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

Protein crystallography data

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

Other elements in 6rnl:

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

Ruthenium (Ru) 4 atoms
Sodium (Na) 1 atom

Potassium Binding Sites:

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

Potassium binding site 1 out of 2 in 6rnl

Go back to Potassium Binding Sites List in 6rnl
Potassium binding site 1 out of 2 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 Potassium with other atoms in the K 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:K101

b:32.0
occ:1.00
O6 D:DG4 2.7 39.8 1.0
O6 C:DG4 2.7 34.0 1.0
O6 A:DG5 2.8 32.0 1.0
O6 B:DG5 2.8 30.2 1.0
O6 D:DG5 2.8 37.9 1.0
O6 B:DG4 2.8 30.7 1.0
O6 C:DG5 2.8 33.1 1.0
O6 A:DG4 2.8 32.8 1.0
C6 D:DG4 3.5 40.8 1.0
O C:HOH204 3.5 31.4 1.0
C6 B:DG4 3.5 30.3 1.0
K C:K101 3.6 54.9 1.0
C6 C:DG4 3.6 35.5 1.0
C6 A:DG4 3.6 35.1 1.0
C6 C:DG5 3.7 34.4 1.0
C6 B:DG5 3.7 32.2 1.0
C6 A:DG5 3.7 30.9 1.0
C6 D:DG5 3.7 38.8 1.0
N1 D:DG4 3.7 40.8 1.0
N1 B:DG4 3.8 30.1 1.0
N1 A:DG4 3.8 35.2 1.0
N1 B:DG5 3.9 33.2 1.0
N1 C:DG4 3.9 35.5 1.0
N1 C:DG5 3.9 34.2 1.0
N1 A:DG5 4.0 28.9 1.0
N1 D:DG5 4.1 38.7 1.0
C5 D:DG4 4.7 42.5 1.0
C5 B:DG4 4.8 30.1 1.0
C5 C:DG4 4.8 39.5 1.0
C5 A:DG4 4.9 37.8 1.0
C5 C:DG5 4.9 38.1 1.0
C5 A:DG5 5.0 33.4 1.0
C2 D:DG4 5.0 42.7 1.0

Potassium binding site 2 out of 2 in 6rnl

Go back to Potassium Binding Sites List in 6rnl
Potassium binding site 2 out of 2 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 Potassium with other atoms in the K 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
C:K101

b:54.9
occ:1.00
O6 D:DG3 2.4 45.3 1.0
O6 C:DG3 2.6 34.1 1.0
O6 B:DG3 2.6 32.8 1.0
O6 A:DG3 2.6 37.1 1.0
O6 B:DG4 2.8 30.7 1.0
O6 C:DG4 2.9 34.0 1.0
O6 A:DG4 3.0 32.8 1.0
O6 D:DG4 3.3 39.8 1.0
C6 D:DG3 3.3 47.4 1.0
C6 C:DG3 3.4 34.7 1.0
C6 B:DG3 3.5 32.0 1.0
N1 C:DG3 3.5 35.4 1.0
K A:K101 3.6 32.0 1.0
N1 D:DG3 3.6 48.9 1.0
C6 A:DG3 3.6 37.4 1.0
C6 B:DG4 3.6 30.3 1.0
N1 B:DG3 3.7 30.8 1.0
C6 A:DG4 3.8 35.1 1.0
C6 C:DG4 3.8 35.5 1.0
N1 A:DG3 3.9 35.8 1.0
N1 B:DG4 3.9 30.1 1.0
N1 A:DG4 4.0 35.2 1.0
C6 D:DG4 4.1 40.8 1.0
N1 D:DG4 4.3 40.8 1.0
N1 C:DG4 4.3 35.5 1.0
N6 B:DA2 4.3 40.6 1.0
C5 D:DG3 4.6 48.9 1.0
C5 C:DG3 4.7 35.6 1.0
N6 D:DA2 4.8 47.8 1.0
C5 B:DG3 4.8 33.2 1.0
C2 C:DG3 4.8 37.6 1.0
C5 A:DG3 4.9 40.5 1.0
C2 D:DG3 4.9 50.9 1.0
C5 B:DG4 4.9 30.1 1.0
C5 C:DG4 5.0 39.5 1.0
C6 B:DA2 5.0 39.2 1.0

Reference:

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
Page generated: Mon Dec 14 01:25:36 2020

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