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

Protein crystallography data

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

Other elements in 8twh:

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

Fluorine (F) 20 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Potassium 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 Potassium atom.
In total 25 binding sites of Potassium where determined in the Crystal Structure of (Gggtt)3GGG G-Quadruplex in Complex with Small Molecule Ligand RHPS4, PDB code: 8twh:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 25 in 8twh

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Potassium binding site 1 out of 25 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 Potassium with other atoms in the K 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:K101

b:36.3
occ:1.00
 O6 A:DG12 2.7 36.9 1.0
O6 A:DG17 2.7 40.3 1.0
O6 A:DG7 2.8 50.0 1.0
O6 A:DG18 2.8 36.5 1.0
O6 A:DG13 2.8 36.5 1.0
O6 A:DG3 2.9 40.5 1.0
O6 A:DG8 2.9 49.0 1.0
O6 A:DG2 3.0 43.0 1.0
C34 A:LG1104 3.2 48.9 1.0
K A:K102 3.3 35.0 1.0
C6 A:DG17 3.6 37.6 1.0
C6 A:DG18 3.6 35.9 1.0
C6 A:DG12 3.7 37.9 1.0
N1 A:DG18 3.7 33.0 1.0
C6 A:DG3 3.7 37.7 1.0
N1 A:DG3 3.7 40.5 1.0
C6 A:DG13 3.7 38.0 1.0
C6 A:DG2 3.8 40.6 1.0
C6 A:DG7 3.8 42.8 1.0
N1 A:DG17 3.8 36.8 1.0
C6 A:DG8 3.9 46.6 1.0
N1 A:DG13 3.9 32.5 1.0
N1 A:DG2 3.9 38.6 1.0
N1 A:DG12 4.0 36.8 1.0
N1 A:DG8 4.0 44.4 1.0
N1 A:DG7 4.1 42.1 1.0
NP5 A:LG1104 4.5 47.1 1.0
C5 A:DG17 4.8 35.0 1.0
C5 A:DG12 4.9 36.1 1.0
C2 A:DG18 4.9 37.0 1.0
C2 A:DG3 5.0 40.2 1.0
C5 A:DG7 5.0 39.7 1.0
C11 A:LG1104 5.0 41.0 1.0
C5 A:DG18 5.0 34.6 1.0

Potassium binding site 2 out of 25 in 8twh

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Potassium binding site 2 out of 25 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 Potassium with other atoms in the K 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:K102

b:35.0
occ:1.00
 O6 A:DG1 2.7 38.9 1.0
O6 A:DG16 2.8 42.0 1.0
O6 A:DG6 2.8 43.6 1.0
O6 A:DG7 2.8 50.0 1.0
O6 A:DG12 2.8 36.9 1.0
O6 A:DG2 2.9 43.0 1.0
O6 A:DG17 3.0 40.3 1.0
O6 A:DG11 3.0 52.5 1.0
K A:K103 3.3 32.3 1.0
K A:K101 3.3 36.3 1.0
C6 A:DG16 3.6 42.7 1.0
C6 A:DG1 3.6 38.3 1.0
C6 A:DG6 3.6 42.4 1.0
C6 A:DG2 3.6 40.6 1.0
C6 A:DG7 3.7 42.8 1.0
N1 A:DG16 3.7 40.5 1.0
C6 A:DG17 3.7 37.6 1.0
C6 A:DG12 3.7 37.9 1.0
N1 A:DG2 3.8 38.6 1.0
N1 A:DG6 3.8 42.1 1.0
C6 A:DG11 3.9 52.5 1.0
N1 A:DG17 3.9 36.8 1.0
N1 A:DG1 3.9 41.0 1.0
N1 A:DG11 4.1 52.5 1.0
N1 A:DG7 4.1 42.1 1.0
N1 A:DG12 4.2 36.8 1.0
C5 A:DG1 4.8 33.2 1.0
C5 A:DG6 4.8 41.9 1.0
C5 A:DG16 4.9 42.8 1.0
C5 A:DG7 4.9 39.7 1.0
C5 A:DG12 4.9 36.1 1.0
C5 A:DG2 4.9 39.2 1.0
C2 A:DG16 5.0 38.8 1.0
C5 A:DG17 5.0 35.0 1.0

