Potassium in PDB 4u5m: Structure of A Left-Handed Dna G-Quadruplex

The structure of Structure of A Left-Handed Dna G-Quadruplex, PDB code: 4u5m was solved by E.Schmitt, Y.Mechulam, A.T.Phan, H.Brahim, W.J.Chung, K.W.Lim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.94 / 1.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	51.886, 51.886, 40.167, 90.00, 90.00, 120.00
R / Rfree (%)	14.1 / 18

The structure of Structure of A Left-Handed Dna G-Quadruplex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Potassium atom in the Structure of A Left-Handed Dna G-Quadruplex (pdb code 4u5m). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Structure of A Left-Handed Dna G-Quadruplex, PDB code: 4u5m:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Structure of A Left-Handed Dna G-Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of A Left-Handed Dna G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K101 b:9.1 occ:1.00 O6 A:DG5 2.8 8.9 0.5 O6 A:DG5 2.8 10.9 0.5 O6 A:DG12 2.8 9.1 1.0 O6 A:DG2 2.8 10.7 1.0 O6 A:DG11 2.8 10.3 1.0 O6 A:DG9 2.8 8.7 1.0 O6 A:DG3 2.9 9.6 1.0 O6 A:DG8 2.9 11.7 1.0 O6 A:DG6 2.9 10.4 1.0 C6 A:DG5 3.5 9.2 0.5 C6 A:DG5 3.5 10.9 0.5 K A:K102 3.6 8.5 1.0 C6 A:DG12 3.6 8.8 1.0 C6 A:DG8 3.7 10.6 1.0 C6 A:DG2 3.7 8.5 1.0 N1 A:DG5 3.7 9.0 0.5 C6 A:DG11 3.7 8.5 1.0 N1 A:DG5 3.7 10.1 0.5 C6 A:DG9 3.7 9.7 1.0 O A:HOH227 3.7 13.3 1.0 C6 A:DG3 3.8 9.6 1.0 C6 A:DG6 3.8 9.8 1.0 N1 A:DG8 3.9 11.0 1.0 N1 A:DG12 3.9 8.6 1.0 N1 A:DG11 4.0 10.5 1.0 N1 A:DG2 4.0 7.8 1.0 N1 A:DG9 4.1 9.4 1.0 N1 A:DG6 4.1 7.8 1.0 N1 A:DG3 4.1 8.3 1.0 C5 A:DG5 4.7 9.0 0.5 C5 A:DG5 4.7 10.5 0.5 C5 A:DG12 4.8 8.7 1.0 C5 A:DG8 4.9 10.8 1.0 C2 A:DG5 4.9 8.7 0.5 C5 A:DG2 4.9 9.4 1.0 C2 A:DG5 4.9 9.9 0.5 C5 A:DG11 4.9 10.9 1.0 C5 A:DG9 4.9 9.3 1.0 C5 A:DG3 4.9 9.7 1.0

Potassium binding site 2 out of 4 in the Structure of A Left-Handed Dna G-Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of A Left-Handed Dna G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:8.5 occ:1.00 O6 A:DG18 2.8 9.9 1.0 O6 A:DG6 2.8 10.4 1.0 O6 A:DG12 2.8 9.1 1.0 O6 A:DG15 2.8 8.7 1.0 O6 A:DG21 2.8 9.3 1.0 O6 A:DG24 2.8 9.8 1.0 O6 A:DG3 2.9 9.6 1.0 O6 A:DG9 2.9 8.7 1.0 K A:K103 3.5 10.2 1.0 K A:K101 3.6 9.1 1.0 C6 A:DG18 3.6 10.0 1.0 C6 A:DG6 3.6 9.8 1.0 C6 A:DG12 3.7 8.8 1.0 C6 A:DG24 3.7 9.5 1.0 C6 A:DG21 3.7 9.0 1.0 C6 A:DG15 3.7 10.0 1.0 C6 A:DG3 3.7 9.6 1.0 C6 A:DG9 3.7 9.7 1.0 N1 A:DG18 3.9 11.0 1.0 N1 A:DG12 4.0 8.6 1.0 N1 A:DG24 4.0 9.2 1.0 N1 A:DG3 4.0 8.3 1.0 N1 A:DG6 4.0 7.8 1.0 N1 A:DG21 4.0 8.2 1.0 N1 A:DG9 4.0 9.4 1.0 N1 A:DG15 4.1 9.8 1.0 C5 A:DG6 4.8 9.6 1.0 C5 A:DG18 4.8 11.0 1.0 C5 A:DG21 4.8 9.6 1.0 C5 A:DG24 4.9 9.9 1.0 C5 A:DG12 4.9 8.7 1.0 C5 A:DG15 4.9 11.1 1.0 C5 A:DG9 4.9 9.3 1.0 C5 A:DG3 4.9 9.7 1.0

