Potassium in PDB 6ftu: Structure of A Quadruplex Forming Sequence From D. Discoideum

The structure of Structure of A Quadruplex Forming Sequence From D. Discoideum, PDB code: 6ftu was solved by A.Guedin, L.Linda, S.Armane, L.Lacroix, J.L.Mergny, S.Thore, L.A.Yatsunyk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.88 / 2.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.060, 135.750, 55.200, 90.00, 93.58, 90.00
R / Rfree (%)	21.8 / 28.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Potassium atom in the Structure of A Quadruplex Forming Sequence From D. Discoideum (pdb code 6ftu). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 21 binding sites of Potassium where determined in the Structure of A Quadruplex Forming Sequence From D. Discoideum, PDB code: 6ftu:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 21 in the Structure of A Quadruplex Forming Sequence From D. Discoideum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of A Quadruplex Forming Sequence From D. Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:65.6 occ:1.00 O6 A:DG7 2.5 52.5 1.0 O6 A:DG23 2.6 69.8 1.0 O6 A:DG24 2.7 50.0 1.0 O6 A:DG18 2.7 62.3 1.0 O6 A:DG17 2.8 58.3 1.0 O6 A:DG8 2.9 48.7 1.0 O6 A:DG3 3.0 49.0 1.0 O6 A:DG4 3.0 48.6 1.0 K A:K102 3.1 62.5 1.0 N1 A:DG18 3.3 57.7 1.0 C6 A:DG18 3.4 61.6 1.0 C6 A:DG7 3.6 51.9 1.0 C6 A:DG23 3.6 64.5 1.0 C6 A:DG17 3.6 60.4 1.0 C6 A:DG24 3.6 50.8 1.0 C6 A:DG8 3.6 57.4 1.0 C6 A:DG3 3.8 51.7 1.0 N1 A:DG4 3.8 50.6 1.0 C6 A:DG4 3.8 52.3 1.0 N1 A:DG8 3.9 63.1 1.0 N1 A:DG17 4.0 53.9 1.0 N1 A:DG7 4.0 51.2 1.0 N1 A:DG23 4.0 60.3 1.0 N1 A:DG3 4.1 47.3 1.0 N1 A:DG24 4.1 48.7 1.0 C2 A:DG18 4.6 55.1 1.0 C5 A:DG17 4.7 60.5 1.0 C5 A:DG18 4.8 60.8 1.0 C5 A:DG7 4.8 52.2 1.0 N6 A:DA22 4.8 78.5 1.0 C5 A:DG24 4.8 49.6 1.0 C5 A:DG23 4.8 62.6 1.0 C5 A:DG8 4.9 57.9 1.0 C5 A:DG3 5.0 54.2 1.0 N2 A:DG18 5.0 53.2 1.0

Potassium binding site 2 out of 21 in the Structure of A Quadruplex Forming Sequence From D. Discoideum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of A Quadruplex Forming Sequence From D. Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:62.5 occ:1.00 O6 A:DG17 2.4 58.3 1.0 O6 A:DG3 2.5 49.0 1.0 O6 A:DG8 2.5 48.7 1.0 O6 A:DG24 2.6 50.0 1.0 O6 A:DG25 2.8 61.9 1.0 O6 A:DG16 3.0 54.3 1.0 K A:K101 3.1 65.6 1.0 O6 A:DG9 3.2 62.8 1.0 O6 A:DG2 3.2 51.8 1.0 C6 A:DG8 3.4 57.4 1.0 K A:K103 3.4 64.4 1.0 C6 A:DG24 3.4 50.8 1.0 C6 A:DG17 3.4 60.4 1.0 C6 A:DG3 3.5 51.7 1.0 N1 A:DG8 3.5 63.1 1.0 C6 A:DG16 3.7 58.0 1.0 C6 A:DG25 3.8 71.8 1.0 N1 A:DG24 3.8 48.7 1.0 C6 A:DG2 3.8 49.8 1.0 N1 A:DG3 3.8 47.3 1.0 N1 A:DG17 3.9 53.9 1.0 N1 A:DG2 3.9 47.9 1.0 C6 A:DG9 3.9 61.7 1.0 N1 A:DG16 4.0 58.4 1.0 N1 A:DG9 4.1 64.3 1.0 N1 A:DG25 4.2 70.7 1.0 C5 A:DG8 4.7 57.9 1.0 C5 A:DG24 4.7 49.6 1.0 C5 A:DG17 4.7 60.5 1.0 C5 A:DG3 4.8 54.2 1.0 C2 A:DG8 4.8 66.9 1.0 C5 A:DG16 4.9 53.7 1.0 C5 A:DG2 4.9 47.2 1.0 O6 A:DG7 4.9 52.5 1.0 C5 A:DG25 5.0 76.7 1.0

