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Ruthenium in PDB 5ls8: Light-Activated Ruthenium Complex Bound to A Dna Quadruplex

Protein crystallography data

The structure of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex, PDB code: 5ls8 was solved by K.T.Mcquaid, H.Abell, 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) 31.72 / 1.78
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 36.625, 36.625, 136.104, 90.00, 90.00, 120.00
R / Rfree (%) 21.4 / 23.3

Other elements in 5ls8:

The structure of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex also contains other interesting chemical elements:

Potassium (K) 2 atoms

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex (pdb code 5ls8). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 6 binding sites of Ruthenium where determined in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex, PDB code: 5ls8:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5; 6;

Ruthenium binding site 1 out of 6 in 5ls8

Go back to Ruthenium Binding Sites List in 5ls8
Ruthenium binding site 1 out of 6 in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru101

b:38.0
occ:1.00
RU A:QHL101 0.0 38.0 1.0
N1 A:QHL101 1.8 37.0 1.0
N9 A:QHL101 1.8 40.0 1.0
N12 A:QHL101 1.8 42.6 1.0
N8 A:QHL101 1.8 49.5 1.0
N5 A:QHL101 1.8 50.1 1.0
N2 A:QHL101 1.8 39.0 1.0
C29 A:QHL101 2.7 39.7 1.0
C10 A:QHL101 2.7 33.2 1.0
C36 A:QHL101 2.7 39.6 1.0
C26 A:QHL101 2.7 46.7 1.0
C19 A:QHL101 2.7 48.8 1.0
C1 A:QHL101 2.7 35.0 1.0
C12 A:QHL101 2.8 44.7 1.0
C30 A:QHL101 2.9 42.3 1.0
C38 A:QHL101 2.9 45.5 1.0
C28 A:QHL101 2.9 48.6 1.0
C2 A:QHL101 2.9 33.7 1.0
C20 A:QHL101 2.9 41.0 1.0
C32 A:QHL101 4.0 40.3 1.0
C35 A:QHL101 4.0 43.2 1.0
C25 A:QHL101 4.1 54.7 1.0
C8 A:QHL101 4.1 33.2 1.0
C22 A:QHL101 4.1 53.5 1.0
C5 A:QHL101 4.1 22.7 1.0
C11 A:QHL101 4.1 40.3 1.0
C31 A:QHL101 4.1 40.0 1.0
C37 A:QHL101 4.1 43.8 1.0
C27 A:QHL101 4.1 48.5 1.0
C21 A:QHL101 4.2 50.8 1.0
C3 A:QHL101 4.2 33.5 1.0
N10 A:QHL101 4.6 41.3 1.0
C9 A:QHL101 4.6 41.9 1.0
N7 A:QHL101 4.6 51.8 1.0
N11 A:QHL101 4.6 44.0 1.0
N6 A:QHL101 4.6 53.3 1.0
O A:HOH205 4.6 39.4 0.5
C4 A:QHL101 4.7 28.9 1.0
O4' C:DG3 4.9 41.1 1.0
O A:HOH209 4.9 50.4 1.0

Ruthenium binding site 2 out of 6 in 5ls8

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Ruthenium binding site 2 out of 6 in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru102

b:37.6
occ:1.00
RU A:QHL102 0.0 37.6 1.0
N12 A:QHL102 2.0 36.3 1.0
N8 A:QHL102 2.0 36.7 1.0
N9 A:QHL102 2.1 33.5 1.0
N5 A:QHL102 2.1 38.3 1.0
N2 A:QHL102 2.1 27.6 1.0
N1 A:QHL102 2.1 39.3 1.0
C36 A:QHL102 2.9 35.7 1.0
C29 A:QHL102 2.9 36.0 1.0
C26 A:QHL102 2.9 53.0 1.0
C19 A:QHL102 2.9 47.7 1.0
C1 A:QHL102 2.9 35.9 1.0
C10 A:QHL102 2.9 31.3 1.0
C38 A:QHL102 3.0 41.0 1.0
C28 A:QHL102 3.0 55.0 1.0
C2 A:QHL102 3.0 32.1 1.0
C30 A:QHL102 3.1 35.1 1.0
C12 A:QHL102 3.1 40.5 1.0
C20 A:QHL102 3.1 44.9 1.0
C35 A:QHL102 4.2 31.3 1.0
C32 A:QHL102 4.2 34.0 1.0
C25 A:QHL102 4.2 54.5 1.0
C5 A:QHL102 4.2 29.3 1.0
C22 A:QHL102 4.2 48.7 1.0
C8 A:QHL102 4.2 31.5 1.0
C37 A:QHL102 4.3 36.5 1.0
C27 A:QHL102 4.3 61.1 1.0
C3 A:QHL102 4.3 34.5 1.0
C31 A:QHL102 4.3 38.9 1.0
C21 A:QHL102 4.3 44.8 1.0
C11 A:QHL102 4.3 37.9 1.0
N11 A:QHL102 4.7 39.3 1.0
N7 A:QHL102 4.8 61.1 1.0
N10 A:QHL102 4.8 38.4 1.0
N6 A:QHL102 4.8 46.8 1.0
C4 A:QHL102 4.8 31.3 1.0
C9 A:QHL102 4.8 35.0 1.0

Ruthenium binding site 3 out of 6 in 5ls8

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Ruthenium binding site 3 out of 6 in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru101

b:35.9
occ:1.00
RU B:QHL101 0.0 35.9 1.0
N9 B:QHL101 1.8 33.3 1.0
N12 B:QHL101 1.8 39.4 1.0
N1 B:QHL101 1.8 37.4 1.0
N5 B:QHL101 1.8 39.4 1.0
N8 B:QHL101 1.8 46.1 1.0
N2 B:QHL101 1.8 38.8 1.0
C29 B:QHL101 2.7 37.3 1.0
C36 B:QHL101 2.7 41.5 1.0
C10 B:QHL101 2.7 44.2 1.0
C1 B:QHL101 2.7 35.9 1.0
C26 B:QHL101 2.7 37.9 1.0
C19 B:QHL101 2.7 46.7 1.0
C30 B:QHL101 2.8 42.8 1.0
C12 B:QHL101 2.9 44.1 1.0
C38 B:QHL101 2.9 42.7 1.0
C28 B:QHL101 2.9 40.1 1.0
C20 B:QHL101 2.9 43.6 1.0
C2 B:QHL101 2.9 37.8 1.0
C32 B:QHL101 4.0 41.4 1.0
C35 B:QHL101 4.0 38.9 1.0
C8 B:QHL101 4.1 41.7 1.0
C25 B:QHL101 4.1 45.5 1.0
C22 B:QHL101 4.1 41.6 1.0
C5 B:QHL101 4.1 32.4 1.0
C31 B:QHL101 4.1 47.8 1.0
C11 B:QHL101 4.1 44.8 1.0
C37 B:QHL101 4.1 43.8 1.0
C27 B:QHL101 4.1 47.4 1.0
C21 B:QHL101 4.1 41.0 1.0
C3 B:QHL101 4.2 33.6 1.0
N10 B:QHL101 4.6 44.8 1.0
N11 B:QHL101 4.6 41.0 1.0
N7 B:QHL101 4.6 41.6 1.0
C9 B:QHL101 4.6 46.3 1.0
N6 B:QHL101 4.6 39.2 1.0
C4 B:QHL101 4.7 34.6 1.0
O4' D:DG3 4.8 39.7 1.0
O B:HOH203 4.9 46.7 1.0

Ruthenium binding site 4 out of 6 in 5ls8

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Ruthenium binding site 4 out of 6 in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ru101

b:39.1
occ:1.00
RU C:QHL101 0.0 39.1 1.0
N9 C:QHL101 1.8 37.7 1.0
N8 C:QHL101 1.8 49.8 1.0
N12 C:QHL101 1.8 43.2 1.0
N5 C:QHL101 1.8 51.0 1.0
N1 C:QHL101 1.8 37.7 1.0
N2 C:QHL101 1.9 43.6 1.0
C26 C:QHL101 2.7 46.9 1.0
C19 C:QHL101 2.7 51.6 1.0
C29 C:QHL101 2.7 44.0 1.0
C36 C:QHL101 2.7 37.7 1.0
C10 C:QHL101 2.8 36.2 1.0
C1 C:QHL101 2.8 36.0 1.0
C30 C:QHL101 2.9 44.1 1.0
C12 C:QHL101 2.9 44.5 1.0
C28 C:QHL101 2.9 50.3 1.0
C38 C:QHL101 2.9 40.2 1.0
C20 C:QHL101 2.9 44.5 1.0
C2 C:QHL101 2.9 34.4 1.0
C25 C:QHL101 4.0 52.8 1.0
C32 C:QHL101 4.0 39.7 1.0
C22 C:QHL101 4.0 56.0 1.0
C35 C:QHL101 4.1 46.0 1.0
C8 C:QHL101 4.1 36.8 1.0
C27 C:QHL101 4.1 46.5 1.0
C31 C:QHL101 4.1 36.8 1.0
C5 C:QHL101 4.1 23.0 1.0
C11 C:QHL101 4.1 41.4 1.0
C37 C:QHL101 4.1 46.1 1.0
C21 C:QHL101 4.1 52.5 1.0
C3 C:QHL101 4.2 34.2 1.0
N7 C:QHL101 4.6 47.3 1.0
N10 C:QHL101 4.6 40.8 1.0
N6 C:QHL101 4.6 50.8 1.0
N11 C:QHL101 4.6 40.6 1.0
C9 C:QHL101 4.7 40.1 1.0
O4' A:DG3 4.7 39.0 1.0
C4 C:QHL101 4.7 31.4 1.0
O C:HOH203 4.8 51.7 1.0

