Cadmium in PDB 3o7s: Crystal Structure of Ru(P-Cymene)/Apo-Fr

The structure of Crystal Structure of Ru(P-Cymene)/Apo-Fr, PDB code: 3o7s was solved by Y.Takezawa, P.Bockmann, N.Sugi, Z.Wang, S.Abe, T.Murakami, T.Hikage, G.Erker, 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)	37.04 / 1.73
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.443, 181.443, 181.443, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 21.7

The structure of Crystal Structure of Ru(P-Cymene)/Apo-Fr also contains other interesting chemical elements:

Ruthenium

(Ru)

3 atoms

The binding sites of Cadmium atom in the Crystal Structure of Ru(P-Cymene)/Apo-Fr (pdb code 3o7s). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Ru(P-Cymene)/Apo-Fr, PDB code: 3o7s:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Crystal Structure of Ru(P-Cymene)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Ru(P-Cymene)/Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd175 b:27.8 occ:0.50 OD2 A:ASP80 2.1 25.1 1.0 OD1 A:ASP80 2.4 12.5 1.0 CG A:ASP80 2.6 16.1 1.0 O A:HOH354 3.5 46.3 1.0 CB A:ASP80 4.1 16.8 1.0 O A:HOH238 4.5 22.3 1.0

Cadmium binding site 2 out of 3 in the Crystal Structure of Ru(P-Cymene)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Ru(P-Cymene)/Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd177 b:27.1 occ:0.50 RU A:RU180 2.3 52.5 0.3 OD1 A:ASP38 2.4 14.6 1.0 O A:HOH338 2.5 26.4 1.0 CG A:ASP38 3.3 13.1 1.0 CB A:ASP38 3.7 10.4 1.0 CA A:ASP38 3.8 10.3 1.0 O A:HOH337 4.1 40.5 1.0 SG A:CYS48 4.2 22.7 1.0 O A:HOH357 4.3 49.4 1.0 CB A:CYS48 4.4 14.8 1.0 O A:HOH243 4.4 23.0 1.0 CG A:GLU45 4.4 18.5 1.0 OD2 A:ASP38 4.5 13.4 1.0 CA A:GLU45 4.5 12.0 1.0 CB A:GLU45 4.6 13.8 1.0 O A:ASP38 4.6 11.1 1.0 CD A:GLU45 4.7 27.2 1.0 C A:ASP38 4.8 10.4 1.0 N A:ASP38 4.8 9.6 1.0 O A:PHE37 4.8 11.8 1.0 OE2 A:GLU45 4.9 33.2 1.0

Cadmium binding site 3 out of 3 in the Crystal Structure of Ru(P-Cymene)/Apo-Fr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Ru(P-Cymene)/Apo-Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd181 b:50.1 occ:0.20 OE2 A:GLU60 2.6 27.6 1.0 OE1 A:GLU60 2.7 27.0 1.0 CD A:GLU60 3.0 23.6 1.0 CD A:GLU56 3.3 15.0 0.5 OE1 A:GLU56 3.4 18.9 0.5 OE2 A:GLU56 3.6 18.9 0.5 CG A:GLU56 3.7 12.4 0.5 O A:HOH293 3.8 39.1 1.0 CG A:GLU60 4.5 17.3 1.0 CB A:GLU56 4.9 11.9 0.5

Y.Takezawa, P.Bockmann, N.Sugi, Z.Wang, S.Abe, T.Murakami, T.Hikage, G.Erker, Y.Watanabe, S.Kitagawa, T.Ueno. Incorporation of Organometallic Ru Complexes Into Apo-Ferritin Cage. J.Chem.Soc.,Dalton Trans. V. 40 2190 2011.
ISSN: ISSN 0300-9246
PubMed: 21113534
DOI: 10.1039/C0DT00955E