Potassium in PDB 6qjo: Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes

The structure of Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes, PDB code: 6qjo was solved by F.R.Winnerdy, B.Bakalar, A.Maity, J.J.Vandana, E.Schmitt, Y.Mechulam, A.T.Phan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.27 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	31.120, 39.270, 53.550, 90.04, 93.03, 89.95
R / Rfree (%)	16.4 / 20.2

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>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Potassium atom in the Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes (pdb code 6qjo). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 15 binding sites of Potassium where determined in the Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes, PDB code: 6qjo:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 15 in the Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:16.6 occ:1.00 O6 A:DG20 2.5 22.0 1.0 O6 A:DG28 2.7 23.6 1.0 O6 A:DG22 2.8 18.1 1.0 O6 A:DG17 2.8 21.0 1.0 O6 A:DG25 2.9 27.9 1.0 O6 A:DG23 3.0 17.5 1.0 O6 A:DG26 3.0 15.7 1.0 O6 A:DG19 3.1 26.8 1.0 C6 A:DG20 3.4 16.3 1.0 C6 A:DG22 3.5 13.4 1.0 K A:K103 3.5 13.5 1.0 C6 A:DG19 3.5 17.9 1.0 N1 A:DG19 3.6 21.9 1.0 N1 A:DG22 3.6 13.6 1.0 C6 A:DG28 3.6 18.6 1.0 C6 A:DG17 3.6 16.4 1.0 C6 A:DG25 3.7 23.4 1.0 N1 A:DG20 3.7 19.4 1.0 C6 A:DG26 3.9 14.4 1.0 C6 A:DG23 3.9 13.4 1.0 N1 A:DG17 3.9 16.2 1.0 N1 A:DG28 4.0 21.5 1.0 N1 A:DG25 4.0 28.9 1.0 N1 A:DG26 4.1 19.3 1.0 N1 A:DG23 4.2 15.8 1.0 C5 A:DG20 4.6 13.3 1.0 C5 A:DG19 4.7 22.2 1.0 C2 A:DG19 4.7 22.7 1.0 C5 A:DG22 4.7 14.9 1.0 C2 A:DG22 4.8 20.0 1.0 C5 A:DG28 4.8 21.9 1.0 C5 A:DG25 4.8 22.4 1.0 C5 A:DG17 4.9 15.5 1.0

Potassium binding site 2 out of 15 in the Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:13.0 occ:1.00 O6 A:DG15 2.7 22.7 1.0 O6 A:DG11 2.8 11.7 1.0 O6 A:DG1 2.8 20.8 1.0 O6 A:DG14 2.8 14.0 1.0 O6 A:DG5 2.8 17.2 1.0 O6 A:DG2 2.9 26.4 1.0 O6 A:DG6 3.0 16.0 1.0 O6 A:DG10 3.1 24.0 1.0 C6 A:DG15 3.5 14.6 1.0 K A:K103 3.5 13.5 1.0 C6 A:DG11 3.6 9.8 1.0 C6 A:DG1 3.6 16.8 1.0 C6 A:DG2 3.7 18.6 1.0 C6 A:DG14 3.7 11.9 1.0 N1 A:DG11 3.7 13.3 1.0 N1 A:DG15 3.7 12.7 1.0 C6 A:DG5 3.8 18.0 1.0 C6 A:DG6 3.8 15.6 1.0 C6 A:DG10 3.9 16.6 1.0 N1 A:DG2 4.0 15.0 1.0 N1 A:DG1 4.0 17.6 1.0 N1 A:DG6 4.0 19.3 1.0 N1 A:DG14 4.1 11.0 1.0 N1 A:DG5 4.2 16.4 1.0 N1 A:DG10 4.3 14.7 1.0 C5 A:DG15 4.7 13.6 1.0 C5 A:DG1 4.8 19.1 1.0 C5 A:DG14 4.8 11.5 1.0 C5 A:DG2 4.8 21.4 1.0 C5 A:DG11 4.8 9.7 1.0 C2 A:DG15 5.0 17.3 1.0 C5 A:DG10 5.0 16.2 1.0 C5 A:DG5 5.0 15.9 1.0 C2 A:DG11 5.0 12.4 1.0

