Potassium in PDB 7xh9: Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex

The structure of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex, PDB code: 7xh9 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)	20.33 / 1.63
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	26.436, 30.341, 30.35, 62.15, 79.96, 79.97
R / Rfree (%)	22.5 / 24.7

The structure of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex also contains other interesting chemical elements:

Strontium

(Sr)

4 atoms

The binding sites of Potassium atom in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex (pdb code 7xh9). 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: 7xh9:
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:28.9 occ:1.00 O6 A:DG4 2.6 37.0 1.0 O6 A:DG11 2.7 36.5 1.0 O6 A:DG8 2.7 34.9 1.0 O6 A:DG15 2.7 36.0 1.0 O6 A:DG3 2.8 30.6 1.0 O6 A:DG10 2.9 35.2 1.0 O6 A:DG14 2.9 34.1 1.0 O6 A:DG7 3.0 32.7 1.0 K A:K102 3.5 30.9 1.0 C6 A:DG8 3.6 36.5 1.0 C6 A:DG4 3.6 38.1 1.0 C6 A:DG14 3.7 35.8 1.0 C6 A:DG3 3.7 36.3 1.0 C6 A:DG11 3.7 39.0 1.0 C6 A:DG15 3.7 37.8 1.0 C6 A:DG10 3.7 37.8 1.0 C6 A:DG7 3.8 35.0 1.0 N1 A:DG8 3.9 35.6 1.0 N1 A:DG4 3.9 35.3 1.0 N1 A:DG14 3.9 34.3 1.0 N1 A:DG11 4.0 36.7 1.0 N1 A:DG15 4.0 39.4 1.0 N1 A:DG10 4.0 34.4 1.0 N1 A:DG3 4.0 32.7 1.0 N1 A:DG7 4.1 35.4 1.0 C5 A:DG3 4.8 34.1 1.0 C5 A:DG14 4.8 35.3 1.0 C5 A:DG8 4.8 36.3 1.0 C5 A:DG4 4.9 36.1 1.0 C5 A:DG10 4.9 36.0 1.0 C5 A:DG15 5.0 39.0 1.0 C5 A:DG7 5.0 34.7 1.0 C5 A:DG11 5.0 38.3 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:30.9 occ:1.00 O6 A:DG2 2.7 33.8 1.0 O6 B:DG1 2.7 32.7 1.0 O6 A:DG13 2.8 32.2 1.0 O6 A:DG10 2.8 35.2 1.0 O6 A:DG7 2.8 32.7 1.0 O6 A:DG3 2.8 30.6 1.0 O6 A:DG14 2.8 34.1 1.0 O6 A:DG6 2.9 33.5 1.0 K A:K103 3.2 30.0 1.0 C6 A:DG2 3.5 33.0 1.0 K A:K101 3.5 28.9 1.0 C6 A:DG13 3.6 34.0 1.0 C6 A:DG7 3.7 35.0 1.0 C6 B:DG1 3.7 33.6 1.0 C6 A:DG10 3.7 37.8 1.0 C6 A:DG6 3.7 33.6 1.0 C6 A:DG3 3.7 36.3 1.0 C6 A:DG14 3.8 35.8 1.0 N1 A:DG2 3.8 36.0 1.0 N1 A:DG13 3.8 34.6 1.0 N1 A:DG7 3.9 35.4 1.0 N1 A:DG6 4.0 33.7 1.0 N1 B:DG1 4.0 35.4 1.0 N1 A:DG3 4.1 32.7 1.0 N1 A:DG10 4.1 34.4 1.0 N1 A:DG14 4.1 34.3 1.0 C5 A:DG2 4.7 36.0 1.0 C5 A:DG13 4.8 31.3 1.0 C5 A:DG10 4.9 36.0 1.0 C5 A:DG7 4.9 34.7 1.0 C5 B:DG1 4.9 34.8 1.0 C5 A:DG6 5.0 34.9 1.0 C5 A:DG14 5.0 35.3 1.0 C5 A:DG3 5.0 34.1 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:30.0 occ:1.00 O6 