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

The structure of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex, PDB code: 7xhd 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)	24.54 / 1.66
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	29.403, 30.917, 31.584, 98.19, 97.15, 109.13
R / Rfree (%)	18.2 / 21.2

The binding sites of Potassium atom in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex (pdb code 7xhd). 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: 7xhd:
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:20.0 occ:1.00 O6 A:DG11 2.7 21.1 1.0 O6 A:DG4 2.7 23.4 1.0 O6 A:DG8 2.7 23.6 1.0 O6 A:DG15 2.8 22.1 1.0 O6 A:DG14 2.9 21.5 1.0 O6 A:DG3 2.9 19.8 1.0 O6 A:DG7 2.9 20.2 1.0 O6 A:DG10 2.9 20.5 1.0 K A:K102 3.5 19.3 1.0 C6 A:DG8 3.6 23.7 1.0 C6 A:DG14 3.6 20.8 1.0 C6 A:DG11 3.6 23.0 1.0 C6 A:DG4 3.7 24.4 1.0 C6 A:DG15 3.7 23.0 1.0 C6 A:DG3 3.7 20.6 1.0 C6 A:DG10 3.8 21.4 1.0 C6 A:DG7 3.8 21.4 1.0 N1 A:DG8 3.9 23.0 1.0 N1 A:DG14 3.9 18.7 1.0 N1 A:DG15 3.9 23.9 1.0 N1 A:DG4 3.9 21.6 1.0 N1 A:DG11 3.9 21.6 1.0 N1 A:DG3 4.0 21.9 1.0 N1 A:DG10 4.1 20.9 1.0 N1 A:DG7 4.2 21.9 1.0 C5 A:DG14 4.8 19.9 1.0 C5 A:DG3 4.9 21.8 1.0 C5 A:DG8 4.9 24.8 1.0 C5 A:DG11 4.9 22.5 1.0 C5 A:DG4 5.0 22.8 1.0 C5 A:DG15 5.0 23.2 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:19.3 occ:1.00 O6 A:DG10 2.7 20.5 1.0 O6 A:DG2 2.8 19.8 1.0 O6 A:DG14 2.8 21.5 1.0 O6 A:DG3 2.8 19.8 1.0 O6 B:DG1 2.8 19.9 1.0 O6 A:DG7 2.8 20.2 1.0 O6 A:DG13 2.9 19.6 1.0 O6 A:DG6 2.9 19.3 1.0 K A:K103 3.3 18.3 1.0 K A:K101 3.5 20.0 1.0 C6 A:DG2 3.6 19.8 1.0 C6 A:DG10 3.6 21.4 1.0 C6 A:DG7 3.7 21.4 1.0 C6 A:DG13 3.7 20.7 1.0 C6 A:DG14 3.7 20.8 1.0 C6 A:DG3 3.7 20.6 1.0 C6 B:DG1 3.7 21.1 1.0 C6 A:DG6 3.7 21.6 1.0 N1 A:DG13 3.9 20.1 1.0 N1 A:DG7 3.9 21.9 1.0 N1 A:DG14 4.0 18.7 1.0 N1 A:DG2 4.0 18.9 1.0 N1 A:DG10 4.0 20.9 1.0 N1 A:DG3 4.0 21.9 1.0 N1 B:DG1 4.0 20.3 1.0 N1 A:DG6 4.1 21.0 1.0 C5 A:DG2 4.8 19.7 1.0 C5 A:DG10 4.8 24.1 1.0 C5 A:DG13 4.9 20.7 1.0 C5 A:DG7 4.9 21.1 1.0 C5 A:DG14 4.9 19.9 1.0 C5 A:DG6 4.9 21.4 1.0 C5 B:DG1 5.0 22.6 1.0 C5 A:DG3 5.0 21.8 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:18.3 occ:1.00 O6 A:DG2 2.8 19.8 1.0 O6 A:DG6 2.8 19.3 1.0 O6 B:DG13 2.8 20.4 1.0 O6 B:DG2 2.8 19.5 1.0 O6 B:DG1 2.8 19.9 1.0 O6 B:DG6 2.8 19.3 1.0 O6 A:DG13 2.9 19.6 1.0 O6 