Ruthenium in PDB 6rsp: L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga)

The structure of L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga), PDB code: 6rsp 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)	33.31 / 1.91
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	47.108, 47.108, 32.460, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.1

The structure of L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga) also contains other interesting chemical elements:

Barium

(Ba)

2 atoms

The binding sites of Ruthenium atom in the L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga) (pdb code 6rsp). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 4 binding sites of Ruthenium where determined in the L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga), PDB code: 6rsp:
Jump to Ruthenium binding site number: 1; 2; 3; 4;

Ruthenium binding site 1 out of 4 in the L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru102 b:47.8 occ:0.24 RU19 A:KHK102 0.0 47.8 0.2 RU19 A:KHK102 0.1 46.8 0.8 N37 A:KHK102 1.9 47.5 0.8 N20 A:KHK102 2.0 51.2 0.8 N24 A:KHK102 2.0 46.6 0.8 N37 A:KHK102 2.0 48.4 0.2 N38 A:KHK102 2.0 47.5 0.2 N15 A:KHK102 2.0 51.1 0.2 N20 A:KHK102 2.0 48.5 0.2 N48 A:KHK102 2.0 46.5 0.2 N24 A:KHK102 2.0 48.1 0.2 N15 A:KHK102 2.0 48.5 0.8 N38 A:KHK102 2.0 48.3 0.8 N48 A:KHK102 2.1 48.2 0.8 C36 A:KHK102 2.7 46.7 0.8 C28 A:KHK102 2.7 46.3 0.8 C17 A:KHK102 2.8 52.3 0.8 C36 A:KHK102 2.8 48.7 0.2 C16 A:KHK102 2.8 50.6 0.8 C43 A:KHK102 2.8 46.7 0.2 C17 A:KHK102 2.8 50.6 0.2 C47 A:KHK102 2.8 46.4 0.2 C16 A:KHK102 2.8 52.2 0.2 C28 A:KHK102 2.8 48.6 0.2 C43 A:KHK102 2.8 48.8 0.8 C47 