Potassium binding site 3 out of 25 in 8twh

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Potassium binding site 3 out of 25 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 Potassium with other atoms in the K 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
A:K103

b:32.3
occ:1.00
 O6 B:DG6 2.7 47.7 1.0
O6 A:DG1 2.7 38.9 1.0
O6 A:DG6 2.8 43.6 1.0
O6 B:DG16 2.8 44.2 1.0
O6 A:DG16 2.8 42.0 1.0
O6 B:DG1 2.8 36.9 1.0
O6 A:DG11 3.0 52.5 1.0
O6 B:DG11 3.1 52.2 1.0
K A:K102 3.3 35.0 1.0
K B:K102 3.3 34.5 1.0
C6 B:DG6 3.5 46.4 1.0
C6 B:DG16 3.5 39.7 1.0
C6 A:DG16 3.6 42.7 1.0
C6 A:DG6 3.6 42.4 1.0
C6 A:DG1 3.7 38.3 1.0
C6 B:DG1 3.7 39.5 1.0
N1 B:DG16 3.7 39.8 1.0
N1 B:DG6 3.8 49.0 1.0
N1 A:DG6 3.8 42.1 1.0
C6 A:DG11 3.8 52.5 1.0
N1 A:DG16 3.8 40.5 1.0
C6 B:DG11 3.9 52.2 1.0
N1 A:DG11 3.9 52.5 1.0
N1 B:DG1 4.0 37.5 1.0
N1 A:DG1 4.1 41.0 1.0
N1 B:DG11 4.1 52.2 1.0
C5 B:DG16 4.8 37.1 1.0
C5 B:DG6 4.8 45.6 1.0
C5 A:DG16 4.8 42.8 1.0
C5 A:DG6 4.9 41.9 1.0
C5 A:DG1 4.9 33.2 1.0
C5 B:DG1 4.9 38.5 1.0
C2 B:DG16 5.0 40.8 1.0

Potassium binding site 4 out of 25 in 8twh

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Potassium binding site 4 out of 25 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 Potassium with other atoms in the K 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:K101

b:34.0
occ:1.00
 O6 B:DG18 2.8 31.6 1.0
O6 B:DG12 2.8 40.0 1.0
O6 B:DG3 2.8 40.8 1.0
O6 B:DG17 2.8 36.9 1.0
O6 B:DG13 2.8 42.6 1.0
O6 B:DG2 2.9 39.4 1.0
O6 B:DG7 2.9 48.3 1.0
O6 B:DG8 3.0 50.6 1.0
C34 B:LG1103 3.3 46.3 1.0
K B:K102 3.4 34.5 1.0
C6 B:DG17 3.5 33.3 1.0
C6 B:DG18 3.6 32.9 1.0
N1 B:DG17 3.6 35.3 1.0
N1 B:DG18 3.7 31.5 1.0
C6 B:DG12 3.7 41.7 1.0
C6 B:DG2 3.7 38.5 1.0
C6 B:DG7 3.7 49.1 1.0
C6 B:DG3 3.7 43.2 1.0
C6 B:DG13 3.7 41.4 1.0
N1 B:DG3 3.9 46.1 1.0
N1 B:DG13 3.9 39.6 1.0
N1 B:DG12 3.9 44.3 1.0
N1 B:DG7 3.9 46.8 1.0
N1 B:DG2 3.9 38.0 1.0
C6 B:DG8 4.0 45.1 1.0
N1 B:DG8 4.2 40.0 1.0
NP5 B:LG1103 4.6 49.1 1.0
C5 B:DG17 4.8 36.2 1.0
C2 B:DG17 4.9 43.3 1.0
C5 B:DG2 4.9 36.4 1.0
C2 B:DG18 5.0 36.6 1.0
C5 B:DG7 5.0 48.9 1.0
C5 B:DG18 5.0 36.5 1.0
C5 B:DG12 5.0 43.4 1.0

