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Potassium in PDB 7otb: Ruthenium Polypridyl Complex Bound to A Unimolecular Chair-Form G- Quadruplex

Protein crystallography data

The structure of Ruthenium Polypridyl Complex Bound to A Unimolecular Chair-Form G- Quadruplex, PDB code: 7otb was solved by K.T.Mcquaid, C.J.Cardin, J.P.Hall, N.G.Paterson, L.Baumgaertner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.29 / 1.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 29.68, 29.68, 113.98, 90, 90, 120
R / Rfree (%) 16.5 / 18.1

Other elements in 7otb:

The structure of Ruthenium Polypridyl Complex Bound to A Unimolecular Chair-Form G- Quadruplex also contains other interesting chemical elements:

Barium (Ba) 1 atom
Ruthenium (Ru) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Ruthenium Polypridyl Complex Bound to A Unimolecular Chair-Form G- Quadruplex (pdb code 7otb). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Ruthenium Polypridyl Complex Bound to A Unimolecular Chair-Form G- Quadruplex, PDB code: 7otb:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 7otb

Go back to Potassium Binding Sites List in 7otb
Potassium binding site 1 out of 4 in the Ruthenium Polypridyl Complex Bound to A Unimolecular Chair-Form G- Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Ruthenium Polypridyl Complex Bound to A Unimolecular Chair-Form G- Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K101

b:19.6
occ:1.00
O6 A:DG1 2.6 19.6 1.0
O6 A:DG9 2.6 21.5 1.0
O6 A:DG13 2.7 23.1 1.0
O6 A:DG14 2.8 21.6 0.5
O6 A:DG14 2.8 21.6 0.5
O6 A:DG21 2.8 20.9 1.0
O6 A:DG20 2.9 20.6 0.5
O6 A:DG8 2.9 22.7 0.5
O6 A:DG20 2.9 22.4 0.5
O6 A:DG2 2.9 23.1 0.5
O6 A:DG8 3.1 21.6 0.5
O6 A:DG2 3.2 23.6 0.5
H1 A:DG13 3.2 26.8 1.0
H1 A:DG9 3.3 24.0 1.0
H1 A:DG21 3.4 23.1 1.0
C6 A:DG13 3.4 20.7 1.0
H1 A:DG14 3.5 25.9 0.5
H1 A:DG20 3.5 23.9 0.5
C6 A:DG1 3.5 20.3 1.0
H1 A:DG1 3.5 21.9 1.0
K A:K102 3.6 17.8 1.0
C6 A:DG9 3.6 21.1 1.0
C6 A:DG20 3.6 20.7 0.5
N1 A:DG13 3.6 22.3 1.0
C6 A:DG14 3.6 22.3 0.5
C6 A:DG20 3.7 20.6 0.5
H1 A:DG20 3.7 26.7 0.5
H1 A:DG2 3.7 27.6 0.5
C6 A:DG8 3.7 21.4 0.5
H1 A:DG14 3.7 27.4 0.5
C6 A:DG14 3.7 22.2 0.5
H1 A:DG8 3.8 26.0 0.5
C6 A:DG21 3.8 20.3 1.0
H1 A:DG8 3.8 27.0 0.5
N1 A:DG9 3.8 20.0 1.0
N1 A:DG20 3.8 19.9 0.5
C6 A:DG2 3.8 23.4 0.5
C6 A:DG8 3.9 21.3 0.5
N1 A:DG14 3.9 21.6 0.5
N1 A:DG1 3.9 18.3 1.0
N1 A:DG21 4.0 19.2 1.0
N1 A:DG20 4.0 22.2 0.5
H1 A:DG2 4.0 29.3 0.5
N1 A:DG8 4.1 21.6 0.5
C6 A:DG2 4.1 23.6 0.5
N1 A:DG14 4.1 22.9 0.5
N1 A:DG2 4.1 23.0 0.5
N1 A:DG8 4.2 22.5 0.5
C52 A:0K8106 4.4 21.4 1.0
N1 A:DG2 4.5 24.4 0.5
C13 A:0K8106 4.6 18.5 1.0
O59 A:0K8106 4.6 19.9 1.0
C5 A:DG20 4.7 21.8 0.5
C5 A:DG13 4.7 22.5 1.0
C5 A:DG1 4.8 20.9 1.0
C5 A:DG20 4.8 21.4 0.5
C5 A:DG8 4.8 21.2 0.5
C5 A:DG14 4.9 22.5 0.5
C2 A:DG13 4.9 23.0 1.0
C53 A:0K8106 4.9 19.1 1.0
C5 A:DG9 4.9 20.6 1.0
C14 A:0K8106 4.9 18.6 1.0
C5 A:DG14 5.0 22.0 0.5
C2 A:DG20 5.0 21.0 0.5