A:KHK102 2.9 48.7 0.8 C21 A:KHK102 3.1 53.4 0.8 C39 A:KHK102 3.1 48.5 0.8 C35 A:KHK102 3.1 47.9 0.8 C39 A:KHK102 3.1 47.9 0.2 C35 A:KHK102 3.1 49.3 0.2 C14 A:KHK102 3.1 53.6 0.2 C25 A:KHK102 3.1 45.7 0.8 C21 A:KHK102 3.1 47.5 0.2 C51 A:KHK102 3.1 45.8 0.2 C14 A:KHK102 3.1 47.6 0.8 C25 A:KHK102 3.1 48.5 0.2 C51 A:KHK102 3.2 48.4 0.8 H66 A:KHK102 3.2 58.2 0.8 H78 A:KHK102 3.2 64.1 0.8 H56 A:KHK102 3.2 64.3 0.2 H78 A:KHK102 3.2 57.0 0.2 H66 A:KHK102 3.2 57.5 0.2 H65 A:KHK102 3.2 59.1 0.2 H65 A:KHK102 3.2 57.5 0.8 H58 A:KHK102 3.2 54.9 0.8 H73 A:KHK102 3.2 54.9 0.2 H58 A:KHK102 3.3 58.2 0.2 H56 A:KHK102 3.3 57.1 0.8 H73 A:KHK102 3.3 58.0 0.8 C18 A:KHK102 4.1 52.2 0.2 C11 A:KHK102 4.1 52.2 0.8 C18 A:KHK102 4.1 55.7 0.8 C32 A:KHK102 4.1 47.1 0.8 C29 A:KHK102 4.1 45.9 0.8 C11 A:KHK102 4.1 55.7 0.2 C32 A:KHK102 4.2 49.1 0.2 C42 A:KHK102 4.2 47.2 0.2 C46 A:KHK102 4.2 45.9 0.2 C29 A:KHK102 4.2 49.0 0.2 C42 A:KHK102 4.2 49.0 0.8 C34 A:KHK102 4.3 48.0 0.8 C46 A:KHK102 4.3 49.0 0.8 C22 A:KHK102 4.3 55.0 0.8 C34 A:KHK102 4.3 49.2 0.2 C40 A:KHK102 4.3 48.2 0.2 C40 A:KHK102 4.3 49.2 0.8 C13 A:KHK102 4.3 55.1 0.2 C26 A:KHK102 4.3 45.6 0.8 C22 A:KHK102 4.3 48.0 0.2 C50 A:KHK102 4.3 45.6 0.2 C13 A:KHK102 4.3 48.3 0.8 C26 A:KHK102 4.3 49.1 0.2 C50 A:KHK102 4.4 49.4 0.8 O2 B:DC2 4.6 44.4 1.0 C33 A:KHK102 4.7 48.0 0.8 C27 A:KHK102 4.7 46.0 0.8 C23 A:KHK102 4.7 55.5 0.8 C33 A:KHK102 4.7 49.2 0.2 C23 A:KHK102 4.7 49.4 0.2 C12 A:KHK102 4.7 55.5 0.2 C41 A:KHK102 4.7 48.0 0.2 C12 A:KHK102 4.7 49.6 0.8 C49 A:KHK102 4.7 45.9 0.2 C41 A:KHK102 4.7 49.1 0.8 C27 A:KHK102 4.7 49.2 0.2 C49 A:KHK102 4.8 49.4 0.8 N2 A:DG9 4.8 58.1 1.0 O4' B:DC2 5.0 51.2 1.0

