Potassium in PDB 6pnk: Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX

The structure of Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX, PDB code: 6pnk was solved by L.A.Yatsunyk, L.Y.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.78 / 2.39
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	60.930, 60.930, 194.342, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 24.9

The structure of Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Potassium atom in the Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX (pdb code 6pnk). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX, PDB code: 6pnk:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX


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 the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:85.4 occ:1.00 O6 A:DG17 2.6 86.2 1.0 O6 A:DG7 2.6 87.4 1.0 O6 A:DG2 2.6 90.7 1.0 O6 A:DG1 2.7 78.8 1.0 O6 A:DG12 2.7 72.0 1.0 O6 A:DG6 2.8 84.3 1.0 O6 A:DG16 2.9 91.8 1.0 O6 A:DG11 3.0 79.2 1.0 K A:K102 3.1 85.0 1.0 K A:K103 3.2 86.4 0.5 C6 A:DG1 3.5 78.0 1.0 C6 A:DG17 3.5 92.0 1.0 C6 A:DG2 3.5 90.0 1.0 C6 A:DG7 3.6 83.2 1.0 C6 A:DG6 3.6 82.5 1.0 C6 A:DG16 3.6 80.1 1.0 C6 A:DG12 3.6 84.2 1.0 N1 A:DG1 3.7 72.6 1.0 N1 A:DG17 3.7 86.5 1.0 N1 A:DG2 3.8 82.8 1.0 N1 A:DG16 3.8 77.2 1.0 N1 A:DG6 3.8 85.3 1.0 C6 A:DG11 3.8 76.8 1.0 N1 A:DG12 3.9 92.5 1.0 N1 A:DG7 4.0 82.5 1.0 N1 A:DG11 4.1 66.0 1.0 C5 A:DG1 4.7 89.5 1.0 C5 A:DG17 4.7 84.3 1.0 C5 A:DG6 4.8 81.3 1.0 C5 A:DG7 4.8 81.2 1.0 C5 A:DG2 4.8 81.2 1.0 C5 A:DG16 4.8 82.6 1.0 C5 A:DG12 4.9 70.2 1.0 C2 A:DG1 4.9 90.9 1.0

Potassium binding site 2 out of 6 in the Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX


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 the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:85.0 occ:1.00 O6 A:DG7 2.7 87.4 1.0 O6 A:DG2 2.7 90.7 1.0 O6 A:DG18 2.7 74.9 1.0 O6 A:DG13 2.7 97.0 1.0 O6 A:DG17 2.8 86.2 1.0 O6 A:DG12 2.8 72.0 1.0 O6 A:DG8 2.8 76.5 1.0 O6 A:DG3 2.8 84.0 1.0 K A:K101 3.1 85.4 1.0 C6 A:DG17 3.5 92.0 1.0 C6 A:DG2 3.5 90.0 1.0 C6 A:DG18 3.6 90.7 1.0 C6 A:DG7 3.6 83.2 1.0 N1 A:DG18 3.7 64.7 1.0 C6 A:DG12 3.7 84.2 1.0 C6 A:DG3 3.7 88.0 1.0 C6 A:DG13 3.7 98.8 1.0 N1 A:DG17 3.7 86.5 1.0 N1 A:DG2 3.8 82.8 1.0 C6 A:DG8 3.8 79.9 1.0 N1 A:DG3 3.9 89.0 1.0 N1 A:DG7 3.9 82.5 1.0 N1 A:DG13 4.0 80.0 1.0 N1 A:DG12 4.0 92.5 1.0 N1 A:DG8 4.0 78.7 1.0 C1 A:MMP104 4.7 98.4 1.0 C5 A:DG17 4.7 84.3 1.0 C5 A:DG2 4.7 81.2 1.0 C5 A:DG7 4.8 81.2 1.0 C5 A:DG18 4.9 86.5 1.0 C5 A:DG12 4.9 70.2 1.0 C2 A:DG17 5.0 93.3 1.0

Potassium binding site 3 out of 6 in the Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX


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 the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:86.4 occ:0.50 O6 A:DG1 2.5 78.8 1.0 O6 A:DG16 2.5 91.8 1.0 O6 A:DG6 2.6 84.3 1.0 O6 A:DG11 2.8 79.2 1.0 K A:K101 3.2 85.4 1.0 C6 A:DG1 3.3 78.0 1.0 C6 A:DG16 3.4 80.1 1.0 C6 A:DG6 3.5 82.5 1.0 N1 A:DG1 3.6 72.6 1.0 N1 A:DG16 3.6 77.2 1.0 C6 A:DG11 3.7 76.8 1.0 N1 A:DG6 3.7 85.3 1.0 N1 A:DG11 3.9 66.0 1.0 C5 A:DG1 4.6 89.5 1.0 C5 A:DG16 4.7 82.6 1.0 C5 A:DG6 4.8 81.3 1.0 C2 A:DG1 4.9 90.9 1.0 C2 A:DG16 4.9 95.8 1.0 C5 A:DG11 5.0 74.1 1.0 C2 A:DG6 5.0 80.6 1.0

Potassium binding site 4 out of 6 in the Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX


