Potassium in PDB 4hli: Dna Dodecamer Containing 5-Hydroxymethyl-Cytosine

The structure of Dna Dodecamer Containing 5-Hydroxymethyl-Cytosine, PDB code: 4hli was solved by B.Spingler, D.Renciuk, M.Vorlickova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.175, 40.590, 65.399, 90.00, 90.00, 90.00
R / Rfree (%)	25.2 / 32.8

The structure of Dna Dodecamer Containing 5-Hydroxymethyl-Cytosine also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Potassium atom in the Dna Dodecamer Containing 5-Hydroxymethyl-Cytosine (pdb code 4hli). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total only one binding site of Potassium was determined in the Dna Dodecamer Containing 5-Hydroxymethyl-Cytosine, PDB code: 4hli:

Potassium binding site 1 out of 1 in the Dna Dodecamer Containing 5-Hydroxymethyl-Cytosine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Dna Dodecamer Containing 5-Hydroxymethyl-Cytosine within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:48.1 occ:1.00 O B:HOH102 2.6 32.9 1.0 O B:HOH104 2.7 28.9 1.0 O2 A:DT8 2.8 36.6 1.0 N3 B:DA6 2.9 23.7 1.0 O4' A:DC9 3.0 24.6 1.0 O4' B:DT7 3.2 42.2 1.0 C2 B:DA6 3.5 21.1 1.0 C4' A:DC9 3.5 26.6 1.0 C4' B:DT7 3.7 43.5 1.0 C1' B:DT7 3.9 38.0 1.0 C5' A:DC9 4.0 29.4 1.0 C2 A:DT8 4.0 34.5 1.0 C4 B:DA6 4.0 25.6 1.0 C1' A:DC9 4.1 30.8 1.0 C1' B:DA6 4.2 41.1 1.0 O A:HOH219 4.2 25.7 1.0 C5' B:DT7 4.3 42.0 1.0 C2 B:DA5 4.4 31.2 1.0 C1' A:DT8 4.4 34.6 1.0 N1 B:DT7 4.5 35.0 1.0 N9 B:DA6 4.5 31.2 1.0 N1 A:DC9 4.6 23.1 1.0 O B:HOH110 4.7 29.8 1.0 N1 A:DT8 4.7 33.8 1.0 C3' A:DC9 4.8 33.4 1.0 N1 B:DA6 4.8 27.2 1.0 O A:HOH215 4.8 41.0 1.0 O4' B:DA6 4.8 34.7 1.0 O2 B:DT7 4.9 47.4 1.0 C2 B:DT7 4.9 39.0 1.0 C3' B:DT7 4.9 42.9 1.0 O2 A:DC9 5.0 28.5 1.0 N3 A:DT8 5.0 35.5 1.0 C2 A:DC9 5.0 27.8 1.0 N3 B:DA5 5.0 22.3 1.0

D.Renciuk, O.Blacque, M.Vorlickova, B.Spingler. Crystal Structures of B-Dna Dodecamer Containing the Epigenetic Modifications 5-Hydroxymethylcytosine or 5-Methylcytosine. Nucleic Acids Res. V. 41 9891 2013.
ISSN: ISSN 0305-1048
PubMed: 23963698
DOI: 10.1093/NAR/GKT738