Potassium binding site 5 out of 25 in 8twh

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Potassium binding site 5 out of 25 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 Potassium with other atoms in the K 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
B:K102

b:34.5
occ:1.00
 O6 B:DG16 2.7 44.2 1.0
O6 B:DG6 2.7 47.7 1.0
O6 B:DG7 2.8 48.3 1.0
O6 B:DG11 2.9 52.2 1.0
O6 B:DG12 2.9 40.0 1.0
O6 B:DG2 2.9 39.4 1.0
O6 B:DG17 2.9 36.9 1.0
O6 B:DG1 2.9 36.9 1.0
K A:K103 3.3 32.3 1.0
K B:K101 3.4 34.0 1.0
C6 B:DG16 3.5 39.7 1.0
C6 B:DG6 3.5 46.4 1.0
C6 B:DG7 3.6 49.1 1.0
C6 B:DG17 3.6 33.3 1.0
C6 B:DG12 3.7 41.7 1.0
N1 B:DG16 3.7 39.8 1.0
N1 B:DG17 3.7 35.3 1.0
C6 B:DG1 3.7 39.5 1.0
C6 B:DG11 3.8 52.2 1.0
C6 B:DG2 3.8 38.5 1.0
N1 B:DG6 3.8 49.0 1.0
N1 B:DG7 3.8 46.8 1.0
N1 B:DG12 4.0 44.3 1.0
N1 B:DG1 4.0 37.5 1.0
N1 B:DG2 4.0 38.0 1.0
N1 B:DG11 4.0 52.2 1.0
C5 B:DG6 4.7 45.6 1.0
C5 B:DG16 4.7 37.1 1.0
C5 B:DG12 4.8 43.4 1.0
C5 B:DG7 4.8 48.9 1.0
C5 B:DG17 4.9 36.2 1.0
C2 B:DG16 4.9 40.8 1.0
C2 B:DG17 4.9 43.3 1.0
C5 B:DG1 5.0 38.5 1.0

Potassium binding site 6 out of 25 in 8twh

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Potassium binding site 6 out of 25 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 Potassium with other atoms in the K 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:K101

b:34.0
occ:1.00
 O6 C:DG17 2.7 34.9 1.0
O6 C:DG7 2.7 39.7 1.0
O6 C:DG13 2.8 38.8 1.0
O6 C:DG2 2.8 40.2 1.0
O6 C:DG3 2.8 42.9 1.0
O6 C:DG8 2.8 35.9 1.0
O6 C:DG12 2.9 37.0 1.0
O6 C:DG18 3.0 31.7 1.0
K C:K102 3.3 27.6 1.0
C34 C:LG1104 3.4 43.7 1.0
C6 C:DG17 3.6 35.0 1.0
C6 C:DG13 3.6 33.8 1.0
C6 C:DG7 3.7 38.4 1.0
C6 C:DG2 3.7 40.8 1.0
C6 C:DG3 3.7 41.1 1.0
N1 C:DG13 3.7 31.4 1.0
C6 C:DG12 3.7 37.1 1.0
C6 C:DG8 3.8 36.9 1.0
N1 C:DG17 3.8 34.0 1.0
C6 C:DG18 3.8 31.7 1.0
N1 C:DG3 3.9 44.4 1.0
N1 C:DG12 3.9 34.0 1.0
N1 C:DG18 3.9 29.1 1.0
N1 C:DG8 4.0 37.3 1.0
N1 C:DG2 4.0 45.7 1.0
N1 C:DG7 4.0 36.8 1.0
NP5 C:LG1104 4.6 38.5 1.0
C5 C:DG17 4.8 38.5 1.0
C5 C:DG2 4.9 38.4 1.0
C5 C:DG13 5.0 36.6 1.0
C5 C:DG7 5.0 40.3 1.0

