Potassium in PDB 7x7g: Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex

The structure of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex, PDB code: 7x7g was solved by K.H.Ngo, C.W.Liew, S.Lattmann, F.R.Winnerdy, A.T.Phan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.63 / 2.19
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	26.173, 31.247, 49.893, 90, 102.9, 90
R / Rfree (%)	25.6 / 26.9

The binding sites of Potassium atom in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex (pdb code 7x7g). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex, PDB code: 7x7g:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


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 A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:21.9 occ:1.00 O6 A:DG8 2.7 19.6 1.0 O6 A:DG15 2.8 28.0 1.0 O6 A:DG11 2.8 22.2 1.0 O6 A:DG4 2.8 26.3 1.0 O6 A:DG3 2.8 26.5 1.0 O6 A:DG14 2.8 28.7 1.0 O6 A:DG7 2.8 21.7 1.0 O6 A:DG10 2.9 24.4 1.0 K A:K102 3.4 12.7 1.0 C6 A:DG8 3.5 23.7 1.0 C6 A:DG10 3.6 25.4 1.0 C6 A:DG14 3.7 29.1 1.0 C6 A:DG4 3.7 29.8 1.0 N1 A:DG8 3.7 25.0 1.0 C6 A:DG15 3.7 28.7 1.0 C6 A:DG3 3.7 29.0 1.0 C6 A:DG7 3.7 26.6 1.0 C6 A:DG11 3.7 28.9 1.0 N1 A:DG4 3.9 27.4 1.0 N1 A:DG10 3.9 23.3 1.0 N1 A:DG15 3.9 27.4 1.0 N1 A:DG14 4.0 28.3 1.0 N1 A:DG11 4.0 29.8 1.0 N1 A:DG7 4.0 24.0 1.0 N1 A:DG3 4.1 25.7 1.0 C5 A:DG8 4.7 24.9 1.0 C5 A:DG10 4.8 27.2 1.0 C5 A:DG14 4.8 29.0 1.0 C5 A:DG3 4.8 30.7 1.0 C5 A:DG7 4.9 28.4 1.0 C2 A:DG8 4.9 26.8 1.0 C5 A:DG15 5.0 28.0 1.0

Potassium binding site 2 out of 5 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


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 A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:12.7 occ:1.00 O6 A:DG10 2.6 24.4 1.0 O6 A:DG2 2.7 26.0 1.0 O6 A:DG7 2.7 21.7 1.0 O6 A:DG3 2.7 26.5 1.0 O6 A:DG14 2.7 28.7 1.0 O6 B:DG1 2.8 22.8 1.0 O6 A:DG6 2.9 20.9 1.0 O6 A:DG13 2.9 22.3 1.0 K A:K101 3.4 21.9 1.0 K A:K103 3.4 10.5 1.0 C6 A:DG2 3.5 27.5 1.0 C6 A:DG10 3.6 25.4 1.0 C6 A:DG7 3.6 26.6 1.0 C6 A:DG14 3.7 29.1 1.0 C6 B:DG1 3.7 24.4 1.0 C6 A:DG3 3.7 29.0 1.0 C6 A:DG6 3.7 23.7 1.0 C6 A:DG13 3.7 25.9 1.0 N1 A:DG2 3.7 26.3 1.0 N1 A:DG7 3.9 24.0 1.0 N1 A:DG13 3.9 24.4 1.0 N1 B:DG1 3.9 23.3 1.0 N1 A:DG14 4.0 28.3 1.0 N1 A:DG10 4.0 23.3 1.0 N1 A:DG6 4.0 24.0 1.0 N1 A:DG3 4.1 25.7 1.0 C5 A:DG2 4.7 27.6 1.0 C5 A:DG10 4.8 27.2 1.0 C5 A:DG7 4.8 28.4 1.0 C5 A:DG6 4.9 24.6 1.0 C5 A:DG14 4.9 29.0 1.0 C5 A:DG3 4.9 30.7 1.0 C5 B:DG1 4.9 24.4 1.0 C5 A:DG13 4.9 28.7 1.0

Potassium binding site 3 out of 5 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