Potassium binding site 2 out of 4 in 7otb

Go back to Potassium Binding Sites List in 7otb
Potassium binding site 2 out of 4 in the Ruthenium Polypridyl Complex Bound to A Unimolecular Chair-Form G- Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Ruthenium Polypridyl Complex Bound to A Unimolecular Chair-Form G- Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K102

b:17.8
occ:1.00
O6 A:DG2 2.6 23.1 0.5
O6 A:DG14 2.7 21.6 0.5
O6 A:DG2 2.7 23.6 0.5
O6 A:DG7 2.7 19.4 1.0
O6 A:DG19 2.7 21.4 1.0
O6 A:DG8 2.7 21.6 0.5
O6 A:DG20 2.8 22.4 0.5
O6 A:DG8 2.8 22.7 0.5
O6 A:DG15 2.8 19.8 1.0
O6 A:DG14 2.8 21.6 0.5
O6 A:DG3 2.8 21.8 1.0
O6 A:DG20 2.9 20.6 0.5
H1 A:DG8 3.3 26.0 0.5
C6 A:DG2 3.4 23.4 0.5
H1 A:DG15 3.4 24.7 1.0
H1 A:DG3 3.4 26.0 1.0
H1 A:DG2 3.4 27.6 0.5
C6 A:DG14 3.5 22.3 0.5
H1 A:DG20 3.5 23.9 0.5
K A:K101 3.6 19.6 1.0
C6 A:DG19 3.6 20.4 1.0
C6 A:DG7 3.6 20.9 1.0
K A:K103 3.6 20.9 1.0
H1 A:DG14 3.6 27.4 0.5
C6 A:DG14 3.6 22.2 0.5
C6 A:DG2 3.6 23.6 0.5
H1 A:DG14 3.6 25.9 0.5
C6 A:DG8 3.6 21.4 0.5
H1 A:DG20 3.6 26.7 0.5
H1 A:DG8 3.7 27.0 0.5
H1 A:DG19 3.7 26.0 1.0
C6 A:DG20 3.7 20.7 0.5
H1 A:DG7 3.7 26.4 1.0
C6 A:DG15 3.7 21.3 1.0
C6 A:DG8 3.7 21.3 0.5
H1 A:DG2 3.7 29.3 0.5
C6 A:DG3 3.7 21.0 1.0
N1 A:DG2 3.7 23.0 0.5
N1 A:DG8 3.8 21.6 0.5
C6 A:DG20 3.8 20.6 0.5
N1 A:DG14 3.9 21.6 0.5
N1 A:DG3 3.9 21.6 1.0
N1 A:DG15 3.9 20.6 1.0
N1 A:DG14 3.9 22.9 0.5
N1 A:DG20 4.0 19.9 0.5
N1 A:DG19 4.0 21.7 1.0
N1 A:DG7 4.0 22.0 1.0
N1 A:DG2 4.0 24.4 0.5
N1 A:DG8 4.1 22.5 0.5
N1 A:DG20 4.1 22.2 0.5
C5 A:DG2 4.5 24.5 0.5
C5 A:DG14 4.6 22.5 0.5
C5 A:DG19 4.7 19.4 1.0
C5 A:DG7 4.7 21.6 1.0
C5 A:DG2 4.7 24.3 0.5
C5 A:DG14 4.8 22.0 0.5
C5 A:DG8 4.9 21.2 0.5
C5 A:DG8 5.0 21.6 0.5
C2 A:DG2 5.0 23.8 0.5
C5 A:DG20 5.0 21.8 0.5