Potassium binding site 3 out of 21 in the Structure of A Quadruplex Forming Sequence From D. Discoideum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of A Quadruplex Forming Sequence From D. Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:64.4 occ:1.00 O6 A:DG9 2.4 62.8 1.0 O6 A:DG25 2.5 61.9 1.0 O6 A:DG16 2.6 54.3 1.0 O6 A:DG26 2.7 64.5 1.0 O6 A:DG2 2.7 51.8 1.0 O6 A:DG1 2.8 55.7 1.0 O6 A:DG15 2.8 61.8 1.0 O6 A:DG10 3.0 72.4 1.0 C6 A:DG25 3.3 71.8 1.0 C6 A:DG9 3.3 61.7 1.0 K A:K102 3.4 62.5 1.0 C6 A:DG16 3.5 58.0 1.0 C6 A:DG2 3.5 49.8 1.0 N1 A:DG2 3.6 47.9 1.0 C6 A:DG26 3.6 66.7 1.0 N1 A:DG16 3.6 58.4 1.0 N1 A:DG25 3.7 70.7 1.0 N1 A:DG9 3.7 64.3 1.0 C6 A:DG15 3.7 53.5 1.0 C6 A:DG1 3.7 59.9 1.0 N1 A:DG26 3.9 66.2 1.0 C6 A:DG10 3.9 66.4 1.0 N1 A:DG15 4.0 55.0 1.0 N1 A:DG1 4.1 61.8 1.0 N1 A:DG10 4.2 65.4 1.0 C5 A:DG25 4.5 76.7 1.0 C5 A:DG9 4.6 57.0 1.0 C5 A:DG16 4.8 53.7 1.0 C5 A:DG2 4.9 47.2 1.0 C5 A:DG1 4.9 56.2 1.0 C2 A:DG2 4.9 47.7 1.0 C2 A:DG16 4.9 57.5 1.0 C5 A:DG26 4.9 68.6 1.0 C2 A:DG25 4.9 72.3 1.0 C5 A:DG15 4.9 53.0 1.0 C2 A:DG9 5.0 63.1 1.0

Potassium binding site 4 out of 21 in the Structure of A Quadruplex Forming Sequence From D. Discoideum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of A Quadruplex Forming Sequence From D. Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:80.9 occ:1.00 O6 B:DG1 2.7 56.0 1.0 O6 B:DG9 2.8 52.3 1.0 O6 B:DG26 2.8 57.1 1.0 O6 B:DG2 2.8 52.4 1.0 O6 B:DG10 2.9 63.9 1.0 O6 B:DG15 3.1 70.3 1.0 O6 B:DG25 3.1 61.1 1.0 O6 B:DG16 3.2 49.7 1.0 C6 B:DG9 3.5 53.1 1.0 N1 B:DG10 3.5 68.6 1.0 C6 B:DG10 3.6 69.9 1.0 C6 B:DG1 3.6 52.6 1.0 K B:K102 3.7 91.5 1.0 C6 B:DG25 3.7 65.4 1.0 C6 B:DG26 3.7 57.9 1.0 N1 B:DG25 3.8 67.2 1.0 N1 B:DG9 3.8 53.5 1.0 C6 B:DG2 3.8 46.3 1.0 N1 B:DG26 3.9 61.3 1.0 N1 B:DG1 3.9 52.1 1.0 C6 B:DG16 4.1 52.9 1.0 C6 B:DG15 4.1 66.4 1.0 N1 B:DG2 4.3 46.1 1.0 C1' B:DC13 4.3 62.0 1.0 N1 B:DG16 4.3 54.9 1.0 N1 B:DG15 4.5 64.5 1.0 C5 B:DG9 4.6 52.7 1.0 O2 B:DC13 4.7 63.5 1.0 N1 B:DC13 4.7 55.8 1.0 C2 B:DG10 4.8 76.0 1.0 C5 B:DG25 4.9 64.7 1.0 C2 B:DC13 4.9 59.7 1.0 C5 B:DG1 4.9 51.2 1.0 C2 B:DG25 4.9 73.3 1.0 C5 B:DG10 5.0 71.7 1.0 C5 B:DG2 5.0 46.0 1.0 C2' B:DC13 5.0 66.9 1.0

