Potassium in PDB 4l0a: X-Ray Structure of An All Lna Quadruplex

The structure of X-Ray Structure of An All Lna Quadruplex, PDB code: 4l0a was solved by I.Russo Krauss, G.Parkinson, A.Merlino, L.Mazzarella, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.70
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	27.670, 27.670, 196.830, 90.00, 90.00, 120.00
R / Rfree (%)	16 / 18

The binding sites of Potassium atom in the X-Ray Structure of An All Lna Quadruplex (pdb code 4l0a). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the X-Ray Structure of An All Lna Quadruplex, PDB code: 4l0a:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the X-Ray Structure of An All Lna Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of X-Ray Structure of An All Lna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:19.5 occ:1.00 O6 D:LCG3 2.8 5.5 1.0 O6 C:LCG4 2.8 3.6 1.0 O6 B:LCG3 2.8 4.6 1.0 O6 D:LCG4 2.9 4.1 1.0 O6 C:LCG3 2.9 4.0 1.0 O6 A:LCG3 3.0 2.6 1.0 O6 B:LCG4 3.0 3.6 1.0 O6 A:LCG4 3.1 5.6 1.0 C6 C:LCG4 3.6 4.5 1.0 K A:K103 3.6 20.5 1.0 C6 D:LCG4 3.7 4.3 1.0 K A:K102 3.7 24.9 1.0 N1 C:LCG4 3.8 4.3 1.0 C6 B:LCG4 3.8 4.6 1.0 C6 D:LCG3 3.8 5.1 1.0 C6 A:LCG4 3.8 3.4 1.0 C6 C:LCG3 3.8 6.2 1.0 C6 B:LCG3 3.8 4.3 1.0 C6 A:LCG3 3.9 3.1 1.0 N1 D:LCG4 3.9 3.0 1.0 N1 A:LCG4 3.9 3.8 1.0 N1 C:LCG3 3.9 6.0 1.0 N1 D:LCG3 4.0 5.3 1.0 N1 B:LCG3 4.0 3.0 1.0 N1 B:LCG4 4.1 4.0 1.0 N1 A:LCG3 4.2 2.6 1.0 C5 C:LCG4 4.7 5.2 1.0 C5 D:LCG4 4.7 4.3 1.0 C5 B:LCG4 4.8 3.8 1.0 C5 A:LCG4 4.9 4.5 1.0 C5 D:LCG3 5.0 4.2 1.0 C2 C:LCG4 5.0 5.2 1.0

Potassium binding site 2 out of 6 in the X-Ray Structure of An All Lna Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of X-Ray Structure of An All Lna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:24.9 occ:1.00 O4 C:TLN5 2.9 7.5 1.0 O4 D:TLN5 2.9 6.2 1.0 O6 B:LCG4 3.0 3.6 1.0 O6 D:LCG4 3.0 4.1 1.0 O4 B:TLN5 3.0 5.7 1.0 O6 A:LCG4 3.1 5.6 1.0 O6 C:LCG4 3.1 3.6 1.0 O4 A:TLN5 3.1 3.5 1.0 K A:K101 3.7 19.5 1.0 C4 C:TLN5 3.7 5.8 1.0 C4 D:TLN5 3.8 5.9 1.0 C4 B:TLN5 3.8 4.6 1.0 N3 C:TLN5 3.8 5.2 1.0 C6 D:LCG4 3.9 4.3 1.0 C6 B:LCG4 4.0 4.6 1.0 C6 A:LCG4 4.0 3.4 1.0 C6 C:LCG4 4.0 4.5 1.0 N3 D:TLN5 4.0 6.2 1.0 C4 A:TLN5 4.0 4.5 1.0 N3 B:TLN5 4.0 6.9 1.0 N1 A:LCG4 4.1 3.8 1.0 N3 A:TLN5 4.1 5.7 1.0 N1 C:LCG4 4.1 4.3 1.0 N1 D:LCG4 4.2 3.0 1.0 N1 B:LCG4 4.2 4.0 1.0 C5 C:TLN5 4.9 5.9 1.0 C5 D:TLN5 5.0 7.4 1.0 C5 B:TLN5 5.0 3.4 1.0

