Potassium in PDB 7dfy: Novel Motif For Left-Handed G-Quadruplex Formation

The structure of Novel Motif For Left-Handed G-Quadruplex Formation, PDB code: 7dfy was solved by P.Das, F.R.Winnerdy, A.Maity, Y.Mechulam, A.T.Phan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.99 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	28.405, 31.601, 77.764, 90, 98.07, 90
R / Rfree (%)	20.1 / 25.9

The structure of Novel Motif For Left-Handed G-Quadruplex Formation also contains other interesting chemical elements:

Strontium

(Sr)

10 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Potassium atom in the Novel Motif For Left-Handed G-Quadruplex Formation (pdb code 7dfy). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 11 binding sites of Potassium where determined in the Novel Motif For Left-Handed G-Quadruplex Formation, PDB code: 7dfy:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 11 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:6.1 occ:1.00 O6 A:DG8 2.7 5.0 1.0 O6 A:DG10 2.7 6.9 1.0 O6 A:DG5 2.7 7.0 1.0 O6 A:DG12 2.9 6.3 1.0 O6 A:DG7 2.9 11.9 1.0 O6 A:DG1 2.9 13.9 1.0 O6 A:DG2 2.9 8.9 1.0 O6 A:DG4 3.2 13.6 1.0 K A:K103 3.5 12.1 1.0 C6 A:DG10 3.6 6.6 1.0 C6 A:DG8 3.6 7.4 1.0 C6 A:DG7 3.6 15.1 1.0 K A:K104 3.6 13.3 1.0 C6 A:DG1 3.7 10.7 1.0 C6 A:DG5 3.7 4.8 1.0 C6 A:DG12 3.8 5.5 1.0 C6 A:DG2 3.8 11.0 1.0 N1 A:DG10 3.8 8.6 1.0 N1 A:DG7 3.9 6.8 1.0 C6 A:DG4 3.9 9.0 1.0 N1 A:DG8 3.9 9.1 1.0 N1 A:DG4 4.0 5.2 1.0 N1 A:DG1 4.0 12.8 1.0 N1 A:DG2 4.1 6.3 1.0 N1 A:DG5 4.1 6.4 1.0 N1 A:DG12 4.2 8.4 1.0 C5 A:DG1 4.8 13.0 1.0 C5 A:DG7 4.8 12.3 1.0 C5 A:DG8 4.8 5.6 1.0 C5 A:DG10 4.8 9.6 1.0 C5 A:DG12 4.9 9.9 1.0 C5 A:DG5 5.0 6.3 1.0 C5 A:DG4 5.0 4.8 1.0

Potassium binding site 2 out of 11 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:7.0 occ:1.00 O6 A:DG16 2.7 10.2 1.0 O6 A:DG19 2.8 5.6 1.0 O6 A:DG24 2.8 9.4 1.0 O6 A:DG22 2.8 9.8 1.0 O6 A:DG26 2.8 13.5 1.0 O6 A:DG18 3.0 6.5 1.0 O6 A:DG15 3.0 9.4 1.0 O6 A:DG21 3.2 5.8 1.0 K A:K103 3.4 12.1 1.0 C6 A:DG16 3.6 10.3 1.0 C6 A:DG24 3.7 8.2 1.0 C6 A:DG19 3.7 8.8 1.0 C6 A:DG26 3.7 12.2 1.0 C6 A:DG15 3.7 5.9 1.0 C6 A:DG18 3.7 5.7 1.0 C6 A:DG22 3.8 10.3 1.0 C6 A:DG21 3.9 3.5 1.0 N1 A:DG24 3.9 13.4 1.0 N1 A:DG15 4.0 4.8 1.0 N1 A:DG18 4.0 11.6 1.0 K A:K105 4.0 59.7 1.0 N1 A:DG26 4.0 7.3 1.0 N1 A:DG21 4.0 3.4 1.0 N1 A:DG19 4.0 6.9 1.0 N1 A:DG16 4.0 7.5 1.0 N1 A:DG22 4.1 3.5 1.0 C5 A:DG16 4.8 7.3 1.0 C5 A:DG18 4.9 9.7 1.0 C5 A:DG15 4.9 5.9 1.0 C5 A:DG24 4.9 4.5 1.0 C5 A:DG19 4.9 7.4 1.0 C5 A:DG26 4.9 8.0 1.0 C5 A:DG22 5.0 9.7 1.0

