Fluorine in PDB 8twh: Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4

The structure of Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4, PDB code: 8twh was solved by L.A.Yatsunyk, K.N.Martin, G.Lam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	128.34 / 2.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.162, 62.667, 256.675, 90, 90, 90
R / Rfree (%)	29.5 / 31.8

The structure of Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4 also contains other interesting chemical elements:

Potassium

(K)

25 atoms

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4 (pdb code 8twh). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 20 binding sites of Fluorine where determined in the Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4, PDB code: 8twh:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 20 in the Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F104 b:54.6 occ:1.00 F30 A:LG1104 0.0 54.6 1.0 C21 A:LG1104 1.3 40.7 1.0 C20 A:LG1104 2.3 39.7 1.0 C22 A:LG1104 2.4 39.5 1.0 N3 A:DG3 3.3 40.5 1.0 C4 A:DG3 3.5 35.8 1.0 C19 A:LG1104 3.6 42.1 1.0 C23 A:LG1104 3.6 45.8 1.0 N9 A:DG3 3.7 44.3 1.0 C1' A:DG3 3.7 50.9 1.0 C2 A:DG3 4.0 40.2 1.0 C2' A:DG3 4.0 51.3 1.0 C24 A:LG1104 4.1 45.7 1.0 C5 A:DG3 4.3 36.0 1.0 N2 A:DG3 4.5 41.7 1.0 C8 A:DG3 4.5 40.8 1.0 N1 A:DG3 4.7 40.5 1.0 C15 A:LG1104 4.8 39.9 1.0 N7 A:DG3 4.9 37.2 1.0 C6 A:DG3 4.9 37.7 1.0

Fluorine binding site 2 out of 20 in the Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F104 b:48.1 occ:1.00 F08 A:LG1104 0.0 48.1 1.0 C04 A:LG1104 1.3 43.4 1.0 C05 A:LG1104 2.3 43.0 1.0 C03 A:LG1104 2.3 36.0 1.0 O4 A:DT14 2.5 43.4 1.0 C4 A:DT14 3.0 41.8 1.0 N3 A:DT14 3.4 46.1 1.0 C4 A:DG13 3.5 38.3 1.0 N3 A:DG13 3.5 38.3 1.0 C2 A:DG13 3.5 34.8 1.0 C06 A:LG1104 3.6 46.9 1.0 C02 A:LG1104 3.6 39.3 1.0 C5 A:DG13 3.6 41.2 1.0 N1 A:DG13 3.6 32.5 1.0 C6 A:DG13 3.7 38.0 1.0 C5 A:DT14 4.0 42.4 1.0 C01 A:LG1104 4.1 43.6 1.0 N9 A:DG13 4.1 38.5 1.0 N2 A:DG13 4.2 33.6 1.0 N7 A:DG13 4.3 42.5 1.0 O6 A:DG13 4.4 36.5 1.0 C2 A:DT14 4.5 50.8 1.0 C7 A:DT14 4.5 39.1 1.0 C8 A:DG13 4.6 40.6 1.0 C11 A:LG1104 4.8 41.0 1.0 C1' A:DG13 4.9 46.0 1.0 C6 A:DT14 4.9 47.6 1.0 C34 A:LG1104 5.0 48.9 1.0

Fluorine binding site 3 out of 20 in the Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F103 b:55.6 occ:1.00 F30 B:LG1103 0.0 55.6 1.0 C21 B:LG1103 1.3 42.3 1.0 C20 B:LG1103 2.3 42.2 1.0 C22 B:LG1103 2.4 37.4 1.0 O4 B:DT5 3.3 65.8 1.0 N3 B:DG3 3.4 41.4 1.0 C19 B:LG1103 3.6 45.1 1.0 C23 B:LG1103 3.6 42.2 1.0 C4 B:DG3 3.7 40.2 1.0 C2 B:DG3 4.0 43.2 1.0 N9 B:DG3 4.0 45.4 1.0 C1' B:DG3 4.0 54.3 1.0 C24 B:LG1103 4.1 47.9 1.0 C4 B:DT5 4.1 61.5 1.0 N3 B:DT5 4.3 67.0 1.0 N2 B:DG3 4.4 43.9 1.0 C2' B:DG3 4.4 56.3 1.0 C5 B:DG3 4.5 37.8 1.0 N1 B:DG3 4.7 46.1 1.0 C15 B:LG1103 4.8 43.1 1.0 C8 B:DG3 4.9 39.6 1.0 C33 C:LG1104 4.9 41.1 1.0 C06 C:LG1104 4.9 44.6 1.0

