1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Reiter, N.J.
Nikstad, L.J.
Allman, A.M.
Johnson, R.J.
Butcher, S.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H13 N2 O8 P S
340.247
n
URIDINE-5'-PHOSPHOROTHIOATE
SP-SULFUR-SUBSTITUTED URIDINE
RNA linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
UK
RNA
RNARFU
2122
1355-8382
9
533
542
10.1261/rna.2199103
12702812
Structure of the U6 RNA intramolecular stem-loop harboring an
S(P)-phosphorothioate modification.
2003
10.2210/pdb1nz1/pdb
pdb_00001nz1
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
A62G, SP phoshphorothioate modified U80
7684.681
SP U6 Intramolecular Stem-Loop RNA
A62G
1
syn
polymer
SP ISL RNA
no
yes
GGUUCCCCUGCAUAAGGA(SSU)GAACC
GGUUCCCCUGCAUAAGGAUGAACC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
0.674
1
19
A
1
A
24
-4.845
A_G1:C24_A
1
0.712
-0.656
0.032
-0.064
-0.711
1
19
A
2
A
23
2.087
A_G2:C23_A
2
-0.186
-0.908
0.052
-0.206
-0.255
1
20
A
3
A
22
-11.622
A_U3:A22_A
3
-0.906
0.582
0.086
-0.150
1.269
1
20
A
4
A
21
-4.926
A_U4:A21_A
4
0.570
-0.894
-0.078
-0.086
-0.245
1
19
A
5
A
20
-0.618
A_C5:G20_A
5
-0.961
-0.097
0.053
-0.183
4.896
1
A
6
A
18
7.897
A_C6:A18_A
6
-4.838
2.281
-0.220
-0.596
-3.237
1
19
A
7
A
17
-3.392
A_C7:G17_A
7
-3.134
0.516
0.086
-0.253
1.602
1
19
A
8
A
16
2.261
A_C8:G16_A
8
0.864
0.694
-0.072
-0.090
0.828
1
20
A
9
A
15
-8.116
A_U9:A15_A
9
-0.707
-0.849
0.051
-0.030
6.029
9
11
A
10
A
14
11.888
A_G10:A14_A
10
6.307
6.595
-0.043
-3.599
4.612
33.705
A
A
1
2
-12.813
A
A
24
23
4.480
-7.370
-0.056
-1.116
AA_G1G2:C23C24_AA
1
-1.644
2.858
32.872
-0.237
-0.280
2.152
44.537
A
A
2
3
28.194
A
A
23
22
3.251
20.626
-1.003
-1.677
AA_G2U3:A22C23_AA
2
0.663
-0.906
39.684
-3.885
1.378
4.251
27.292
A
A
3
4
-10.028
A
A
22
21
4.068
-4.709
0.513
-1.364
AA_U3U4:A21A22_AA
3
0.689
-1.467
26.882
-1.387
-0.866
2.138
41.877
A
A
4
5
40.064
A
A
21
20
3.570
26.594
0.122
-1.079
AA_U4C5:G20A21_AA
4
-0.906
1.364
32.634
-4.271
-0.265
3.898
60.690
A
A
5
6
4.148
A
A
20
18
5.110
4.148
4.405
0.165
AA_C5C6:A18G20_AA
5
-16.050
16.052
58.591
-0.119
-5.451
2.459
22.634
A
A
6
7
24.009
A
A
18
17
3.694
9.141
-0.949
-2.014
AA_C6C7:G17A18_AA
6
2.416
-6.346
20.588
-8.409
3.284
3.377
39.199
A
A
7
8
3.006
A
A
17
16
3.263
2.007
1.186
-0.669
AA_C7C8:G16G17_AA
7
6.706
-10.045
38.593
-1.242
-0.947
1.817
27.763
A
A
8
9
32.984
A
A
16
15
3.120
15.010
-1.926
-1.525
AA_C8U9:A15G16_AA
8
0.148
-0.325
23.423
-6.150
4.044
3.772
68.840
A
A
9
10
-25.652
A
A
15
14
4.549
-28.207
2.295
0.115
AA_U9G10:A14A15_AA
9
-11.895
10.818
62.424
1.515
-2.626
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2003-05-13
1
1
2008-04-29
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
Solution structure of the U6 intramolecular stem-loop RNA
Refined solution structure of the U6 intramolecular stem-loop RNA using residual dipolar couplings (RDCs)
U80G U6 Intramolecular Stem-Loop RNA from Saccharomyces cerevisiae
RCSB
Y
RCSB
2003-02-14
REL
Synthetic RNA (Dharmacon, Inc.) was prepared containing an SP phosphorothioate modification at nucleotide U80. The Sp RNA was separated from the Rp RNA diastereomer using reverse-phase high pressure liquid chromatography.