Potassium binding site 3 out of 15 in the Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:13.5 occ:1.00 O6 A:DG10 2.5 24.0 1.0 O6 A:DG17 2.8 21.0 1.0 O6 A:DG1 2.8 20.8 1.0 O6 A:DG23 2.8 17.5 1.0 O6 A:DG14 2.8 14.0 1.0 O6 A:DG26 2.9 15.7 1.0 O6 A:DG20 3.1 22.0 1.0 O6 A:DG5 3.1 17.2 1.0 K A:K101 3.5 16.6 1.0 C6 A:DG10 3.5 16.6 1.0 K A:K102 3.5 13.0 1.0 C6 A:DG26 3.6 14.4 1.0 C6 A:DG17 3.6 16.4 1.0 C6 A:DG1 3.7 16.8 1.0 C6 A:DG23 3.7 13.4 1.0 C6 A:DG14 3.7 11.9 1.0 N1 A:DG26 3.7 19.3 1.0 C6 A:DG20 3.8 16.3 1.0 C6 A:DG5 3.9 18.0 1.0 N1 A:DG10 3.9 14.7 1.0 N1 A:DG17 4.0 16.2 1.0 N1 A:DG1 4.0 17.6 1.0 N1 A:DG23 4.0 15.8 1.0 N1 A:DG14 4.0 11.0 1.0 N1 A:DG20 4.1 19.4 1.0 N1 A:DG5 4.3 16.4 1.0 C5 A:DG10 4.7 16.2 1.0 C5 A:DG17 4.8 15.5 1.0 C5 A:DG26 4.8 16.4 1.0 C5 A:DG20 4.9 13.3 1.0 C5 A:DG23 4.9 12.8 1.0 C5 A:DG1 4.9 19.1 1.0 C5 A:DG14 4.9 11.5 1.0 C2 A:DG26 5.0 19.2 1.0

Potassium binding site 4 out of 15 in the Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:35.7 occ:1.00 OP1 A:DT3 2.8 46.5 1.0 O A:HOH207 3.8 40.2 1.0 O D:HOH218 3.9 19.4 1.0 P A:DT3 4.1 39.6 1.0 O5' A:DT3 4.5 35.6 1.0 OP2 D:DT12 4.6 22.6 1.0 OP2 A:DT3 4.7 28.2 1.0 OP1 A:DT4 4.9 17.6 1.0 C5' A:DT3 5.0 30.4 1.0

Potassium binding site 5 out of 15 in the Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:17.6 occ:1.00 O6 B:DG25 2.6 20.8 1.0 O6 B:DG23 2.7 24.2 1.0 O6 B:DG28 2.8 20.4 1.0 O6 B:DG19 2.8 18.1 1.0 O6 B:DG26 2.8 19.3 1.0 O6 B:DG20 3.0 12.9 1.0 O6 B:DG17 3.1 19.5 1.0 C6 B:DG25 3.3 14.5 1.0 O6 B:DG22 3.3 34.0 1.0 C6 B:DG19 3.5 14.5 1.0 C6 B:DG26 3.5 13.3 1.0 N1 B:DG25 3.5 21.6 1.0 K B:K103 3.6 14.2 1.0 N1 B:DG19 3.6 15.1 1.0 C6 B:DG28 3.6 16.9 1.0 C6 B:DG23 3.7 19.7 1.0 C6 B:DG20 3.8 9.7 1.0 N1 B:DG26 3.8 11.9 1.0 C6 B:DG17 3.9 11.6 1.0 C6 B:DG22 3.9 21.3 1.0 N1 B:DG28 3.9 14.9 1.0 N1 B:DG20 4.0 12.0 1.0 N1 B:DG22 4.1 20.5 1.0 N1 B:DG23 4.1 18.4 1.0 N1 B:DG17 4.2 13.1 1.0 C5 B:DG25 4.5 21.2 1.0 C5 B:DG26 4.7 10.2 1.0 C5 B:DG19 4.7 16.3 1.0 C2 B:DG25 4.7 24.7 1.0 C2 B:DG19 4.8 16.7 1.0 C5 B:DG28 4.8 21.3 1.0 C5 B:DG23 4.9 22.9 1.0 C5 B:DG20 4.9 12.4 1.0 C5 B:DG22 5.0 13.2 1.0 C2 B:DG26 5.0 18.6 1.0

Potassium binding site 6 out of 15 in the Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:16.0 occ:1.00 O6 B:DG6 2.5 26.9 1.0 O6 B:DG1 2.5 17.9 1.0 O6 B:DG10 2.6 18.1 1.0 O6 B:DG14 2.8 19.0 1.0 O6 B:DG2 2.9 22.3 1.0 O6 B:DG5 2.9 23.8 1.0 O6 B:DG15 3.0 14.9 1.0 O6 B:DG11 3.1 35.7 1.0 O B:HOH202 3.4 15.5 1.0 C6 B:DG1 3.4 14.5 1.0 K B:K103 3.4 14.2 1.0 C6 B:DG6 3.4 22.1 1.0 C6 B:DG10 3.6 11.3 1.0 C6 B:DG2 3.7 16.9 1.0 N1 B:DG1 3.7 16.9 1.0 N1 B:DG6 3.7 18.8 1.0 C6 B:DG14 3.7 10.3 1.0 C6 B:DG5 3.8 16.8 1.0 C6 B:DG15 3.8 13.4 1.0 C6 B:DG11 3.8 26.0 1.0 N1 B:DG15 4.0 10.2 1.0 N1 B:DG10 4.0 13.0 1.0 N1 B:DG5 4.0 17.1 1.0 N1 B:DG14 4.1 12.5 1.0 N1 B:DG2 4.1 17.0 1.0 N1 B:DG11 4.2 24.1 1.0 N2 B:DG8 4.5 29.3 1.0 C5 B:DG1 4.7 12.0 1.0 C5 B:DG10 4.8 12.3 1.0 C5 B:DG2 4.8 20.6 1.0 C5 B:DG6 4.8 19.1 1.0 C5 B:DG11 4.8 20.3 1.0 N1 B:DG8 4.8 22.7 1.0 C5 B:DG5 4.9 14.7 1.0 C2 B:DG8 4.9 24.5 1.0 C5 B:DG14 4.9 11.2 1.0 C5 B:DG15 5.0 14.6 1.0 C2 B:DG1 5.0 15.2 1.0