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 A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:10.5 occ:1.00 O6 B:DG6 2.6 18.9 1.0 O6 A:DG6 2.7 20.9 1.0 O6 A:DG1 2.8 17.8 1.0 O6 B:DG2 2.9 20.0 1.0 O6 B:DG13 2.9 18.7 1.0 O6 B:DG1 2.9 22.8 1.0 O6 A:DG13 2.9 22.3 1.0 O6 A:DG2 2.9 26.0 1.0 K B:K101 3.4 13.0 1.0 K A:K102 3.4 12.7 1.0 C6 B:DG6 3.5 22.8 1.0 C6 A:DG6 3.6 23.7 1.0 C6 A:DG1 3.7 23.2 1.0 C6 B:DG2 3.7 23.2 1.0 C6 B:DG1 3.7 24.4 1.0 C6 B:DG13 3.7 23.0 1.0 C6 A:DG2 3.8 27.5 1.0 C6 A:DG13 3.8 25.9 1.0 N1 B:DG6 3.8 21.5 1.0 N1 B:DG2 3.9 29.0 1.0 N1 A:DG1 3.9 27.5 1.0 N1 A:DG6 3.9 24.0 1.0 N1 B:DG13 4.0 24.2 1.0 N1 A:DG13 4.0 24.4 1.0 N1 B:DG1 4.0 23.3 1.0 N1 A:DG2 4.0 26.3 1.0 C5 B:DG6 4.8 24.9 1.0 C5 B:DG1 4.9 24.4 1.0 C5 A:DG6 4.9 24.6 1.0 C5 A:DG1 4.9 21.1 1.0 C5 B:DG2 5.0 26.1 1.0 C5 A:DG2 5.0 27.6 1.0

Potassium binding site 4 out of 5 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


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 A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:13.0 occ:1.00 O6 B:DG10 2.6 26.1 1.0 O6 B:DG7 2.7 24.1 1.0 O6 B:DG14 2.8 26.8 1.0 O6 B:DG3 2.8 24.4 1.0 O6 B:DG2 2.9 20.0 1.0 O6 A:DG1 2.9 17.8 1.0 O6 B:DG13 3.0 18.7 1.0 O6 B:DG6 3.1 18.9 1.0 K B:K102 3.4 14.7 1.0 K A:K103 3.4 10.5 1.0 C6 B:DG10 3.6 24.3 1.0 C6 B:DG7 3.6 26.2 1.0 C6 B:DG2 3.6 23.2 1.0 C6 B:DG3 3.7 27.4 1.0 C6 B:DG14 3.7 27.0 1.0 C6 A:DG1 3.7 23.2 1.0 C6 B:DG13 3.7 23.0 1.0 C6 B:DG6 3.8 22.8 1.0 N1 B:DG7 3.8 26.1 1.0 N1 B:DG2 3.8 29.0 1.0 N1 B:DG10 3.9 25.1 1.0 N1 B:DG3 3.9 26.1 1.0 N1 B:DG13 3.9 24.2 1.0 N1 B:DG14 3.9 30.7 1.0 N1 A:DG1 3.9 27.5 1.0 N1 B:DG6 4.0 21.5 1.0 C5 B:DG2 4.8 26.1 1.0 C5 B:DG7 4.8 25.8 1.0 C5 B:DG10 4.9 23.2 1.0 C5 B:DG3 4.9 27.9 1.0 C5 B:DG6 4.9 24.9 1.0 C5 B:DG14 5.0 27.4 1.0 C5 A:DG1 5.0 21.1 1.0 C5 B:DG13 5.0 27.6 1.0

Potassium binding site 5 out of 5 in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex


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 A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:14.7 occ:1.00 O6 B:DG8 2.7 23.1 1.0 O6 B:DG11 2.8 23.5 1.0 O6 B:DG15 2.8 25.2 1.0 O6 B:DG4 2.8 26.1 1.0 O6 B:DG3 2.9 24.4 1.0 O6 B:DG14 3.0 26.8 1.0 O6 B:DG7 3.1 24.1 1.0 O6 B:DG10 3.1 26.1 1.0 K B:K101 3.4 13.0 1.0 C6 B:DG8 3.5 25.5 1.0 C6 B:DG4 3.7 26.8 1.0 N1 B:DG8 3.7 28.0 1.0 C6 B:DG11 3.7 24.6 1.0 C6 B:DG3 3.7 27.4 1.0 C6 B:DG15 3.7 28.9 1.0 C6 B:DG14 3.7 27.0 1.0 N1 B:DG4 3.8 27.2 1.0 C6 B:DG10 3.8 24.3 1.0 C6 B:DG7 3.8 26.2 1.0 N1 B:DG11 3.9 28.0 1.0 N1 B:DG15 3.9 28.3 1.0 N1 B:DG3 3.9 26.1 1.0 N1 B:DG14 4.0 30.7 1.0 N1 B:DG10 4.0 25.1 1.0 N1 B:DG7 4.0 26.1 1.0 C5 B:DG8 4.8 24.7 1.0 C5 B:DG3 4.9 27.9 1.0 C5 B:DG14 4.9 27.4 1.0 C5 B:DG10 4.9 23.2 1.0 C2 B:DG8 4.9 27.9 1.0

K.H.Ngo, C.W.Liew, S.Lattmann, F.R.Winnerdy, A.T.Phan. Crystal Structures of An Hiv-1 Integrase Aptamer: Formation of A Water-Mediated A.G.G.G.G Pentad in An Interlocked G-Quadruplex Biochem.Biophys.Res.Commun. 2022.
ISSN: ESSN 1090-2104