A:DG1 2.9 19.7 1.0 K A:K102 3.3 19.3 1.0 K B:K101 3.3 18.8 1.0 C6 A:DG2 3.6 19.8 1.0 C6 B:DG13 3.7 20.5 1.0 C6 B:DG1 3.7 21.1 1.0 C6 A:DG6 3.7 21.6 1.0 C6 B:DG2 3.7 20.4 1.0 C6 A:DG13 3.7 20.7 1.0 C6 A:DG1 3.7 20.1 1.0 C6 B:DG6 3.8 19.3 1.0 N1 A:DG2 3.9 18.9 1.0 N1 B:DG13 3.9 21.3 1.0 N1 A:DG13 4.0 20.1 1.0 N1 A:DG6 4.0 21.0 1.0 N1 B:DG2 4.0 19.9 1.0 N1 B:DG1 4.0 20.3 1.0 N1 A:DG1 4.0 20.1 1.0 N1 B:DG6 4.1 19.1 1.0 C5 B:DG1 4.8 22.6 1.0 C5 A:DG2 4.9 19.7 1.0 C5 B:DG13 4.9 20.1 1.0 C5 A:DG6 4.9 21.4 1.0 C5 B:DG2 4.9 21.0 1.0 C5 A:DG1 5.0 19.9 1.0 C5 A:DG13 5.0 20.7 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:18.8 occ:1.00 O6 B:DG14 2.7 20.0 1.0 O6 B:DG7 2.7 20.4 1.0 O6 B:DG10 2.7 19.5 1.0 O6 B:DG3 2.8 18.9 1.0 O6 B:DG2 2.8 19.5 1.0 O6 A:DG1 2.8 19.7 1.0 O6 B:DG6 2.9 19.3 1.0 O6 B:DG13 2.9 20.4 1.0 K A:K103 3.3 18.3 1.0 K B:K102 3.4 19.1 1.0 C6 B:DG2 3.6 20.4 1.0 C6 B:DG7 3.7 20.6 1.0 C6 B:DG10 3.7 19.2 1.0 C6 B:DG14 3.7 20.6 1.0 C6 B:DG3 3.7 20.9 1.0 C6 B:DG6 3.7 19.3 1.0 C6 A:DG1 3.7 20.1 1.0 C6 B:DG13 3.7 20.5 1.0 N1 B:DG2 3.9 19.9 1.0 N1 B:DG6 3.9 19.1 1.0 N1 B:DG7 4.0 19.4 1.0 N1 B:DG13 4.0 21.3 1.0 N1 B:DG3 4.0 21.0 1.0 N1 B:DG14 4.0 19.6 1.0 N1 B:DG10 4.0 18.6 1.0 N1 A:DG1 4.0 20.1 1.0 C5 B:DG2 4.8 21.0 1.0 C5 B:DG10 4.9 20.1 1.0 C5 B:DG6 4.9 20.5 1.0 C5 A:DG1 4.9 19.9 1.0 C5 B:DG7 4.9 19.5 1.0 C5 B:DG14 4.9 20.9 1.0 C5 B:DG13 4.9 20.1 1.0 C5 B:DG3 5.0 20.3 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:19.1 occ:1.00 O6 B:DG11 2.7 20.5 1.0 O6 B:DG8 2.7 21.6 1.0 O6 B:DG15 2.7 21.9 1.0 O6 B:DG4 2.7 20.3 1.0 O6 B:DG3 2.9 18.9 1.0 O6 B:DG10 2.9 19.5 1.0 O6 B:DG14 2.9 20.0 1.0 O6 B:DG7 3.0 20.4 1.0 K B:K101 3.4 18.8 1.0 C6 B:DG8 3.6 22.5 1.0 C6 B:DG14 3.7 20.6 1.0 C6 B:DG4 3.7 22.9 1.0 C6 B:DG11 3.7 22.2 1.0 C6 B:DG3 3.7 20.9 1.0 C6 B:DG15 3.7 21.7 1.0 C6 B:DG10 3.7 19.2 1.0 C6 B:DG7 3.7 20.6 1.0 N1 B:DG8 3.9 20.8 1.0 N1 B:DG4 3.9 23.1 1.0 N1 B:DG14 3.9 19.6 1.0 N1 B:DG11 4.0 21.4 1.0 N1 B:DG15 4.0 22.4 1.0 N1 B:DG3 4.0 21.0 1.0 N1 B:DG10 4.1 18.6 1.0 N1 B:DG7 4.1 19.4 1.0 C5 B:DG3 4.8 20.3 1.0 C5 B:DG14 4.8 20.9 1.0 C5 B:DG7 4.9 19.5 1.0 C5 B:DG8 4.9 20.0 1.0 C5 B:DG10 4.9 20.1 1.0 C5 B:DG4 5.0 23.4 1.0 C5 B:DG11 5.0 21.8 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. V. 613 153 2022.
ISSN: ESSN 1090-2104
PubMed: 35561583
DOI: 10.1016/J.BBRC.2022.04.020