Magnesium in PDB 7ooo: The Crystal Structure of A Dna:Rna Hybrid Duplex Sequence Cttttctttg Containing An Lna-Amide-Lna Modification

The structure of The Crystal Structure of A Dna:Rna Hybrid Duplex Sequence Cttttctttg Containing An Lna-Amide-Lna Modification, PDB code: 7ooo was solved by C.Thorpe, J.Hardwick, M.A.Mcdonough, J.P.Hall, Y.R.Baker, A.H.El-Sagheer, T.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.08 / 2.57
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	49.15, 49.15, 90.96, 90, 90, 120
R / Rfree (%)	23.3 / 25.1

The binding sites of Magnesium atom in the The Crystal Structure of A Dna:Rna Hybrid Duplex Sequence Cttttctttg Containing An Lna-Amide-Lna Modification (pdb code 7ooo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Crystal Structure of A Dna:Rna Hybrid Duplex Sequence Cttttctttg Containing An Lna-Amide-Lna Modification, PDB code: 7ooo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Crystal Structure of A Dna:Rna Hybrid Duplex Sequence Cttttctttg Containing An Lna-Amide-Lna Modification


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of A Dna:Rna Hybrid Duplex Sequence Cttttctttg Containing An Lna-Amide-Lna Modification within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:86.0 occ:0.44 O31 B:05A13 2.3 80.9 1.0 C11 B:05A13 3.1 75.4 1.0 C2' B:05A13 3.5 75.4 1.0 C1' B:05A13 4.0 77.7 1.0 C4' B:05A13 4.4 81.2 1.0 C3' B:05A13 4.6 77.8 1.0 O4' B:05A13 4.6 84.4 1.0 O3' B:05A13 4.8 77.0 1.0 C5' B:DT14 4.9 71.7 1.0

Magnesium binding site 2 out of 2 in the The Crystal Structure of A Dna:Rna Hybrid Duplex Sequence Cttttctttg Containing An Lna-Amide-Lna Modification


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of A Dna:Rna Hybrid Duplex Sequence Cttttctttg Containing An Lna-Amide-Lna Modification within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:98.1 occ:1.00 O3' B:DT17 4.2 84.3 1.0 N7 D:A9 4.3 83.1 1.0 N7 D:G10 4.3 80.9 1.0 OP1 B:DT18 4.4 93.7 1.0 O6 D:G10 4.6 72.8 1.0 N6 D:A9 4.7 82.5 1.0 C4' B:DT17 4.9 81.3 1.0

Y.R.Baker, C.Thorpe, J.Chen, L.M.Poller, L.Cox, P.Kumar, W.F.Lim, L.Lie, G.Mcclorey, S.Epple, D.Singleton, M.A.Mcdonough, J.S.Hardwick, K.E.Christensen, M.J.A.Wood, J.P.Hall, A.H.El-Sagheer, T.Brown. An Lna-Amide Modification That Enhances the Cell Uptake and Activity of Phosphorothioate Exon-Skipping Oligonucleotides. Nat Commun V. 13 4036 2022.
ISSN: ESSN 2041-1723
PubMed: 35821218
DOI: 10.1038/S41467-022-31636-2