2N3R | pdb_00002n3r

NMR structure of the II-III-VI three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	1D 1H watergate	2 mM [U-15N] RNA (62-MER)	90% H2O/10% D2O		6.5	ambient	288
2	2D 1H-15N HSQC	2 mM [U-15N] RNA (62-MER)	90% H2O/10% D2O		6.5	ambient	288
3	2D 1H-15N HSQC NH2 only	2 mM [U-15N] RNA (62-MER)	90% H2O/10% D2O		6.5	ambient	288
4	2D HNN COSY	2 mM [U-15N] RNA (62-MER)	90% H2O/10% D2O		6.5	ambient	288
5	2D 1H-1H NOESY	2 mM [U-15N] RNA (62-MER)	90% H2O/10% D2O		6.5	ambient	288
6	2D 1H-15N CPMG-NOESY	2 mM [U-15N] RNA (62-MER)	90% H2O/10% D2O		6.5	ambient	288
7	3D 15N-edited NOESY-HSQC	2 mM [U-15N] RNA (62-MER)	90% H2O/10% D2O		6.5	ambient	288
8	3D 15N/13C-edited NOESY-HSQC	2 mM [U-13C; U-15N] RNA (62-MER)	90% H2O/10% D2O		6.5	ambient	288
9	2D G-specific H(NC)-TOCSY-(C)H	2 mM [U-13C; U-15N] RNA (62-MER)	90% H2O/10% D2O		6.5	ambient	288
10	2D A-specific H(NC)-TOCSY-(C)H	2 mM [U-13C; U-15N] RNA (62-MER)	90% H2O/10% D2O		6.5	ambient	288
11	2D 1H-15N MQ-(HC)N(C)H	2 mM [U-13C; U-15N] RNA (62-MER)	100% D2O		6.5	ambient	298
12	2D 1H-13C HSQC	2 mM [U-13C; U-15N] RNA (62-MER)	100% D2O		6.5	ambient	298
13	2D 1H-13C HMQC	2 mM [U-13C; U-15N] RNA (62-MER)	100% D2O		6.5	ambient	298
14	3D HCCH-COSY	2 mM [U-13C; U-15N] RNA (62-MER)	100% D2O		6.5	ambient	298
15	3D HCCH-TOCSY	2 mM [U-13C; U-15N] RNA (62-MER)	100% D2O		6.5	ambient	298
16	3D 13C-edited NOESY-HSQC	2 mM [U-13C; U-15N] RNA (62-MER)	100% D2O		6.5	ambient	298
17	2D 1H-13C HSQC	2 mM [U-13C; U-15N]-Ade RNA (62-MER)	100% D2O		6.5	ambient	298
18	2D 1H-13C HMQC	2 mM [U-13C; U-15N]-Ade RNA (62-MER)	100% D2O		6.5	ambient	298
19	3D HCCH-COSY	2 mM [U-13C; U-15N]-Ade RNA (62-MER)	100% D2O		6.5	ambient	298
20	3D HCCH-TOCSY	2 mM [U-13C; U-15N]-Ade RNA (62-MER)	100% D2O		6.5	ambient	298
21	3D 13C-edited NOESY-HSQC	2 mM [U-13C; U-15N]-Ade RNA (62-MER)	100% D2O		6.5	ambient	298
22	2D 1H-13C HSQC	2 mM [U-13C; U-15N]-Cyt RNA (62-MER)	100% D2O		6.5	ambient	298
23	2D 1H-13C HMQC	2 mM [U-13C; U-15N]-Cyt RNA (62-MER)	100% D2O		6.5	ambient	298
24	3D HCCH-COSY	2 mM [U-13C; U-15N]-Cyt RNA (62-MER)	100% D2O		6.5	ambient	298
25	3D HCCH-TOCSY	2 mM [U-13C; U-15N]-Cyt RNA (62-MER)	100% D2O		6.5	ambient	298
26	3D 13C-edited NOESY-HSQC	2 mM [U-13C; U-15N]-Cyt RNA (62-MER)	100% D2O		6.5	ambient	298
27	2D 1H-13C HSQC	2.5 mM [U-13C; U-15N]-Gua RNA (62-MER)	100% D2O		6.5	ambient	298
28	2D 1H-13C HMQC	2.5 mM [U-13C; U-15N]-Gua RNA (62-MER)	100% D2O		6.5	ambient	298
29	3D HCCH-COSY	2.5 mM [U-13C; U-15N]-Gua RNA (62-MER)	100% D2O		6.5	ambient	298
30	3D HCCH-TOCSY	2.5 mM [U-13C; U-15N]-Gua RNA (62-MER)	100% D2O		6.5	ambient	298
31	3D 13C-edited NOESY-HSQC	2.5 mM [U-13C; U-15N]-Gua RNA (62-MER)	100% D2O		6.5	ambient	298

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

NMR Refinement
Method	Details	Software
simulated annealing		NMRDraw

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	500
Conformers Submitted Total Number	21
Representative Model	1 (minimized average structure)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2	data analysis	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	data analysis	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5	data analysis	CCPNMR		CCPN
6	chemical shift assignment	CCPNMR		CCPN
7	peak picking	CCPNMR		CCPN
8	structure solution	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
9	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore