Magnesium in PDB 8pfq: Rna Structure with 1-Methylpseudoridine, P1 Space Group

The structure of Rna Structure with 1-Methylpseudoridine, P1 Space Group, PDB code: 8pfq 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)	23.38 / 1.01
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	26.763, 27.037, 29.141, 62.59, 63.8, 88.7
R / Rfree (%)	15.4 / 17.5

The binding sites of Magnesium atom in the Rna Structure with 1-Methylpseudoridine, P1 Space Group (pdb code 8pfq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Rna Structure with 1-Methylpseudoridine, P1 Space Group, PDB code: 8pfq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Rna Structure with 1-Methylpseudoridine, P1 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, P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:49.9 occ:1.00 O B:HOH249 2.1 23.8 1.0 O B:HOH281 2.2 31.1 1.0 O A:HOH247 2.3 17.7 1.0 O A:HOH260 2.4 15.0 1.0 O A:HOH263 3.4 24.3 1.0 O A:HOH258 3.5 27.0 1.0 O B:HOH236 3.9 18.7 1.0 H62 A:A5 4.1 12.1 1.0 O A:HOH224 4.2 15.1 1.0 H41 A:C3 4.4 11.4 1.0 O B:HOH280 4.4 24.6 1.0 O A:HOH226 4.7 14.2 1.0 H5 A:C3 4.7 11.0 1.0 O2 B:B8H27 4.8 11.0 1.0 N4 A:C3 4.8 9.5 1.0 O A:HOH261 4.8 18.0 1.0 N6 A:A5 4.8 10.1 1.0 O6 A:G4 4.9 9.9 1.0 H61 A:A6 4.9 11.5 1.0 H8 B:B8H27 4.9 13.5 1.0 H61 A:A5 5.0 12.1 1.0 H62 A:A6 5.0 11.5 1.0 N7 A:G4 5.0 11.6 1.0

Magnesium binding site 2 out of 3 in the Rna Structure with 1-Methylpseudoridine, P1 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, P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:49.5 occ:1.00 O A:HOH232 2.1 18.4 1.0 O A:HOH276 2.2 41.5 1.0 O A:HOH230 2.3 17.5 1.0 O A:HOH283 3.2 20.6 1.0 O B:HOH212 3.4 22.5 1.0 O A:HOH262 3.7 25.9 1.0 O A:HOH218 3.8 15.7 1.0 O B:HOH259 4.1 24.3 1.0 O A:HOH257 4.2 23.6 1.0 H62 A:A9 4.2 10.0 1.0 O6 A:G10 4.3 8.7 1.0 N7 A:A9 4.4 8.9 1.0 O A:HOH235 4.5 21.6 1.0 H41 A:C11 4.6 10.9 1.0 N7 A:G10 4.7 8.7 1.0 N6 A:A9 4.9 8.3 1.0 H42 A:C11 5.0 10.9 1.0

Magnesium binding site 3 out of 3 in the Rna Structure with 1-Methylpseudoridine, P1 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rna Structure with 1-Methylpseudoridine, P1 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:15.8 occ:1.00 O B:HOH243 2.0 13.6 1.0 O B:HOH283 2.0 20.1 1.0 O B:HOH282 2.0 26.5 1.0 O B:HOH235 2.0 16.3 1.0 O B:HOH230 2.1 18.9 1.0 O A:HOH281 2.2 23.6 1.0 H62 B:A29 3.9 11.2 1.0 O B:HOH210 4.0 17.7 1.0 O A:HOH219 4.0 14.5 1.0 O B:HOH204 4.1 20.3 1.0 O B:HOH258 4.1 18.4 1.0 N7 B:A29 4.2 9.6 1.0 N7 B:G30 4.4 8.9 1.0 O6 B:G30 4.4 8.9 1.0 O A:HOH268 4.5 40.2 1.0 N6 B:A29 4.6 9.3 1.0 H41 B:C31 4.7 11.5 1.0 C5 B:A29 5.0 9.7 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