Fluorine binding site 4 out of 20 in the Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4 within 5.0Å range: probe atom residue distance (Å) B Occ B:F103 b:48.6 occ:1.00 F08 B:LG1103 0.0 48.6 1.0 C04 B:LG1103 1.3 43.1 1.0 C05 B:LG1103 2.3 37.7 1.0 C03 B:LG1103 2.3 43.1 1.0 O4 B:DT14 2.8 44.0 1.0 C4 B:DT14 2.9 39.9 1.0 N3 B:DT14 2.9 41.9 1.0 C06 B:LG1103 3.6 38.4 1.0 C2 B:DG13 3.6 39.8 1.0 N1 B:DG13 3.6 39.6 1.0 C4 B:DG13 3.6 43.2 1.0 C02 B:LG1103 3.6 42.3 1.0 N3 B:DG13 3.6 41.5 1.0 C5 B:DG13 3.7 41.0 1.0 C6 B:DG13 3.7 41.4 1.0 O C:HOH202 3.8 34.1 1.0 C5 B:DT14 3.8 40.7 1.0 C2 B:DT14 3.8 43.4 1.0 C01 B:LG1103 4.1 38.2 1.0 C23 C:LG1104 4.2 43.5 1.0 N2 B:DG13 4.2 38.5 1.0 N9 B:DG13 4.3 40.5 1.0 O6 B:DG13 4.3 42.6 1.0 N7 B:DG13 4.4 42.8 1.0 NP5 C:LG1104 4.4 38.5 1.0 O2 B:DT14 4.4 49.2 1.0 C34 C:LG1104 4.5 43.7 1.0 C6 B:DT14 4.5 40.3 1.0 N1 B:DT14 4.5 40.6 1.0 C03 C:LG1104 4.6 37.9 1.0 C24 C:LG1104 4.6 42.0 1.0 C7 B:DT14 4.6 42.7 1.0 C8 B:DG13 4.7 40.0 1.0 C11 B:LG1103 4.8 43.6 1.0 C34 B:LG1103 4.9 46.3 1.0

Fluorine binding site 5 out of 20 in the Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4 within 5.0Å range: probe atom residue distance (Å) B Occ C:F104 b:54.0 occ:1.00 F30 C:LG1104 0.0 54.0 1.0 C21 C:LG1104 1.3 46.0 1.0 C20 C:LG1104 2.3 44.6 1.0 C22 C:LG1104 2.4 44.7 1.0 N3 C:DG3 3.3 42.0 1.0 C19 C:LG1104 3.6 44.3 1.0 C23 C:LG1104 3.6 43.5 1.0 C2 C:DG3 3.7 44.5 1.0 C4 C:DG3 3.7 37.8 1.0 N2 C:DG3 4.0 44.3 1.0 C24 C:LG1104 4.1 42.0 1.0 N9 C:DG3 4.1 42.7 1.0 C1' C:DG3 4.3 51.3 1.0 N1 C:DG3 4.4 44.4 1.0 C5 C:DG3 4.5 37.5 1.0 C15 C:LG1104 4.8 42.0 1.0 C33 B:LG1103 4.8 39.2 1.0 C6 C:DG3 4.8 41.1 1.0 C2' C:DG3 4.9 51.2 1.0

