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

The structure of Dna Dodecamer Containing 5-Hydroxymethyl Cytosine, PDB code: 4glh 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)	41.78 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.637, 41.767, 63.997, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 27.6

The binding sites of Potassium atom in the Dna Dodecamer Containing 5-Hydroxymethyl Cytosine (pdb code 4glh). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Dna Dodecamer Containing 5-Hydroxymethyl Cytosine, PDB code: 4glh:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 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:K101 b:30.9 occ:0.80 O2 A:DT7 2.7 27.4 1.0 O2 B:DT7 2.7 27.2 1.0 O B:HOH205 2.8 30.0 1.0 O B:HOH204 2.9 29.4 1.0 O4' A:DT8 3.1 29.4 1.0 O4' B:DT8 3.3 29.7 1.0 C4' A:DT8 3.6 30.6 1.0 C4' B:DT8 3.7 31.9 1.0 C2 A:DT7 3.9 26.1 1.0 C2 B:DT7 3.9 25.2 1.0 C5' B:DT8 4.1 32.6 1.0 C1' A:DT8 4.1 28.1 1.0 C5' A:DT8 4.1 31.1 1.0 C1' B:DT7 4.3 27.1 1.0 C1' A:DT7 4.3 27.9 1.0 C2 B:DA6 4.3 26.4 1.0 C2 A:DA6 4.4 23.9 1.0 C1' B:DT8 4.4 29.2 1.0 N1 A:DT8 4.5 26.3 1.0 K B:K101 4.5 29.8 0.5 N1 B:DT7 4.6 26.4 1.0 N1 A:DT7 4.6 27.2 1.0 O2 A:DT8 4.8 27.2 1.0 N1 B:DT8 4.8 28.7 1.0 C2 A:DT8 4.8 26.4 1.0 N3 B:DT7 4.8 24.2 1.0 N3 A:DT7 4.8 25.6 1.0 O B:HOH207 4.9 28.6 1.0 C3' A:DT8 4.9 30.6 1.0 N3 B:DA6 4.9 26.1 1.0 O2 B:DT8 5.0 27.5 1.0 O4' B:DT7 5.0 28.2 1.0

Potassium binding site 2 out of 2 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 2 of Dna Dodecamer Containing 5-Hydroxymethyl Cytosine within 5.0Å range: probe atom residue distance (Å) B Occ B:K101 b:29.8 occ:0.50 O2 A:DT8 2.7 27.2 1.0 N3 B:DA6 2.8 26.1 1.0 O B:HOH208 2.9 33.6 1.0 O B:HOH204 2.9 29.4 1.0 O4' A:5HC9 3.2 31.3 1.0 O4' B:DT7 3.3 28.2 1.0 C2 B:DA6 3.4 26.4 1.0 C4' A:5HC9 3.5 31.8 1.0 C4' B:DT7 3.7 31.0 1.0 C2 A:DT8 3.8 26.4 1.0 C5' A:5HC9 3.9 32.1 1.0 C4 B:DA6 4.0 23.5 1.0 C1' B:DT7 4.1 27.1 1.0 C1' B:DA6 4.1 28.6 1.0 C1' A:5HC9 4.2 30.2 1.0 C1' A:DT8 4.3 28.1 1.0 C5' B:DT7 4.3 32.6 1.0 C2 B:DA5 4.4 24.0 1.0 N9 B:DA6 4.5 28.0 1.0 K A:K101 4.5 30.9 0.8 N1 A:DT8 4.5 26.3 1.0 O A:HOH203 4.6 29.2 1.0 N1 B:DT7 4.6 26.4 1.0 O4' B:DA6 4.7 29.6 1.0 N1 B:DA6 4.7 23.7 1.0 N1 A:5HC9 4.7 29.1 1.0 O2 B:DT7 4.7 27.2 1.0 N3 A:DT8 4.8 24.9 1.0 O4' A:DT8 4.8 29.4 1.0 C2 B:DT7 4.9 25.2 1.0 O B:HOH223 4.9 34.2 1.0 C3' A:5HC9 4.9 33.6 1.0 O5' A:5HC9 5.0 33.0 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