Magnesium in PDB 8tdy: 16MER Self-Complementary Duplex Rna with D:U Pair Sequence 1

The structure of 16MER Self-Complementary Duplex Rna with D:U Pair Sequence 1, PDB code: 8tdy was solved by Z.Fang, X.Jia, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.68 / 1.66
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	41.146, 41.146, 125.047, 90, 90, 120
R / Rfree (%)	19.6 / 22.4

The binding sites of Magnesium atom in the 16MER Self-Complementary Duplex Rna with D:U Pair Sequence 1 (pdb code 8tdy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the 16MER Self-Complementary Duplex Rna with D:U Pair Sequence 1, PDB code: 8tdy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the 16MER Self-Complementary Duplex Rna with D:U Pair Sequence 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 16MER Self-Complementary Duplex Rna with D:U Pair Sequence 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:15.8 occ:1.00 O A:HOH243 1.7 16.0 1.0 O A:HOH257 2.1 21.0 1.0 O A:HOH253 2.5 20.3 1.0 O A:HOH204 2.5 27.4 1.0 O A:HOH215 2.6 22.6 1.0 O A:HOH210 2.6 17.7 1.0 N7 A:A3 3.0 6.8 1.0 O A:HOH206 3.2 22.5 1.0 C8 A:A3 3.6 6.7 1.0 OP2 A:A3 4.0 14.6 1.0 C5 A:A3 4.0 8.3 1.0 N6 A:A3 4.4 7.4 1.0 C6 A:A3 4.6 5.5 1.0 N7 A:G4 4.7 9.4 1.0 O A:HOH205 4.8 18.8 1.0 N9 A:A3 4.8 6.5 1.0 O A:HOH237 4.9 17.7 1.0 O6 A:G4 5.0 8.4 1.0

Magnesium binding site 2 out of 2 in the 16MER Self-Complementary Duplex Rna with D:U Pair Sequence 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 16MER Self-Complementary Duplex Rna with D:U Pair Sequence 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:30.6 occ:1.00 O A:HOH256 2.1 27.1 1.0 O A:HOH222 2.4 22.9 1.0 O A:HOH254 2.5 18.6 1.0 O A:HOH251 2.5 26.9 1.0 O A:HOH246 2.5 32.1 1.0 N7 A:A6 2.9 17.9 1.0 O A:HOH232 3.2 23.8 1.0 O A:HOH237 3.5 17.7 1.0 C8 A:A6 3.6 11.3 1.0 C5 A:A6 4.1 11.7 1.0 OP2 A:A6 4.1 16.1 1.0 N7 A:N6G5 4.2 12.9 1.0 O A:HOH207 4.2 28.7 1.0 O A:HOH214 4.3 26.6 1.0 N6 A:A6 4.4 16.8 1.0 C8 A:N6G5 4.6 10.4 1.0 C6 A:A6 4.7 10.5 1.0 C5 A:N6G5 4.8 9.2 1.0 N9 A:A6 4.9 11.0 1.0

X.Jia, Z.Fang, S.C.Kim, D.Ding, L.Zhou, J.W.Szostak. Diaminopurine in Nonenzymatic Rna Template Copying. J.Am.Chem.Soc. 2024.
ISSN: ESSN 1520-5126
PubMed: 38818863
DOI: 10.1021/JACS.4C02560