Ruthenium binding site 2 out of 4 in the L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru102 b:46.8 occ:0.76 RU19 A:KHK102 0.0 46.8 0.8 RU19 A:KHK102 0.1 47.8 0.2 N37 A:KHK102 1.9 48.4 0.2 N24 A:KHK102 2.0 48.1 0.2 N38 A:KHK102 2.0 48.3 0.8 N20 A:KHK102 2.0 48.5 0.2 N15 A:KHK102 2.0 48.5 0.8 N37 A:KHK102 2.0 47.5 0.8 N24 A:KHK102 2.0 46.6 0.8 N20 A:KHK102 2.0 51.2 0.8 N48 A:KHK102 2.0 48.2 0.8 N48 A:KHK102 2.0 46.5 0.2 N15 A:KHK102 2.0 51.1 0.2 N38 A:KHK102 2.1 47.5 0.2 C36 A:KHK102 2.7 48.7 0.2 C28 A:KHK102 2.7 48.6 0.2 C43 A:KHK102 2.8 48.8 0.8 C16 A:KHK102 2.8 50.6 0.8 C17 A:KHK102 2.8 50.6 0.2 C28 A:KHK102 2.8 46.3 0.8 C36 A:KHK102 2.8 46.7 0.8 C17 A:KHK102 2.8 52.3 0.8 C16 A:KHK102 2.8 52.2 0.2 C47 A:KHK102 2.8 48.7 0.8 C47 A:KHK102 2.8 46.4 0.2 C43 A:KHK102 2.8 46.7 0.2 C39 A:KHK102 3.0 48.5 0.8 C35 A:KHK102 3.0 49.3 0.2 C21 A:KHK102 3.0 47.5 0.2 C14 A:KHK102 3.1 47.6 0.8 C25 A:KHK102 3.1 48.5 0.2 C25 A:KHK102 3.1 45.7 0.8 C21 A:KHK102 3.1 53.4 0.8 C35 A:KHK102 3.1 47.9 0.8 C51 A:KHK102 3.1 45.8 0.2 C39 A:KHK102 3.1 47.9 0.2 C14 A:KHK102 3.1 53.6 0.2 C51 A:KHK102 3.1 48.4 0.8 H66 A:KHK102 3.2 58.2 0.8 H78 A:KHK102 3.2 57.0 0.2 H56 A:KHK102 3.2 57.1 0.8 H65 A:KHK102 3.2 59.1 0.2 H58 A:KHK102 3.2 54.9 0.8 H73 A:KHK102 3.2 54.9 0.2 H78 A:KHK102 3.2 64.1 0.8 H66 A:KHK102 3.3 57.5 0.2 H58 A:KHK102 3.3 58.2 0.2 H65 A:KHK102 3.3 57.5 0.8 H56 A:KHK102 3.3 64.3 0.2 H73 A:KHK102 3.3 58.0 0.8 C32 A:KHK102 4.1 49.1 0.2 C18 A:KHK102 4.1 52.2 0.2 C11 A:KHK102 4.1 52.2 0.8 C29 A:KHK102 4.1 49.0 0.2 C18 A:KHK102 4.1 55.7 0.8 C42 A:KHK102 4.1 49.0 0.8 C11 A:KHK102 4.1 55.7 0.2 C29 A:KHK102 4.2 45.9 0.8 C32 A:KHK102 4.2 47.1 0.8 C46 A:KHK102 4.2 49.0 0.8 C34 A:KHK102 4.2 49.2 0.2 C46 A:KHK102 4.2 45.9 0.2 C40 A:KHK102 4.2 49.2 0.8 C42 A:KHK102 4.2 47.2 0.2 C22 A:KHK102 4.2 48.0 0.2 C13 A:KHK102 4.3 48.3 0.8 C26 A:KHK102 4.3 49.1 0.2 C26 A:KHK102 4.3 45.6 0.8 C34 A:KHK102 4.3 48.0 0.8 C22 A:KHK102 4.3 55.0 0.8 C50 A:KHK102 4.3 45.6 0.2 C40 A:KHK102 4.3 48.2 0.2 C13 A:KHK102 4.3 55.1 0.2 C50 A:KHK102 4.4 49.4 0.8 O2 B:DC2 4.6 44.4 1.0 C33 A:KHK102 4.6 49.2 0.2 C41 A:KHK102 4.7 49.1 0.8 C23 A:KHK102 4.7 49.4 0.2 C27 A:KHK102 4.7 49.2 0.2 C12 A:KHK102 4.7 49.6 0.8 C27 A:KHK102 4.7 46.0 0.8 C23 A:KHK102 4.7 55.5 0.8 C33 A:KHK102 4.7 48.0 0.8 C12 A:KHK102 4.7 55.5 0.2 C41 A:KHK102 4.8 48.0 0.2 C49 A:KHK102 4.8 45.9 0.2 C49 A:KHK102 4.8 49.4 0.8 N2 A:DG9 4.8 58.1 1.0 O4' B:DC2 4.9 51.2 1.0 H67 A:KHK102 5.0 59.0 0.8 H64 A:KHK102 5.0 59.0 0.2

