Potassium in PDB 8ebo: Homopurine Parallel G-Quadruplex From Human Chromosome 7 Stabilized By K+ Ions

The structure of Homopurine Parallel G-Quadruplex From Human Chromosome 7 Stabilized By K+ Ions, PDB code: 8ebo was solved by E.V.Chen, L.A.Yatsunyk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.71 / 1.98
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	42.053, 47.474, 119.597, 90, 90, 90
R / Rfree (%)	23.1 / 27.9

The structure of Homopurine Parallel G-Quadruplex From Human Chromosome 7 Stabilized By K+ Ions also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Potassium atom in the Homopurine Parallel G-Quadruplex From Human Chromosome 7 Stabilized By K+ Ions (pdb code 8ebo). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Homopurine Parallel G-Quadruplex From Human Chromosome 7 Stabilized By K+ Ions, PDB code: 8ebo:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Homopurine Parallel G-Quadruplex From Human Chromosome 7 Stabilized By K+ Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Homopurine Parallel G-Quadruplex From Human Chromosome 7 Stabilized By K+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:70.7 occ:1.00 O6 A:DG21 2.4 74.2 1.0 O6 A:DG8 2.7 66.3 1.0 O6 A:DG9 2.7 81.8 1.0 O6 A:DG13 2.7 78.4 1.0 O6 A:DG5 2.8 87.4 1.0 O6 A:DG20 2.8 74.9 1.0 O6 A:DG12 2.9 62.3 1.0 O6 A:DG4 2.9 78.8 1.0 K A:K103 3.5 69.7 1.0 C6 A:DG21 3.5 92.2 1.0 C6 A:DG13 3.5 76.7 1.0 C6 A:DG8 3.6 75.5 1.0 N1 A:DG13 3.6 77.1 1.0 C6 A:DG9 3.6 77.2 1.0 C6 A:DG20 3.6 86.9 1.0 C6 A:DG5 3.7 85.0 1.0 C6 A:DG12 3.7 68.8 1.0 C6 A:DG4 3.7 84.4 1.0 N1 A:DG9 3.8 66.1 1.0 N1 A:DG5 3.8 76.4 1.0 N1 A:DG12 3.9 69.5 1.0 N1 A:DG8 3.9 55.8 1.0 C1 A:MMP101 3.9 74.5 1.0 N1 A:DG20 3.9 69.0 1.0 N1 A:DG21 4.0 85.0 1.0 N1 A:DG4 4.0 80.3 1.0 C5 A:DG21 4.7 89.8 1.0 C5 A:DG8 4.8 66.5 1.0 C5 A:DG20 4.8 79.2 1.0 C5 A:DG12 4.8 58.1 1.0 C2 A:DG13 4.9 80.7 1.0 C5 A:DG4 4.9 65.3 1.0 C5 A:DG13 4.9 66.9 1.0 C5 A:DG9 4.9 75.6 1.0 C5 A:DG5 5.0 76.9 1.0

Potassium binding site 2 out of 3 in the Homopurine Parallel G-Quadruplex From Human Chromosome 7 Stabilized By K+ Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Homopurine Parallel G-Quadruplex From Human Chromosome 7 Stabilized By K+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:69.7 occ:1.00 O6 A:DG20 2.6 74.9 1.0 O6 A:DG7 2.6 73.6 1.0 O6 A:DG8 2.7 66.3 1.0 O6 A:DG11 2.7 60.8 1.0 O6 A:DG19 2.8 69.8 1.0 O6 A:DG4 2.8 78.8 1.0 O6 A:DG3 2.8 79.8 1.0 O6 A:DG12 3.0 62.3 1.0 K A:K104 3.2 65.5 1.0 K A:K102 3.5 70.7 1.0 C6 A:DG7 3.5 74.1 1.0 C6 A:DG3 3.5 85.9 1.0 C6 A:DG20 3.6 86.9 1.0 C6 A:DG19 3.6 74.0 1.0 C6 A:DG8 3.6 75.5 1.0 C6 A:DG11 3.6 63.0 1.0 C6 A:DG4 3.7 84.4 1.0 N1 A:DG3 3.8 79.4 1.0 N1 A:DG19 3.8 85.1 1.0 C6 A:DG12 3.8 68.8 1.0 N1 A:DG11 3.9 59.8 1.0 N1 A:DG4 3.9 80.3 1.0 N1 A:DG8 3.9 55.8 1.0 N1 A:DG20 3.9 69.0 1.0 N1 A:DG7 4.0 68.0 1.0 N1 A:DG12 4.1 69.5 1.0 C5 A:DG7 4.7 65.8 1.0 C5 A:DG3 4.8 72.2 1.0 C5 A:DG19 4.8 69.1 1.0 C5 A:DG8 4.8 66.5 1.0 C5 A:DG20 4.8 79.2 1.0 C5 A:DG11 4.8 57.4 1.0 C5 A:DG4 4.9 65.3 1.0 O6 A:DG21 4.9 74.2 1.0 C2 A:DG3 5.0 81.6 1.0

Potassium binding site 3 out of 3 in the Homopurine Parallel G-Quadruplex From Human Chromosome 7 Stabilized By K+ Ions


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Homopurine Parallel G-Quadruplex From Human Chromosome 7 Stabilized By K+ Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:65.5 occ:1.00 O6 A:DG3 2.5 79.8 1.0 O6 A:DG7 2.6 73.6 1.0 O6 A:DG19 2.7 69.8 1.0 O6 A:DG1 2.8 79.2 1.0 O6 A:DG18 2.8 68.9 1.0 O6 A:DG11 2.9 60.8 1.0 K A:K103 3.2 69.7 1.0 C6 A:DG3 3.4 85.9 1.0 C6 A:DG19 3.5 74.0 1.0 C6 A:DG7 3.6 74.1 1.0 C6 A:DG1 3.7 75.3 1.0 C6 A:DG11 3.7 63.0 1.0 C6 A:DG18 3.7 66.1 1.0 N1 A:DG19 3.7 85.1 1.0 N1 A:DG3 3.7 79.4 1.0 N1 A:DG11 4.0 59.8 1.0 N1 A:DG7 4.0 68.0 1.0 N1 A:DG18 4.1 63.9 1.0 N1 A:DG1 4.3 84.2 1.0 C5 A:DG1 4.7 78.5 1.0 C5 A:DG3 4.7 72.2 1.0 C5 A:DG7 4.8 65.8 1.0 C5 A:DG19 4.8 69.1 1.0 C5 A:DG18 4.9 62.3 1.0 C5 A:DG11 4.9 57.4 1.0 C2 A:DG19 5.0 78.8 1.0

M.Ye, E.V.Chen, S.H.Pfeil, K.N.Martin, T.Atrafi, S.Yun, Z.Martinez, L.A.Yatsunyk. Homopurine Guanine-Rich Sequences in Complex with N-Methyl Mesoporphyrin IX Form Parallel G-Quadruplex Dimers and Display A Unique Symmetry Tetrad. Bioorg.Med.Chem. V. 77 17112 2022.
ISSN: ESSN 1464-3391
PubMed: 36508994
DOI: 10.1016/J.BMC.2022.117112