Sodium 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
Ruthenium	(Ru)	4 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the L-[Ru(Tap)2(Dppz)]2+ Bound to the G-Quadruplex Forming Sequence D(Tagggtt), PDB code: 6rnl:

Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na104 b:63.8 occ:1.00 O A:HOH221 2.4 39.5 1.0 O A:HOH216 2.5 46.0 1.0 O A:HOH211 2.5 53.8 1.0 N6 A:RKL102 2.8 47.6 1.0 H23 A:RKL102 2.9 59.3 1.0 O A:HOH225 3.2 31.1 0.5 C22 A:RKL102 3.6 48.5 1.0 C23 A:RKL102 3.6 49.5 1.0 H21 A:RKL102 3.7 55.5 1.0 C21 A:RKL102 3.7 46.3 1.0 O A:HOH209 4.1 29.5 0.6 O D:HOH213 4.2 30.2 0.7 O A:HOH214 4.7 33.3 0.7 C7 A:DT6 4.9 33.8 1.0 C19 A:RKL102 4.9 47.9 1.0 C24 A:RKL102 4.9 50.8 1.0 H24 A:RKL103 5.0 37.0 1.0 C20 A:RKL102 5.0 45.4 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