Fluorine binding site 6 out of 20 in the Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4 within 5.0Å range: probe atom residue distance (Å) B Occ C:F104 b:35.9 occ:1.00 F08 C:LG1104 0.0 35.9 1.0 C04 C:LG1104 1.3 34.5 1.0 C05 C:LG1104 2.3 38.1 1.0 C03 C:LG1104 2.3 37.9 1.0 O4 C:DT14 2.9 40.3 1.0 N3 C:DT14 3.0 45.2 1.0 C4 C:DT14 3.1 39.1 1.0 O C:HOH202 3.1 34.1 1.0 N3 C:DG13 3.2 38.5 1.0 C2 C:DG13 3.2 35.5 1.0 C4 C:DG13 3.3 39.1 1.0 N1 C:DG13 3.5 31.4 1.0 C06 C:LG1104 3.6 44.6 1.0 C02 C:LG1104 3.6 43.4 1.0 C5 C:DG13 3.6 36.6 1.0 C6 C:DG13 3.7 33.8 1.0 N2 C:DG13 3.8 33.8 1.0 C2 C:DT14 3.9 42.4 1.0 N9 C:DG13 4.1 38.0 1.0 C5 C:DT14 4.1 29.8 1.0 C01 C:LG1104 4.1 46.3 1.0 C23 B:LG1103 4.3 42.2 1.0 O2 C:DT14 4.4 44.1 1.0 N7 C:DG13 4.5 41.7 1.0 NP5 B:LG1103 4.5 49.1 1.0 C03 B:LG1103 4.5 43.1 1.0 O6 C:DG13 4.5 38.8 1.0 C8 C:DG13 4.6 40.9 1.0 C34 B:LG1103 4.6 46.3 1.0 C24 B:LG1103 4.7 47.9 1.0 N1 C:DT14 4.7 43.5 1.0 C1' C:DG13 4.7 40.3 1.0 C6 C:DT14 4.7 38.1 1.0 C11 C:LG1104 4.8 38.2 1.0 C7 C:DT14 4.9 32.1 1.0 C34 C:LG1104 4.9 43.7 1.0

Fluorine binding site 7 out of 20 in the Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4 within 5.0Å range: probe atom residue distance (Å) B Occ D:F103 b:62.5 occ:1.00 F30 D:LG1103 0.0 62.5 1.0 C21 D:LG1103 1.3 55.1 1.0 C20 D:LG1103 2.3 52.7 1.0 C22 D:LG1103 2.4 48.5 1.0 N3 D:DG3 3.2 41.1 1.0 C19 D:LG1103 3.6 50.6 1.0 C23 D:LG1103 3.6 45.9 1.0 C2 D:DG3 3.7 47.2 1.0 O4 D:DT5 3.7 72.8 1.0 C4 D:DG3 3.8 43.6 1.0 N2 D:DG3 4.0 45.3 1.0 C24 D:LG1103 4.1 47.1 1.0 N9 D:DG3 4.2 42.4 1.0 C1' D:DG3 4.2 53.7 1.0 C4 D:DT5 4.5 73.5 1.0 N1 D:DG3 4.6 50.4 1.0 N3 D:DT5 4.6 70.6 1.0 C5 D:DG3 4.7 44.5 1.0 C2' D:DG3 4.8 59.7 1.0 C15 D:LG1103 4.8 46.7 1.0

Fluorine binding site 8 out of 20 in the Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4 within 5.0Å range: probe atom residue distance (Å) B Occ D:F103 b:45.9 occ:1.00 F08 D:LG1103 0.0 45.9 1.0 C04 D:LG1103 1.3 39.7 1.0 C05 D:LG1103 2.3 40.3 1.0 C03 D:LG1103 2.3 40.8 1.0 O4 D:DT14 2.9 43.1 1.0 C4 D:DT14 3.1 40.8 1.0 N3 D:DG13 3.2 38.9 1.0 C4 D:DG13 3.3 39.0 1.0 C2 D:DG13 3.3 39.1 1.0 N3 D:DT14 3.3 39.6 1.0 N1 D:DG13 3.5 33.4 1.0 C5 D:DG13 3.5 40.4 1.0 C06 D:LG1103 3.6 43.4 1.0 C02 D:LG1103 3.6 42.0 1.0 C6 D:DG13 3.7 36.3 1.0 N2 D:DG13 3.9 39.7 1.0 N9 D:DG13 4.0 41.1 1.0 C5 D:DT14 4.0 36.5 1.0 C01 D:LG1103 4.1 43.0 1.0 C2 D:DT14 4.3 43.9 1.0 N7 D:DG13 4.3 40.8 1.0 C23 E:LG1104 4.3 45.1 1.0 C03 E:LG1104 4.4 37.8 1.0 O6 D:DG13 4.4 36.7 1.0 NP5 E:LG1104 4.4 42.1 1.0 C8 D:DG13 4.5 42.1 1.0 C24 E:LG1104 4.6 42.8 1.0 C34 E:LG1104 4.6 48.3 1.0 C1' D:DG13 4.6 44.8 1.0 C7 D:DT14 4.7 40.1 1.0 C6 D:DT14 4.8 44.6 1.0 C11 D:LG1103 4.8 42.3 1.0 O2 D:DT14 4.9 47.1 1.0 N1 D:DT14 4.9 46.9 1.0 C34 D:LG1103 4.9 45.9 1.0