Potassium binding site 3 out of 6 in the X-Ray Structure of An All Lna Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of X-Ray Structure of An All Lna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:20.5 occ:1.00 O6 C:LCG2 2.8 6.3 1.0 O6 A:LCG2 2.8 6.1 1.0 O6 B:LCG2 2.9 4.2 1.0 O6 D:LCG2 2.9 6.6 1.0 O6 C:LCG3 3.0 4.0 1.0 O6 B:LCG3 3.1 4.6 1.0 O6 D:LCG3 3.1 5.5 1.0 O6 A:LCG3 3.2 2.6 1.0 K A:K101 3.6 19.5 1.0 C6 C:LCG3 3.7 6.2 1.0 C6 A:LCG2 3.7 6.6 1.0 C6 C:LCG2 3.7 5.9 1.0 C6 B:LCG3 3.8 4.3 1.0 C6 D:LCG3 3.8 5.1 1.0 C6 B:LCG2 3.8 4.7 1.0 N1 A:LCG2 3.9 5.0 1.0 C6 D:LCG2 3.9 5.0 1.0 C6 A:LCG3 3.9 3.1 1.0 N1 C:LCG3 3.9 6.0 1.0 N1 C:LCG2 3.9 4.5 1.0 N1 B:LCG3 4.0 3.0 1.0 N1 B:LCG2 4.0 4.3 1.0 N1 D:LCG3 4.0 5.3 1.0 N1 A:LCG3 4.0 2.6 1.0 N1 D:LCG2 4.1 6.4 1.0 C5 C:LCG3 4.7 6.1 1.0 C5 B:LCG3 4.8 3.3 1.0 C5 D:LCG3 4.8 4.2 1.0 C5 A:LCG3 5.0 3.8 1.0 C5 A:LCG2 5.0 4.6 1.0 C5 C:LCG2 5.0 5.1 1.0

Potassium binding site 4 out of 6 in the X-Ray Structure of An All Lna Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of X-Ray Structure of An All Lna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ E:K3003 b:22.8 occ:1.00 O6 G:LCG2 2.8 5.3 1.0 O6 E:LCG2 2.8 6.4 1.0 O6 F:LCG2 2.8 5.3 1.0 O6 H:LCG2 3.0 5.7 1.0 O6 E:LCG3 3.0 3.0 1.0 O6 F:LCG3 3.1 2.0 1.0 O6 G:LCG3 3.1 5.1 1.0 O6 H:LCG3 3.2 5.4 1.0 K E:K3004 3.6 20.5 1.0 C6 E:LCG3 3.7 4.8 1.0 C6 E:LCG2 3.7 5.1 1.0 C6 G:LCG2 3.8 6.7 1.0 C6 F:LCG2 3.8 5.8 1.0 C6 F:LCG3 3.8 3.0 1.0 C6 G:LCG3 3.8 3.8 1.0 C6 H:LCG3 3.9 6.5 1.0 N1 E:LCG2 3.9 4.3 1.0 C6 H:LCG2 3.9 6.6 1.0 N1 E:LCG3 4.0 3.4 1.0 N1 F:LCG3 4.0 5.0 1.0 N1 F:LCG2 4.0 5.1 1.0 N1 G:LCG3 4.0 3.8 1.0 N1 H:LCG3 4.0 4.3 1.0 N1 G:LCG2 4.1 7.4 1.0 N1 H:LCG2 4.1 6.1 1.0 C5 E:LCG3 4.7 2.6 1.0 C5 G:LCG3 4.8 2.8 1.0 C5 F:LCG3 4.8 3.4 1.0 C5 H:LCG3 4.9 5.6 1.0 C5 E:LCG2 5.0 4.0 1.0 C5 G:LCG2 5.0 7.3 1.0