Potassium binding site 7 out of 25 in 8twh

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Potassium binding site 7 out of 25 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 Potassium with other atoms in the K 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
C:K102

b:27.6
occ:1.00
 O6 C:DG16 2.7 33.8 1.0
O6 C:DG1 2.8 35.0 1.0
O6 C:DG11 2.8 42.1 1.0
O6 C:DG2 2.9 40.2 1.0
O6 C:DG6 2.9 32.1 1.0
O6 C:DG12 3.0 37.0 1.0
O6 C:DG7 3.0 39.7 1.0
O6 C:DG17 3.1 34.9 1.0
K C:K103 3.3 27.0 1.0
K C:K101 3.3 34.0 1.0
C6 C:DG1 3.6 38.8 1.0
C6 C:DG16 3.6 36.7 1.0
C6 C:DG6 3.6 36.9 1.0
C6 C:DG11 3.7 40.0 1.0
C6 C:DG2 3.7 40.8 1.0
C6 C:DG7 3.8 38.4 1.0
C6 C:DG12 3.8 37.1 1.0
N1 C:DG6 3.8 38.7 1.0
C6 C:DG17 3.8 35.0 1.0
N1 C:DG1 3.8 41.8 1.0
N1 C:DG16 3.9 36.6 1.0
N1 C:DG17 3.9 34.0 1.0
N1 C:DG2 3.9 45.7 1.0
N1 C:DG11 4.0 37.7 1.0
N1 C:DG7 4.1 36.8 1.0
N1 C:DG12 4.1 34.0 1.0
C5 C:DG6 4.8 43.5 1.0
C5 C:DG1 4.8 39.7 1.0
C5 C:DG16 4.8 40.4 1.0
C5 C:DG7 4.9 40.3 1.0
C5 C:DG11 4.9 41.1 1.0
C5 C:DG2 4.9 38.4 1.0
C2 C:DG6 5.0 39.7 1.0
C5 C:DG12 5.0 33.7 1.0

Potassium binding site 8 out of 25 in 8twh

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Potassium binding site 8 out of 25 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 Potassium with other atoms in the K 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
C:K103

b:27.0
occ:1.00
 O6 D:DG1 2.7 40.0 1.0
O6 C:DG6 2.7 32.1 1.0
O6 D:DG11 2.8 37.3 1.0
O6 C:DG16 2.8 33.8 1.0
O6 C:DG11 2.8 42.1 1.0
O6 D:DG16 2.8 32.7 1.0
O6 D:DG6 2.8 42.9 1.0
O6 C:DG1 2.9 35.0 1.0
K D:K102 3.3 31.2 1.0
K C:K102 3.3 27.6 1.0
C6 D:DG1 3.5 40.5 1.0
C6 C:DG11 3.6 40.0 1.0
C6 C:DG16 3.6 36.7 1.0
C6 D:DG11 3.6 39.5 1.0
C6 D:DG16 3.6 35.9 1.0
C6 C:DG6 3.6 36.9 1.0
C6 D:DG6 3.6 43.8 1.0
C6 C:DG1 3.7 38.8 1.0
N1 D:DG1 3.8 40.4 1.0
N1 D:DG11 3.8 41.7 1.0
N1 C:DG11 3.8 37.7 1.0
N1 C:DG6 3.8 38.7 1.0
N1 C:DG16 3.9 36.6 1.0
N1 D:DG16 3.9 38.2 1.0
N1 D:DG6 3.9 44.2 1.0
N1 C:DG1 4.1 41.8 1.0
C5 D:DG1 4.8 41.3 1.0
C5 C:DG16 4.8 40.4 1.0
C5 D:DG16 4.8 36.6 1.0
C5 C:DG11 4.9 41.1 1.0
C5 D:DG6 4.9 42.7 1.0
C5 D:DG11 4.9 39.5 1.0
C5 C:DG6 4.9 43.5 1.0
C5 C:DG1 5.0 39.7 1.0