Potassium binding site 3 out of 4 in 7otb

Go back to Potassium Binding Sites List in 7otb
Potassium binding site 3 out of 4 in the Ruthenium Polypridyl Complex Bound to A Unimolecular Chair-Form G- Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Ruthenium Polypridyl Complex Bound to A Unimolecular Chair-Form G- Quadruplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:20.9
occ:1.00
O4 A:DT16 2.8 25.1 1.0
O A:HOH266 2.8 34.9 1.0
O6 A:DG7 2.8 19.4 1.0
O6 A:DG3 2.8 21.8 1.0
O2 A:DT5 2.9 26.5 1.0
O2 A:DT18 2.9 25.1 1.0
O6 A:DG19 2.9 21.4 1.0
O6 A:DG15 2.9 19.8 1.0
H1 A:DG7 3.4 26.4 1.0
H3 A:DT5 3.4 31.5 1.0
H1 A:DG19 3.5 26.0 1.0
K A:K102 3.6 17.8 1.0
C6 A:DG3 3.6 21.0 1.0
C6 A:DG7 3.6 20.9 1.0
C2 A:DT18 3.7 25.5 1.0
C6 A:DG15 3.7 21.3 1.0
C6 A:DG19 3.7 20.4 1.0
C2 A:DT5 3.7 27.2 1.0
H1 A:DG3 3.7 26.0 1.0
N1 A:DG7 3.8 22.0 1.0
N3 A:DT5 3.9 26.2 1.0
N1 A:DG19 4.0 21.7 1.0
C4 A:DT16 4.0 22.8 1.0
O A:HOH201 4.0 33.7 0.7
H3 A:DT18 4.0 30.6 1.0
H1 A:DG15 4.0 24.7 1.0
N1 A:DG3 4.0 21.6 1.0
N1 A:DG15 4.2 20.6 1.0
N3 A:DT18 4.2 25.5 1.0
H1' A:DT18 4.3 30.9 1.0
H3 A:DT16 4.3 27.0 1.0
H73 A:DT16 4.3 29.8 1.0
N1 A:DT18 4.6 25.0 1.0
N3 A:DT16 4.6 22.5 1.0
C5 A:DG15 4.6 21.0 1.0
C5 A:DG3 4.7 22.2 1.0
H4' A:DA6 4.7 39.1 0.4
H4' A:DA6 4.9 39.1 0.6
C5 A:DG7 4.9 21.6 1.0
C1' A:DT18 4.9 25.8 1.0
H1' A:DT5 5.0 35.1 1.0
C5 A:DG19 5.0 19.4 1.0

Potassium binding site 4 out of 4 in 7otb

Go back to Potassium Binding Sites List in 7otb
Potassium binding site 4 out of 4 in the Ruthenium Polypridyl Complex Bound to A Unimolecular Chair-Form G- Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Ruthenium Polypridyl Complex Bound to A Unimolecular Chair-Form G- Quadruplex within 5.0Å range:

Reference:

K.T.Mcquaid, S.Takahashi, L.Baumgaertner, D.J.Cardin, N.G.Paterson, J.P.Hall, N.Sugimoto, C.J.Cardin. Ruthenium Polypyridyl Complex Bound to A Unimolecular Chair-Form G-Quadruplex. J.Am.Chem.Soc. V. 144 5956 2022.
ISSN: ESSN 1520-5126
PubMed: 35324198
DOI: 10.1021/JACS.2C00178
Page generated: Wed Apr 5 09:46:15 2023

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