Ruthenium 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:

Cadmium

(Cd)

3 atoms

The binding sites of Ruthenium 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 Ruthenium atom.
In total 3 binding sites of Ruthenium where determined in the Crystal Structure of Ru(P-Cymene)/Apo-Fr, PDB code: 3o7s:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium 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 Ruthenium with other atoms in the Ru 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:Ru176 b:34.2 occ:1.00 NE2 A:HIS49 2.1 19.1 1.0 NE2 A:HIS173 2.2 31.6 1.0 OE2 A:GLU53 2.2 26.6 1.0 C9 A:MML179 2.5 42.1 1.0 C10 A:MML179 2.5 42.0 1.0 C2 A:MML179 2.6 42.8 1.0 C5 A:MML179 2.6 42.9 1.0 C4 A:MML179 2.6 42.5 1.0 C3 A:MML179 2.6 42.5 1.0 CD2 A:HIS173 2.9 31.6 1.0 CD2 A:HIS49 3.0 20.5 1.0 CE1 A:HIS49 3.1 21.0 1.0 CD A:GLU53 3.3 19.7 1.0 CE1 A:HIS173 3.4 32.7 1.0 C8 A:MML179 3.5 43.8 1.0 C6 A:MML179 3.6 43.5 1.0 C1 A:MML179 3.6 43.4 1.0 CG A:GLU53 3.8 18.1 1.0 ND1 A:HIS49 4.2 21.1 1.0 CG A:HIS49 4.2 14.6 1.0 CG A:HIS173 4.2 30.2 1.0 ND1 A:HIS173 4.4 31.8 1.0 OE1 A:GLU53 4.4 24.6 1.0 C7 A:MML179 4.8 44.2 1.0

Ruthenium 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 Ruthenium with other atoms in the Ru 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:Ru178 b:52.5 occ:0.40 NE2 A:HIS114 2.1 45.1 1.0 SG A:CYS126 2.1 53.3 1.0 CD2 A:HIS114 3.0 44.4 1.0 CE1 A:HIS114 3.1 46.0 1.0 O A:HOH331 3.3 32.6 1.0 CB A:CYS126 3.8 52.8 1.0 CG A:HIS114 4.2 43.9 1.0 O A:CYS126 4.2 53.1 1.0 ND1 A:HIS114 4.2 45.5 1.0 CA A:CYS126 4.5 52.6 1.0 C A:CYS126 4.6 52.8 1.0 OG A:SER118 4.8 52.2 1.0

Ruthenium 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 Ruthenium with other atoms in the Ru 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:Ru180 b:52.5 occ:0.30 CD A:CD177 2.3 27.1 0.5 O A:HOH337 2.8 40.5 1.0 SG A:CYS48 3.0 22.7 1.0 OD1 A:ASP38 3.6 14.6 1.0 O A:HOH317 3.9 40.1 1.0 O A:HOH357 3.9 49.4 1.0 CB A:CYS48 4.0 14.8 1.0 CG A:ASP38 4.2 13.1 1.0 O A:HOH271 4.3 45.6 1.0 O A:HOH338 4.4 26.4 1.0 CG A:GLU45 4.4 18.5 1.0 CB A:ASP38 4.5 10.4 1.0 OE2 A:GLU45 4.5 33.2 1.0 CD A:GLU45 4.8 27.2 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