Magnesium in PDB 8pfk: Rna Structure with 1-Methylpseudoridine, C2 Space Group

The structure of Rna Structure with 1-Methylpseudoridine, C2 Space Group, PDB code: 8pfk was solved by B.Spingler, K.Mcauley, P.Nievergelt, A.Thorn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.75 / 1.32
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	41.295, 34.777, 31.685, 90, 128.07, 90
R / Rfree (%)	14.5 / 18.3

The binding sites of Magnesium atom in the Rna Structure with 1-Methylpseudoridine, C2 Space Group (pdb code 8pfk). 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 Structure with 1-Methylpseudoridine, C2 Space Group, PDB code: 8pfk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rna Structure with 1-Methylpseudoridine, C2 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna Structure with 1-Methylpseudoridine, C2 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:25.0 occ:1.00 O A:HOH242 1.9 22.4 1.0 O A:HOH295 2.1 26.0 1.0 O A:HOH227 2.1 22.3 1.0 O A:HOH289 2.1 29.4 1.0 O A:HOH211 2.2 19.3 1.0 O A:HOH282 2.2 34.5 1.0 O A:HOH218 3.8 33.3 1.0 O A:HOH201 3.9 36.3 1.0 H62 A:A9 4.1 14.1 1.0 O A:HOH258 4.3 26.5 1.0 N7 A:A9 4.3 12.8 1.0 O A:HOH230 4.3 18.1 1.0 O6 A:G10 4.3 12.2 1.0 N7 A:G10 4.4 13.3 1.0 H41 A:C11 4.7 17.1 1.0 N6 A:A9 4.8 11.7 1.0 O A:HOH216 4.8 25.8 1.0 H5 A:U8 4.9 21.7 1.0

Magnesium binding site 2 out of 2 in the Rna Structure with 1-Methylpseudoridine, C2 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rna Structure with 1-Methylpseudoridine, C2 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:22.4 occ:1.00 O A:HOH243 2.0 14.6 1.0 O A:HOH235 2.1 16.5 1.0 O A:HOH283 2.2 22.2 1.0 O A:HOH254 2.8 26.9 1.0 H62 A:A5 3.6 16.3 1.0 O A:HOH228 4.1 19.0 1.0 O A:HOH293 4.2 39.9 1.0 H41 A:C3 4.2 15.5 1.0 O A:HOH270 4.3 22.1 1.0 N6 A:A5 4.4 13.5 1.0 O6 A:G4 4.4 12.3 1.0 H5 A:C3 4.5 14.0 1.0 N7 A:G4 4.5 13.6 1.0 H61 A:A5 4.5 16.3 1.0 N4 A:C3 4.6 12.9 1.0 O A:HOH240 4.7 17.6 1.0 C5 A:C3 4.8 11.6 1.0 O A:HOH268 4.8 34.4 1.0 C4 A:C3 4.9 11.3 1.0 H42 A:C3 5.0 15.5 1.0

P.Nievergelt, F.Berliat, K.Mcauley, C.R.Dorgan, R.M.Van Well, A.Thorn, B.Spingler. Rna Oligomers at Atomic Resolution Containing 1-Methylpseudouridine, An Essential Building Block of Mrna Vaccines. Chemmedchem 00600 2024.
ISSN: ESSN 1860-7187
PubMed: 38235959
DOI: 10.1002/CMDC.202300600