Magnesium in PDB 4c5x: Ultra High Resolution Dickerson-Drew Dodecamer B-Dna with 5-Hydroxymethyl-Cytosine Modification

The structure of Ultra High Resolution Dickerson-Drew Dodecamer B-Dna with 5-Hydroxymethyl-Cytosine Modification, PDB code: 4c5x was solved by M.Mcdonough, A.H.El-Sagheer, T.Brown, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.2 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.300, 40.270, 64.880, 90.00, 90.00, 90.00
R / Rfree (%)	14.21 / 17.34

The binding sites of Magnesium atom in the Ultra High Resolution Dickerson-Drew Dodecamer B-Dna with 5-Hydroxymethyl-Cytosine Modification (pdb code 4c5x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Ultra High Resolution Dickerson-Drew Dodecamer B-Dna with 5-Hydroxymethyl-Cytosine Modification, PDB code: 4c5x:

Magnesium binding site 1 out of 1 in the Ultra High Resolution Dickerson-Drew Dodecamer B-Dna with 5-Hydroxymethyl-Cytosine Modification


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ultra High Resolution Dickerson-Drew Dodecamer B-Dna with 5-Hydroxymethyl-Cytosine Modification within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:14.9 occ:1.00 O A:HOH2029 2.0 16.9 1.0 O A:HOH2018 2.1 16.2 1.0 O A:HOH2019 2.1 14.8 1.0 O A:HOH2071 2.1 17.8 1.0 O A:HOH2072 2.1 16.2 1.0 O A:HOH2073 2.1 14.8 1.0 O B:HOH2047 4.1 18.0 1.0 O A:HOH2001 4.2 29.5 1.0 O6 B:DG22 4.3 16.3 1.0 O5 B:5HC21 4.4 23.2 1.0 N7 A:DG2 4.4 14.2 1.0 O6 A:DG2 4.4 13.4 1.0 O A:HOH2004 4.4 24.7 1.0 C5 A:DC1 4.5 17.2 1.0 O B:HOH2046 4.7 34.2 1.0 O A:HOH2030 4.7 42.5 1.0 C6 A:DC1 4.8 15.5 1.0 N4 A:DC3 4.9 16.8 1.0

L.Lercher, M.A.Mcdonough, A.H.El-Sagheer, A.Thalhammer, S.Kriaucionis, T.Brown, C.J.Schofield. Structural Insights Into How 5-Hydroxymethylation Influences Transcription Factor Binding. Chem.Commun.(Camb.) V. 50 1794 2014.
ISSN: ISSN 1359-7345
PubMed: 24287551
DOI: 10.1039/C3CC48151D