Ruthenium in PDB 3wvw: Crystal Structure of Ruco/Apo-Wtfr

The structure of Crystal Structure of Ruco/Apo-Wtfr, PDB code: 3wvw 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)	21.43 / 2.00
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.863, 181.863, 181.863, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.9

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

Cadmium

(Cd)

3 atoms

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

Ruthenium binding site 1 out of 3 in the Crystal Structure of Ruco/Apo-Wtfr


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-Wtfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru213 b:46.1 occ:0.40 NE2 A:HIS114 2.5 20.2 1.0 OE2 A:GLU130 2.5 21.1 1.0 CE1 A:HIS114 2.6 17.0 1.0 O2 A:EDO210 3.2 44.4 1.0 CB A:CYS126 3.4 21.3 1.0 CD A:GLU130 3.8 24.1 1.0 CD2 A:HIS114 3.8 16.4 1.0 ND1 A:HIS114 3.9 19.9 1.0 SG A:CYS126 4.0 23.2 1.0 CD A:CD201 4.3 48.1 0.1 OE1 A:GLU130 4.5 36.1 1.0 CG A:HIS114 4.5 17.3 1.0 C2 A:EDO210 4.5 42.2 1.0 CA A:CYS126 4.5 17.6 1.0 CG A:GLU130 4.7 21.8 1.0 C A:CYS126 4.8 18.6 1.0 C1 A:EDO210 4.8 38.9 1.0 O A:CYS126 4.9 19.1 1.0

Ruthenium binding site 2 out of 3 in the Crystal Structure of Ruco/Apo-Wtfr


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-Wtfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru214 b:50.5 occ:0.30 NE2 A:HIS132 2.4 37.2 1.0 CE1 A:HIS132 3.0 36.1 1.0 O A:HOH415 3.4 48.9 1.0 CD2 A:HIS132 3.6 34.5 1.0 ND1 A:HIS132 4.2 37.8 1.0 NH2 A:ARG64 4.4 46.0 1.0 CG A:HIS132 4.5 32.9 1.0 OG A:SER131 4.8 39.2 1.0

Ruthenium binding site 3 out of 3 in the Crystal Structure of Ruco/Apo-Wtfr


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Crystal Structure of Ruco/Apo-Wtfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru215 b:45.8 occ:0.70 RU A:RU1215 0.0 45.8 0.7 C1 A:RU1215 2.0 42.9 0.7 C2 A:RU1215 2.0 33.2 0.7 OE1 A:GLU45 2.3 48.1 1.0 SG A:CYS48 2.7 17.2 1.0 O A:HOH367 2.7 32.5 1.0 O2 A:RU1215 3.2 34.0 0.7 O1 A:RU1215 3.2 47.1 0.7 CD A:GLU45 3.3 38.7 1.0 CB A:CYS48 3.6 14.1 1.0 OE2 A:GLU45 3.6 38.3 1.0 OD1 A:ASP38 3.9 18.0 1.0 CG A:ASP38 4.4 15.7 1.0 CG A:GLU45 4.6 26.3 1.0 CB A:ASP38 4.6 14.2 1.0 O A:GLU45 4.7 12.5 1.0 CA A:CYS48 4.8 13.3 1.0 N A:HIS49 4.8 13.2 1.0 C A:CYS48 4.9 13.4 1.0 CA A:GLU45 4.9 15.5 1.0 CD A:ARG52 5.0 35.4 1.0 NH1 A:ARG52 5.0 52.0 1.0

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