Potassium in PDB 7d5e: Left-Handed G-Quadruplex Containing Two Bulges

The structure of Left-Handed G-Quadruplex Containing Two Bulges, PDB code: 7d5e was solved by P.Das, A.Maity, K.H.Ngo, F.R.Winnerdy, B.Bakalar, Y.Mechulam, E.Schmitt, A.T.Phan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.09 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	29.1, 39.81, 54.97, 90, 91.28, 90
R / Rfree (%)	18.4 / 21.4

The structure of Left-Handed G-Quadruplex Containing Two Bulges also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Potassium atom in the Left-Handed G-Quadruplex Containing Two Bulges (pdb code 7d5e). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Left-Handed G-Quadruplex Containing Two Bulges, PDB code: 7d5e:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:11.1 occ:1.00 O6 A:DG15 2.8 9.3 1.0 O6 A:DG10 2.8 10.2 1.0 O6 A:DG21 2.8 11.1 1.0 O6 A:DG2 2.8 11.7 1.0 O6 A:DG13 2.8 11.8 1.0 O6 A:DG6 2.8 11.5 1.0 O6 A:DG24 2.9 11.2 1.0 O6 A:DG18 2.9 10.3 1.0 K A:K103 3.5 11.2 1.0 K A:K102 3.6 10.0 1.0 C6 A:DG21 3.6 10.6 1.0 C6 A:DG10 3.6 10.2 1.0 C6 A:DG15 3.7 9.5 1.0 C6 A:DG24 3.7 11.3 1.0 C6 A:DG2 3.7 10.7 1.0 C6 A:DG13 3.7 9.5 1.0 C6 A:DG6 3.7 11.2 1.0 C6 A:DG18 3.7 11.1 1.0 N1 A:DG21 3.9 11.8 1.0 N1 A:DG10 4.0 9.6 1.0 N1 A:DG24 4.0 10.7 1.0 N1 A:DG15 4.0 10.1 1.0 N1 A:DG6 4.0 9.9 1.0 N1 A:DG13 4.0 10.2 1.0 N1 A:DG2 4.0 10.4 1.0 N1 A:DG18 4.1 11.3 1.0 C5 A:DG10 4.8 11.1 1.0 C5 A:DG21 4.8 11.5 1.0 C5 A:DG24 4.8 11.9 1.0 C5 A:DG15 4.9 10.6 1.0 C5 A:DG2 4.9 12.0 1.0 C5 A:DG13 4.9 9.3 1.0 C5 A:DG6 4.9 10.5 1.0 C5 A:DG18 5.0 11.7 1.0

Potassium binding site 2 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:10.0 occ:1.00 O6 A:DG26 2.7 11.9 1.0 O6 A:DG23 2.8 10.9 1.0 O6 A:DG15 2.8 9.3 1.0 O6 A:DG20 2.8 13.6 1.0 O6 A:DG18 2.9 10.3 1.0 O6 A:DG17 2.9 14.5 1.0 O6 A:DG24 3.0 11.2 1.0 O6 A:DG21 3.0 11.1 1.0 C6 A:DG23 3.6 10.4 1.0 C6 A:DG20 3.6 11.6 1.0 K A:K101 3.6 11.1 1.0 C6 A:DG26 3.6 10.8 1.0 C6 A:DG15 3.7 9.5 1.0 C6 A:DG17 3.7 12.4 1.0 C6 A:DG18 3.8 11.1 1.0 N1 A:DG23 3.8 10.3 1.0 N1 A:DG20 3.8 11.9 1.0 C6 A:DG21 3.9 10.6 1.0 C6 A:DG24 3.9 11.3 1.0 N1 A:DG17 3.9 13.1 1.0 N1 A:DG26 3.9 11.3 1.0 N1 A:DG15 4.0 10.1 1.0 N1 A:DG18 4.1 11.3 1.0 N1 A:DG24 4.2 10.7 1.0 N1 A:DG21 4.2 11.8 1.0 C5 A:DG23 4.8 11.6 1.0 C5 A:DG20 4.8 12.6 1.0 C5 A:DG15 4.8 10.6 1.0 C5 A:DG17 4.9 13.5 1.0 C5 A:DG26 4.9 11.6 1.0 C5 A:DG18 5.0 11.7 1.0

