Magnesium in PDB 6u8u: Rna Duplex Bound with Tna 3'-3' Imidazolium Dimer

The structure of Rna Duplex Bound with Tna 3'-3' Imidazolium Dimer, PDB code: 6u8u was solved by J.W.Szostak, W.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.40
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	43.956, 43.956, 84.516, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 26.7

The binding sites of Magnesium atom in the Rna Duplex Bound with Tna 3'-3' Imidazolium Dimer (pdb code 6u8u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rna Duplex Bound with Tna 3'-3' Imidazolium Dimer, PDB code: 6u8u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rna Duplex Bound with Tna 3'-3' Imidazolium Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna Duplex Bound with Tna 3'-3' Imidazolium Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:65.8 occ:1.00 O A:HOH205 1.9 38.2 1.0 O A:HOH206 2.1 59.6 1.0 O A:HOH202 2.1 62.2 1.0 O A:HOH201 3.1 54.3 1.0 N4 A:C6 3.9 49.3 1.0 C4 A:C6 5.0 55.3 1.0

Magnesium binding site 2 out of 2 in the Rna Duplex Bound with Tna 3'-3' Imidazolium Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rna Duplex Bound with Tna 3'-3' Imidazolium Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:42.2 occ:1.00 O B:HOH204 1.9 59.4 1.0 O B:HOH203 2.0 46.6 1.0 O A:HOH203 2.2 51.1 1.0 O B:HOH201 2.2 53.8 1.0 N4 B:C6 3.5 40.6 1.0 O4 B:U7 4.6 46.1 1.0 N6 A:A10 4.6 51.2 1.0 C4 B:C6 4.7 45.0 1.0

W.Zhang, S.C.Kim, C.P.Tam, V.S.Lelyveld, S.Bala, J.C.Chaput, J.W.Szostak. Structural Interpretation of the Effects of Threo-Nucleotides on Nonenzymatic Template-Directed Polymerization Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962