Ruthenium in PDB 5nbe: [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2

The structure of [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2, PDB code: 5nbe was solved by K.T.Mcquaid, J.P.Hall, C.J.Cardin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.89 / 1.51
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	47.880, 47.880, 29.140, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19

The structure of [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2 also contains other interesting chemical elements:

Barium

(Ba)

1 atom

The binding sites of Ruthenium atom in the [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2 (pdb code 5nbe). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2, PDB code: 5nbe:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in the [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru101 b:16.2 occ:0.66 RU A:QHL101 0.0 16.2 0.7 RU A:QHL101 0.0 19.4 0.3 N5 A:QHL101 1.8 20.4 0.3 N8 A:QHL101 1.8 20.6 0.3 N12 A:QHL101 1.8 21.1 0.3 N9 A:QHL101 1.8 21.1 0.3 N2 A:QHL101 1.9 20.9 0.3 N1 A:QHL101 1.9 21.1 0.3 N1 A:QHL101 1.9 17.9 0.7 N9 A:QHL101 1.9 16.0 0.7 N5 A:QHL101 1.9 17.1 0.7 N2 A:QHL101 1.9 18.2 0.7 N12 A:QHL101 1.9 15.8 0.7 N8 A:QHL101 1.9 17.4 0.7 C26 A:QHL101 2.7 20.2 0.3 C19 A:QHL101 2.7 20.3 0.3 C36 A:QHL101 2.7 21.2 0.3 C29 A:QHL101 2.7 21.4 0.3 C1 A:QHL101 2.7 20.6 0.3 C10 A:QHL101 2.7 20.4 0.3 C10 A:QHL101 2.8 17.9 0.7 C36 A:QHL101 2.8 15.0 0.7 C1 A:QHL101 2.8 17.6 0.7 C29 A:QHL101 2.8 15.1 0.7 C26 A:QHL101 2.8 17.2 0.7 C19 A:QHL101 2.8 17.8 0.7 C38 A:QHL101 2.9 20.9 0.3 C30 A:QHL101 2.9 21.0 0.3 C20 A:QHL101 2.9 20.6 0.3 C28 A:QHL101 2.9 21.0 0.3 C2 A:QHL101 2.9 20.9 0.3 C12 A:QHL101 2.9 20.9 0.3 C12 A:QHL101 2.9 18.5 0.7 C20 A:QHL101 3.0 16.8 0.7 C2 A:QHL101 3.0 18.1 0.7 C28 A:QHL101 3.0 16.6 0.7 C38 A:QHL101 3.0 15.7 0.7 C30 A:QHL101 3.0 15.4 0.7 C25 A:QHL101 4.0 21.0 0.3 C22 A:QHL101 4.0 20.6 0.3 C35 A:QHL101 4.0 21.5 0.3 C32 A:QHL101 4.1 21.4 0.3 C5 A:QHL101 4.1 20.8 0.3 C8 A:QHL101 4.1 20.7 0.3 C8 A:QHL101 4.1 18.3 0.7 C27 A:QHL101 4.1 21.2 0.3 C21 A:QHL101 4.1 20.6 0.3 C37 A:QHL101 4.1 21.5 0.3 C31 A:QHL101 4.1 21.1 0.3 C5 A:QHL101 4.2 18.2 0.7 C35 A:QHL101 4.2 15.5 0.7 C32 A:QHL101 4.2 15.1 0.7 C3 A:QHL101 4.2 20.9 0.3 C11 A:QHL101 4.2 21.1 0.3 C25 A:QHL101 4.2 17.8 0.7 C22 A:QHL101 4.2 17.6 0.7 C11 A:QHL101 4.2 18.5 0.7 C21 A:QHL101 4.2 17.2 0.7 C3 A:QHL101 4.3 18.4 0.7 C37 A:QHL101 4.3 15.2 0.7 C27 A:QHL101 4.3 17.4 0.7 C31 A:QHL101 4.3 15.2 0.7 O2 A:DC2 4.6 18.6 1.0 N7 A:QHL101 4.6 21.1 0.3 N6 A:QHL101 4.6 20.8 0.3 N11 A:QHL101 4.6 21.6 0.3 N10 A:QHL101 4.6 21.8 0.3 C4 A:QHL101 4.7 21.3 0.3 C9 A:QHL101 4.7 21.0 0.3 C9 A:QHL101 4.7 19.5 0.7 C4 A:QHL101 4.7 18.4 0.7 N11 A:QHL101 4.8 16.0 0.7 N6 A:QHL101 4.8 17.9 0.7 N10 A:QHL101 4.8 15.0 0.7 N7 A:QHL101 4.8 17.5 0.7 O4' A:DC2 4.9 22.2 1.0 O A:HOH259 4.9 26.4 1.0 C24 A:QHL101 5.0 20.4 0.3