sample
Solution structure based on 322 NOE derived distance restraints, 144 dihedral angle restraints, 25 hydrogen bond restraints, and 40 residual dipolar copupling restraints.
structures with the lowest energy
100
17
2D NOESY
HSQC
HSQC
2D NOESY
2D TOCSY
50 mM NaCl
7.0
ambient
283
K
50 mM NaCl
7.2
ambient
303
K
50 mM NaCl
7.0
ambient
303
K
Torsion angle and molecular dynamics, simulated annealing, residual dipolar coupling
15
lowest energy
0.8-1.2 mM RNA, 50 mM NaCL, pH 7.0
H2O
0.8-1.2 mM RNA, 50 mM NaCL, pH 7.0, 17 mg/mL PF1 Phage
H2O
0.8-1.2 mM RNA, 50 mM NaCL, pH 7.0
D2O
Bruker
collection
XwinNMR
2.6
Accelrys
processing
Felix
98
Goddard, T.D. and D.G. Kneller
data analysis
Sparky
3
Brunger
structure solution
CNS
1.1
Brunger
refinement
X-PLOR
3.1
750
Bruker
DMX
600
Bruker
DMX
500
Bruker
DMX
400
Bruker
DMX
G
1
n
1
G
1
A
G
2
n
2
G
2
A
U
3
n
3
U
3
A
U
4
n
4
U
4
A
C
5
n
5
C
5
A
C
6
n
6
C
6
A
C
7
n
7
C
7
A
C
8
n
8
C
8
A
U
9
n
9
U
9
A
G
10
n
10
G
10
A
C
11
n
11
C
11
A
A
12
n
12
A
12
A
U
13
n
13
U
13
A
A
14
n
14
A
14
A
A
15
n
15
A
15
A
G
16
n
16
G
16
A
G
17
n
17
G
17
A
A
18
n
18
A
18
A
SSU
19
n
19
SSU
19
A
G
20
n
20
G
20
A
A
21
n
21
A
21
A
A
22
n
22
A
22
A
C
23
n
23
C
23
A
C
24
n
24
C
24
A
author_defined_assembly
1
monomeric
A
SSU
19
URIDINE-5'-PHOSPHOROTHIOATE
A
SSU
19
U
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
A
HO2'
O4'
C
A
11
12
1.53
3
A
A
HO2'
O4'
C
A
11
12
1.47
5
A
A
O2'
H2'
A
U
12
13
1.45
5
A
A
H2'
OP2
G
A
10
12
1.58
6
A
A
HO2'
O4'
C
A
11
12
1.47
6
A
A
HO2'
O5'
G
A
17
18
1.51
7
A
A
H2'
OP2
G
A
10
12
1.57
8
A
A
H2'
OP2
G
A
10
12
1.51
9
A
A
HO2'
O5'
C
U
8
9
1.26
10
A
A
HO2'
O5'
G
A
20
21
1.46
10
A
A
H2'
OP2
G
A
10
12
1.53
11
A
A
HO2'
O5'
C
U
8
9
1.30
11
A
A
H2'
OP2
G
A
10
12
1.47
12
A
A
HO2'
O4'
C
A
11
12
1.42
12
A
A
O2'
H8
C
A
11
12
1.43
12
A
A
O2'
H2'
G
C
10
11
1.47
12
A
A
O2'
H5''
C
A
11
12
1.49
12
A
A
HO2'
O4'
C
C
23
24
1.59
14
A
A
H2'
OP2
G
A
10
12
1.49
14
A
A
HO2'
O4'
C
C
5
6
1.54
15
A
A
O2'
H5'
U
C
4
5
1.58
16
A
A
HO2'
O4'
C
A
11
12
1.37
16
A
A
O2'
H8
C
A
11
12
1.42
16
A
A
O2'
H2'
G
C
10
11
1.48
17
A
A
HO2'
O4'
C
A
11
12
1.33
17
A
A
O2'
H8
C
A
11
12
1.38
17
A
A
O2'
H2'
G
C
10
11
1.38
1
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
1
-2.64
0.40
106.40
103.76
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
1
4.69
0.50
113.10
117.79
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
1
-2.77
0.40
106.40
103.63
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
1
4.59
0.50
113.10
117.69
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
1
-2.56
0.40
106.40
103.84
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
1
3.60
0.50
113.80
117.40
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
1
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
1
3.70
0.50
113.80
117.50
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
1
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
1
-2.70
0.40
106.40
103.70
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
1
4.65
0.50
113.10
117.75
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
1
-2.58
0.40
106.40
103.82
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
1
3.78
0.50
113.80
117.58
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
1
4.58
0.50
113.10
117.68
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
1
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
1
3.68
0.50
113.80
117.48
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
1
3.73
0.50
113.80
117.53
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
2
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
2
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
2
4.62
0.50
113.10
117.72
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
2
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
2
4.64
0.50
113.10
117.74
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
2
-2.60
0.40
106.40
103.80
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
2
3.69
0.50
113.80
117.49
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
2
3.82
0.50
113.80
117.62
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
2
3.72
0.50
113.80
117.52
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
2
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
2
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
2
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
2
-2.74
0.40
106.40
103.66
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
2
3.75
0.50
113.80
117.55
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
2
4.66
0.50
113.10
117.76
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
2
-2.78
0.40
106.40
103.63
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
2
3.71
0.50
113.80
117.51
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
2
3.72
0.50
113.80
117.52
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
3
4.45
0.50
113.10
117.55
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
3
-2.64
0.40
106.40
103.76
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
3
4.57
0.50
113.10
117.67
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
3
-2.74
0.40
106.40
103.66
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
3
4.66
0.50
113.10
117.76
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
3
-2.59
0.40
106.40
103.81
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
3
3.68