Potassium binding site 9 out of 25 in 8twh

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Potassium binding site 9 out of 25 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 Potassium with other atoms in the K 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
D:K101

b:39.5
occ:1.00
 O6 D:DG13 2.7 36.7 1.0
O6 D:DG12 2.7 41.1 1.0
O6 D:DG17 2.8 32.3 1.0
O6 D:DG7 2.8 45.8 1.0
O6 D:DG2 2.8 41.9 1.0
O6 D:DG18 2.8 28.2 1.0
O6 D:DG8 2.9 43.3 1.0
O6 D:DG3 2.9 43.3 1.0
K D:K102 3.1 31.2 1.0
C6 D:DG7 3.5 43.5 1.0
N1 D:DG7 3.5 39.0 1.0
C34 D:LG1103 3.5 45.9 1.0
C6 D:DG17 3.5 33.3 1.0
C6 D:DG13 3.6 36.3 1.0
C6 D:DG12 3.6 40.5 1.0
C6 D:DG2 3.7 42.3 1.0
N1 D:DG17 3.7 31.7 1.0
C6 D:DG18 3.7 31.2 1.0
C6 D:DG3 3.8 44.8 1.0
C6 D:DG8 3.8 43.3 1.0
N1 D:DG13 3.9 33.4 1.0
N1 D:DG3 3.9 50.4 1.0
N1 D:DG2 3.9 41.3 1.0
N1 D:DG12 3.9 40.4 1.0
N1 D:DG18 4.0 35.3 1.0
N1 D:DG8 4.1 43.1 1.0
C2 D:DG7 4.7 43.3 1.0
C5 D:DG7 4.8 48.1 1.0
C5 D:DG17 4.8 37.5 1.0
NP5 D:LG1103 4.8 44.9 1.0
C5 D:DG12 4.9 39.4 1.0
C5 D:DG13 4.9 40.4 1.0
C5 D:DG2 4.9 40.1 1.0
C2 D:DG17 5.0 39.1 1.0

Potassium binding site 10 out of 25 in 8twh

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Potassium binding site 10 out of 25 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 Potassium with other atoms in the K 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
D:K102

b:31.2
occ:1.00
 O6 D:DG16 2.6 32.7 1.0
O6 D:DG6 2.7 42.9 1.0
O6 D:DG12 2.8 41.1 1.0
O6 D:DG7 2.8 45.8 1.0
O6 D:DG1 2.8 40.0 1.0
O6 D:DG2 2.9 41.9 1.0
O6 D:DG11 2.9 37.3 1.0
O6 D:DG17 2.9 32.3 1.0
K D:K101 3.1 39.5 1.0
K C:K103 3.3 27.0 1.0
C6 D:DG7 3.5 43.5 1.0
N1 D:DG7 3.5 39.0 1.0
C6 D:DG6 3.6 43.8 1.0
C6 D:DG16 3.6 35.9 1.0
C6 D:DG1 3.6 40.5 1.0
C6 D:DG11 3.7 39.5 1.0
C6 D:DG12 3.7 40.5 1.0
C6 D:DG2 3.8 42.3 1.0
C6 D:DG17 3.8 33.3 1.0
N1 D:DG11 3.9 41.7 1.0
N1 D:DG6 3.9 44.2 1.0
N1 D:DG1 3.9 40.4 1.0
N1 D:DG16 4.0 38.2 1.0
N1 D:DG17 4.0 31.7 1.0
N1 D:DG2 4.0 41.3 1.0
N1 D:DG12 4.1 40.4 1.0
C2 D:DG7 4.7 43.3 1.0
C5 D:DG7 4.7 48.1 1.0
C5 D:DG16 4.8 36.6 1.0
C5 D:DG6 4.8 42.7 1.0
C5 D:DG1 4.8 41.3 1.0
C5 D:DG11 4.9 39.5 1.0
C5 D:DG12 4.9 39.4 1.0

Reference:

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.
Page generated: Sat Sep 28 22:14:54 2024

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