Cadmium in PDB 3o7r: Crystal Structure of Ru(P-Cymene)/Apo-H49AFR

The structure of Crystal Structure of Ru(P-Cymene)/Apo-H49AFR, PDB code: 3o7r 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)	24.28 / 1.90
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.703, 181.703, 181.703, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.7

The structure of Crystal Structure of Ru(P-Cymene)/Apo-H49AFR also contains other interesting chemical elements:

Ruthenium

(Ru)

2 atoms

The binding sites of Cadmium atom in the Crystal Structure of Ru(P-Cymene)/Apo-H49AFR (pdb code 3o7r). 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-H49AFR, PDB code: 3o7r:
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-H49AFR


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-H49AFR within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd175 b:23.2 occ:0.50 OD2 A:ASP80 1.6 3.3 1.0 O A:HOH225 2.4 20.7 1.0 OD1 A:ASP80 2.4 14.7 1.0 CG A:ASP80 2.4 15.6 1.0 CB A:ASP80 4.0 14.7 1.0 O A:HOH210 4.4 17.5 1.0

Cadmium binding site 2 out of 3 in the Crystal Structure of Ru(P-Cymene)/Apo-H49AFR


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-H49AFR within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd176 b:41.2 occ:0.30 OE1 A:GLU60 2.4 29.2 1.0 CD A:GLU60 3.1 26.1 1.0 OE2 A:GLU60 3.1 33.2 1.0 O A:HOH285 3.6 48.8 1.0 OE2 A:GLU56 4.0 32.8 1.0 CD A:GLU56 4.2 23.1 1.0 CG A:GLU56 4.3 20.2 1.0 CG A:GLU60 4.6 19.9 1.0 CG A:GLU57 4.6 17.4 1.0 OE2 A:GLU53 4.7 33.5 1.0 OE1 A:GLU56 4.9 33.3 1.0

Cadmium binding site 3 out of 3 in the Crystal Structure of Ru(P-Cymene)/Apo-H49AFR


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-H49AFR within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd177 b:42.2 occ:0.70 O A:HOH367 2.2 41.9 1.0 OE1 A:GLU45 2.2 37.6 1.0 O A:HOH346 2.2 38.2 1.0 OD1 A:ASP38 2.5 15.8 1.0 CG A:ASP38 3.4 15.5 1.0 CD A:GLU45 3.5 34.4 1.0 CB A:ASP38 3.7 12.0 1.0 CA A:ASP38 3.8 12.5 1.0 OE2 A:GLU45 4.2 38.5 1.0 SG A:CYS48 4.2 22.3 1.0 CB A:CYS48 4.2 14.5 1.0 CA A:GLU45 4.3 14.5 1.0 O A:HOH222 4.4 20.6 1.0 CB A:GLU45 4.5 15.0 1.0 CG A:GLU45 4.5 22.8 1.0 OD2 A:ASP38 4.6 17.5 1.0 N A:ASP38 4.7 11.9 1.0 O A:PHE37 4.7 13.8 1.0 O A:ASP38 4.8 13.1 1.0 C A:ASP38 4.8 12.7 1.0

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