Ruthenium in PDB 3wvu: Crystal Structure of Ruco/Apo-R52CFR

The structure of Crystal Structure of Ruco/Apo-R52CFR, PDB code: 3wvu was solved by K.Fujita, Y.Tanaka, S.Abe, T.Hikage, T.Kuchimaru, S.Kizaka-Kondoh, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.26 / 1.92
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.575, 181.575, 181.575, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.3

The structure of Crystal Structure of Ruco/Apo-R52CFR also contains other interesting chemical elements:

Cadmium

(Cd)

3 atoms

The binding sites of Ruthenium atom in the Crystal Structure of Ruco/Apo-R52CFR (pdb code 3wvu). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the Crystal Structure of Ruco/Apo-R52CFR, PDB code: 3wvu:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in the Crystal Structure of Ruco/Apo-R52CFR


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Crystal Structure of Ruco/Apo-R52CFR within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru213 b:46.7 occ:0.70 SG A:CYS52 2.2 25.9 1.0 SG A:CYS48 2.3 21.8 1.0 O A:CYS48 2.9 11.7 1.0 CB A:CYS52 3.2 15.5 1.0 O A:HOH403 3.2 37.9 1.0 C A:CYS48 3.3 12.6 1.0 CB A:CYS48 3.7 16.6 1.0 CA A:CYS48 3.8 13.4 1.0 RU A:RU214 4.0 44.5 0.7 O A:GLY34 4.1 14.7 1.0 N A:HIS49 4.1 13.1 1.0 C A:GLY34 4.2 13.5 1.0 CA A:GLY34 4.2 12.5 1.0 ND1 A:HIS49 4.2 26.7 0.5 CA A:CYS52 4.4 13.0 1.0 CA A:HIS49 4.4 14.9 0.5 CA A:HIS49 4.5 14.7 0.5 N A:CYS52 4.5 12.4 1.0 O A:HOH402 4.7 23.6 1.0 CE1 A:HIS49 4.9 27.2 0.5 N A:PHE35 4.9 13.2 1.0

Ruthenium binding site 2 out of 2 in the Crystal Structure of Ruco/Apo-R52CFR


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Crystal Structure of Ruco/Apo-R52CFR within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru214 b:44.5 occ:0.70 OE2 A:GLU45 2.5 52.5 1.0 SG A:CYS48 2.7 21.8 1.0 CD A:GLU45 3.2 40.2 1.0 CE1 A:HIS49 3.3 27.2 0.5 OE1 A:GLU45 3.4 57.4 1.0 ND1 A:HIS49 3.7 26.7 0.5 CB A:CYS48 3.7 16.6 1.0 OD1 A:ASP38 3.7 17.1 1.0 RU A:RU213 4.0 46.7 0.7 NE2 A:HIS49 4.2 27.1 0.5 CG A:ASP38 4.4 14.4 1.0 CG A:GLU45 4.6 26.1 1.0 CB A:ASP38 4.6 11.9 1.0 O A:GLU45 4.7 10.7 1.0 CG A:HIS49 4.8 22.4 0.5 CA A:GLU45 4.9 14.8 1.0 CD2 A:HIS49 5.0 26.9 0.5

K.Fujita, Y.Tanaka, T.Sho, S.Ozeki, S.Abe, T.Hikage, T.Kuchimaru, S.Kizaka-Kondoh, T.Ueno. Intracellular Co Release From Composite of Ferritin and Ruthenium Carbonyl Complexes. J.Am.Chem.Soc. V. 136 16902 2014.
ISSN: ISSN 0002-7863
PubMed: 25352251
DOI: 10.1021/JA508938F