Potassium in PDB 6kfl: Crystal Structure of A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4

The structure of Crystal Structure of A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4, PDB code: 6kfl was solved by Y.S.Zhang, G.N.Parkinson, D.G.Wei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.06 / 1.92
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	48.152, 47.192, 38.133, 90.00, 113.15, 90.00
R / Rfree (%)	21.8 / 26.2

The structure of Crystal Structure of A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4 also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Potassium atom in the Crystal Structure of A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4 (pdb code 6kfl). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4, PDB code: 6kfl:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Crystal Structure of A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4


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 A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:20.8 occ:1.00 O6 A:DG6 2.6 26.1 1.0 O6 B:DG6 2.6 24.3 1.0 O6 B:DG7 2.7 13.3 1.0 O6 B:DG2 2.8 19.5 1.0 O6 A:DG2 2.8 23.3 1.0 O6 A:DG7 2.9 16.9 1.0 O6 B:DG1 2.9 15.1 1.0 O6 A:DG1 3.0 14.0 1.0 K A:K102 3.5 12.1 1.0 C6 B:DG7 3.5 13.1 1.0 C6 A:DG6 3.5 24.7 1.0 C6 B:DG6 3.6 21.5 1.0 C6 A:DG2 3.7 24.4 1.0 C6 B:DG2 3.7 23.1 1.0 C6 A:DG7 3.7 16.8 1.0 C6 B:DG1 3.8 12.9 1.0 N1 A:DG6 3.8 25.8 1.0 C6 A:DG1 3.8 16.8 1.0 N1 B:DG7 3.8 15.3 1.0 N1 B:DG6 3.9 20.6 1.0 N1 A:DG2 4.0 23.8 1.0 N1 A:DG7 4.0 19.6 1.0 N1 B:DG2 4.0 21.8 1.0 N1 B:DG1 4.1 14.9 1.0 N1 A:DG1 4.1 17.1 1.0 C5 A:DC5 4.4 48.2 1.0 C6 A:DC5 4.5 50.9 1.0 C4 A:DC5 4.6 48.0 1.0 C5 B:DG7 4.8 15.4 1.0 N1 A:DC5 4.8 54.4 1.0 C5 B:DG6 4.8 23.6 1.0 C5 A:DG6 4.8 26.8 1.0 N3 A:DC5 4.9 48.6 1.0 C5 A:DG7 5.0 19.0 1.0 C5 B:DG1 5.0 13.6 1.0 C2 A:DC5 5.0 51.6 1.0

Potassium binding site 2 out of 4 in the Crystal Structure of A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4


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 A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:12.1 occ:1.00 O6 B:DG12 2.7 11.2 1.0 O6 A:DG9 2.7 11.0 1.0 O6 A:DG12 2.8 10.6 1.0 O6 A:DG1 2.8 14.0 1.0 O6 B:DG9 2.8 9.7 1.0 O6 A:DG7 2.8 16.9 1.0 O6 B:DG7 2.8 13.3 1.0 O6 B:DG1 2.9 15.1 1.0 K A:K103 3.4 9.6 1.0 K A:K101 3.5 20.8 1.0 C6 B:DG12 3.6 10.4 1.0 C6 A:DG9 3.6 11.6 1.0 C6 A:DG7 3.7 16.8 1.0 C6 B:DG7 3.7 13.1 1.0 C6 B:DG9 3.7 13.3 1.0 C6 A:DG12 3.7 10.5 1.0 C6 A:DG1 3.7 16.8 1.0 C6 B:DG1 3.8 12.9 1.0 N1 B:DG12 3.9 10.9 1.0 N1 A:DG7 3.9 19.6 1.0 N1 B:DG9 4.0 15.2 1.0 N1 A:DG9 4.0 14.6 1.0 N1 B:DG7 4.0 15.3 1.0 N1 A:DG1 4.0 17.1 1.0 N1 A:DG12 4.0 10.2 1.0 N1 B:DG1 4.1 14.9 1.0 C5 B:DG12 4.7 11.5 1.0 C5 B:DG7 4.9 15.4 1.0 C5 A:DG9 4.9 14.9 1.0 C5 A:DG12 4.9 11.0 1.0 C5 B:DG9 4.9 12.4 1.0 C5 A:DG1 4.9 17.4 1.0 C5 A:DG7 4.9 19.0 1.0

