Magnesium in PDB 4g6r: Minimal Hairpin Ribozyme in the Transition State with G8I Variation

The structure of Minimal Hairpin Ribozyme in the Transition State with G8I Variation, PDB code: 4g6r was solved by J.A.Liberman, J.L.Jenkins, J.Krucinska, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.17 / 2.83
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.127, 93.127, 128.867, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 22

The binding sites of Magnesium atom in the Minimal Hairpin Ribozyme in the Transition State with G8I Variation (pdb code 4g6r). 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 Minimal Hairpin Ribozyme in the Transition State with G8I Variation, PDB code: 4g6r:

Magnesium binding site 1 out of 1 in the Minimal Hairpin Ribozyme in the Transition State with G8I Variation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Minimal Hairpin Ribozyme in the Transition State with G8I Variation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:0.8 occ:1.00 O B:HOH203 2.0 87.4 1.0 O A:HOH202 2.1 92.2 1.0 O B:HOH201 2.1 98.7 1.0 O A:HOH201 2.1 91.6 1.0 O B:HOH202 2.2 93.6 1.0 O B:HOH204 2.2 88.3 1.0 O6 B:G12 4.2 77.9 1.0 N7 B:G12 4.2 76.5 1.0 O6 B:G13 4.3 75.9 1.0 O3 A:SO4101 4.4 92.5 0.7 C6 B:G12 4.8 75.0 1.0 C5 B:G12 4.8 74.3 1.0 O6 B:G11 5.0 88.8 1.0 N7 B:G13 5.0 77.0 1.0

J.A.Liberman, M.Guo, J.L.Jenkins, J.Krucinska, Y.Chen, P.R.Carey, J.E.Wedekind. A Transition-State Interaction Shifts Nucleobase Ionization Toward Neutrality to Facilitate Small Ribozyme Catalysis. J.Am.Chem.Soc. V. 134 16933 2012.
ISSN: ISSN 0002-7863
PubMed: 22989273
DOI: 10.1021/JA3070528