Potassium in PDB 9c46: Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter

The structure of Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter, PDB code: 9c46 was solved by E.R.Xing, L.A.Yatsunyk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.10 / 2.39
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.137, 31.491, 31.5, 90, 104.31, 90
R / Rfree (%)	23.3 / 25.4

The structure of Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Potassium atom in the Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter (pdb code 9c46). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter, PDB code: 9c46:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:51.9 occ:1.00 O6 A:DG9 2.7 58.6 1.0 O6 A:DG12 2.7 62.0 1.0 O6 A:DG6 2.9 65.7 1.0 O6 A:DG3 2.9 56.7 1.0 O6 A:DG7 2.9 47.7 1.0 O6 A:DG10 3.0 43.7 1.0 O6 A:DG1 3.0 44.1 1.0 O6 A:DG4 3.2 49.0 1.0 C6 A:DG9 3.4 59.5 1.0 N1 A:DG9 3.6 60.6 1.0 C6 A:DG6 3.6 54.3 1.0 C6 A:DG12 3.6 59.2 1.0 K A:K102 3.6 44.6 1.0 N1 A:DG6 3.7 55.3 1.0 C6 A:DG3 3.7 56.5 1.0 C6 A:DG10 3.7 46.7 1.0 C6 A:DG7 3.9 48.9 1.0 N1 A:DG12 3.9 57.8 1.0 N1 A:DG3 3.9 53.8 1.0 N1 A:DG10 4.0 47.4 1.0 C6 A:DG1 4.0 47.7 1.0 C6 A:DG4 4.1 47.9 1.0 N1 A:DG7 4.2 52.7 1.0 N1 A:DG4 4.3 43.5 1.0 N1 A:DG1 4.4 53.8 1.0 C5 A:DG9 4.6 65.8 1.0 C2 A:DG9 4.8 64.6 1.0 C5 A:DG12 4.8 60.5 1.0 C5 A:DG6 4.8 52.7 1.0 C5 A:DG10 4.9 53.8 1.0 C2 A:DG6 4.9 59.0 1.0 C5 A:DG3 4.9 54.5 1.0

Potassium binding site 2 out of 4 in the Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:44.6 occ:1.00 O6 A:DG10 2.6 43.7 1.0 O6 A:DG1 2.7 44.1 1.0 O6 A:DG15 2.8 36.2 1.0 O6 A:DG21 2.8 44.9 1.0 O6 A:DG24 2.9 35.1 1.0 O6 A:DG18 2.9 43.6 1.0 O6 A:DG7 3.0 47.7 1.0 O6 A:DG4 3.2 49.0 1.0 K A:K103 3.4 24.1 1.0 C6 A:DG10 3.5 46.7 1.0 C6 A:DG1 3.6 47.7 1.0 K A:K101 3.6 51.9 1.0 C6 A:DG21 3.6 38.6 1.0 C6 A:DG15 3.6 41.6 1.0 N1 A:DG10 3.7 47.4 1.0 C6 A:DG24 3.7 36.7 1.0 C6 A:DG18 3.7 40.8 1.0 N1 A:DG21 3.9 47.2 1.0 C6 A:DG7 3.9 48.9 1.0 C6 A:DG4 4.0 47.9 1.0 N1 A:DG15 4.0 37.2 1.0 N1 A:DG18 4.0 30.9 1.0 N1 A:DG24 4.0 31.6 1.0 N1 A:DG1 4.0 53.8 1.0 N1 A:DG4 4.2 43.5 1.0 N1 A:DG7 4.2 52.7 1.0 C5 A:DG10 4.7 53.8 1.0 C5 A:DG1 4.8 44.8 1.0 C5 A:DG15 4.8 39.4 1.0 C5 A:DG21 4.8 38.6 1.0 C5 A:DG18 4.9 35.4 1.0 C2 A:DG10 4.9 54.9 1.0 C5 A:DG24 4.9 43.5 1.0

Potassium binding site 3 out of 4 in the Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:24.1 occ:1.00 O6 A:DG22 2.7 26.9 1.0 O6 A:DG21 2.7 44.9 1.0 O6 A:DG15 2.7 36.2 1.0 O6 A:DG18 2.7 43.6 1.0 O6 A:DG24 2.7 35.1 1.0 O6 A:DG16 2.9 22.7 1.0 O6 A:DG25 3.0 23.4 1.0 O6 A:DG19 3.1 37.0 1.0 K A:K104 3.3 28.8 0.5 K A:K102 3.4 44.6 1.0 C6 A:DG21 3.5 38.6 1.0 C6 A:DG22 3.5 29.8 1.0 C6 A:DG18 3.6 40.8 1.0 C6 A:DG24 3.6 36.7 1.0 C6 A:DG15 3.6 41.6 1.0 N1 A:DG21 3.7 47.2 1.0 C6 A:DG16 3.7 37.8 1.0 C6 A:DG19 3.7 28.2 1.0 C6 A:DG25 3.7 27.6 1.0 N1 A:DG19 3.8 20.6 1.0 N1 A:DG18 3.9 30.9 1.0 N1 A:DG24 3.9 31.6 1.0 N1 A:DG22 3.9 32.3 1.0 N1 A:DG25 4.0 29.7 1.0 N1 A:DG16 4.0 40.3 1.0 N1 A:DG15 4.0 37.2 1.0 C5 A:DG22 4.7 32.1 1.0 C5 A:DG21 4.7 38.6 1.0 C5 A:DG24 4.8 43.5 1.0 C5 A:DG15 4.8 39.4 1.0 C5 A:DG18 4.8 35.4 1.0 C5 A:DG16 4.9 29.1 1.0 C5 A:DG25 4.9 32.5 1.0 C5 A:DG19 4.9 30.7 1.0 C2 A:DG21 5.0 44.6 1.0

Potassium binding site 4 out of 4 in the Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Right-Left Hybrid Parallel G-Quadruplex From SLC2A1 Promoter within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:28.8 occ:0.50 O6 A:DG16 2.7 22.7 1.0 O6 A:DG22 2.7 26.9 1.0 O6 A:DG19 2.7 37.0 1.0 O6 A:DG25 2.7 23.4 1.0 K A:K103 3.3 24.1 1.0 C6 A:DG16 3.6 37.8 1.0 C6 A:DG19 3.6 28.2 1.0 C6 A:DG22 3.6 29.8 1.0 C6 A:DG25 3.7 27.6 1.0 N1 A:DG19 3.8 20.6 1.0 N1 A:DG16 3.9 40.3 1.0 N1 A:DG25 3.9 29.7 1.0 N1 A:DG22 4.0 32.3 1.0 C5 A:DG22 4.8 32.1 1.0 C5 A:DG16 4.8 29.1 1.0 C5 A:DG19 4.9 30.7 1.0 C5 A:DG25 4.9 32.5 1.0

P.Seth, E.Xing, A.D.Hendrickson, K.Li, R.Monsen, J.B.Chaires, S.Neidle, L.A.Yatsunyk. Interaction of N-Methylmesoporphyrin IX with A Hybrid Left-/Right-Handed G-Quadruplex Motif From the Promoter of the SLC2A1 Gene. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 39704129
DOI: 10.1093/NAR/GKAE1208