Potassium binding site 3 out of 11 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:12.1 occ:1.00 O6 A:DG26 2.8 13.5 1.0 O6 A:DG2 2.8 8.9 1.0 O6 A:DG8 2.9 5.0 1.0 O6 A:DG12 2.9 6.3 1.0 O6 A:DG22 2.9 9.8 1.0 O6 A:DG16 2.9 10.2 1.0 O6 A:DG5 3.0 7.0 1.0 O6 A:DG19 3.0 5.6 1.0 K A:K102 3.4 7.0 1.0 K A:K101 3.5 6.1 1.0 C6 A:DG2 3.7 11.0 1.0 C6 A:DG26 3.7 12.2 1.0 C6 A:DG8 3.7 7.4 1.0 C6 A:DG22 3.7 10.3 1.0 C6 A:DG19 3.8 8.8 1.0 C6 A:DG12 3.8 5.5 1.0 C6 A:DG16 3.8 10.3 1.0 C6 A:DG5 3.8 4.8 1.0 N1 A:DG2 4.0 6.3 1.0 N1 A:DG8 4.0 9.1 1.0 N1 A:DG26 4.0 7.3 1.0 N1 A:DG22 4.0 3.5 1.0 N1 A:DG19 4.1 6.9 1.0 N1 A:DG12 4.1 8.4 1.0 N1 A:DG5 4.1 6.4 1.0 N1 A:DG16 4.2 7.5 1.0 C5 A:DG8 4.9 5.6 1.0 C5 A:DG2 4.9 8.8 1.0 C5 A:DG26 4.9 8.0 1.0 C5 A:DG22 4.9 9.7 1.0 C5 A:DG5 4.9 6.3 1.0 C5 A:DG16 5.0 7.3 1.0 C5 A:DG19 5.0 7.4 1.0 C5 A:DG12 5.0 9.9 1.0

Potassium binding site 4 out of 11 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:13.3 occ:1.00 O2 B:DT25 2.6 16.7 1.0 O6 A:DG4 2.6 13.6 1.0 O6 A:DG7 2.7 11.9 1.0 O6 A:DG1 2.9 13.9 1.0 O A:HOH254 3.0 10.6 1.0 O A:HOH252 3.0 15.5 1.0 O6 A:DG10 3.2 6.9 1.0 C6 A:DG4 3.5 9.0 1.0 K A:K101 3.6 6.1 1.0 C6 A:DG7 3.6 15.1 1.0 O B:HOH216 3.7 31.9 1.0 C2 B:DT25 3.7 17.9 1.0 N1 A:DG4 3.8 5.2 1.0 C6 A:DG1 3.8 10.7 1.0 C6 A:DG10 3.9 6.6 1.0 N1 A:DG7 4.0 6.8 1.0 N1 A:DG10 4.2 8.6 1.0 N1 A:DG1 4.2 12.8 1.0 C1' B:DT25 4.3 17.6 1.0 C2' B:DT25 4.4 20.3 1.0 O A:HOH210 4.4 17.9 1.0 N1 B:DT25 4.5 22.6 1.0 N3 B:DT25 4.7 21.9 1.0 C5 A:DG4 4.8 4.8 1.0 C5 A:DG7 4.9 12.3 1.0

