Potassium in PDB 6au4: Crystal Structure of the Major Quadruplex Formed in the Human C-Myc Promoter

The structure of Crystal Structure of the Major Quadruplex Formed in the Human C-Myc Promoter, PDB code: 6au4 was solved by S.Stump, T.C.Mou, S.R.Sprang, N.R.Natale, H.D.Beall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.91 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	65.663, 69.811, 32.952, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 24.6

The binding sites of Potassium atom in the Crystal Structure of the Major Quadruplex Formed in the Human C-Myc Promoter (pdb code 6au4). 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 Major Quadruplex Formed in the Human C-Myc Promoter, PDB code: 6au4:
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 Major Quadruplex Formed in the Human C-Myc Promoter


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 Major Quadruplex Formed in the Human C-Myc Promoter within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:40.4 occ:1.00 O6 A:DG14 2.5 67.6 1.0 O6 A:DG9 2.7 50.7 1.0 O6 A:DG13 2.7 41.1 1.0 O6 A:DG8 2.7 40.3 1.0 O6 A:DG4 2.7 54.0 1.0 O6 A:DG17 2.7 39.2 1.0 O6 A:DG5 2.7 65.4 1.0 O6 A:DG18 2.8 50.6 1.0 K A:K102 3.4 50.4 1.0 C6 A:DG14 3.5 61.2 1.0 C6 A:DG8 3.6 43.0 1.0 C6 A:DG4 3.6 48.1 1.0 C6 A:DG13 3.6 44.0 1.0 C6 A:DG9 3.6 54.7 1.0 C6 A:DG17 3.6 41.8 1.0 C6 A:DG18 3.6 51.3 1.0 C6 A:DG5 3.7 57.1 1.0 N1 A:DG8 3.8 51.4 1.0 N1 A:DG14 3.9 69.3 1.0 N1 A:DG4 3.9 47.0 1.0 N1 A:DG18 3.9 50.2 1.0 N1 A:DG9 3.9 54.2 1.0 N1 A:DG5 4.0 55.2 1.0 N1 A:DG13 4.0 38.6 1.0 N1 A:DG17 4.0 40.7 1.0 C5 A:DG14 4.7 59.9 1.0 C5 A:DG13 4.7 55.0 1.0 C5 A:DG8 4.8 43.9 1.0 C5 A:DG17 4.8 48.8 1.0 C5 A:DG4 4.8 59.4 1.0 C5 A:DG18 4.9 59.9 1.0 C5 A:DG9 4.9 54.9 1.0 C5 A:DG5 5.0 49.0 1.0

Potassium binding site 2 out of 6 in the Crystal Structure of the Major Quadruplex Formed in the Human C-Myc Promoter


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 Major Quadruplex Formed in the Human C-Myc Promoter within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:50.4 occ:1.00 O6 A:DG15 2.6 55.7 1.0 O6 A:DG14 2.7 67.6 1.0 O6 A:DG10 2.7 56.7 1.0 O6 A:DG6 2.8 62.1 1.0 O6 A:DG19 2.8 73.3 1.0 O6 A:DG18 2.8 50.6 1.0 O6 A:DG9 2.8 50.7 1.0 O6 A:DG5 3.0 65.4 1.0 K A:K101 3.4 40.4 1.0 C6 A:DG10 3.5 62.2 1.0 C6 A:DG14 3.5 61.2 1.0 N1 A:DG10 3.6 63.7 1.0 C6 A:DG15 3.6 62.4 1.0 C6 A:DG9 3.6 54.7 1.0 C6 A:DG18 3.6 51.3 1.0 C6 A:DG6 3.7 53.7 1.0 C6 A:DG19 3.8 62.5 1.0 C6 A:DG5 3.8 57.1 1.0 N1 A:DG14 3.8 69.3 1.0 N1 A:DG9 3.9 54.2 1.0 N1 A:DG15 3.9 59.7 1.0 N1 A:DG6 3.9 54.0 1.0 N1 A:DG18 4.0 50.2 1.0 N1 A:DG5 4.0 55.2 1.0 N1 A:DG19 4.1 56.3 1.0 C6 B:DA22 4.2 0.8 1.0 N6 B:DA22 4.3 0.6 1.0 N1 B:DA22 4.4 1.0 1.0 C5 A:DG14 4.7 59.9 1.0 C5 B:DA22 4.7 0.0 1.0 C5 A:DG10 4.8 59.9 1.0 C5 A:DG9 4.8 54.9 1.0 C2 A:DG10 4.8 65.6 1.0 C5 A:DG18 4.9 59.9 1.0 C5 A:DG15 4.9 50.3 1.0 C5 A:DG5 4.9 49.0 1.0 C2 B:DA22 4.9 0.5 1.0

Potassium binding site 3 out of 6 in the Crystal Structure of the Major Quadruplex Formed in the Human C-Myc Promoter


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 Major Quadruplex Formed in the Human C-Myc Promoter within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:42.2 occ:1.00 O6 B:DG13 2.6 62.1 1.0 O6 B:DG17 2.7 44.0 1.0 O6 B:DG4 2.7 67.4 1.0 O6 B:DG8 2.7 40.8 1.0 K B:K102 3.3 42.5 1.0 C6 B:DG17 3.5 46.4 1.0 C6 B:DG13 3.5 56.3 1.0 C6 B:DG8 3.6 38.6 1.0 C6 B:DG4 3.6 58.5 1.0 N1 B:DG17 3.8 55.1 1.0 N1 B:DG8 3.9 50.7 1.0 N1 B:DG13 3.9 55.7 1.0 N1 B:DG4 4.0 54.3 1.0 C5 B:DG17 4.7 49.8 1.0 C5 B:DG13 4.7 52.1 1.0 C5 B:DG4 4.8 58.2 1.0 C5 B:DG8 4.8 49.5 1.0

