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

The structure of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex, PDB code: 7xie 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)	26.33 / 1.97
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	26.577, 29.628, 29.584, 63.69, 78.16, 78.19
R / Rfree (%)	20.7 / 23.7

The binding sites of Potassium atom in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex (pdb code 7xie). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex, PDB code: 7xie:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 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:24.0 occ:1.00 O6 A:DG11 2.6 27.1 1.0 O6 A:DG8 2.7 22.5 1.0 O6 A:DG15 2.7 27.0 1.0 O6 A:DG4 2.7 26.4 1.0 O6 A:DG14 2.8 28.3 1.0 O6 A:DG10 2.8 22.6 1.0 O6 A:DG7 2.8 26.7 1.0 O6 A:DG3 3.0 25.6 1.0 K A:K102 3.5 23.4 1.0 C6 A:DG8 3.6 26.6 1.0 C6 A:DG14 3.6 27.3 1.0 C6 A:DG10 3.6 27.3 1.0 C6 A:DG11 3.6 29.4 1.0 C6 A:DG4 3.7 28.1 1.0 C6 A:DG15 3.7 29.3 1.0 C6 A:DG7 3.7 27.5 1.0 C6 A:DG3 3.8 26.8 1.0 N1 A:DG8 3.9 26.8 1.0 N1 A:DG10 3.9 23.6 1.0 N1 A:DG4 3.9 26.6 1.0 N1 A:DG11 4.0 31.7 1.0 N1 A:DG14 4.0 24.0 1.0 N1 A:DG7 4.1 22.8 1.0 N1 A:DG15 4.1 30.4 1.0 N1 A:DG3 4.1 23.3 1.0 C5 A:DG14 4.7 29.2 1.0 C5 A:DG10 4.8 26.4 1.0 C5 A:DG8 4.8 27.6 1.0 C5 A:DG7 4.9 25.6 1.0 C5 A:DG11 4.9 26.4 1.0 C5 A:DG4 5.0 26.8 1.0 C5 A:DG15 5.0 29.0 1.0

Potassium binding site 2 out of 7 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:23.4 occ:1.00 O6 A:DG7 2.7 26.7 1.0 O6 A:DG6 2.8 22.8 1.0 O6 B:DG1 2.8 26.1 1.0 O6 A:DG2 2.8 22.5 1.0 O6 A:DG14 2.8 28.3 1.0 O6 A:DG13 2.8 23.8 1.0 O6 A:DG10 2.9 22.6 1.0 O6 A:DG3 2.9 25.6 1.0 K A:K103 3.3 22.0 1.0 K A:K101 3.5 24.0 1.0 C6 A:DG7 3.6 27.5 1.0 C6 A:DG6 3.6 24.9 1.0 C6 A:DG2 3.6 24.3 1.0 C6 A:DG13 3.6 25.2 1.0 C6 B:DG1 3.7 26.6 1.0 C6 A:DG14 3.7 27.3 1.0 C6 A:DG3 3.8 26.8 1.0 C6 A:DG10 3.8 27.3 1.0 N1 A:DG7 3.9 22.8 1.0 N1 A:DG6 3.9 25.1 1.0 N1 A:DG2 4.0 26.2 1.0 N1 A:DG13 4.0 21.8 1.0 N1 A:DG3 4.0 23.3 1.0 N1 B:DG1 4.0 26.6 1.0 N1 A:DG14 4.1 24.0 1.0 N1 A:DG10 4.1 23.6 1.0 C5 A:DG6 4.8 22.0 1.0 C5 A:DG2 4.8 26.5 1.0 C5 A:DG7 4.8 25.6 1.0 C5 A:DG13 4.8 24.8 1.0 C5 B:DG1 4.9 25.6 1.0 C5 A:DG10 5.0 26.4 1.0 C5 A:DG14 5.0 29.2 1.0 C5 A:DG3 5.0 25.8 1.0

Potassium binding site 3 out of 7 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:22.0 occ:1.00 O6 B:DG6 2.7 21.0 1.0 O6 B:DG2 2.7 22.1 1.0 O6 A:DG6 2.7 22.8 1.0 O6 A:DG1 2.7 25.4 1.0 O6 A:DG2 2.8 22.5 1.0 O6 A:DG13 2.8 23.8 1.0 O6 B:DG13 2.8 21.3 1.0 O6 B:DG1 2.8 26.1 1.0 K B:K101 3.2 21.8 1.0 K A:K102 3.3 23.4 1.0 C6 B:DG6 3.6 25.4 1.0 C6 A:DG6 3.6 24.9 1.0 C6 B:DG2 3.6 24.4 1.0 C6 A:DG1 3.6 27.3 1.0 C6 A:DG13 3.7 25.2 1.0 C6 A:DG2 3.7 24.3 1.0 C6 B:DG13 3.7 26.6 1.0 C6 B:DG1 3.7 26.6 1.0 N1 B:DG6 3.8 24.1 1.0 N1 A:DG6 3.9 25.1 1.0 N1 B:DG2 3.9 24.7 1.0 N1 A:DG2 4.0 26.2 1.0 N1 B:DG13 4.0 23.5 1.0 N1 A:DG13 4.0 21.8 1.0 N1 A:DG1 4.0 26.4 1.0 N1 B:DG1 4.1 26.6 1.0 C5 A:DG6 4.8 22.0 1.0 C5 B:DG6 4.8 21.9 1.0 C5 A:DG1 4.8 27.4 1.0 C5 B:DG2 4.9 25.5 1.0 C5 B:DG1 4.9 25.6 1.0 C5 A:DG13 4.9 24.8 1.0 C5 B:DG13 4.9 24.7 1.0 C5 A:DG2 4.9 26.5 1.0

