Ruthenium in PDB 6rnl: L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt)

The structure of L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt), PDB code: 6rnl 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)	32.29 / 1.88
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	38.514, 38.514, 128.804, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 21.5

The structure of L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt) also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Ruthenium atom in the L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt) (pdb code 6rnl). 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(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt), PDB code: 6rnl:
Jump to Ruthenium binding site number: 1; 2; 3; 4;

Ruthenium binding site 1 out of 4 in the L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru102 b:42.1 occ:1.00 RU A:RKL102 0.0 42.1 1.0 N8 A:RKL102 2.1 47.5 1.0 N12 A:RKL102 2.1 47.3 1.0 N2 A:RKL102 2.1 37.9 1.0 N9 A:RKL102 2.1 47.4 1.0 N5 A:RKL102 2.1 45.5 1.0 N1 A:RKL102 2.1 38.8 1.0 C29 A:RKL102 2.9 49.0 1.0 C36 A:RKL102 2.9 49.2 1.0 C1 A:RKL102 2.9 35.7 1.0 C26 A:RKL102 2.9 49.3 1.0 C19 A:RKL102 2.9 47.9 1.0 C10 A:RKL102 2.9 35.8 1.0 C38 A:RKL102 3.1 50.7 1.0 C2 A:RKL102 3.1 37.5 1.0 C20 A:RKL102 3.1 45.4 1.0 C12 A:RKL102 3.1 37.3 1.0 C28 A:RKL102 3.1 50.1 1.0 C30 A:RKL102 3.1 49.8 1.0 H2 A:RKL102 3.2 44.9 1.0 H12 A:RKL102 3.2 44.7 1.0 H38 A:RKL102 3.2 60.8 1.0 H20 A:RKL102 3.2 54.4 1.0 H28 A:RKL102 3.2 60.0 1.0 H30 A:RKL102 3.3 59.7 1.0 C32 A:RKL102 4.2 50.9 1.0 C35 A:RKL102 4.2 51.5 1.0 C5 A:RKL102 4.2 36.1 1.0 C22 A:RKL102 4.2 48.5 1.0 C25 A:RKL102 4.2 51.4 1.0 C8 A:RKL102 4.2 35.6 1.0 C31 A:RKL102 4.3 51.5 1.0 C37 A:RKL102 4.4 53.5 1.0 C21 A:RKL102 4.4 46.3 1.0 C11 A:RKL102 4.4 36.7 1.0 C3 A:RKL102 4.4 37.4 1.0 C27 A:RKL102 4.4 51.6 1.0 O4 A:DT6 4.7 32.6 1.0 N10 A:RKL102 4.8 51.5 1.0 N11 A:RKL102 4.8 53.7 1.0 N6 A:RKL102 4.8 47.6 1.0 C7 A:DT6 4.8 33.8 1.0 C4 A:RKL102 4.8 37.4 1.0 N7 A:RKL102 4.8 52.1 1.0 C9 A:RKL102 4.9 36.2 1.0

Ruthenium binding site 2 out of 4 in the L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru103 b:32.8 occ:1.00 RU A:RKL103 0.0 32.8 1.0 N12 A:RKL103 2.1 32.1 1.0 N8 A:RKL103 2.1 33.3 1.0 N1 A:RKL103 2.1 29.7 1.0 N2 A:RKL103 2.1 31.7 1.0 N9 A:RKL103 2.1 31.7 1.0 N5 A:RKL103 2.1 31.0 1.0 C36 A:RKL103 2.8 33.6 1.0 C29 A:RKL103 2.8 32.0 1.0 C1 A:RKL103 2.9 32.0 1.0 C10 A:RKL103 2.9 30.7 1.0 C26 A:RKL103 2.9 31.8 1.0 C19 A:RKL103 2.9 31.3 1.0 C2 A:RKL103 3.1 33.8 1.0 C28 A:RKL103 3.1 35.4 1.0 C38 A:RKL103 3.1 33.0 1.0 C12 A:RKL103 3.1 29.7 1.0 C30 A:RKL103 3.1 33.1 1.0 C20 A:RKL103 3.1 32.8 1.0 H2 A:RKL103 3.2 40.5 1.0 H12 A:RKL103 3.2 35.5 1.0 H28 A:RKL103 3.2 42.4 1.0 H20 A:RKL103 3.2 39.3 1.0 H38 A:RKL103 3.2 39.5 1.0 H30 A:RKL103 3.2 39.7 1.0 C32 A:RKL103 4.2 32.2 1.0 C35 A:RKL103 4.2 37.0 1.0 C5 A:RKL103 4.2 34.9 1.0 C25 A:RKL103 4.2 31.8 1.0 C8 A:RKL103 4.2 32.2 1.0 C22 A:RKL103 4.3 32.2 1.0 C31 A:RKL103 4.3 32.9 1.0 C37 A:RKL103 4.4 35.3 1.0 C27 A:RKL103 4.4 35.3 1.0 C3 A:RKL103 4.4 35.5 1.0 C11 A:RKL103 4.4 31.5 1.0 O4 B:DT7 4.4 38.3 1.0 C21 A:RKL103 4.4 34.6 1.0 O B:HOH108 4.6 31.2 1.0 O2 A:DT6 4.7 35.0 1.0 N10 A:RKL103 4.7 31.1 1.0 N11 A:RKL103 4.8 37.0 1.0 O A:HOH218 4.8 36.6 1.0 N7 A:RKL103 4.8 33.2 1.0 C4 A:RKL103 4.8 35.7 1.0 N6 A:RKL103 4.9 34.0 1.0 C9 A:RKL103 4.9 31.5 1.0

