5LWJ

Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa.

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	0.66 mM GTP Class II RNA (34-MER), 1.32 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 900
2	3D 1H-13C NOESY aliphatic	1.1 mM [U-13C; U-15N]-Ade GTP Class II RNA (34-MER), 2.2 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 800
3	3D 1H-13C NOESY aliphatic3D 1H-13C NOESY aliphatic	0.82 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura GTP Class II RNA (34-MER), 1.64 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 900
4	3D 1H-13C NOESY aliphatic	0.73 mM [U-13C; U-15N]-Cyt GTP Class II RNA (34-MER), 1.46 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 900
5	2D 1H-13C NOESY aromatic	1.1 mM [U-13C; U-15N]-Ade GTP Class II RNA (34-MER), 2.2 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 900
6	2D 2D 1H-13C NOESY aromatic	0.82 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura GTP Class II RNA (34-MER), 1.64 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 25 mM H2O, 100 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 950
7	3D 1H-13C NOESY aromatic	0.73 mM [U-13C; U-15N]-Cyt GTP Class II RNA (34-MER), 1.46 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 900
8	3D HCCH-TOCSY	1.1 mM [U-13C; U-15N]-Ade GTP Class II RNA (34-MER), 2.2 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
9	3D HCCH-TOCSY	0.82 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura GTP Class II RNA (34-MER), 1.64 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
10	3D HCCH-TOCSY	0.73 mM [U-13C; U-15N]-Cyt GTP Class II RNA (34-MER), 1.46 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
11	3D HCCH-COSY	1.1 mM [U-13C; U-15N]-Ade GTP Class II RNA (34-MER), 2.2 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
12	3D HCCH-COSY	0.82 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura GTP Class II RNA (34-MER), 1.64 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
13	3D HCCH-COSY	0.73 mM [U-13C; U-15N]-Cyt GTP Class II RNA (34-MER), 1.46 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
14	2D 1H-15N HNN-COSY	0.5 mM [U-99% 15N] GTP Class II RNA (34-MER), 1 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium phosphate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	283	Bruker AVANCE 600
15	2D 1H-13C HNCO	0.82 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura GTP Class II RNA (34-MER), 1.64 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 800
16	2D 1H-13C H5(6)C5(6)C4NH3	0.73 mM [U-13C; U-15N]-Cyt GTP Class II RNA (34-MER), 1.46 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 700
17	2D 1H-13C H5(6)C5(6)C4N4H4	0.73 mM [U-13C; U-15N]-Cyt GTP Class II RNA (34-MER), 1.46 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 700
18	2D 1H-15N HCN aromatic	1.1 mM [U-13C; U-15N]-Ade GTP Class II RNA (34-MER), 2.2 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
19	2D 1H-15N HCN aromatic	0.82 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura GTP Class II RNA (34-MER), 1.64 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
20	2D 1H-15N HCN aromatic	0.73 mM [U-13C; U-15N]-Cyt GTP Class II RNA (34-MER), 1.46 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 800
21	2D 1H-15N HCN aliphatic	1.1 mM [U-13C; U-15N]-Ade GTP Class II RNA (34-MER), 2.2 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
22	2D 1H-15N HCN aliphatic	0.82 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura GTP Class II RNA (34-MER), 1.64 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
23	2D 1H-15N HCN aliphatic	0.73 mM [U-13C; U-15N]-Cyt GTP Class II RNA (34-MER), 1.46 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 800
24	D 1H-15N 2bond-HSQC	0.5 mM [U-99% 15N] GTP Class II RNA (34-MER), 1 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium phosphate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
25	2D 1H-1H HCCH-TOCSY (adenine)	1.1 mM [U-13C; U-15N]-Ade GTP Class II RNA (34-MER), 2.2 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
26	2D 1H-31P H(C)P	1.1 mM [U-13C; U-15N]-Ade GTP Class II RNA (34-MER), 2.2 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