Potassium binding site 3 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:11.2 occ:1.00 O6 A:DG4 2.7 11.9 1.0 O6 A:DG8 2.7 11.4 1.0 O6 A:DG2 2.8 11.7 1.0 O6 A:DG13 2.8 11.8 1.0 O6 A:DG12 2.8 11.7 1.0 O6 A:DG10 2.9 10.2 1.0 O6 A:DG1 2.9 14.4 1.0 O6 A:DG6 3.0 11.5 1.0 K A:K101 3.5 11.1 1.0 C6 A:DG8 3.6 11.7 1.0 C6 A:DG4 3.6 11.7 1.0 C6 A:DG2 3.7 10.7 1.0 C6 A:DG12 3.7 10.7 1.0 C6 A:DG13 3.7 9.5 1.0 C6 A:DG1 3.7 12.6 1.0 C6 A:DG10 3.8 10.2 1.0 N1 A:DG8 3.9 10.6 1.0 C6 A:DG6 3.9 11.2 1.0 N1 A:DG4 3.9 11.7 1.0 N1 A:DG12 3.9 11.5 1.0 N1 A:DG1 3.9 11.0 1.0 N1 A:DG13 4.0 10.2 1.0 N1 A:DG2 4.0 10.4 1.0 N1 A:DG10 4.1 9.6 1.0 N1 A:DG6 4.2 9.9 1.0 C5 A:DG8 4.8 11.5 1.0 C5 A:DG2 4.8 12.0 1.0 C5 A:DG12 4.9 10.9 1.0 C5 A:DG1 4.9 12.2 1.0 C5 A:DG13 4.9 9.3 1.0 C5 A:DG4 4.9 11.1 1.0 C5 A:DG10 5.0 11.1 1.0

Potassium binding site 4 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:10.2 occ:1.00 O6 B:DG15 2.8 10.8 1.0 O6 B:DG10 2.8 9.7 1.0 O6 B:DG2 2.8 9.8 1.0 O6 B:DG21 2.8 9.1 1.0 O6 B:DG6 2.8 10.3 1.0 O6 B:DG24 2.9 10.0 1.0 O6 B:DG13 2.9 10.5 1.0 O6 B:DG18 2.9 11.1 1.0 K B:K103 3.5 10.0 1.0 K B:K102 3.6 10.4 1.0 C6 B:DG10 3.6 9.8 1.0 C6 B:DG15 3.6 9.9 1.0 C6 B:DG21 3.7 9.2 1.0 C6 B:DG24 3.7 9.5 1.0 C6 B:DG2 3.7 10.3 1.0 C6 B:DG6 3.7 9.3 1.0 C6 B:DG13 3.8 9.3 1.0 C6 B:DG18 3.8 10.0 1.0 N1 B:DG21 3.9 10.3 1.0 N1 B:DG10 4.0 9.8 1.0 N1 B:DG15 4.0 10.4 1.0 N1 B:DG6 4.0 8.8 1.0 N1 B:DG24 4.0 9.0 1.0 N1 B:DG2 4.1 10.2 1.0 N1 B:DG13 4.1 9.2 1.0 N1 B:DG18 4.1 9.9 1.0 C5 B:DG15 4.8 9.1 1.0 C5 B:DG10 4.8 10.6 1.0 C5 B:DG21 4.8 9.8 1.0 C5 B:DG24 4.9 9.6 1.0 C5 B:DG2 4.9 10.8 1.0 C5 B:DG6 4.9 9.1 1.0

Potassium binding site 5 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:10.4 occ:1.00 O6 B:DG23 2.7 10.3 1.0 O6 B:DG15 2.7 10.8 1.0 O6 B:DG26 2.8 11.1 1.0 O6 B:DG18 2.9 11.1 1.0 O6 B:DG20 2.9 13.2 1.0 O6 B:DG17 2.9 11.1 1.0 O6 B:DG24 2.9 10.0 1.0 O6 B:DG21 3.0 9.1 1.0 C6 B:DG23 3.5 10.0 1.0 K B:K101 3.6 10.2 1.0 C6 B:DG15 3.6 9.9 1.0 C6 B:DG20 3.6 12.1 1.0 C6 B:DG17 3.7 10.2 1.0 C6 B:DG26 3.7 10.7 1.0 C6 B:DG18 3.8 10.0 1.0 N1 B:DG23 3.8 10.4 1.0 N1 B:DG20 3.8 11.6 1.0 C6 B:DG21 3.9 9.2 1.0 C6 B:DG24 3.9 9.5 1.0 N1 B:DG17 3.9 11.1 1.0 N1 B:DG15 4.0 10.4 1.0 N1 B:DG26 4.0 10.5 1.0 N1 B:DG18 4.1 9.9 1.0 N1 B:DG24 4.2 9.0 1.0 N1 B:DG21 4.2 10.3 1.0 C3 B:SPM106 4.6 60.3 1.0 C5 B:DG23 4.7 9.7 1.0 C5 B:DG15 4.8 9.1 1.0 C5 B:DG20 4.8 12.2 1.0 C5 B:DG17 4.9 11.5 1.0 C5 B:DG18 5.0 11.2 1.0 N1 B:SPM106 5.0 28.8 1.0 C5 B:DG26 5.0 10.4 1.0