Ruthenium binding site 3 out of 4 in the L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ru102 b:46.6 occ:0.46 RU19 B:KHK102 0.0 46.6 0.5 RU19 B:KHK102 0.0 46.3 0.5 N20 B:KHK102 2.0 51.2 0.5 N37 B:KHK102 2.0 47.6 0.5 N37 B:KHK102 2.0 48.2 0.5 N38 B:KHK102 2.0 47.6 0.5 N24 B:KHK102 2.0 46.0 0.5 N38 B:KHK102 2.0 48.2 0.5 N15 B:KHK102 2.0 51.2 0.5 N15 B:KHK102 2.0 48.7 0.5 N20 B:KHK102 2.0 48.7 0.5 N48 B:KHK102 2.0 46.0 0.5 N24 B:KHK102 2.0 48.9 0.5 N48 B:KHK102 2.1 48.9 0.5 C36 B:KHK102 2.7 48.6 0.5 C28 B:KHK102 2.8 45.3 0.5 C36 B:KHK102 2.8 46.0 0.5 C28 B:KHK102 2.8 48.9 0.5 C16 B:KHK102 2.8 50.3 0.5 C17 B:KHK102 2.8 52.0 0.5 C47 B:KHK102 2.8 45.3 0.5 C43 B:KHK102 2.8 46.0 0.5 C17 B:KHK102 2.8 50.3 0.5 C16 B:KHK102 2.8 52.0 0.5 C43 B:KHK102 2.8 48.5 0.5 C47 B:KHK102 2.8 48.9 0.5 C39 B:KHK102 3.0 47.5 0.5 C21 B:KHK102 3.1 53.1 0.5 C35 B:KHK102 3.1 47.9 0.5 C14 B:KHK102 3.1 53.0 0.5 C25 B:KHK102 3.1 43.8 0.5 C21 B:KHK102 3.1 47.0 0.5 C39 B:KHK102 3.1 47.7 0.5 C14 B:KHK102 3.1 47.0 0.5 C51 B:KHK102 3.1 43.8 0.5 C35 B:KHK102 3.1 47.7 0.5 C25 B:KHK102 3.1 48.6 0.5 C51 B:KHK102 3.1 48.5 0.5 H66 B:KHK102 3.2 57.0 0.5 H78 B:KHK102 3.2 63.7 0.5 H56 B:KHK102 3.2 63.6 0.5 H78 B:KHK102 3.2 56.5 0.5 H65 B:KHK102 3.2 57.5 0.5 H56 B:KHK102 3.2 56.4 0.5 H58 B:KHK102 3.2 52.6 0.5 H73 B:KHK102 3.2 52.6 0.5 H66 B:KHK102 3.2 57.2 0.5 H65 B:KHK102 3.3 57.3 0.5 H58 B:KHK102 3.3 58.3 0.5 H73 B:KHK102 3.3 58.3 0.5 C11 B:KHK102 4.1 52.2 0.5 C18 B:KHK102 4.1 55.5 0.5 C18 B:KHK102 4.1 52.2 0.5 C11 B:KHK102 4.1 55.5 0.5 C32 B:KHK102 4.1 49.2 0.5 C29 B:KHK102 4.1 44.7 0.5 C32 B:KHK102 4.2 46.9 0.5 C29 B:KHK102 4.2 49.8 0.5 C46 B:KHK102 4.2 44.7 0.5 C42 B:KHK102 4.2 46.9 0.5 C42 B:KHK102 4.2 49.2 0.5 C46 B:KHK102 4.2 49.8 0.5 C40 B:KHK102 4.2 48.6 0.5 C34 B:KHK102 4.3 48.5 0.5 C22 B:KHK102 4.3 54.8 0.5 C26 B:KHK102 4.3 43.6 0.5 C13 B:KHK102 4.3 54.8 0.5 C40 B:KHK102 4.3 48.1 0.5 C22 B:KHK102 4.3 47.8 0.5 C13 B:KHK102 4.3 47.7 0.5 C50 B:KHK102 4.3 43.7 0.5 C34 B:KHK102 4.3 48.1 0.5 C26 B:KHK102 4.3 49.5 0.5 C50 B:KHK102 4.4 49.6 0.5 C33 B:KHK102 4.7 49.1 0.5 C27 B:KHK102 4.7 44.2 0.5 C41 B:KHK102 4.7 49.1 0.5 C23 B:KHK102 4.7 55.4 0.5 C12 B:KHK102 4.7 49.5 0.5 O2 A:DC2 4.7 48.4 1.0 C12 B:KHK102 4.7 55.4 0.5 C23 B:KHK102 4.7 49.5 0.5 C49 B:KHK102 4.7 44.2 0.5 C41 B:KHK102 4.7 48.0 0.5 C33 B:KHK102 4.7 48.1 0.5 C27 B:KHK102 4.7 49.8 0.5 N2 B:DG9 4.8 54.8 1.0 C49 B:KHK102 4.8 50.0 0.5 O4' A:DC2 5.0 51.5 1.0