Potassium binding site 3 out of 4 in the Structure of A Left-Handed Dna G-Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of A Left-Handed Dna G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:10.2 occ:1.00 O6 A:DG26 2.8 13.1 1.0 O6 A:DG15 2.8 8.7 1.0 O6 A:DG24 2.8 9.8 1.0 O6 A:DG18 2.8 9.9 1.0 O6 A:DG20 2.9 12.3 1.0 O6 A:DG17 2.9 13.7 1.0 O6 A:DG21 2.9 9.3 1.0 O6 A:DG23 2.9 13.0 1.0 K A:K102 3.5 8.5 1.0 C6 A:DG20 3.6 11.7 1.0 C6 A:DG26 3.7 13.9 1.0 C6 A:DG17 3.7 12.4 1.0 C6 A:DG23 3.7 9.8 1.0 C6 A:DG15 3.7 10.0 1.0 C6 A:DG24 3.7 9.5 1.0 C6 A:DG18 3.7 10.0 1.0 C6 A:DG21 3.8 9.0 1.0 N1 A:DG20 3.8 9.5 1.0 N1 A:DG23 3.9 8.9 1.0 N1 A:DG17 3.9 11.1 1.0 N1 A:DG26 3.9 12.5 1.0 N1 A:DG15 4.0 9.8 1.0 N1 A:DG24 4.1 9.2 1.0 N1 A:DG18 4.1 11.0 1.0 N1 A:DG21 4.1 8.2 1.0 C5 A:DG20 4.8 11.6 1.0 C5 A:DG17 4.9 13.3 1.0 C5 A:DG15 4.9 11.1 1.0 C5 A:DG23 4.9 9.8 1.0 C5 A:DG26 4.9 12.9 1.0 C5 A:DG18 4.9 11.0 1.0 C5 A:DG24 5.0 9.9 1.0

Potassium binding site 4 out of 4 in the Structure of A Left-Handed Dna G-Quadruplex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of A Left-Handed Dna G-Quadruplex within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:13.2 occ:1.00 O4 A:DT13 2.6 16.3 1.0 O2 A:DT1 2.7 12.5 1.0 O A:HOH227 2.9 13.3 1.0 C2 A:DT1 3.4 11.2 1.0 N3 A:DT1 3.7 10.8 1.0 C4 A:DT13 3.8 14.7 1.0 C7 A:DT13 4.3 15.7 1.0 N1 A:DT1 4.4 11.9 1.0 C5 A:DT13 4.5 14.9 1.0 O A:HOH225 4.6 12.1 1.0 O6 A:DG2 4.8 10.7 1.0 N3 A:DT13 4.8 14.9 1.0 C4 A:DT1 4.9 10.8 1.0 C1' A:DT1 4.9 12.7 1.0

W.J.Chung, B.Heddi, E.Schmitt, K.W.Lim, Y.Mechulam, A.T.Phan. Structure of A Left-Handed Dna G-Quadruplex. Proc.Natl.Acad.Sci.Usa 2015.
ISSN: ESSN 1091-6490
PubMed: 25695967
DOI: 10.1073/PNAS.1418718112