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 the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:87.2 occ:1.00 O6 B:DG8 2.6 96.3 1.0 O6 B:DG2 2.7 0.6 1.0 O6 B:DG17 2.7 0.9 1.0 O6 B:DG3 2.7 79.2 1.0 O6 B:DG18 2.8 0.1 1.0 O6 B:DG13 2.8 84.3 1.0 O6 B:DG12 2.8 83.0 1.0 O6 B:DG7 2.8 92.2 1.0 K B:K103 3.3 93.0 1.0 C6 B:DG17 3.5 0.2 1.0 C6 B:DG2 3.6 0.9 1.0 C6 B:DG8 3.6 90.4 1.0 C6 B:DG12 3.6 0.4 1.0 C6 B:DG7 3.6 95.9 1.0 C6 B:DG18 3.7 0.2 1.0 C6 B:DG13 3.7 82.9 1.0 C6 B:DG3 3.7 93.0 1.0 N1 B:DG17 3.8 0.4 1.0 N1 B:DG18 3.8 96.9 1.0 N1 B:DG8 3.8 91.0 1.0 C1 B:MMP104 3.8 88.3 0.5 N1 B:DG2 3.8 86.5 1.0 N1 B:DG7 3.9 0.7 1.0 N1 B:DG12 3.9 0.1 1.0 N1 B:DG13 3.9 80.6 1.0 N1 B:DG3 4.1 84.9 1.0 C5 B:DG17 4.8 0.6 1.0 C5 B:DG2 4.8 93.1 1.0 C5 B:DG7 4.9 91.8 1.0 C1 B:MMP104 4.9 99.7 0.5 C5 B:DG12 4.9 97.5 1.0 C5 B:DG8 4.9 0.3 1.0 N1 B:MMP104 5.0 99.6 0.5

Potassium binding site 5 out of 6 in the Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX


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 the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:0.4 occ:0.50 O6 B:DG1 2.7 95.8 1.0 O6 B:DG16 2.7 83.6 1.0 O6 B:DG6 2.8 90.7 1.0 O6 B:DG11 3.0 94.2 1.0 K B:K103 3.3 93.0 1.0 C6 B:DG16 3.5 99.5 1.0 C6 B:DG1 3.6 1.0 1.0 N1 B:DG16 3.7 96.5 1.0 C6 B:DG6 3.7 0.4 1.0 N1 B:DG1 3.8 86.9 1.0 C6 B:DG11 3.8 81.5 1.0 N1 B:DG6 4.0 0.7 1.0 N1 B:DG11 4.0 83.9 1.0 C5 B:DG16 4.8 95.2 1.0 C5 B:DG1 4.8 0.3 1.0 C2 B:DG16 4.9 0.4 1.0 C5 B:DG6 5.0 0.2 1.0

Potassium binding site 6 out of 6 in the Crystal Structure of the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX


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 the G-Quadruplex Formed By (Gggtt)3GGG in Complex with N-Methylmesoporphryin IX within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:93.0 occ:1.00 O6 B:DG2 2.6 0.6 1.0 O6 B:DG7 2.6 92.2 1.0 O6 B:DG16 2.8 83.6 1.0 O6 B:DG17 2.8 0.9 1.0 O6 B:DG1 2.8 95.8 1.0 O6 B:DG6 2.9 90.7 1.0 O6 B:DG12 2.9 83.0 1.0 O6 B:DG11 3.0 94.2 1.0 K B:K101 3.3 87.2 1.0 K B:K102 3.3 0.4 0.5 C6 B:DG2 3.4 0.9 1.0 C6 B:DG7 3.5 95.9 1.0 C6 B:DG16 3.6 99.5 1.0 C6 B:DG17 3.6 0.2 1.0 C6 B:DG1 3.6 1.0 1.0 N1 B:DG2 3.6 86.5 1.0 C6 B:DG6 3.7 0.4 1.0 C6 B:DG12 3.8 0.4 1.0 N1 B:DG16 3.8 96.5 1.0 N1 B:DG17 3.8 0.4 1.0 N1 B:DG1 3.8 86.9 1.0 N1 B:DG7 3.9 0.7 1.0 C6 B:DG11 3.9 81.5 1.0 N1 B:DG6 4.0 0.7 1.0 N1 B:DG12 4.0 0.1 1.0 N1 B:DG11 4.1 83.9 1.0 C5 B:DG2 4.7 93.1 1.0 C5 B:DG7 4.8 91.8 1.0 C5 B:DG16 4.9 95.2 1.0 C5 B:DG1 4.9 0.3 1.0 C5 B:DG6 4.9 0.2 1.0 C2 B:DG2 4.9 96.7 1.0 C5 B:DG17 4.9 0.6 1.0 O6 B:DG8 5.0 96.3 1.0

L.Y.Lin, S.Mccarthy, B.M.Powell, Y.Manurung, I.M.Xiang, W.L.Dean, B.Chaires, L.A.Yatsunyk. Biophysical and X-Ray Structural Studies of the (Gggtt)3GGG G-Quadruplex in Complex with N-Methyl Mesoporphyrin IX. Plos One V. 15 41513 2020.
ISSN: ESSN 1932-6203
PubMed: 33206666
DOI: 10.1371/JOURNAL.PONE.0241513