Potassium binding site 7 out of 15 in the Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:14.2 occ:1.00 O6 B:DG26 2.4 19.3 1.0 O6 B:DG20 2.6 12.9 1.0 O6 B:DG5 2.8 23.8 1.0 O6 B:DG10 2.8 18.1 1.0 O6 B:DG1 3.0 17.9 1.0 O6 B:DG17 3.0 19.5 1.0 O6 B:DG14 3.1 19.0 1.0 O6 B:DG23 3.1 24.2 1.0 C6 B:DG26 3.3 13.3 1.0 C6 B:DG20 3.4 9.7 1.0 K B:K102 3.4 16.0 1.0 C6 B:DG5 3.5 16.8 1.0 K B:K101 3.6 17.6 1.0 N1 B:DG5 3.6 17.1 1.0 C6 B:DG10 3.7 11.3 1.0 C6 B:DG1 3.7 14.5 1.0 N1 B:DG20 3.7 12.0 1.0 N1 B:DG26 3.7 11.9 1.0 C6 B:DG17 3.9 11.6 1.0 C6 B:DG23 3.9 19.7 1.0 C6 B:DG14 3.9 10.3 1.0 N1 B:DG1 4.0 16.9 1.0 N1 B:DG17 4.0 13.1 1.0 N1 B:DG14 4.1 12.5 1.0 N1 B:DG10 4.1 13.0 1.0 N1 B:DG23 4.2 18.4 1.0 C5 B:DG26 4.4 10.2 1.0 C5 B:DG20 4.6 12.4 1.0 C5 B:DG10 4.8 12.3 1.0 C5 B:DG5 4.8 14.7 1.0 C5 B:DG1 4.8 12.0 1.0 C2 B:DG5 4.9 15.4 1.0 O6 B:DG6 4.9 26.9 1.0 C5 B:DG23 5.0 22.9 1.0 C2 B:DG20 5.0 14.2 1.0

Potassium binding site 8 out of 15 in the Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes within 5.0Å range: probe atom residue distance (Å) B Occ C:K101 b:16.4 occ:1.00 O6 C:DG25 2.5 18.6 1.0 O6 C:DG28 2.6 23.3 1.0 O6 C:DG20 2.6 23.1 1.0 O6 C:DG23 3.0 24.0 1.0 O6 C:DG17 3.1 23.4 1.0 O6 C:DG26 3.1 22.8 1.0 O6 C:DG22 3.1 21.9 1.0 C6 C:DG25 3.2 17.0 1.0 O6 C:DG19 3.3 33.3 1.0 N1 C:DG25 3.4 17.9 1.0 C6 C:DG20 3.5 14.4 1.0 C6 C:DG28 3.5 20.0 1.0 K C:K103 3.6 12.5 1.0 N1 C:DG22 3.7 20.1 1.0 C6 C:DG22 3.7 11.7 1.0 N1 C:DG20 3.7 15.3 1.0 N1 C:DG28 3.8 19.7 1.0 C6 C:DG17 3.8 16.6 1.0 C6 C:DG19 3.8 24.7 1.0 C6 C:DG26 3.8 16.5 1.0 C6 C:DG23 3.9 18.0 1.0 N1 C:DG19 4.0 21.1 1.0 N1 C:DG26 4.1 16.9 1.0 N1 C:DG17 4.2 16.4 1.0 N1 C:DG23 4.3 21.4 1.0 C5 C:DG25 4.5 27.1 1.0 C2 C:DG25 4.6 19.7 1.0 C5 C:DG20 4.7 19.4 1.0 C5 C:DG28 4.8 23.2 1.0 C2 C:DG22 4.8 18.5 1.0 C5 C:DG19 4.9 25.2 1.0 C5 C:DG22 4.9 18.7 1.0 C5 C:DG17 4.9 21.9 1.0 C2 C:DG19 5.0 18.8 1.0 C5 C:DG26 5.0 23.6 1.0

