Magnesium in PDB 9mdw: 16MER Self-Complementary Duplex Rna with All Watson-Crick Base Pairs

The structure of 16MER Self-Complementary Duplex Rna with All Watson-Crick Base Pairs, PDB code: 9mdw 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)	41.40 / 1.42
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	41.159, 41.159, 124.195, 90, 90, 120
R / Rfree (%)	18.1 / 22

The binding sites of Magnesium atom in the 16MER Self-Complementary Duplex Rna with All Watson-Crick Base Pairs (pdb code 9mdw). 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 All Watson-Crick Base Pairs, PDB code: 9mdw:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the 16MER Self-Complementary Duplex Rna with All Watson-Crick Base Pairs


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 All Watson-Crick Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:24.6 occ:1.00 O A:HOH236 2.0 21.7 1.0 O A:HOH296 2.0 37.1 1.0 O A:HOH294 2.1 37.5 1.0 O A:HOH242 2.2 23.4 1.0 O A:HOH217 2.3 21.3 1.0 O A:HOH284 3.7 36.1 1.0 N6 A:A6 4.0 14.8 1.0 N7 A:A6 4.1 14.0 1.0 O A:HOH298 4.3 32.7 1.0 O A:HOH263 4.3 24.9 1.0 O A:HOH293 4.4 33.0 1.0 N7 A:G7 4.4 10.1 1.0 O6 A:G7 4.5 11.2 1.0 O A:HOH249 4.5 29.5 1.0 O A:HOH234 4.5 21.2 1.0 C5 A:A6 4.7 13.7 1.0 C6 A:A6 4.7 13.3 1.0 O A:HOH270 4.8 32.9 1.0

Magnesium binding site 2 out of 3 in the 16MER Self-Complementary Duplex Rna with All Watson-Crick Base Pairs


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 All Watson-Crick Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:15.8 occ:0.33 OP1 A:G7 2.1 17.3 1.0 O A:HOH252 2.1 20.4 1.0 P A:G7 3.4 16.2 1.0 MG A:MG103 3.5 12.2 0.3 O5' A:G7 3.7 15.6 1.0 O A:HOH267 4.1 20.7 1.0 C5' A:G7 4.3 12.3 1.0 O3' A:A6 4.3 13.2 1.0 O A:HOH290 4.5 35.2 1.0 OP2 A:G7 4.5 14.5 1.0 C4' A:G7 4.9 11.8 1.0

Magnesium binding site 3 out of 3 in the 16MER Self-Complementary Duplex Rna with All Watson-Crick Base Pairs


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 All Watson-Crick Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:12.2 occ:0.33 O2' A:A6 2.7 15.4 1.0 O3' A:A6 3.0 13.2 1.0 OP1 A:G7 3.2 17.3 1.0 O5' A:G7 3.5 15.6 1.0 P A:G7 3.5 16.2 1.0 MG A:MG102 3.5 15.8 0.3 C2' A:A6 3.8 13.5 1.0 C3' A:A6 3.9 14.0 1.0 C4' A:A6 4.3 13.6 1.0 O A:HOH286 4.5 38.1 0.3 C5' A:G7 4.7 12.3 1.0 C1' A:A6 4.9 13.0 1.0 OP2 A:G7 5.0 14.5 1.0 C4' A:G7 5.0 11.8 1.0

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