27	2D 1H-31P H(C)P	0.82 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura GTP Class II RNA (34-MER), 1.64 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
28	2D 1H-31P H(C)P	0.73 mM [U-13C; U-15N]-Cyt GTP Class II RNA (34-MER), 1.46 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
29	2D HCCH-COSY	0.66 mM GTP Class II RNA (34-MER), 1.32 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
30	2D 1H-13C long-rangeH8(C8)C5(N1)H1	0.82 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura GTP Class II RNA (34-MER), 1.64 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 25 mM H2O, 100 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
31	2D CMPG NOESY	0.5 mM [U-99% 15N] GTP Class II RNA (34-MER), 1 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium phosphate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 800
32	3D 1H-13C NOESY aliphatic	0.66 mM GTP Class II RNA (34-MER), 1.32 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 800
33	3D 1H-13C NOESY aromatic	0.66 mM GTP Class II RNA (34-MER), 1.32 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 900
34	lr-2D-HNN-COSY	1.3 mM [U-15N]-Gua, [U-15N]-Ade GTP Class II RNA (34-MER), 2.6 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
35	2D-HNN-COSY NH2	1.3 mM [U-15N]-Gua, [U-15N]-Ade GTP Class II RNA (34-MER), 2.6 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
36	3D 13C-F1 filtered, 13C-F3-edited NOESY HSQC	1.1 mM [U-13C; U-15N]-Ade GTP Class II RNA (34-MER), 2.2 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 800
37	3D 13C-F1 filtered, 13C-F3-edited NOESY HSQC	0.82 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura GTP Class II RNA (34-MER), 1.64 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 900
38	3D 13C-F1 filtered, 13C-F3-edited NOESY HSQC	0.73 mM [U-13C; U-15N]-Cyt GTP Class II RNA (34-MER), 1.46 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 800
39	2D 1H-15N HSQC	0.5 mM [U-99% 15N] GTP Class II RNA (34-MER), 1 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium phosphate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	283	Bruker AVANCE 600
40	2D 1H-15N HSQC NH2 only	0.5 mM [U-99% 15N] GTP Class II RNA (34-MER), 1 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium phosphate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	283	Bruker AVANCE 800
41	2D 1H-13C HSQC aromatic	1.2 mM [U-99% 13C; U-99% 15N] GTP Class II RNA (34-MER), 2.4 mM GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 950
42	2D 1H-13C HSQC aliphatic	1.2 mM [U-99% 13C; U-99% 15N] GTP Class II RNA (34-MER), 2.4 mM GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 800
43	2D 15N-F2 edited 1H,1H NOESY	0.9 mM GTP Class II RNA (34-MER), 1.8 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O	95% H2O/5% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 800
44	3D HCCH-TOCSY-CCH-E.COSY	1.1 mM [U-13C; U-15N]-Ade GTP Class II RNA (34-MER), 2.2 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
45	3D HCCH-TOCSY-CCH-E.COSY	0.73 mM [U-13C; U-15N]-Cyt GTP Class II RNA (34-MER), 1.46 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600
46	3D HCCH-TOCSY-CCH-E.COSY	0.82 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura GTP Class II RNA (34-MER), 1.64 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O	100% D2O	potassium chloride (25) mM	6.3	1 atm	293	Bruker AVANCE 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
2	Bruker	AVANCE	600
7	Bruker	AVANCE	700
6	Bruker	AVANCE	800
5	Bruker	AVANCE	900
4	Bruker	AVANCE	950

NMR Refinement
Method	Details	Software
molecular dynamics		OPAL

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (target function)

Computation: NMR Software
#	Classification	Version	Software Name	Author
4	collection	TopSpin	3.5	Bruker Biospin
5	processing	TopSpin	3.5	Bruker Biospin
10	data analysis	TopSpin	3.5	Bruker Biospin
6	chemical shift assignment	CARA	1.8.4.2	Keller and Wuthrich
7	peak picking	CARA	1.8.4.2	Keller and Wuthrich
8	structure calculation	CYANA	3.97	Guntert, Mumenthaler and Wuthrich
9	refinement	OPAL		Luginbuhl, Guntert, Billeter, Wuthrich

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.

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5LWJ

Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa.