesting chemical elements:

Cadmium

(Cd)

2 atoms

The binding sites of Palladium atom in the Apo-Fr with Low Content of Pd Ions (pdb code 2z5p). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 6 binding sites of Palladium where determined in the Apo-Fr with Low Content of Pd Ions, PDB code: 2z5p:
Jump to Palladium binding site number: 1; 2; 3; 4; 5; 6;

Palladium binding site 1 out of 6 in the Apo-Fr with Low Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 1 of Apo-Fr with Low Content of Pd Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd201 b:28.3 occ:0.30 CD A:GLU130 1.9 25.0 0.3 OE1 A:GLU130 2.2 25.2 0.3 CG A:GLU130 2.3 25.2 0.3 OE2 A:GLU130 2.4 24.4 0.3 SG A:CYS126 2.5 28.1 0.5 NE2 A:HIS114 2.6 26.0 0.9 O A:CYS126 3.1 27.2 0.6 PD A:PD204 3.2 0.9 0.2 CD2 A:HIS114 3.2 25.6 0.9 PD A:PD202 3.2 46.1 0.3 C A:CYS126 3.6 27.2 0.6 CB A:CYS126 3.7 27.6 0.5 CE1 A:HIS114 3.7 25.7 0.7 CB A:CYS126 3.7 27.3 0.5 CB A:GLU130 3.8 25.1 0.3 CA A:CYS126 4.0 27.2 0.5 CA A:CYS126 4.0 27.4 0.5 CG A:HIS114 4.4 24.0 0.9 N A:ASP127 4.5 27.1 1.0 ND1 A:HIS114 4.6 25.5 0.8 CA A:GLU130 4.7 25.1 0.6 N A:GLU130 4.8 24.5 0.6 SG A:CYS126 4.8 29.9 0.5 CD1 A:LEU134 5.0 23.1 1.0

Palladium binding site 2 out of 6 in the Apo-Fr with Low Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 2 of Apo-Fr with Low Content of Pd Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd202 b:46.1 occ:0.30 SG A:CYS126 2.6 28.1 0.5 PD A:PD201 3.2 28.3 0.3 CG A:GLU130 3.2 25.2 0.3 OE2 A:GLU130 3.4 24.4 0.3 CA A:ASP127 3.4 26.7 1.0 N A:ASP127 3.4 27.1 1.0 C A:CYS126 3.6 27.2 0.6 CD A:GLU130 3.7 25.0 0.3 O A:CYS126 3.7 27.2 0.6 CB A:ASP127 3.9 26.7 0.3 CB A:CYS126 4.0 27.3 0.5 CB A:GLU130 4.2 25.1 0.3 CB A:CYS126 4.2 27.6 0.5 OD1 A:ASP127 4.2 27.5 0.3 CA A:CYS126 4.5 27.2 0.5 CA A:CYS126 4.5 27.4 0.5 PD A:PD204 4.6 0.9 0.2 CG A:ASP127 4.6 27.0 0.3 C A:ASP127 4.7 26.2 1.0 OE1 A:GLU130 4.7 25.2 0.3 O A:PRO123 5.0 24.0 0.9 O A:ASP127 5.0 26.2 0.6

Palladium binding site 3 out of 6 in the Apo-Fr with Low Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 3 of Apo-Fr with Low Content of Pd Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd203 b:65.4 occ:0.30 OE1 A:GLU45 2.2 16.4 0.5 PD A:PD206 2.5 0.5 0.2 SG A:CYS48 2.5 13.5 1.0 O A:HOH1194 2.6 37.9 1.0 OD1 A:ASP38 3.2 13.0 1.0 CD A:GLU45 3.5 17.2 0.5 CB A:CYS48 3.5 11.3 1.0 CG A:ASP38 3.6 11.4 1.0 CB A:ASP38 3.6 9.3 1.0 OE2 A:GLU45 4.2 17.9 0.5 OD2 A:ASP38 4.5 11.5 1.0 CG A:GLU45 4.5 14.7 0.5 CA A:ASP38 4.5 9.1 1.0 O A:HOH1223 4.6 56.6 1.0 CG A:GLU45 4.7 14.7 0.5 CB A:GLU45 4.8 13.0 0.5 CA A:CYS48 4.9 11.2 1.0 CD A:ARG52 4.9 20.1 1.0 O A:GLU45 5.0 12.3 1.0

Palladium binding site 4 out of 6 in the Apo-Fr with Low Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 4 of Apo-Fr with Low Content of Pd Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd204 b:0.9 occ:0.20 O A:HOH1218 2.4 58.0 1.0 SG A:CYS126 2.5 28.1 0.5 NE2 A:HIS114 2.5 26.0 0.9 CE1 A:HIS114 2.6 25.7 0.7 PD A:PD201 3.2 28.3 0.3 CB A:CYS126 3.2 27.6 0.5 CB A:CYS126 3.2 27.3 0.5 SG A:CYS126 3.3 29.9 0.5 CD2 A:HIS114 3.8 25.6 0.9 ND1 A:HIS114 3.8 25.5 0.8 CA A:CYS126 4.4 27.2 0.5 CG A:HIS114 4.4 24.0 0.9 CA A:CYS126 4.4 27.4 0.5 PD A:PD202 4.6 46.1 0.3 CB A:SER118 4.9 27.0 1.0 OG A:SER118 4.9 27.4 0.6 CD A:GLU130 5.0 25.0 0.3

Palladium binding site 5 out of 6 in the Apo-Fr with Low Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 5 of Apo-Fr with Low Content of Pd Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd205 b:0.9 occ:0.20 NE2 A:HIS49 2.0 13.7 0.5 CD2 A:HIS49 2.9 13.4 0.5 CE1 A:HIS49 3.1 13.8 0.5 O A:HOH1224 3.4 45.8 1.0 CG A:GLU53 3.5 14.5 0.5 CD A:GLU53 3.9 18.9 0.5 OE1 A:GLU53 4.0 22.1 0.5 CG A:HIS49 4.1 11.4 0.5 ND1 A:HIS49 4.2 14.5 0.5 CG A:GLU53 4.3 16.0 0.5 OE2 A:GLU53 4.7 21.0 0.5 CB A:GLU53 4.8 13.1 0.5 CB A:GLU53 4.8 12.8 0.5

Palladium binding site 6 out of 6 in the Apo-Fr with Low Content of Pd Ions


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 6 of Apo-Fr with Low Content of Pd Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd206 b:0.5 occ:0.20 SG A:CYS48 2.4 13.5 1.0 PD A:PD203 2.5 65.4 0.3 O A:HOH1223 3.2 56.6 1.0 N A:HIS49 3.3 10.8 1.0 CB A:CYS48 3.3 11.3 1.0 C A:CYS48 3.5 11.1 1.0 CA A:HIS49 3.6 10.5 1.0 CD A:ARG52 3.8 20.1 1.0 O A:HOH1194 3.9 37.9 1.0 CB A:HIS49 4.0 10.9 1.0 O A:CYS48 4.0 11.3 1.0 CA A:CYS48 4.1 11.2 1.0 OE1 A:GLU45 4.1 16.4 0.5 O A:GLU45 4.1 12.3 1.0 CG A:ARG52 4.4 15.4 1.0 NH2 A:ARG52 4.6 26.2 0.7 CG A:GLU45 4.8 14.7 0.5 ND1 A:HIS49 4.9 14.5 0.5 CB A:ARG52 4.9 12.6 1.0 CG A:HIS49 4.9 11.4 0.5 NE A:ARG52 5.0 22.5 0.8

T.Ueno, M.Abe, K.Hirata, S.Abe, M.Suzuki, N.Shimizu, M.Yamamoto, M.Takata, Y.Watanabe. Process of Accumulation of Metal Ions on the Interior Surface of Apo-Ferritin: Crystal Structures of A Series of Apo-Ferritins Containing Variable Quantities of Pd(II) Ions. J.Am.Chem.Soc. V. 131 5094 2009.
ISSN: ISSN 0002-7863
PubMed: 19317403
DOI: 10.1021/JA806688S