Ruthenium in PDB 6gld: Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2

The structure of Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2, PDB code: 6gld 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)	29.80 / 1.06
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	42.136, 42.136, 39.092, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 15.8

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

Bromine	(Br)	2 atoms
Barium	(Ba)	1 atom

The binding sites of Ruthenium atom in the Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2 (pdb code 6gld). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2, PDB code: 6gld:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in the Intercalation of [Ru(Tap)2(11-Br-Dppz)]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 Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ru102 b:9.1 occ:0.34 RU1 B:F3K102 0.0 9.1 0.3 RU1 B:F3K102 0.1 15.1 0.7 N05 B:F3K102 2.0 13.3 0.7 N08 B:F3K102 2.0 14.4 0.7 N11 B:F3K102 2.1 11.5 0.7 N03 B:F3K102 2.1 9.8 0.3 N05 B:F3K102 2.1 9.5 0.3 N08 B:F3K102 2.1 9.7 0.3 N09 B:F3K102 2.1 11.0 0.3 N04 B:F3K102 2.1 10.8 0.3 N11 B:F3K102 2.1 10.8 0.3 N04 B:F3K102 2.1 11.6 0.7 N09 B:F3K102 2.1 12.7 0.7 N03 B:F3K102 2.1 13.0 0.7 C21 B:F3K102 2.7 13.4 0.7 C28 B:F3K102 2.7 16.6 0.7 C21 B:F3K102 2.8 9.7 0.3 C28 B:F3K102 2.8 10.2 0.3 C36 B:F3K102 2.9 11.7 0.3 C32 B:F3K102 2.9 12.8 0.3 C13 B:F3K102 2.9 10.7 0.3 C14 B:F3K102 2.9 11.1 0.3 C36 B:F3K102 2.9 11.4 0.7 C32 B:F3K102 2.9 11.3 0.7 C14 B:F3K102 2.9 12.5 0.7 C13 B:F3K102 3.0 13.6 0.7 C12 B:F3K102 3.1 10.6 0.3 C38 B:F3K102 3.1 11.0 0.7 C19 B:F3K102 3.1 14.1 0.7 C29 B:F3K102 3.1 12.4 0.3 C27 B:F3K102 3.1 15.8 0.7 C16 B:F3K102 3.1 11.6 0.3 C12 B:F3K102 3.1 13.6 0.7 C38 B:F3K102 3.1 11.6 0.3 C16 B:F3K102 3.1 13.0 0.7 C19 B:F3K102 3.1 9.9 0.3 C27 B:F3K102 3.1 10.8 0.3 H121 B:F3K102 3.1 12.7 0.3 C29 B:F3K102 3.1 12.4 0.7 H121 B:F3K102 3.2 16.4 0.7 H381 B:F3K102 3.2 13.2 0.7 H291 B:F3K102 3.2 14.9 0.3 H161 B:F3K102 3.2 15.6 0.7 H161 B:F3K102 3.2 14.0 0.3 H381 B:F3K102 3.2 13.9 0.3 H191 B:F3K102 3.2 16.9 0.7 H271 B:F3K102 3.2 18.9 0.7 H271 B:F3K102 3.2 12.9 0.3 H191 B:F3K102 3.3 11.8 0.3 H291 B:F3K102 3.3 14.8 0.7 C22 B:F3K102 4.1 16.3 0.7 C25 B:F3K102 4.1 16.3 0.7 C22 B:F3K102 4.2 10.2 0.3 C25 B:F3K102 4.2 10.5 0.3 C31 B:F3K102 4.2 13.3 0.3 C35 B:F3K102 4.2 12.8 0.3 C09 B:F3K102 4.2 11.6 0.3 C35 B:F3K102 4.2 11.7 0.7 C15 B:F3K102 4.2 11.1 0.3 C31 B:F3K102 4.3 11.3 0.7 C15 B:F3K102 4.3 13.6 0.7 C09 B:F3K102 4.3 12.5 0.7 C20 B:F3K102 4.3 15.0 0.7 C26 B:F3K102 4.3 17.0 0.7 C11 B:F3K102 4.3 11.8 0.3 C37 B:F3K102 4.3 13.7 0.7 C30 B:F3K102 4.4 13.4 0.3 C20 B:F3K102 4.4 11.1 0.3 C17 B:F3K102 4.4 12.5 0.3 C37 B:F3K102 4.4 11.9 0.3 C26 B:F3K102 4.4 12.5 0.3 C11 B:F3K102 4.4 14.9 0.7 C17 B:F3K102 4.4 14.3 0.7 C30 B:F3K102 4.4 12.5 0.7 O B:HOH239 4.6 13.5 1.0 N06 B:F3K102 4.7 14.2 0.7 N07 B:F3K102 4.7 17.6 0.7 O2 B:DC2 4.7 13.2 1.0 N06 B:F3K102 4.8 10.7 0.3 N07 B:F3K102 4.8 11.9 0.3 N10 B:F3K102 4.8 12.5 0.3 C10 B:F3K102 4.8 12.9 0.3 N12 B:F3K102 4.8 11.5 0.3 N12 B:F3K102 4.8 12.5 0.7 C18 B:F3K102 4.8 11.8 0.3 C18 B:F3K102 4.9 16.3 0.7 C10 B:F3K102 4.9 13.4 0.7 N10 B:F3K102 4.9 11.7 0.7 O B:HOH244 5.0 14.4 1.0

