Potassium in PDB 6ldm: Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1

The structure of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1, PDB code: 6ldm was solved by A.Traczyk, D.J.Gill, W.L.Chong, D.Rhodes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.09 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	84.680, 70.200, 64.850, 90.00, 97.72, 90.00
R / Rfree (%)	20.3 / 23.3

The structure of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 also contains other interesting chemical elements:

Sodium

(Na)

11 atoms

The binding sites of Potassium atom in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 (pdb code 6ldm). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1, PDB code: 6ldm:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:51.5 occ:1.00 O6 B:DG9 2.6 62.9 1.0 O6 B:DG17 2.7 66.3 1.0 O6 B:DG5 2.7 63.8 1.0 O6 B:DG12 2.8 58.5 1.0 O6 B:DG13 2.8 52.9 1.0 O6 B:DG8 2.9 62.3 1.0 O6 B:DG4 2.9 61.2 1.0 O6 B:DG16 3.0 63.5 1.0 K B:K102 3.2 48.2 1.0 C6 B:DG9 3.6 63.7 1.0 C6 B:DG17 3.6 66.1 1.0 C6 B:DG8 3.6 63.3 1.0 C6 B:DG5 3.6 63.8 1.0 C6 B:DG12 3.7 58.3 1.0 C6 B:DG4 3.7 61.4 1.0 C6 B:DG13 3.7 52.8 1.0 C6 B:DG16 3.8 62.9 1.0 NA B:NA109 3.8 73.2 1.0 N1 B:DG9 3.8 64.1 1.0 N1 B:DG8 3.9 63.1 1.0 N1 B:DG4 3.9 61.5 1.0 N1 B:DG17 3.9 65.5 1.0 N1 B:DG5 3.9 63.5 1.0 N1 B:DG16 4.0 62.2 1.0 N1 B:DG12 4.0 57.8 1.0 N1 B:DG13 4.0 53.0 1.0 C5 B:DG8 4.8 65.3 1.0 C5 B:DG12 4.8 58.7 1.0 C5 B:DG17 4.9 66.7 1.0 C5 B:DG9 4.9 64.7 1.0 C5 B:DG4 4.9 61.9 1.0 C5 B:DG5 4.9 65.0 1.0 C5 B:DG16 5.0 62.8 1.0

Potassium binding site 2 out of 5 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:K102 b:48.2 occ:1.00 O6 B:DG8 2.7 62.3 1.0 O6 B:DG4 2.7 61.2 1.0 O6 B:DG12 2.8 58.5 1.0 O6 B:DG3 2.8 63.3 1.0 O6 B:DG7 2.8 59.4 1.0 O6 B:DG15 2.8 55.9 1.0 O6 B:DG16 2.9 63.5 1.0 O6 B:DG11 3.0 61.6 1.0 K B:K101 3.2 51.5 1.0 K B:K103 3.4 45.2 0.5 C6 B:DG8 3.6 63.3 1.0 C6 B:DG4 3.6 61.4 1.0 C6 B:DG3 3.6 63.4 1.0 C6 B:DG12 3.6 58.3 1.0 C6 B:DG7 3.7 60.6 1.0 C6 B:DG16 3.7 62.9 1.0 C6 B:DG15 3.7 55.6 1.0 N1 B:DG8 3.8 63.1 1.0 N1 B:DG4 3.8 61.5 1.0 N1 B:DG16 3.9 62.2 1.0 C6 B:DG11 3.9 61.1 1.0 N1 B:DG12 4.0 57.8 1.0 N1 B:DG15 4.0 55.3 1.0 N1 B:DG3 4.0 63.1 1.0 N1 B:DG7 4.0 60.6 1.0 N1 B:DG11 4.2 60.6 1.0 C5 B:DG3 4.7 64.5 1.0 C5 B:DG7 4.8 62.5 1.0 C5 B:DG4 4.9 61.9 1.0 C5 B:DG8 4.9 65.3 1.0 C5 B:DG12 4.9 58.7 1.0 C5 B:DG15 4.9 55.4 1.0

Potassium binding site 3 out of 5 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:K103 b:45.2 occ:0.50 O6 B:DG3 2.6 63.3 1.0 O6 B:DG7 2.8 59.4 1.0 O6 B:DG15 2.8 55.9 1.0 O6 B:DG11 3.0 61.6 1.0 K B:K102 3.4 48.2 1.0 C6 B:DG3 3.5 63.4 1.0 C6 B:DG15 3.6 55.6 1.0 C6 B:DG7 3.7 60.6 1.0 C6 B:DG11 3.8 61.1 1.0 N1 B:DG15 3.9 55.3 1.0 N1 B:DG3 4.0 63.1 1.0 N1 B:DG7 4.1 60.6 1.0 N1 B:DG11 4.1 60.6 1.0 C5 B:DG3 4.7 64.5 1.0 C5 B:DG15 4.9 55.4 1.0 C5 B:DG7 4.9 62.5 1.0

Potassium binding site 4 out of 5 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:K104 b:97.5 occ:1.00 OP2 B:DG3 2.1 92.1 1.0 O5' B:DG3 2.7 86.6 1.0 P B:DG3 2.9 91.9 1.0 C5' B:DG3 3.0 81.0 1.0 C3' B:DG3 3.8 74.2 1.0 C4' B:DG3 3.8 75.8 1.0 C2' B:DG3 3.9 72.1 1.0 O3' B:DT2 4.0 96.2 1.0 OP1 B:DG3 4.0 91.9 1.0 NA B:NA112 4.3 92.5 1.0 O4' B:DG3 4.5 72.7 1.0 OP2 B:DT1 4.8 0.2 1.0 C1' B:DG3 4.8 70.6 1.0 C3' B:DT2 5.0 0.4 1.0

Potassium binding site 5 out of 5 in the Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:K105 b:0.3 occ:1.00 O3' B:DT18 2.1 83.3 1.0 C3' B:DT18 2.9 82.3 1.0 C2' B:DT18 3.8 81.7 1.0 C4' B:DT18 4.2 81.5 1.0 O5' B:DT18 4.8 81.5 1.0 C5' B:DT18 4.9 81.5 1.0 C1' B:DT18 5.0 81.1 1.0

A.Traczyk, D.J.Gill, W.L.Chong, D.Rhodes. Structural Basis of G-Quadruplex Dna Recognition By the Yeast Telomeric Protein RAP1 Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962