Potassium binding site 5 out of 11 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range: probe atom residue distance (Å) B Occ A:K105 b:59.7 occ:1.00 O A:HOH263 2.5 12.8 1.0 O6 A:DG15 2.8 9.4 1.0 O6 A:DG21 3.1 5.8 1.0 O6 A:DG18 3.1 6.5 1.0 O6 A:DG24 3.2 9.4 1.0 C6 A:DG15 3.8 5.9 1.0 C6 A:DG24 3.9 8.2 1.0 K A:K102 4.0 7.0 1.0 C6 A:DG21 4.0 3.5 1.0 C6 A:DG18 4.0 5.7 1.0 N1 A:DG15 4.2 4.8 1.0 N1 A:DG24 4.2 13.4 1.0 N1 A:DG21 4.2 3.4 1.0 N1 A:DG18 4.4 11.6 1.0 O A:HOH236 4.8 17.6 1.0 C5 A:DG15 5.0 5.9 1.0

Potassium binding site 6 out of 11 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range: probe atom residue distance (Å) B Occ A:K106 b:28.9 occ:1.00 OP1 A:DG22 2.7 3.4 1.0 P A:DG22 3.9 12.7 1.0 O3' A:DG21 4.4 7.5 1.0 C3' A:DG21 4.4 17.1 1.0 OP2 A:DG22 4.5 8.8 1.0 C4' A:DG21 4.7 15.6 1.0 C5' A:DG21 4.8 10.9 1.0 OP2 A:DG21 4.9 18.3 1.0

Potassium binding site 7 out of 11 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:23.9 occ:1.00 O6 B:DG10 2.8 25.9 1.0 O6 B:DG4 2.8 33.1 1.0 O6 B:DG7 2.8 31.4 1.0 O6 B:DG12 2.8 21.3 1.0 O6 B:DG5 2.9 35.1 1.0 O6 B:DG1 2.9 27.2 1.0 O6 B:DG8 3.0 42.0 1.0 O6 B:DG2 3.0 27.2 1.0 C6 B:DG4 3.5 25.3 1.0 C6 B:DG1 3.6 19.6 1.0 K B:K103 3.6 33.0 1.0 C6 B:DG7 3.6 33.0 1.0 C6 B:DG12 3.6 24.5 1.0 C6 B:DG10 3.7 21.1 1.0 N1 B:DG1 3.7 20.7 1.0 N1 B:DG4 3.7 26.6 1.0 C6 B:DG5 3.8 34.0 1.0 C6 B:DG8 3.8 30.5 1.0 C6 B:DG2 3.8 27.5 1.0 N1 B:DG10 3.9 18.7 1.0 N1 B:DG8 4.0 25.1 1.0 N1 B:DG7 4.0 33.7 1.0 N1 B:DG12 4.0 22.3 1.0 O B:HOH204 4.0 33.4 1.0 N1 B:DG2 4.1 36.6 1.0 N1 B:DG5 4.1 30.6 1.0 C5 B:DG4 4.7 26.1 1.0 C5 B:DG12 4.7 21.6 1.0 C5 B:DG7 4.7 35.3 1.0 C5 B:DG1 4.7 18.1 1.0 C2 B:DG1 4.9 20.6 1.0 C2 B:DG4 4.9 35.6 1.0 C5 B:DG5 5.0 32.3 1.0 C5 B:DG10 5.0 22.3 1.0