B:DG13 2.8 32.9 1.0 O6 A:DG2 2.8 33.8 1.0 O6 B:DG2 2.8 33.7 1.0 O6 B:DG6 2.8 34.2 1.0 O6 A:DG13 2.8 32.2 1.0 O6 A:DG1 2.8 33.0 1.0 O6 A:DG6 2.8 33.5 1.0 O6 B:DG1 2.9 32.7 1.0 K A:K102 3.2 30.9 1.0 K B:K101 3.3 31.5 1.0 C6 A:DG13 3.6 34.0 1.0 C6 B:DG13 3.6 32.0 1.0 C6 A:DG2 3.7 33.0 1.0 C6 A:DG1 3.7 35.5 1.0 C6 B:DG2 3.7 36.7 1.0 C6 B:DG6 3.7 31.8 1.0 C6 A:DG6 3.7 33.6 1.0 C6 B:DG1 3.8 33.6 1.0 N1 A:DG13 3.9 34.6 1.0 N1 B:DG13 3.9 34.1 1.0 N1 A:DG2 3.9 36.0 1.0 N1 A:DG6 4.0 33.7 1.0 N1 B:DG6 4.0 36.6 1.0 N1 B:DG2 4.0 35.7 1.0 N1 A:DG1 4.0 35.0 1.0 N1 B:DG1 4.1 35.4 1.0 C5 A:DG1 4.8 36.8 1.0 C5 A:DG13 4.9 31.3 1.0 C5 B:DG13 4.9 32.5 1.0 C5 A:DG2 4.9 36.0 1.0 C5 B:DG1 4.9 34.8 1.0 C5 B:DG2 4.9 36.8 1.0 C5 B:DG6 5.0 36.5 1.0 C5 A:DG6 5.0 34.9 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:31.5 occ:1.00 O6 B:DG10 2.7 35.7 1.0 O6 B:DG3 2.7 31.9 1.0 O6 A:DG1 2.7 33.0 1.0 O6 B:DG2 2.7 33.7 1.0 O6 B:DG13 2.8 32.9 1.0 O6 B:DG7 2.8 35.8 1.0 O6 B:DG14 2.9 35.2 1.0 O6 B:DG6 2.9 34.2 1.0 K A:K103 3.3 30.0 1.0 K B:K102 3.5 30.3 1.0 C6 B:DG2 3.6 36.7 1.0 C6 B:DG13 3.6 32.0 1.0 C6 B:DG7 3.6 37.0 1.0 C6 B:DG10 3.6 38.1 1.0 C6 B:DG3 3.7 35.8 1.0 C6 A:DG1 3.7 35.5 1.0 C6 B:DG6 3.7 31.8 1.0 C6 B:DG14 3.8 35.8 1.0 N1 B:DG7 3.9 38.3 1.0 N1 B:DG2 3.9 35.7 1.0 N1 B:DG13 3.9 34.1 1.0 N1 B:DG3 4.0 36.0 1.0 N1 A:DG1 4.0 35.0 1.0 N1 B:DG6 4.0 36.6 1.0 N1 B:DG10 4.0 33.6 1.0 N1 B:DG14 4.1 35.3 1.0 C5 B:DG2 4.7 36.8 1.0 C5 B:DG10 4.8 36.2 1.0 C5 B:DG13 4.8 32.5 1.0 C5 B:DG7 4.9 35.8 1.0 C5 A:DG1 4.9 36.8 1.0 C5 B:DG3 4.9 34.5 1.0 C5 B:DG6 4.9 36.5 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:30.3 occ:1.00 O6 B:DG4 2.6 37.9 1.0 O6 B:DG8 2.7 40.9 1.0 O6 B:DG11 2.7 39.5 1.0 O6 B:DG15 2.7 35.0 1.0 O6 B:DG3 2.8 31.9 1.0 O6 B:DG14 2.9 35.2 1.0 O6 B:DG10 2.9 35.7 1.0 O6 B:DG7 2.9 35.8 1.0 K B:K101 3.5 31.5 1.0 C6 B:DG4 3.6 40.9 1.0 C6 B:DG8 3.6 47.7 1.0 C6 B:DG3 3.6 35.8 1.0 C6 B:DG14 3.7 35.8 1.0 C6 B:DG15 3.7 38.0 1.0 C6 B:DG10 3.7 38.1 1.0 C6 B:DG11 3.7 41.6 1.0 C6 B:DG7 3.8 37.0 1.0 N1 B:DG4 3.8 42.1 1.0 N1 B:DG8 3.9 44.0 1.0 N1 B:DG14 3.9 35.3 1.0 N1 B:DG15 4.0 38.1 1.0 N1 B:DG10 4.0 33.6 1.0 N1 B:DG3 4.0 36.0 1.0 N1 B:DG11 4.0 36.0 1.0 N1 B:DG7 4.1 38.3 1.0 C5 B:DG3 4.7 34.5 1.0 C5 B:DG14 4.8 32.5 1.0 C5 B:DG8 4.8 46.7 1.0 C5 B:DG4 4.9 36.8 1.0 C5 B:DG10 4.9 36.2 1.0 C5 B:DG7 4.9 35.8 1.0 C5 B:DG15 5.0 39.2 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