Potassium binding site 4 out of 6 in the Crystal Structure of the Major Quadruplex Formed in the Human C-Myc Promoter


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 Major Quadruplex Formed in the Human C-Myc Promoter within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:42.5 occ:1.00 O6 B:DG5 2.5 62.9 1.0 O6 B:DG13 2.6 62.1 1.0 O6 B:DG14 2.6 68.7 1.0 O6 B:DG17 2.6 44.0 1.0 O6 B:DG9 2.7 45.7 1.0 O6 B:DG18 2.8 49.7 1.0 O6 B:DG4 2.8 67.4 1.0 O6 B:DG8 2.8 40.8 1.0 K B:K103 3.3 48.0 1.0 K B:K101 3.3 42.2 1.0 C6 B:DG13 3.5 56.3 1.0 C6 B:DG5 3.5 55.4 1.0 C6 B:DG17 3.5 46.4 1.0 C6 B:DG14 3.5 54.5 1.0 C6 B:DG8 3.6 38.6 1.0 C6 B:DG9 3.6 59.2 1.0 C6 B:DG4 3.7 58.5 1.0 C6 B:DG18 3.7 50.4 1.0 N1 B:DG5 3.9 44.7 1.0 N1 B:DG17 3.9 55.1 1.0 N1 B:DG13 3.9 55.7 1.0 N1 B:DG8 3.9 50.7 1.0 N1 B:DG14 3.9 67.9 1.0 N1 B:DG9 3.9 54.0 1.0 N1 B:DG4 4.0 54.3 1.0 N1 B:DG18 4.0 62.1 1.0 C5 B:DG13 4.7 52.1 1.0 C5 B:DG14 4.7 56.3 1.0 C5 B:DG17 4.7 49.8 1.0 C5 B:DG5 4.8 55.5 1.0 C5 B:DG8 4.8 49.5 1.0 C5 B:DG9 4.9 50.7 1.0 C5 B:DG4 4.9 58.2 1.0 C5 B:DG18 4.9 56.5 1.0

Potassium binding site 5 out of 6 in the Crystal Structure of the Major Quadruplex Formed in the Human C-Myc Promoter


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 Major Quadruplex Formed in the Human C-Myc Promoter within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:48.0 occ:1.00 O6 B:DG10 2.6 59.3 1.0 O6 B:DG15 2.6 57.3 1.0 O6 B:DG14 2.6 68.7 1.0 O6 B:DG6 2.7 61.1 1.0 O6 B:DG19 2.8 73.8 1.0 O6 B:DG18 2.9 49.7 1.0 O6 B:DG9 2.9 45.7 1.0 O6 B:DG5 3.0 62.9 1.0 K B:K102 3.3 42.5 1.0 C6 B:DG10 3.5 62.8 1.0 C6 B:DG14 3.5 54.5 1.0 C6 B:DG15 3.5 59.1 1.0 C6 B:DG6 3.7 52.5 1.0 N1 B:DG10 3.7 64.5 1.0 C6 B:DG9 3.7 59.2 1.0 C6 B:DG5 3.7 55.4 1.0 C6 B:DG19 3.8 72.3 1.0 C6 B:DG18 3.8 50.4 1.0 N1 B:DG15 3.8 59.5 1.0 N1 B:DG6 3.9 52.5 1.0 N1 B:DG14 3.9 67.9 1.0 N1 B:DG9 4.0 54.0 1.0 N1 B:DG5 4.0 44.7 1.0 N1 B:DG19 4.0 71.8 1.0 N1 B:DG18 4.1 62.1 1.0 C6 A:DA22 4.4 84.9 1.0 N6 A:DA22 4.5 85.2 1.0 N1 A:DA22 4.5 88.7 1.0 C5 B:DG14 4.7 56.3 1.0 C5 B:DG5 4.8 55.5 1.0 C5 B:DG10 4.8 59.7 1.0 C5 B:DG15 4.8 61.5 1.0 C5 A:DA22 4.8 79.1 1.0 C5 B:DG9 4.9 50.7 1.0 C5 B:DG18 5.0 56.5 1.0 C5 B:DG6 5.0 55.1 1.0 C2 B:DG10 5.0 67.7 1.0

Potassium binding site 6 out of 6 in the Crystal Structure of the Major Quadruplex Formed in the Human C-Myc Promoter


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 Major Quadruplex Formed in the Human C-Myc Promoter within 5.0Å range: probe atom residue distance (Å) B Occ B:K104 b:95.0 occ:1.00 O4 B:DT7 2.7 72.4 1.0 O B:HOH206 3.3 60.6 1.0 C4 B:DT7 3.6 71.8 1.0 O B:HOH208 3.8 70.9 1.0 N3 B:DT7 3.9 64.5 1.0 C5 B:DT7 5.0 71.5 1.0

S.Stump, T.C.Mou, S.R.Sprang, N.R.Natale, H.D.Beall. Crystal Structure of the Major Quadruplex Formed in the Promoter Region of the Human C-Myc Oncogene. Plos One V. 13 05584 2018.
ISSN: ESSN 1932-6203
PubMed: 30312328
DOI: 10.1371/JOURNAL.PONE.0205584