Potassium binding site 3 out of 4 in the Crystal Structure of A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4


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 A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:9.6 occ:1.00 O6 B:DG13 2.7 8.6 1.0 O6 B:DG12 2.7 11.2 1.0 O6 A:DG12 2.8 10.6 1.0 O6 A:DG10 2.8 8.6 1.0 O6 A:DG13 2.8 7.8 1.0 O6 B:DG10 2.9 7.4 1.0 O6 B:DG9 2.9 9.7 1.0 O6 A:DG9 2.9 11.0 1.0 K A:K102 3.4 12.1 1.0 K A:K104 3.4 16.3 1.0 C6 B:DG13 3.6 8.7 1.0 C6 A:DG10 3.6 12.8 1.0 C6 B:DG12 3.6 10.4 1.0 C6 A:DG12 3.7 10.5 1.0 C6 B:DG10 3.7 11.2 1.0 C6 A:DG13 3.7 7.8 1.0 C6 A:DG9 3.8 11.6 1.0 C6 B:DG9 3.8 13.3 1.0 N1 B:DG13 3.9 11.3 1.0 N1 B:DG10 4.0 11.1 1.0 N1 B:DG12 4.0 10.9 1.0 N1 A:DG10 4.0 13.8 1.0 N1 A:DG12 4.0 10.2 1.0 N1 A:DG13 4.0 7.8 1.0 N1 A:DG9 4.1 14.6 1.0 N1 B:DG9 4.1 15.2 1.0 C5 B:DG13 4.8 9.2 1.0 C5 A:DG10 4.8 15.3 1.0 C5 A:DG12 4.9 11.0 1.0 C5 B:DG10 4.9 10.7 1.0 C5 B:DG12 4.9 11.5 1.0 C5 A:DG13 4.9 8.2 1.0

Potassium binding site 4 out of 4 in the Crystal Structure of A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4


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 A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:16.3 occ:1.00 O6 B:DG13 2.8 8.6 1.0 O6 A:DG10 2.9 8.6 1.0 O6 A:DG13 2.9 7.8 1.0 O6 B:DG10 3.0 7.4 1.0 N1 A:DA14 3.3 15.4 0.5 K A:K103 3.4 9.6 1.0 N1 B:DA14 3.5 9.6 0.5 C6 B:DG13 3.7 8.7 1.0 C2 A:DA14 3.8 18.0 0.5 C6 A:DG10 3.8 12.8 1.0 C6 A:DG13 3.8 7.8 1.0 C6 B:DG10 3.8 11.2 1.0 C2 B:DA14 3.9 11.6 0.5 N1 B:DG13 4.0 11.3 1.0 N1 A:DG10 4.0 13.8 1.0 N1 B:DG10 4.1 11.1 1.0 N1 A:DG13 4.1 7.8 1.0 C2 A:DA14 4.2 20.6 0.5 C6 A:DA14 4.4 20.1 0.5 C6 B:DA14 4.5 10.3 0.5 N6 A:DA14 4.7 19.9 0.5 N6 B:DA14 4.8 8.3 0.5 N7 B:DA14 4.9 9.0 0.5 N1 A:DA14 4.9 19.7 0.5 C5 B:DG13 4.9 9.2 1.0 N3 A:DA14 4.9 17.2 0.5

Y.S.Zhang, G.N.Parkinson, D.G.Wei. Crystal Structure of A Two-Quartet Dna G-Quadruplex Complexed with the Porphyrin TMPYP4 To Be Published.