Potassium binding site 5 out of 21 in the Structure of A Quadruplex Forming Sequence From D. Discoideum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of A Quadruplex Forming Sequence From D. Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:91.5 occ:1.00 O6 B:DG3 2.5 49.1 1.0 O6 B:DG24 2.6 66.1 1.0 O6 B:DG16 2.6 49.7 1.0 O6 B:DG25 2.7 61.1 1.0 O6 B:DG17 2.7 56.4 1.0 O6 B:DG8 2.8 51.4 1.0 O6 B:DG2 3.0 52.4 1.0 O6 B:DG9 3.2 52.3 1.0 C6 B:DG24 3.3 68.6 1.0 N1 B:DG24 3.4 62.7 1.0 C6 B:DG16 3.4 52.9 1.0 K B:K103 3.5 73.4 1.0 C6 B:DG3 3.5 46.1 1.0 C6 B:DG17 3.6 53.7 1.0 C6 B:DG8 3.6 55.0 1.0 N1 B:DG16 3.7 54.9 1.0 C6 B:DG25 3.7 65.4 1.0 K B:K101 3.7 80.9 1.0 C6 B:DG2 3.7 46.3 1.0 N1 B:DG8 3.8 52.0 1.0 N1 B:DG17 3.8 49.2 1.0 N1 B:DG3 3.9 42.5 1.0 N1 B:DG2 4.0 46.1 1.0 N1 B:DG25 4.1 67.2 1.0 C6 B:DG9 4.2 53.1 1.0 N1 B:DG9 4.4 53.5 1.0 C5 B:DG16 4.5 49.4 1.0 C5 B:DG24 4.6 72.7 1.0 C2 B:DG24 4.6 70.7 1.0 C5 B:DG3 4.7 44.6 1.0 C5 B:DG17 4.9 49.1 1.0 C5 B:DG8 4.9 57.7 1.0 C2 B:DG16 4.9 55.7 1.0 C5 B:DG2 4.9 46.0 1.0 C5 B:DG25 4.9 64.7 1.0 C2 B:DG8 5.0 57.4 1.0

Potassium binding site 6 out of 21 in the Structure of A Quadruplex Forming Sequence From D. Discoideum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of A Quadruplex Forming Sequence From D. Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:73.4 occ:1.00 O6 B:DG7 2.6 63.4 1.0 O6 B:DG23 2.6 57.8 1.0 O6 B:DG4 2.8 43.5 1.0 O6 B:DG18 2.8 48.3 1.0 O6 B:DG24 2.9 66.1 1.0 O6 B:DG17 3.0 56.4 1.0 O6 B:DG8 3.0 51.4 1.0 O6 B:DG3 3.1 49.1 1.0 C6 B:DG23 3.4 66.3 1.0 C6 B:DG24 3.4 68.6 1.0 N1 B:DG24 3.5 62.7 1.0 N1 B:DG23 3.5 59.1 1.0 K B:K102 3.5 91.5 1.0 C6 B:DG7 3.5 60.6 1.0 C6 B:DG4 3.6 40.9 1.0 C6 B:DG18 3.7 50.9 1.0 N1 B:DG4 3.7 40.7 1.0 C6 B:DG8 3.7 55.0 1.0 C6 B:DG17 3.8 53.7 1.0 N1 B:DG8 3.8 52.0 1.0 N1 B:DG7 3.8 56.9 1.0 N1 B:DG18 3.9 50.8 1.0 C6 B:DG3 3.9 46.1 1.0 N1 B:DG17 4.0 49.2 1.0 N1 B:DG3 4.3 42.5 1.0 C2 B:DG24 4.6 70.7 1.0 C5 B:DG24 4.6 72.7 1.0 C5 B:DG23 4.7 65.4 1.0 C2 B:DG23 4.7 57.5 1.0 N6 B:DA22 4.7 98.0 1.0 C5 B:DG7 4.8 58.6 1.0 C5 B:DG17 4.9 49.1 1.0 C5 B:DG8 5.0 57.7 1.0 C5 B:DG4 5.0 41.3 1.0 C5 B:DG18 5.0 51.7 1.0 C2 B:DG8 5.0 57.4 1.0