Fluorine binding site 9 out of 20 in the Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4 within 5.0Å range: probe atom residue distance (Å) B Occ E:F104 b:48.1 occ:1.00 F30 E:LG1104 0.0 48.1 1.0 C21 E:LG1104 1.3 41.5 1.0 C20 E:LG1104 2.3 41.3 1.0 C22 E:LG1104 2.4 42.3 1.0 C19 E:LG1104 3.6 44.7 1.0 N3 E:DG3 3.6 36.8 1.0 C23 E:LG1104 3.6 45.1 1.0 C4 E:DG3 3.8 37.1 1.0 C2 E:DG3 4.1 37.3 1.0 C24 E:LG1104 4.1 42.8 1.0 N9 E:DG3 4.1 41.0 1.0 C1' E:DG3 4.3 49.3 1.0 C5 E:DG3 4.5 36.5 1.0 C2' E:DG3 4.5 51.8 1.0 N2 E:DG3 4.5 39.4 1.0 N1 E:DG3 4.7 43.1 1.0 C15 E:LG1104 4.7 44.7 1.0 C8 E:DG3 4.9 41.4 1.0 C6 E:DG3 4.9 41.6 1.0 C06 D:LG1103 5.0 43.4 1.0

Fluorine binding site 10 out of 20 in the Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4 within 5.0Å range: probe atom residue distance (Å) B Occ E:F104 b:43.7 occ:1.00 F08 E:LG1104 0.0 43.7 1.0 C04 E:LG1104 1.3 41.4 1.0 C05 E:LG1104 2.3 42.4 1.0 C03 E:LG1104 2.3 37.8 1.0 O4 E:DT14 2.8 46.3 1.0 C4 E:DT14 3.0 45.5 1.0 N3 E:DT14 3.0 38.7 1.0 C4 E:DG13 3.4 38.5 1.0 C5 E:DG13 3.5 40.6 1.0 N1 E:DG13 3.5 37.1 1.0 N3 E:DG13 3.5 36.1 1.0 C2 E:DG13 3.5 37.6 1.0 C6 E:DG13 3.6 40.6 1.0 C06 E:LG1104 3.6 45.3 1.0 C02 E:LG1104 3.6 41.6 1.0 C5 E:DT14 3.9 39.2 1.0 C2 E:DT14 4.0 33.6 1.0 C23 D:LG1103 4.1 45.9 1.0 C01 E:LG1104 4.1 42.4 1.0 N9 E:DG13 4.1 40.2 1.0 N7 E:DG13 4.2 43.7 1.0 O6 E:DG13 4.2 41.4 1.0 NP5 D:LG1103 4.3 44.9 1.0 N2 E:DG13 4.3 33.0 1.0 C03 D:LG1103 4.4 40.8 1.0 C24 D:LG1103 4.4 47.1 1.0 C8 E:DG13 4.4 42.9 1.0 C34 D:LG1103 4.5 45.9 1.0 O2 E:DT14 4.5 34.7 1.0 C6 E:DT14 4.6 37.4 1.0 N1 E:DT14 4.7 37.7 1.0 C7 E:DT14 4.7 41.8 1.0 C11 E:LG1104 4.8 39.4 1.0 C1' E:DG13 4.9 40.6 1.0 C34 E:LG1104 5.0 48.3 1.0

G.Lam, K.N.Martin, L.A.Yatsunyk. Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4 To Be Published.