Ruthenium binding site 5 out of 6 in 5ls8

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Ruthenium binding site 5 out of 6 in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 5 of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ru102

b:38.1
occ:1.00
RU C:QHL102 0.0 38.1 1.0
N12 C:QHL102 2.0 36.9 1.0
N2 C:QHL102 2.0 25.5 1.0
N9 C:QHL102 2.0 40.8 1.0
N1 C:QHL102 2.0 36.8 1.0
N8 C:QHL102 2.1 44.8 1.0
N5 C:QHL102 2.1 36.3 1.0
C36 C:QHL102 2.9 41.9 1.0
C29 C:QHL102 2.9 39.0 1.0
C1 C:QHL102 2.9 36.0 1.0
C10 C:QHL102 2.9 34.6 1.0
C19 C:QHL102 2.9 51.0 1.0
C26 C:QHL102 2.9 54.5 1.0
C38 C:QHL102 3.0 41.7 1.0
C2 C:QHL102 3.0 33.8 1.0
C12 C:QHL102 3.0 42.1 1.0
C28 C:QHL102 3.1 56.8 1.0
C30 C:QHL102 3.1 40.4 1.0
C20 C:QHL102 3.1 45.1 1.0
C35 C:QHL102 4.2 35.2 1.0
C32 C:QHL102 4.2 36.9 1.0
C5 C:QHL102 4.2 32.3 1.0
C8 C:QHL102 4.2 31.6 1.0
C22 C:QHL102 4.2 46.5 1.0
C25 C:QHL102 4.2 57.0 1.0
C37 C:QHL102 4.3 39.9 1.0
C3 C:QHL102 4.3 35.5 1.0
C11 C:QHL102 4.3 39.2 1.0
C31 C:QHL102 4.3 40.3 1.0
C27 C:QHL102 4.3 61.2 1.0
C21 C:QHL102 4.3 48.6 1.0
N11 C:QHL102 4.7 43.1 1.0
N10 C:QHL102 4.7 38.8 1.0
C4 C:QHL102 4.8 31.1 1.0
N7 C:QHL102 4.8 57.2 1.0
N6 C:QHL102 4.8 51.0 1.0
C9 C:QHL102 4.8 34.6 1.0
C16 A:QHL102 5.0 38.7 1.0

Ruthenium binding site 6 out of 6 in 5ls8

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Ruthenium binding site 6 out of 6 in the Light-Activated Ruthenium Complex Bound to A Dna Quadruplex


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 6 of Light-Activated Ruthenium Complex Bound to A Dna Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ru101

b:36.5
occ:1.00
RU D:QHL101 0.0 36.5 1.0
N9 D:QHL101 1.8 35.0 1.0
N1 D:QHL101 1.8 38.8 1.0
N12 D:QHL101 1.8 42.0 1.0
N5 D:QHL101 1.8 38.2 1.0
N8 D:QHL101 1.8 47.5 1.0
N2 D:QHL101 1.8 36.4 1.0
C29 D:QHL101 2.7 36.1 1.0
C36 D:QHL101 2.7 41.2 1.0
C10 D:QHL101 2.7 39.9 1.0
C1 D:QHL101 2.7 38.1 1.0
C19 D:QHL101 2.7 45.5 1.0
C26 D:QHL101 2.7 40.5 1.0
C30 D:QHL101 2.8 42.0 1.0
C12 D:QHL101 2.8 46.0 1.0
C38 D:QHL101 2.9 43.9 1.0
C20 D:QHL101 2.9 41.2 1.0
C28 D:QHL101 2.9 42.5 1.0
C2 D:QHL101 2.9 32.0 1.0
C32 D:QHL101 4.0 39.6 1.0
C35 D:QHL101 4.0 43.7 1.0
C8 D:QHL101 4.0 40.6 1.0
C5 D:QHL101 4.1 22.6 1.0
C22 D:QHL101 4.1 41.9 1.0
C25 D:QHL101 4.1 48.0 1.0
C31 D:QHL101 4.1 48.0 1.0
C11 D:QHL101 4.1 39.3 1.0
C37 D:QHL101 4.1 46.6 1.0
C21 D:QHL101 4.1 39.5 1.0
C27 D:QHL101 4.1 50.5 1.0
C3 D:QHL101 4.2 30.9 1.0
N10 D:QHL101 4.6 46.1 1.0
N11 D:QHL101 4.6 45.4 1.0
C9 D:QHL101 4.6 45.9 1.0
N6 D:QHL101 4.6 39.3 1.0
N7 D:QHL101 4.6 43.3 1.0
C4 D:QHL101 4.7 29.5 1.0
O4' B:DG3 4.9 41.3 1.0

Reference:

K.Mcquaid, H.Abell, S.P.Gurung, D.R.Allan, G.Winter, T.Sorensen, D.J.Cardin, J.A.Brazier, C.J.Cardin, J.P.Hall. Structural Studies Reveal Enantiospecific Recognition of A Dna G-Quadruplex By A Ruthenium Polypyridyl Complex. Angew.Chem.Int.Ed.Engl. V. 58 9881 2019.
ISSN: ESSN 1521-3773
PubMed: 30958918
DOI: 10.1002/ANIE.201814502
Page generated: Wed Dec 16 02:08:37 2020

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