Ruthenium binding site 4 out of 4 in the L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ru102 b:46.3 occ:0.54 RU19 B:KHK102 0.0 46.3 0.5 RU19 B:KHK102 0.0 46.6 0.5 N37 B:KHK102 2.0 48.2 0.5 N38 B:KHK102 2.0 48.2 0.5 N24 B:KHK102 2.0 48.9 0.5 N24 B:KHK102 2.0 46.0 0.5 N37 B:KHK102 2.0 47.6 0.5 N38 B:KHK102 2.0 47.6 0.5 N15 B:KHK102 2.0 48.7 0.5 N20 B:KHK102 2.0 51.2 0.5 N20 B:KHK102 2.0 48.7 0.5 N48 B:KHK102 2.0 46.0 0.5 N15 B:KHK102 2.0 51.2 0.5 N48 B:KHK102 2.0 48.9 0.5 C36 B:KHK102 2.7 48.6 0.5 C28 B:KHK102 2.7 48.9 0.5 C28 B:KHK102 2.8 45.3 0.5 C43 B:KHK102 2.8 48.5 0.5 C36 B:KHK102 2.8 46.0 0.5 C16 B:KHK102 2.8 50.3 0.5 C47 B:KHK102 2.8 45.3 0.5 C17 B:KHK102 2.8 52.0 0.5 C43 B:KHK102 2.8 46.0 0.5 C17 B:KHK102 2.8 50.3 0.5 C47 B:KHK102 2.8 48.9 0.5 C16 B:KHK102 2.8 52.0 0.5 C39 B:KHK102 3.0 47.5 0.5 C35 B:KHK102 3.1 47.9 0.5 C21 B:KHK102 3.1 47.0 0.5 C14 B:KHK102 3.1 47.0 0.5 C25 B:KHK102 3.1 43.8 0.5 C21 B:KHK102 3.1 53.1 0.5 C51 B:KHK102 3.1 43.8 0.5 C25 B:KHK102 3.1 48.6 0.5 C39 B:KHK102 3.1 47.7 0.5 C14 B:KHK102 3.1 53.0 0.5 C35 B:KHK102 3.1 47.7 0.5 C51 B:KHK102 3.1 48.5 0.5 H66 B:KHK102 3.2 57.0 0.5 H78 B:KHK102 3.2 56.5 0.5 H56 B:KHK102 3.2 56.4 0.5 H78 B:KHK102 3.2 63.7 0.5 H58 B:KHK102 3.2 52.6 0.5 H65 B:KHK102 3.2 57.5 0.5 H73 B:KHK102 3.2 52.6 0.5 H56 B:KHK102 3.2 63.6 0.5 H66 B:KHK102 3.2 57.2 0.5 H58 B:KHK102 3.3 58.3 0.5 H73 B:KHK102 3.3 58.3 0.5 H65 B:KHK102 3.3 57.3 0.5 C32 B:KHK102 4.1 49.2 0.5 C11 B:KHK102 4.1 52.2 0.5 C29 B:KHK102 4.1 49.8 0.5 C18 B:KHK102 4.1 52.2 0.5 C18 B:KHK102 4.1 55.5 0.5 C29 B:KHK102 4.1 44.7 0.5 C42 B:KHK102 4.1 49.2 0.5 C11 B:KHK102 4.1 55.5 0.5 C32 B:KHK102 4.2 46.9 0.5 C46 B:KHK102 4.2 44.7 0.5 C42 B:KHK102 4.2 46.9 0.5 C46 B:KHK102 4.2 49.8 0.5 C40 B:KHK102 4.2 48.6 0.5 C34 B:KHK102 4.2 48.5 0.5 C26 B:KHK102 4.3 43.6 0.5 C22 B:KHK102 4.3 47.8 0.5 C13 B:KHK102 4.3 47.7 0.5 C26 B:KHK102 4.3 49.5 0.5 C50 B:KHK102 4.3 43.7 0.5 C22 B:KHK102 4.3 54.8 0.5 C40 B:KHK102 4.3 48.1 0.5 C13 B:KHK102 4.3 54.8 0.5 C34 B:KHK102 4.3 48.1 0.5 C50 B:KHK102 4.3 49.6 0.5 C33 B:KHK102 4.7 49.1 0.5 C41 B:KHK102 4.7 49.1 0.5 C27 B:KHK102 4.7 44.2 0.5 O2 A:DC2 4.7 48.4 1.0 C27 B:KHK102 4.7 49.8 0.5 C12 B:KHK102 4.7 49.5 0.5 C23 B:KHK102 4.7 49.5 0.5 C49 B:KHK102 4.7 44.2 0.5 C23 B:KHK102 4.7 55.4 0.5 C41 B:KHK102 4.7 48.0 0.5 C33 B:KHK102 4.7 48.1 0.5 C12 B:KHK102 4.7 55.4 0.5 C49 B:KHK102 4.8 50.0 0.5 N2 B:DG9 4.8 54.8 1.0 O4' A:DC2 4.9 51.5 1.0

K.T.Mcquaid, J.P.Hall, C.J.Cardin. L-[Ru(Phen)2(11-NO2-Dppz)]2+ Bound to the Oligonucleotide Sequence D(Tcggcgccga) To Be Published.