Magnesium in PDB 8f5c: Mirror-Image Dna Containing 2'-Ome-L-Dc Modification

The structure of Mirror-Image Dna Containing 2'-Ome-L-Dc Modification, PDB code: 8f5c was solved by W.Zhang, Y.Dantsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.71 / 1.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	41.9, 41.9, 23.82, 90, 90, 90
R / Rfree (%)	19.3 / 20.4

The binding sites of Magnesium atom in the Mirror-Image Dna Containing 2'-Ome-L-Dc Modification (pdb code 8f5c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mirror-Image Dna Containing 2'-Ome-L-Dc Modification, PDB code: 8f5c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mirror-Image Dna Containing 2'-Ome-L-Dc Modification


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mirror-Image Dna Containing 2'-Ome-L-Dc Modification within 5.0Å range:

Magnesium binding site 2 out of 2 in the Mirror-Image Dna Containing 2'-Ome-L-Dc Modification


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mirror-Image Dna Containing 2'-Ome-L-Dc Modification within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:22.6 occ:0.60 O A:HOH239 2.1 23.0 0.6 OP2 A:0DG3 2.2 24.7 1.0 O A:HOH231 2.2 33.2 0.6 O A:HOH237 2.2 34.0 0.6 P A:0DG3 3.6 21.9 1.0 C5' A:0DG3 4.1 19.5 1.0 O5' A:0DG3 4.2 20.0 1.0 O3' A:XE62 4.5 20.1 1.0 OP1 A:0DG3 4.5 22.2 1.0 O A:HOH203 4.5 33.7 1.0 O A:HOH220 4.5 25.4 0.5

Y.Dantsu, W.Zhang. Synthesis and Structural Characterization of 2'-Deoxy-2'-Methoxy-L-Cytidine Nucleic Acids Chemistryselect 2023.
ISSN: ESSN 2365-6549
DOI: 10.1002/SLCT.202301966