Potassium binding site 6 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:10.0 occ:1.00 O6 B:DG4 2.7 10.5 1.0 O6 B:DG8 2.7 11.0 1.0 O6 B:DG12 2.8 11.0 1.0 O6 B:DG1 2.8 11.6 1.0 O6 B:DG13 2.9 10.5 1.0 O6 B:DG2 2.9 9.8 1.0 O6 B:DG10 2.9 9.7 1.0 O6 B:DG6 3.0 10.3 1.0 K B:K101 3.5 10.2 1.0 C6 B:DG4 3.6 9.7 1.0 C6 B:DG8 3.6 11.0 1.0 C6 B:DG1 3.6 9.6 1.0 C6 B:DG12 3.6 9.9 1.0 C6 B:DG13 3.7 9.3 1.0 C6 B:DG10 3.7 9.8 1.0 C6 B:DG2 3.7 10.3 1.0 N1 B:DG1 3.9 8.7 1.0 N1 B:DG4 3.9 10.9 1.0 C6 B:DG6 3.9 9.3 1.0 N1 B:DG8 3.9 10.6 1.0 N1 B:DG12 3.9 9.9 1.0 N1 B:DG13 4.0 9.2 1.0 N1 B:DG10 4.0 9.8 1.0 N1 B:DG2 4.1 10.2 1.0 N1 B:DG6 4.2 8.8 1.0 C5 B:DG1 4.8 10.6 1.0 C5 B:DG12 4.8 9.2 1.0 C5 B:DG4 4.9 10.3 1.0 C5 B:DG8 4.9 10.3 1.0 C5 B:DG13 4.9 10.2 1.0 C5 B:DG2 4.9 10.8 1.0 C5 B:DG10 4.9 10.6 1.0

Potassium binding site 7 out of 7 in the Left-Handed G-Quadruplex Containing Two Bulges


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Left-Handed G-Quadruplex Containing Two Bulges within 5.0Å range: probe atom residue distance (Å) B Occ B:K104 b:34.6 occ:1.00 N1 B:SPM106 3.0 28.8 1.0 N3 B:DT22 3.0 15.5 1.0 O B:HOH269 3.1 39.8 1.0 C2 B:SPM106 3.6 55.9 1.0 O2 B:DT22 3.7 16.5 1.0 O4 B:DT22 3.8 17.1 1.0 C2 B:DT22 3.8 15.2 1.0 C4 B:DT22 3.8 15.7 1.0 C6 B:DG20 4.0 12.1 1.0 C4 B:SPM106 4.0 29.4 1.0 C3 B:SPM106 4.0 60.3 1.0 N1 B:DG20 4.1 11.6 1.0 C5 B:DG20 4.1 12.2 1.0 C4 B:DG20 4.3 10.9 1.0 N5 B:SPM106 4.3 57.5 1.0 O6 B:DG20 4.3 13.2 1.0 C2 B:DG20 4.4 12.0 1.0 C6 B:SPM106 4.5 15.1 1.0 O2 B:DT19 4.5 21.3 1.0 N3 B:DG20 4.5 11.8 1.0 N7 B:DG20 4.7 12.8 1.0 O B:HOH256 4.9 26.2 1.0 N9 B:DG20 5.0 12.0 1.0

P.Das, K.H.Ngo, F.R.Winnerdy, A.Maity, B.Bakalar, Y.Mechulam, E.Schmitt, A.T.Phan. Bulges in Left-Handed G-Quadruplexes. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33503265
DOI: 10.1093/NAR/GKAA1259