Ruthenium binding site 2 out of 2 in the [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of [Ru(Tap)2(Dppz-11-Cn)]2+ Bound to D(Tcggcgccga)2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru101 b:19.4 occ:0.34 RU A:QHL101 0.0 19.4 0.3 RU A:QHL101 0.0 16.2 0.7 N5 A:QHL101 1.8 20.4 0.3 N9 A:QHL101 1.8 21.1 0.3 N8 A:QHL101 1.8 20.6 0.3 N1 A:QHL101 1.8 21.1 0.3 N12 A:QHL101 1.8 21.1 0.3 N2 A:QHL101 1.8 20.9 0.3 N2 A:QHL101 1.9 18.2 0.7 N1 A:QHL101 1.9 17.9 0.7 N5 A:QHL101 1.9 17.1 0.7 N9 A:QHL101 1.9 16.0 0.7 N12 A:QHL101 1.9 15.8 0.7 N8 A:QHL101 1.9 17.4 0.7 C26 A:QHL101 2.7 20.2 0.3 C19 A:QHL101 2.7 20.3 0.3 C1 A:QHL101 2.7 20.6 0.3 C10 A:QHL101 2.7 20.4 0.3 C29 A:QHL101 2.7 21.4 0.3 C36 A:QHL101 2.7 21.2 0.3 C10 A:QHL101 2.7 17.9 0.7 C1 A:QHL101 2.7 17.6 0.7 C36 A:QHL101 2.8 15.0 0.7 C29 A:QHL101 2.8 15.1 0.7 C19 A:QHL101 2.8 17.8 0.7 C26 A:QHL101 2.8 17.2 0.7 C30 A:QHL101 2.9 21.0 0.3 C20 A:QHL101 2.9 20.6 0.3 C12 A:QHL101 2.9 20.9 0.3 C2 A:QHL101 2.9 20.9 0.3 C28 A:QHL101 2.9 21.0 0.3 C38 A:QHL101 2.9 20.9 0.3 C20 A:QHL101 2.9 16.8 0.7 C2 A:QHL101 2.9 18.1 0.7 C12 A:QHL101 2.9 18.5 0.7 C38 A:QHL101 3.0 15.7 0.7 C30 A:QHL101 3.0 15.4 0.7 C28 A:QHL101 3.0 16.6 0.7 C25 A:QHL101 4.0 21.0 0.3 C22 A:QHL101 4.0 20.6 0.3 C32 A:QHL101 4.1 21.4 0.3 C35 A:QHL101 4.1 21.5 0.3 C8 A:QHL101 4.1 20.7 0.3 C5 A:QHL101 4.1 20.8 0.3 C8 A:QHL101 4.1 18.3 0.7 C5 A:QHL101 4.1 18.2 0.7 C31 A:QHL101 4.1 21.1 0.3 C21 A:QHL101 4.1 20.6 0.3 C27 A:QHL101 4.1 21.2 0.3 C11 A:QHL101 4.2 21.1 0.3 C3 A:QHL101 4.2 20.9 0.3 C37 A:QHL101 4.2 21.5 0.3 C35 A:QHL101 4.2 15.5 0.7 C32 A:QHL101 4.2 15.1 0.7 C22 A:QHL101 4.2 17.6 0.7 C25 A:QHL101 4.2 17.8 0.7 C3 A:QHL101 4.2 18.4 0.7 C11 A:QHL101 4.2 18.5 0.7 C21 A:QHL101 4.2 17.2 0.7 C37 A:QHL101 4.3 15.2 0.7 C31 A:QHL101 4.3 15.2 0.7 C27 A:QHL101 4.3 17.4 0.7 O2 A:DC2 4.6 18.6 1.0 N7 A:QHL101 4.6 21.1 0.3 N6 A:QHL101 4.6 20.8 0.3 N10 A:QHL101 4.6 21.8 0.3 C9 A:QHL101 4.6 21.0 0.3 N11 A:QHL101 4.6 21.6 0.3 C4 A:QHL101 4.6 21.3 0.3 C4 A:QHL101 4.7 18.4 0.7 C9 A:QHL101 4.7 19.5 0.7 N11 A:QHL101 4.8 16.0 0.7 N6 A:QHL101 4.8 17.9 0.7 N10 A:QHL101 4.8 15.0 0.7 N7 A:QHL101 4.8 17.5 0.7 O A:HOH259 4.9 26.4 1.0 O4' A:DC2 4.9 22.2 1.0

K.Mcquaid, J.P.Hall, J.A.Brazier, D.J.Cardin, C.J.Cardin. X-Ray Crystal Structures Show Dna Stacking Advantage of Terminal Nitrile Substitution in Ru-Dppz Complexes. Chemistry V. 24 15859 2018.
ISSN: ISSN 0947-6539
PubMed: 30063271
DOI: 10.1002/CHEM.201803021