Magnesium in PDB 7lyf: Dengue Virus Rna Promoter Stem-Loop A Fused with Trna-Scaffold

The structure of Dengue Virus Rna Promoter Stem-Loop A Fused with Trna-Scaffold, PDB code: 7lyf was solved by E.H.Lee, K.H.Choi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.69 / 3.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	30.924, 137.558, 336.877, 90, 90, 90
R / Rfree (%)	22.6 / 26.8

The binding sites of Magnesium atom in the Dengue Virus Rna Promoter Stem-Loop A Fused with Trna-Scaffold (pdb code 7lyf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Dengue Virus Rna Promoter Stem-Loop A Fused with Trna-Scaffold, PDB code: 7lyf:

Magnesium binding site 1 out of 1 in the Dengue Virus Rna Promoter Stem-Loop A Fused with Trna-Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dengue Virus Rna Promoter Stem-Loop A Fused with Trna-Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:129.3 occ:1.00 O6 A:G5 2.0 131.0 1.0 O4 A:U130 3.0 151.8 1.0 C6 A:G5 3.1 136.8 1.0 O6 A:G6 3.1 136.2 1.0 O4 A:U129 3.8 147.9 1.0 C5 A:G5 3.9 138.9 1.0 N7 A:G6 3.9 133.2 1.0 C6 A:G6 4.0 131.3 1.0 N7 A:G5 4.0 138.9 1.0 N1 A:G5 4.1 132.6 1.0 N4 A:C131 4.1 132.0 1.0 C4 A:U130 4.1 142.7 1.0 C5 A:G6 4.3 132.8 1.0 N6 A:A7 4.7 136.9 1.0 N3 A:U130 4.7 139.6 1.0 C4 A:U129 4.8 150.9 1.0

E.Lee, P.J.Bujalowski, T.Teramoto, K.Gottipati, S.D.Scott, R.Padmanabhan, K.H.Choi. Structures of Flavivirus Rna Promoters Suggest Two Binding Modes with NS5 Polymerase Nat Commun 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-22846-1