Ruthenium binding site 3 out of 4 in the L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ru102 b:53.7 occ:1.00 RU C:RKL102 0.0 53.7 1.0 N1 C:RKL102 2.1 43.7 1.0 N8 C:RKL102 2.1 62.9 1.0 N12 C:RKL102 2.1 55.0 1.0 N2 C:RKL102 2.1 45.7 1.0 N9 C:RKL102 2.1 55.0 1.0 N5 C:RKL102 2.1 63.1 1.0 C36 C:RKL102 2.9 56.6 1.0 C26 C:RKL102 2.9 67.8 1.0 C29 C:RKL102 2.9 56.4 1.0 C10 C:RKL102 2.9 39.6 1.0 C1 C:RKL102 2.9 40.7 1.0 C19 C:RKL102 2.9 67.6 1.0 C12 C:RKL102 3.0 39.4 1.0 C2 C:RKL102 3.1 44.1 1.0 C28 C:RKL102 3.1 66.2 1.0 C38 C:RKL102 3.1 55.8 1.0 C20 C:RKL102 3.1 67.3 1.0 C30 C:RKL102 3.1 55.5 1.0 H2 C:RKL102 3.2 52.8 1.0 H12 C:RKL102 3.2 47.2 1.0 H28 C:RKL102 3.2 79.4 1.0 H38 C:RKL102 3.2 66.9 1.0 H20 C:RKL102 3.2 80.7 1.0 H30 C:RKL102 3.3 66.6 1.0 C32 C:RKL102 4.2 58.2 1.0 C25 C:RKL102 4.2 70.8 1.0 C8 C:RKL102 4.2 37.2 1.0 C35 C:RKL102 4.2 58.5 1.0 C22 C:RKL102 4.2 70.7 1.0 C5 C:RKL102 4.2 38.5 1.0 C31 C:RKL102 4.3 56.6 1.0 C11 C:RKL102 4.3 38.0 1.0 C37 C:RKL102 4.3 56.8 1.0 C3 C:RKL102 4.3 42.5 1.0 C27 C:RKL102 4.3 68.8 1.0 C21 C:RKL102 4.4 70.2 1.0 N10 C:RKL102 4.7 57.5 1.0 N7 C:RKL102 4.8 70.5 1.0 N11 C:RKL102 4.8 57.8 1.0 N6 C:RKL102 4.8 71.3 1.0 C9 C:RKL102 4.8 37.6 1.0 C4 C:RKL102 4.8 40.6 1.0

Ruthenium binding site 4 out of 4 in the L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ru101 b:37.8 occ:1.00 RU D:RKL101 0.0 37.8 1.0 N8 D:RKL101 2.1 34.1 1.0 N2 D:RKL101 2.1 36.7 1.0 N9 D:RKL101 2.1 41.8 1.0 N5 D:RKL101 2.1 32.2 1.0 N12 D:RKL101 2.1 44.6 1.0 N1 D:RKL101 2.1 40.1 1.0 C26 D:RKL101 2.9 31.4 1.0 C29 D:RKL101 2.9 45.7 1.0 C1 D:RKL101 2.9 38.1 1.0 C36 D:RKL101 2.9 46.3 1.0 C19 D:RKL101 2.9 29.9 1.0 C10 D:RKL101 2.9 39.8 1.0 C2 D:RKL101 3.0 36.0 1.0 C12 D:RKL101 3.1 42.6 1.0 C20 D:RKL101 3.1 31.0 1.0 C38 D:RKL101 3.1 48.6 1.0 C28 D:RKL101 3.1 35.1 1.0 C30 D:RKL101 3.1 43.1 1.0 H2 D:RKL101 3.2 43.2 1.0 H12 D:RKL101 3.2 51.1 1.0 H20 D:RKL101 3.2 37.1 1.0 H38 D:RKL101 3.2 58.2 1.0 H30 D:RKL101 3.3 51.6 1.0 H28 D:RKL101 3.3 42.1 1.0 C5 D:RKL101 4.2 38.4 1.0 C32 D:RKL101 4.2 48.3 1.0 C35 D:RKL101 4.2 49.1 1.0 C8 D:RKL101 4.2 41.6 1.0 C25 D:RKL101 4.2 32.6 1.0 C22 D:RKL101 4.2 29.1 1.0 C3 D:RKL101 4.3 36.9 1.0 C31 D:RKL101 4.3 45.5 1.0 C37 D:RKL101 4.4 50.8 1.0 C11 D:RKL101 4.4 44.0 1.0 C21 D:RKL101 4.4 30.2 1.0 C27 D:RKL101 4.4 35.7 1.0 N10 D:RKL101 4.8 47.5 1.0 N11 D:RKL101 4.8 50.4 1.0 C4 D:RKL101 4.8 37.9 1.0 N6 D:RKL101 4.8 29.0 1.0 C9 D:RKL101 4.8 43.4 1.0 N7 D:RKL101 4.9 35.0 1.0

K.Mcquaid, J.P.Hall, L.Baumgaertner, D.J.Cardin, C.J.Cardin. Three Thymine/Adenine Binding Modes of the Ruthenium Complex Lambda-[Ru(Tap)2(Dppz)]2+to the G-Quadruplex Forming Sequence D(Tagggtt) Shown By X-Ray Crystallography. Chem.Commun.(Camb.) V. 55 9116 2019.
ISSN: ESSN 1364-548X
PubMed: 31298665
DOI: 10.1039/C9CC04316K