Potassium binding site 9 out of 15 in the Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes within 5.0Å range: probe atom residue distance (Å) B Occ C:K102 b:14.1 occ:1.00 O6 C:DG1 2.5 25.4 1.0 O6 C:DG6 2.5 19.9 1.0 O6 C:DG11 2.6 13.9 1.0 O6 C:DG2 2.7 30.5 1.0 O6 C:DG5 2.9 20.8 1.0 O6 C:DG15 2.9 26.8 1.0 O6 C:DG14 3.0 16.3 1.0 O6 C:DG10 3.1 18.7 1.0 C6 C:DG6 3.4 15.3 1.0 C6 C:DG1 3.4 17.8 1.0 C6 C:DG2 3.4 25.1 1.0 C6 C:DG15 3.6 21.1 1.0 K C:K103 3.6 12.5 1.0 C6 C:DG11 3.6 22.6 1.0 N1 C:DG6 3.6 20.3 1.0 N1 C:DG2 3.6 21.2 1.0 C6 C:DG5 3.7 14.3 1.0 N1 C:DG1 3.7 21.2 1.0 C6 C:DG14 3.8 14.0 1.0 N1 C:DG15 3.9 14.7 1.0 C6 C:DG10 3.9 13.4 1.0 N1 C:DG11 4.0 25.3 1.0 N1 C:DG5 4.0 12.3 1.0 N1 C:DG14 4.2 15.0 1.0 N1 C:DG10 4.3 22.8 1.0 C5 C:DG2 4.6 24.4 1.0 C5 C:DG15 4.6 22.9 1.0 C5 C:DG1 4.6 14.0 1.0 C5 C:DG6 4.7 12.0 1.0 N1 C:DG8 4.7 20.4 1.0 N2 C:DG8 4.7 28.9 1.0 C5 C:DG5 4.8 16.7 1.0 C5 C:DG11 4.8 17.0 1.0 C2 C:DG2 4.9 20.6 1.0 C2 C:DG6 4.9 16.2 1.0 C2 C:DG15 5.0 17.7 1.0

Potassium binding site 10 out of 15 in the Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Dna Containing Both Right- and Left-Handed Parallel-Stranded G- Quadruplexes within 5.0Å range: probe atom residue distance (Å) B Occ C:K103 b:12.5 occ:1.00 O6 C:DG26 2.5 22.8 1.0 O6 C:DG10 2.6 18.7 1.0 O6 C:DG17 2.7 23.4 1.0 O6 C:DG23 2.8 24.0 1.0 O6 C:DG5 2.9 20.8 1.0 O6 C:DG20 3.0 23.1 1.0 O6 C:DG14 3.0 16.3 1.0 O6 C:DG1 3.1 25.4 1.0 C6 C:DG26 3.4 16.5 1.0 C6 C:DG10 3.5 13.4 1.0 K C:K102 3.6 14.1 1.0 C6 C:DG20 3.6 14.4 1.0 C6 C:DG17 3.6 16.6 1.0 K C:K101 3.6 16.4 1.0 C6 C:DG23 3.6 18.0 1.0 C6 C:DG5 3.7 14.3 1.0 N1 C:DG20 3.8 15.3 1.0 N1 C:DG10 3.8 22.8 1.0 C6 C:DG14 3.8 14.0 1.0 N1 C:DG26 3.9 16.9 1.0 C6 C:DG1 3.9 17.8 1.0 N1 C:DG5 3.9 12.3 1.0 N1 C:DG23 3.9 21.4 1.0 N1 C:DG17 4.0 16.4 1.0 N1 C:DG14 4.1 15.0 1.0 N1 C:DG1 4.2 21.2 1.0 C5 C:DG26 4.6 23.6 1.0 C5 C:DG20 4.7 19.4 1.0 C5 C:DG10 4.8 14.3 1.0 C5 C:DG17 4.8 21.9 1.0 C5 C:DG23 4.8 18.3 1.0 C5 C:DG5 4.9 16.7 1.0 C2 C:DG20 5.0 17.3 1.0 C5 C:DG1 5.0 14.0 1.0 C5 C:DG14 5.0 14.6 1.0

F.R.Winnerdy, B.Bakalar, A.Maity, J.J.Vandana, Y.Mechulam, E.Schmitt, A.T.Phan. uc(Nmr) Solution and X-Ray Crystal Structures of A Dna Molecule Containing Both Right- and Left-Handed Parallel-Stranded G-Quadruplexes. Nucleic Acids Res. V. 47 8272 2019.
ISSN: ESSN 1362-4962
PubMed: 31216034
DOI: 10.1093/NAR/GKZ349