Potassium binding site 4 out of 7 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 A:K104 b:36.2 occ:1.00 OP1 A:DG15 2.6 31.5 1.0 P A:DG15 4.0 34.4 1.0 C5' A:DG15 4.5 38.4 1.0 O5' A:DG15 4.6 36.5 1.0 O A:HOH215 4.6 38.4 1.0 OP2 A:DG15 4.6 29.1 1.0

Potassium binding site 5 out of 7 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:K101 b:21.8 occ:1.00 O6 B:DG7 2.7 25.3 1.0 O6 A:DG1 2.8 25.4 1.0 O6 B:DG13 2.8 21.3 1.0 O6 B:DG2 2.8 22.1 1.0 O6 B:DG10 2.8 25.4 1.0 O6 B:DG3 2.8 25.8 1.0 O6 B:DG6 2.8 21.0 1.0 O6 B:DG14 2.9 29.1 1.0 K A:K103 3.2 22.0 1.0 K B:K102 3.5 25.4 1.0 C6 B:DG7 3.6 27.9 1.0 C6 B:DG2 3.6 24.4 1.0 C6 B:DG6 3.6 25.4 1.0 C6 B:DG13 3.6 26.6 1.0 C6 A:DG1 3.7 27.3 1.0 C6 B:DG3 3.7 26.6 1.0 C6 B:DG10 3.8 27.9 1.0 C6 B:DG14 3.8 29.4 1.0 N1 B:DG7 3.9 27.4 1.0 N1 B:DG2 3.9 24.7 1.0 N1 B:DG6 3.9 24.1 1.0 N1 B:DG3 3.9 22.6 1.0 N1 A:DG1 4.0 26.4 1.0 N1 B:DG13 4.0 23.5 1.0 N1 B:DG14 4.1 28.6 1.0 N1 B:DG10 4.1 26.4 1.0 C5 B:DG2 4.8 25.5 1.0 C5 B:DG7 4.8 25.7 1.0 C5 B:DG6 4.8 21.9 1.0 C5 B:DG13 4.8 24.7 1.0 C5 A:DG1 4.9 27.4 1.0 C5 B:DG10 5.0 27.1 1.0 C5 B:DG3 5.0 26.7 1.0

Potassium binding site 6 out of 7 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 6 of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:25.4 occ:1.00 O6 B:DG11 2.6 30.8 1.0 O6 B:DG8 2.7 25.9 1.0 O6 B:DG15 2.7 28.5 1.0 O6 B:DG4 2.7 28.3 1.0 O6 B:DG10 2.7 25.4 1.0 O6 B:DG14 2.8 29.1 1.0 O6 B:DG7 2.9 25.3 1.0 O6 B:DG3 3.0 25.8 1.0 K B:K101 3.5 21.8 1.0 C6 B:DG8 3.6 31.1 1.0 C6 B:DG14 3.6 29.4 1.0 C6 B:DG10 3.6 27.9 1.0 C6 B:DG11 3.6 30.7 1.0 C6 B:DG4 3.7 30.4 1.0 C6 B:DG15 3.7 32.2 1.0 C6 B:DG7 3.8 27.9 1.0 C6 B:DG3 3.8 26.6 1.0 N1 B:DG8 3.9 29.8 1.0 N1 B:DG10 3.9 26.4 1.0 N1 B:DG11 3.9 31.9 1.0 N1 B:DG14 3.9 28.6 1.0 N1 B:DG4 4.0 29.9 1.0 N1 B:DG15 4.1 28.5 1.0 N1 B:DG7 4.1 27.4 1.0 N1 B:DG3 4.1 22.6 1.0 C5 B:DG14 4.7 30.3 1.0 C5 B:DG10 4.8 27.1 1.0 C5 B:DG8 4.8 31.2 1.0 C5 B:DG4 4.9 27.5 1.0 C5 B:DG11 4.9 29.7 1.0 C5 B:DG15 4.9 31.2 1.0 C5 B:DG7 5.0 25.7 1.0

Potassium binding site 7 out of 7 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 7 of Crystal Structure of A Dimeric Interlocked Parallel G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:34.2 occ:1.00 OP1 B:DG15 2.6 33.4 1.0 P B:DG15 3.9 36.6 1.0 O5' B:DG15 4.5 35.3 1.0 OP2 B:DG15 4.6 29.4 1.0 C5' B:DG15 4.8 35.7 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