Potassium binding site 7 out of 21 in the Structure of A Quadruplex Forming Sequence From D. Discoideum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of A Quadruplex Forming Sequence From D. Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ C:K101 b:74.8 occ:1.00 O6 C:DG25 2.6 53.8 1.0 O6 C:DG2 2.7 47.4 1.0 O6 C:DG9 2.8 57.9 1.0 O6 C:DG8 2.8 56.8 1.0 O6 C:DG16 2.8 58.3 1.0 O6 C:DG24 2.9 60.7 1.0 O6 C:DG3 2.9 48.1 1.0 O6 C:DG17 3.0 57.5 1.0 C6 C:DG25 3.5 58.4 1.0 C6 C:DG2 3.5 51.5 1.0 C6 C:DG8 3.5 57.9 1.0 K C:K103 3.5 71.1 1.0 N1 C:DG8 3.5 63.9 1.0 C6 C:DG24 3.6 69.5 1.0 C6 C:DG16 3.6 55.6 1.0 N1 C:DG25 3.6 56.7 1.0 C6 C:DG9 3.7 63.7 1.0 N1 C:DG2 3.7 51.9 1.0 C6 C:DG3 3.8 48.3 1.0 N1 C:DG16 3.9 51.5 1.0 N1 C:DG24 3.9 67.6 1.0 C6 C:DG17 3.9 66.0 1.0 N1 C:DG9 4.0 65.1 1.0 N1 C:DG3 4.0 46.1 1.0 K C:K102 4.1 72.1 1.0 N1 C:DG17 4.2 61.0 1.0 C5 C:DG2 4.7 48.6 1.0 C2 C:DG8 4.7 65.6 1.0 C5 C:DG8 4.8 57.3 1.0 C5 C:DG25 4.8 59.5 1.0 C5 C:DG24 4.8 64.8 1.0 C5 C:DG16 4.9 49.2 1.0 C2 C:DG25 4.9 63.6 1.0 C5 C:DG9 4.9 63.7 1.0 C2 C:DG2 4.9 55.7 1.0

Potassium binding site 8 out of 21 in the Structure of A Quadruplex Forming Sequence From D. Discoideum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Structure of A Quadruplex Forming Sequence From D. Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ C:K102 b:72.1 occ:1.00 O6 C:DG4 2.6 51.8 1.0 O6 C:DG18 2.7 52.4 1.0 O6 C:DG23 2.8 59.1 1.0 O6 C:DG7 2.9 55.7 1.0 O6 C:DG3 3.0 48.1 1.0 N1 C:DG4 3.0 47.3 1.0 O6 C:DG17 3.1 57.5 1.0 C6 C:DG4 3.2 50.2 1.0 O6 C:DG8 3.2 56.8 1.0 O6 C:DG24 3.6 60.7 1.0 C6 C:DG18 3.6 54.3 1.0 C6 C:DG3 3.7 48.3 1.0 C6 C:DG7 3.8 65.2 1.0 C6 C:DG17 3.8 66.0 1.0 N1 C:DG18 3.8 48.2 1.0 C6 C:DG23 3.9 60.2 1.0 N1 C:DG17 3.9 61.0 1.0 N1 C:DG7 3.9 60.4 1.0 C6 C:DG8 4.0 57.9 1.0 K C:K101 4.1 74.8 1.0 N1 C:DG3 4.1 46.1 1.0 N1 C:DG23 4.2 63.6 1.0 C2 C:DG4 4.3 49.1 1.0 N1 C:DG8 4.4 63.9 1.0 C6 C:DG24 4.4 69.5 1.0 N6 C:DA22 4.5 72.3 1.0 N1 C:DG24 4.5 67.6 1.0 C5 C:DG4 4.6 45.5 1.0 N2 C:DG4 4.6 42.4 1.0 C5 C:DG3 4.7 54.0 1.0 C5 C:DG18 5.0 54.2 1.0