Potassium binding site 8 out of 11 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:31.9 occ:1.00 O6 B:DG19 2.7 29.8 1.0 O6 B:DG16 2.8 30.3 1.0 O6 B:DG22 2.8 25.0 1.0 O6 B:DG21 2.8 38.4 1.0 O6 B:DG18 2.9 29.1 1.0 O6 B:DG24 3.0 28.0 1.0 O6 B:DG26 3.0 21.8 1.0 O6 B:DG15 3.1 43.9 1.0 K B:K103 3.4 33.0 1.0 C6 B:DG19 3.5 29.0 1.0 C6 B:DG18 3.6 33.5 1.0 C6 B:DG16 3.6 36.9 1.0 C6 B:DG21 3.7 30.3 1.0 C6 B:DG15 3.7 38.8 1.0 C6 B:DG22 3.8 31.8 1.0 N1 B:DG18 3.8 41.7 1.0 N1 B:DG15 3.8 38.7 1.0 N1 B:DG19 3.8 33.8 1.0 C6 B:DG24 3.9 22.6 1.0 C6 B:DG26 3.9 20.6 1.0 N1 B:DG16 3.9 40.1 1.0 N1 B:DG21 4.1 26.5 1.0 N1 B:DG22 4.1 29.1 1.0 N1 B:DG24 4.1 22.0 1.0 N1 B:DG26 4.2 20.8 1.0 C5 B:DG18 4.7 36.6 1.0 C5 B:DG21 4.8 32.0 1.0 C5 B:DG19 4.8 30.9 1.0 C5 B:DG16 4.9 35.5 1.0 C5 B:DG15 4.9 33.3 1.0 C2 B:DG15 4.9 36.6 1.0 C2 B:DG18 5.0 41.4 1.0 C5 B:DG22 5.0 31.3 1.0

Potassium binding site 9 out of 11 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:33.0 occ:1.00 O6 B:DG12 2.7 21.3 1.0 O6 B:DG2 2.8 27.2 1.0 O6 B:DG5 2.8 35.1 1.0 O6 B:DG16 2.8 30.3 1.0 O6 B:DG22 2.8 25.0 1.0 O6 B:DG26 2.9 21.8 1.0 O6 B:DG19 2.9 29.8 1.0 O6 B:DG8 3.1 42.0 1.0 K B:K102 3.4 31.9 1.0 C6 B:DG12 3.6 24.5 1.0 K B:K101 3.6 23.9 1.0 C6 B:DG2 3.7 27.5 1.0 C6 B:DG19 3.7 29.0 1.0 C6 B:DG16 3.7 36.9 1.0 C6 B:DG5 3.7 34.0 1.0 C6 B:DG22 3.7 31.8 1.0 C6 B:DG26 3.8 20.6 1.0 C6 B:DG8 3.8 30.5 1.0 N1 B:DG12 3.9 22.3 1.0 N1 B:DG19 3.9 33.8 1.0 N1 B:DG8 4.0 25.1 1.0 N1 B:DG16 4.0 40.1 1.0 N1 B:DG26 4.0 20.8 1.0 N1 B:DG2 4.0 36.6 1.0 N1 B:DG22 4.0 29.1 1.0 N1 B:DG5 4.1 30.6 1.0 C5 B:DG12 4.8 21.6 1.0 C5 B:DG5 4.8 32.3 1.0 C5 B:DG2 4.9 21.5 1.0 C5 B:DG22 4.9 31.3 1.0 C5 B:DG16 4.9 35.5 1.0 C5 B:DG19 4.9 30.9 1.0

Potassium binding site 10 out of 11 in the Novel Motif For Left-Handed G-Quadruplex Formation


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Novel Motif For Left-Handed G-Quadruplex Formation within 5.0Å range: probe atom residue distance (Å) B Occ B:K104 b:115.5 occ:1.00 O6 B:DG24 3.5 28.0 1.0 C6 B:DG24 3.7 22.6 1.0 N1 B:DG24 4.1 22.0 1.0 O6 B:DG15 4.2 43.9 1.0 C5 B:DG24 4.3 21.5 1.0 O6 B:DG21 4.4 38.4 1.0 N1 B:DG21 4.6 26.5 1.0 C6 B:DG21 4.8 30.3 1.0 N7 B:DG24 4.8 24.5 1.0 C2 B:DG24 4.9 22.4 1.0 O2 B:DT23 5.0 43.8 1.0

P.Das, F.R.Winnerdy, A.Maity, Y.Mechulam, A.T.Phan. A Novel Minimal Motif For Left-Handed G-Quadruplex Formation. Chem.Commun.(Camb.) V. 57 2527 2021.
ISSN: ESSN 1364-548X
PubMed: 33690751
DOI: 10.1039/D0CC08146A