Ruthenium binding site 2 out of 2 in the Intercalation of [Ru(Tap)2(11-Br-Dppz)]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 Intercalation of [Ru(Tap)2(11-Br-Dppz)]2+ Bound to D(Tcggcgccga)2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ru102 b:15.1 occ:0.66 RU1 B:F3K102 0.0 15.1 0.7 RU1 B:F3K102 0.1 9.1 0.3 N03 B:F3K102 2.0 9.8 0.3 N08 B:F3K102 2.0 9.7 0.3 N04 B:F3K102 2.0 10.8 0.3 N05 B:F3K102 2.1 13.3 0.7 N08 B:F3K102 2.1 14.4 0.7 N03 B:F3K102 2.1 13.0 0.7 N04 B:F3K102 2.1 11.6 0.7 N11 B:F3K102 2.1 11.5 0.7 N09 B:F3K102 2.1 12.7 0.7 N05 B:F3K102 2.1 9.5 0.3 N09 B:F3K102 2.1 11.0 0.3 N11 B:F3K102 2.1 10.8 0.3 C28 B:F3K102 2.8 10.2 0.3 C13 B:F3K102 2.8 10.7 0.3 C21 B:F3K102 2.8 13.4 0.7 C21 B:F3K102 2.8 9.7 0.3 C14 B:F3K102 2.8 11.1 0.3 C28 B:F3K102 2.8 16.6 0.7 C14 B:F3K102 2.9 12.5 0.7 C13 B:F3K102 2.9 13.6 0.7 C36 B:F3K102 2.9 11.4 0.7 C32 B:F3K102 2.9 11.3 0.7 C32 B:F3K102 2.9 12.8 0.3 C36 B:F3K102 2.9 11.7 0.3 C12 B:F3K102 3.0 10.6 0.3 C12 B:F3K102 3.0 13.6 0.7 C16 B:F3K102 3.0 11.6 0.3 C27 B:F3K102 3.1 10.8 0.3 C16 B:F3K102 3.1 13.0 0.7 C29 B:F3K102 3.1 12.4 0.7 C19 B:F3K102 3.1 14.1 0.7 C38 B:F3K102 3.1 11.0 0.7 C29 B:F3K102 3.1 12.4 0.3 C27 B:F3K102 3.1 15.8 0.7 H121 B:F3K102 3.1 16.4 0.7 C38 B:F3K102 3.1 11.6 0.3 H121 B:F3K102 3.1 12.7 0.3 C19 B:F3K102 3.2 9.9 0.3 H161 B:F3K102 3.2 14.0 0.3 H161 B:F3K102 3.2 15.6 0.7 H271 B:F3K102 3.2 12.9 0.3 H291 B:F3K102 3.2 14.9 0.3 H291 B:F3K102 3.2 14.8 0.7 H381 B:F3K102 3.2 13.2 0.7 H381 B:F3K102 3.2 13.9 0.3 H191 B:F3K102 3.2 16.9 0.7 H271 B:F3K102 3.2 18.9 0.7 H191 B:F3K102 3.3 11.8 0.3 C25 B:F3K102 4.1 10.5 0.3 C09 B:F3K102 4.1 11.6 0.3 C22 B:F3K102 4.2 16.3 0.7 C22 B:F3K102 4.2 10.2 0.3 C25 B:F3K102 4.2 16.3 0.7 C15 B:F3K102 4.2 11.1 0.3 C15 B:F3K102 4.2 13.6 0.7 C09 B:F3K102 4.2 12.5 0.7 C35 B:F3K102 4.2 11.7 0.7 C31 B:F3K102 4.3 11.3 0.7 C31 B:F3K102 4.3 13.3 0.3 C35 B:F3K102 4.3 12.8 0.3 C11 B:F3K102 4.3 11.8 0.3 C26 B:F3K102 4.3 12.5 0.3 C17 B:F3K102 4.3 12.5 0.3 C11 B:F3K102 4.3 14.9 0.7 C20 B:F3K102 4.4 15.0 0.7 C17 B:F3K102 4.4 14.3 0.7 C26 B:F3K102 4.4 17.0 0.7 C30 B:F3K102 4.4 12.5 0.7 C37 B:F3K102 4.4 13.7 0.7 C30 B:F3K102 4.4 13.4 0.3 C20 B:F3K102 4.4 11.1 0.3 C37 B:F3K102 4.4 11.9 0.3 O B:HOH239 4.6 13.5 1.0 C10 B:F3K102 4.7 12.9 0.3 N07 B:F3K102 4.7 11.9 0.3 N06 B:F3K102 4.8 14.2 0.7 O2 B:DC2 4.8 13.2 1.0 C18 B:F3K102 4.8 11.8 0.3 N07 B:F3K102 4.8 17.6 0.7 N06 B:F3K102 4.8 10.7 0.3 C10 B:F3K102 4.8 13.4 0.7 C18 B:F3K102 4.8 16.3 0.7 N12 B:F3K102 4.8 12.5 0.7 N10 B:F3K102 4.9 12.5 0.3 N12 B:F3K102 4.9 11.5 0.3 N10 B:F3K102 4.9 11.7 0.7

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