Potassium binding site 9 out of 21 in the Structure of A Quadruplex Forming Sequence From D. Discoideum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Structure of A Quadruplex Forming Sequence From D. Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ C:K103 b:71.1 occ:1.00 O6 C:DG10 2.5 54.8 1.0 O6 C:DG15 2.6 56.8 1.0 O6 C:DG26 2.7 52.2 1.0 O6 C:DG1 2.8 59.7 1.0 O6 C:DG16 2.8 58.3 1.0 O6 C:DG2 2.8 47.4 1.0 O6 C:DG25 2.9 53.8 1.0 O6 C:DG9 3.0 57.9 1.0 C6 C:DG15 3.5 55.7 1.0 K C:K101 3.5 74.8 1.0 C6 C:DG2 3.5 51.5 1.0 C6 C:DG10 3.5 52.8 1.0 C6 C:DG25 3.6 58.4 1.0 C6 C:DG1 3.6 58.5 1.0 N1 C:DG2 3.6 51.9 1.0 C6 C:DG26 3.6 54.8 1.0 C6 C:DG16 3.7 55.6 1.0 N1 C:DG1 3.7 57.9 1.0 N1 C:DG25 3.8 56.7 1.0 N1 C:DG15 3.8 54.9 1.0 C6 C:DG9 3.8 63.7 1.0 N1 C:DG26 3.9 54.4 1.0 N1 C:DG10 4.0 51.1 1.0 N1 C:DG16 4.0 51.5 1.0 N1 C:DG9 4.1 65.1 1.0 O2 C:DC13 4.5 68.2 1.0 C1' C:DC13 4.5 65.7 1.0 C2 C:DC13 4.7 65.8 1.0 C5 C:DG25 4.7 59.5 1.0 C5 C:DG15 4.7 58.1 1.0 N1 C:DC13 4.7 63.9 1.0 C5 C:DG10 4.8 54.0 1.0 C5 C:DG2 4.8 48.6 1.0 C2 C:DG2 4.8 55.7 1.0 C5 C:DG1 4.8 53.8 1.0 C5 C:DG16 4.9 49.2 1.0 C2 C:DG25 4.9 63.6 1.0 C5 C:DG9 4.9 63.7 1.0 C5 C:DG26 5.0 55.2 1.0

Potassium binding site 10 out of 21 in the Structure of A Quadruplex Forming Sequence From D. Discoideum


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Structure of A Quadruplex Forming Sequence From D. Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ D:K101 b:84.7 occ:1.00 O6 D:DG7 2.4 82.1 1.0 O6 D:DG18 2.6 89.9 1.0 O6 D:DG4 3.0 49.8 1.0 N1 D:DG4 3.1 48.4 1.0 O6 D:DG8 3.3 75.1 1.0 O6 D:DG17 3.4 70.2 1.0 O6 D:DG23 3.4 80.4 1.0 C6 D:DG7 3.4 75.7 1.0 O6 D:DG3 3.5 51.6 1.0 C6 D:DG4 3.5 51.2 1.0 C6 D:DG18 3.5 96.2 1.0 O6 D:DG24 3.6 80.9 1.0 K D:K102 3.7 82.8 1.0 N1 D:DG18 3.7 0.9 1.0 N1 D:DG7 3.7 62.4 1.0 C6 D:DG17 4.0 71.0 1.0 C6 D:DG3 4.0 50.9 1.0 C6 D:DG8 4.0 71.7 1.0 N1 D:DG17 4.1 64.0 1.0 N1 D:DG3 4.1 51.2 1.0 N1 D:DG8 4.2 64.5 1.0 C6 D:DG23 4.3 90.4 1.0 N1 D:DG23 4.3 88.2 1.0 C2 D:DG4 4.3 52.3 1.0 C2 D:DA6 4.4 66.8 1.0 N2 D:DG4 4.5 55.9 1.0 C6 D:DG24 4.5 87.1 1.0 N1 D:DA6 4.6 66.9 1.0 N1 D:DG24 4.6 83.7 1.0 C5 D:DG7 4.8 82.5 1.0 C5 D:DG18 4.9 96.8 1.0 C5 D:DG4 4.9 49.0 1.0 N3 D:DA6 5.0 60.7 1.0

A.Guedin, L.Y.Lin, S.Armane, L.Lacroix, J.L.Mergny, S.Thore, L.A.Yatsunyk. Quadruplexes in 'Dicty': Crystal Structure of A Four-Quartet G-Quadruplex Formed By G-Rich Motif Found in the Dictyostelium Discoideum Genome. Nucleic Acids Res. V. 46 5297 2018.
ISSN: ESSN 1362-4962
PubMed: 29718337
DOI: 10.1093/NAR/GKY290