Potassium binding site 5 out of 6 in the X-Ray Structure of An All Lna Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of X-Ray Structure of An All Lna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ E:K3004 b:20.5 occ:1.00 O6 H:LCG4 2.8 2.5 1.0 O6 F:LCG3 2.9 2.0 1.0 O6 H:LCG3 2.9 5.4 1.0 O6 E:LCG3 2.9 3.0 1.0 O6 F:LCG4 3.0 3.3 1.0 O6 G:LCG3 3.0 5.1 1.0 O6 E:LCG4 3.0 3.6 1.0 O6 G:LCG4 3.0 2.0 1.0 C6 H:LCG4 3.6 3.6 1.0 K E:K3003 3.6 22.8 1.0 C6 F:LCG4 3.7 3.8 1.0 K E:K3005 3.7 23.1 1.0 C6 G:LCG4 3.8 4.5 1.0 C6 H:LCG3 3.8 6.5 1.0 N1 H:LCG4 3.8 4.4 1.0 C6 E:LCG4 3.8 4.3 1.0 C6 F:LCG3 3.8 3.0 1.0 N1 F:LCG4 3.9 4.4 1.0 C6 G:LCG3 3.9 3.8 1.0 C6 E:LCG3 3.9 4.8 1.0 N1 G:LCG4 4.0 4.5 1.0 N1 H:LCG3 4.0 4.3 1.0 N1 E:LCG4 4.0 3.9 1.0 N1 F:LCG3 4.0 5.0 1.0 N1 G:LCG3 4.1 3.8 1.0 N1 E:LCG3 4.2 3.4 1.0 C5 H:LCG4 4.7 3.6 1.0 C5 F:LCG4 4.7 2.9 1.0 C5 G:LCG4 4.8 5.5 1.0 C5 E:LCG4 4.9 4.6 1.0

Potassium binding site 6 out of 6 in the X-Ray Structure of An All Lna Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of X-Ray Structure of An All Lna Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ E:K3005 b:23.1 occ:1.00 O4 E:TLN5 2.8 5.5 1.0 O4 F:TLN5 2.9 6.0 1.0 O4 G:TLN5 2.9 6.9 1.0 O6 E:LCG4 3.0 3.6 1.0 O6 G:LCG4 3.1 2.0 1.0 O4 H:TLN5 3.1 6.2 1.0 O6 F:LCG4 3.1 3.3 1.0 O6 H:LCG4 3.2 2.5 1.0 C4 E:TLN5 3.6 4.9 1.0 K E:K3004 3.7 20.5 1.0 C4 F:TLN5 3.8 5.7 1.0 N3 F:TLN5 3.8 6.7 1.0 C4 G:TLN5 3.8 7.8 1.0 N3 E:TLN5 3.9 5.5 1.0 C6 E:LCG4 3.9 4.3 1.0 C6 G:LCG4 4.0 4.5 1.0 C4 H:TLN5 4.0 6.4 1.0 C6 F:LCG4 4.0 3.8 1.0 N1 E:LCG4 4.1 3.9 1.0 C6 H:LCG4 4.1 3.6 1.0 N3 G:TLN5 4.1 7.1 1.0 N1 F:LCG4 4.1 4.4 1.0 N3 H:TLN5 4.2 9.1 1.0 N1 G:LCG4 4.2 4.5 1.0 N1 H:LCG4 4.3 4.4 1.0 C5 E:TLN5 4.9 3.5 1.0

I.Russo Krauss, G.N.Parkinson, A.Merlino, C.A.Mattia, A.Randazzo, E.Novellino, L.Mazzarella, F.Sica. A Regular Thymine Tetrad and A Peculiar Supramolecular Assembly in the First Crystal Structure of An All-Lna G-Quadruplex. Acta Crystallogr.,Sect.D V. 70 362 2014.
ISSN: ISSN 0907-4449
PubMed: 24531470
DOI: 10.1107/S1399004713028095