Magnesium in PDB 9mdy: 16MER Self-Complementary Duplex Rna with S(2)U:A Pair Sequence 2

The structure of 16MER Self-Complementary Duplex Rna with S(2)U:A Pair Sequence 2, PDB code: 9mdy 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)	40.97 / 1.36
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	40.995, 40.995, 122.92, 90, 90, 120
R / Rfree (%)	18.6 / 21.8

The binding sites of Magnesium atom in the 16MER Self-Complementary Duplex Rna with S(2)U:A Pair Sequence 2 (pdb code 9mdy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the 16MER Self-Complementary Duplex Rna with S(2)U:A Pair Sequence 2, PDB code: 9mdy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the 16MER Self-Complementary Duplex Rna with S(2)U:A Pair Sequence 2


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 S(2)U:A Pair Sequence 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:25.4 occ:1.00 O A:HOH248 1.9 20.3 1.0 O A:HOH299 2.0 39.7 1.0 O A:HOH295 2.1 29.1 1.0 O A:HOH217 2.2 25.2 1.0 O A:HOH219 2.2 27.6 1.0 O A:HOH300 2.2 34.8 1.0 N6 A:A6 4.0 18.6 1.0 O A:HOH273 4.1 37.6 1.0 N7 A:A6 4.1 16.7 1.0 O A:HOH277 4.2 29.9 1.0 O A:HOH260 4.3 25.8 1.0 N7 A:G7 4.4 11.9 1.0 O6 A:G7 4.4 13.8 1.0 O A:HOH244 4.4 19.1 1.0 O A:HOH294 4.5 47.7 1.0 C5 A:A6 4.7 14.9 1.0 C6 A:A6 4.7 16.3 1.0

Magnesium binding site 2 out of 3 in the 16MER Self-Complementary Duplex Rna with S(2)U:A Pair Sequence 2


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 S(2)U:A Pair Sequence 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:27.6 occ:1.00 O A:HOH211 1.9 25.5 1.0 O A:HOH280 2.0 24.8 1.0 O A:HOH236 2.1 17.7 1.0 O A:HOH286 2.3 29.2 1.0 O A:HOH254 3.7 33.3 1.0 O A:HOH279 3.8 23.0 1.0 O A:HOH218 3.9 28.4 1.0 O A:HOH245 3.9 35.3 1.0 N7 A:A3 3.9 9.3 1.0 N6 A:A3 4.3 9.3 1.0 O6 A:G4 4.3 11.6 1.0 O A:HOH244 4.4 19.1 1.0 C5 A:A3 4.6 8.6 1.0 N7 A:G4 4.7 12.2 1.0 N6 A:A5 4.7 14.6 1.0 C6 A:A3 4.8 8.7 1.0 C8 A:A3 4.8 9.8 1.0 O A:HOH222 4.9 26.3 1.0

Magnesium binding site 3 out of 3 in the 16MER Self-Complementary Duplex Rna with S(2)U:A Pair Sequence 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 16MER Self-Complementary Duplex Rna with S(2)U:A Pair Sequence 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:23.0 occ:0.33 O2' A:C13 2.6 12.6 1.0 O A:HOH257 3.0 21.4 0.3 O3' A:C13 3.1 11.4 1.0 C5' A:U14 3.6 12.6 1.0 C2' A:C13 3.7 11.6 1.0 C3' A:C13 3.8 11.8 1.0 OP1 A:U14 4.0 14.9 1.0 P A:U14 4.0 12.6 1.0 C4' A:C13 4.1 11.9 1.0 O5' A:U14 4.2 11.3 1.0 O A:HOH285 4.5 21.0 0.3 C4' A:U14 4.5 9.9 1.0 O4' A:U14 4.7 9.6 1.0 C1' A:C13 4.8 12.3 1.0 O4' A:C13 5.0 12.5 1.0

Z.Fang, X.Jia, J.W.Szostak. Nonenzymatic Rna Copying with A Potentially Primordial Genetic Alphabet To Be Published.