1YN2

Solution structure of the Neurospora VS ribozyme stem-loop V in the presence of MgCl2 with modeling of bound manganese ions

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N CPMG-NOESY	0.8 mM to 2.0 mM of unlabeled, 15N, or 13C/15N SL5	[10 mM d11-Tris pH 7.0, 50 mM NaCl, 0.05 mM NaN3, 40 mM MgCl2] or [ 10 mM d11-Tris pH 7.0, 0.05 mM NaN3, 20 mM or 46 mM MgCl2]; 90% H2O, 10% D2O or 100% D2O; in some cases 0 uM, 10 uM, 20 uM, 40 uM, or 80 uM MnCl2 were added.	variable (see sample details)	7.0	ambient	298
2	3D 13C-EDITED HMQC-NOESY	0.8 mM to 2.0 mM of unlabeled, 15N, or 13C/15N SL5	[10 mM d11-Tris pH 7.0, 50 mM NaCl, 0.05 mM NaN3, 40 mM MgCl2] or [ 10 mM d11-Tris pH 7.0, 0.05 mM NaN3, 20 mM or 46 mM MgCl2]; 90% H2O, 10% D2O or 100% D2O; in some cases 0 uM, 10 uM, 20 uM, 40 uM, or 80 uM MnCl2 were added.	variable (see sample details)	7.0	ambient	298
3	2D HNN-COSY	0.8 mM to 2.0 mM of unlabeled, 15N, or 13C/15N SL5	[10 mM d11-Tris pH 7.0, 50 mM NaCl, 0.05 mM NaN3, 40 mM MgCl2] or [ 10 mM d11-Tris pH 7.0, 0.05 mM NaN3, 20 mM or 46 mM MgCl2]; 90% H2O, 10% D2O or 100% D2O; in some cases 0 uM, 10 uM, 20 uM, 40 uM, or 80 uM MnCl2 were added.	variable (see sample details)	7.0	ambient	298
4	3D HCCH E.COSY	0.8 mM to 2.0 mM of unlabeled, 15N, or 13C/15N SL5	[10 mM d11-Tris pH 7.0, 50 mM NaCl, 0.05 mM NaN3, 40 mM MgCl2] or [ 10 mM d11-Tris pH 7.0, 0.05 mM NaN3, 20 mM or 46 mM MgCl2]; 90% H2O, 10% D2O or 100% D2O; in some cases 0 uM, 10 uM, 20 uM, 40 uM, or 80 uM MnCl2 were added.	variable (see sample details)	7.0	ambient	298
5	2D 1H-13C CT-HSQC	0.8 mM to 2.0 mM of unlabeled, 15N, or 13C/15N SL5	[10 mM d11-Tris pH 7.0, 50 mM NaCl, 0.05 mM NaN3, 40 mM MgCl2] or [ 10 mM d11-Tris pH 7.0, 0.05 mM NaN3, 20 mM or 46 mM MgCl2]; 90% H2O, 10% D2O or 100% D2O; in some cases 0 uM, 10 uM, 20 uM, 40 uM, or 80 uM MnCl2 were added.	variable (see sample details)	7.0	ambient	298
6	2D 1H-15N HSQC	0.8 mM to 2.0 mM of unlabeled, 15N, or 13C/15N SL5	[10 mM d11-Tris pH 7.0, 50 mM NaCl, 0.05 mM NaN3, 40 mM MgCl2] or [ 10 mM d11-Tris pH 7.0, 0.05 mM NaN3, 20 mM or 46 mM MgCl2]; 90% H2O, 10% D2O or 100% D2O; in some cases 0 uM, 10 uM, 20 uM, 40 uM, or 80 uM MnCl2 were added.	variable (see sample details)	7.0	ambient	298
7	1D 31P	0.8 mM to 2.0 mM of unlabeled, 15N, or 13C/15N SL5	[10 mM d11-Tris pH 7.0, 50 mM NaCl, 0.05 mM NaN3, 40 mM MgCl2] or [ 10 mM d11-Tris pH 7.0, 0.05 mM NaN3, 20 mM or 46 mM MgCl2]; 90% H2O, 10% D2O or 100% D2O; in some cases 0 uM, 10 uM, 20 uM, 40 uM, or 80 uM MnCl2 were added.	variable (see sample details)	7.0	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600

NMR Refinement
Method	Details	Software
SIMULATED ANNEALING, MOLECULAR DYNAMICS	Conformer 1 represents the minimized average structure, the 10 following structures represent the ensemble of low-energy structures	X-PLOR

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	46
Conformers Submitted Total Number	11
Representative Model	1 (minimized average structure)

Additional NMR Experimental Information
Details	Bound manganese ions were modeled using distance restraints derived from Mn-induced paramagnetic line broadening

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	X-PLOR	NIH-2.0.6	Brunger, A.
2	data analysis	NMRPipe	most current	Delaglio, F.
3	data analysis	NMRView	5.0.3	Johnson, B.
4	data analysis	MOLMOL	2K.2	Koradi, R.
5	refinement	X-PLOR	NIH-2.0.6	Brunger, A.

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.