0.50
113.80
117.48
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
3
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
3
3.65
0.50
113.80
117.45
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
3
4.65
0.50
113.10
117.75
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
3
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
3
4.51
0.50
113.10
117.61
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
3
-2.72
0.40
106.40
103.68
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
3
3.75
0.50
113.80
117.55
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
3
4.61
0.50
113.10
117.71
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
3
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
3
3.74
0.50
113.80
117.54
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
3
3.74
0.50
113.80
117.54
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
4
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
4
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
4
4.59
0.50
113.10
117.69
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
4
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
4
4.67
0.50
113.10
117.77
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
4
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
4
3.60
0.50
113.80
117.40
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
4
3.69
0.50
113.80
117.49
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
4
3.73
0.50
113.80
117.53
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
4
4.46
0.50
113.10
117.56
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
4
-2.57
0.40
106.40
103.83
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
4
4.59
0.50
113.10
117.69
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
4
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
4
3.84
0.50
113.80
117.64
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
4
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
4
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
4
3.79
0.50
113.80
117.59
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
4
3.74
0.50
113.80
117.54
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
5
4.51
0.50
113.10
117.61
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
5
-2.64
0.40
106.40
103.76
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
5
4.57
0.50
113.10
117.67
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
5
-2.63
0.40
106.40
103.77
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
5
4.69
0.50
113.10
117.79
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
5
-2.55
0.40
106.40
103.85
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
5
3.51
0.50
113.80
117.31
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
5
3.83
0.50
113.80
117.63
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
5
3.70
0.50
113.80
117.50
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
5
4.58
0.50
113.10
117.68
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
5
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
5
4.65
0.50
113.10
117.75
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
5
-2.57
0.40
106.40
103.83
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
5
3.73
0.50
113.80
117.53
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
5
4.49
0.50
113.10
117.59
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
5
-2.60
0.40
106.40
103.80
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
5
3.83
0.50
113.80
117.63
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
5
3.71
0.50
113.80
117.51
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
6
4.46
0.50
113.10
117.56
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
6
-2.59
0.40
106.40
103.81
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
6
4.49
0.50
113.10
117.59
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
6
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
6
4.69
0.50
113.10
117.79
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
6
-2.53
0.40
106.40
103.87
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
6
3.66
0.50
113.80
117.46
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
6
3.67
0.50
113.80
117.47
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
6
3.67
0.50
113.80
117.47
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
6
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
6
-2.64
0.40
106.40
103.76
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
6
4.57
0.50
113.10
117.67
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
6
-2.63
0.40
106.40
103.77
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
6
3.88
0.50
113.80
117.68
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
6
4.49
0.50
113.10
117.59
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
6
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
6
3.68
0.50
113.80
117.48
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
6
3.66
0.50
113.80
117.46
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
7
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
7
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
7
4.57
0.50
113.10
117.67
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
7
-2.61
0.40
106.40
103.79
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
7
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
7
-2.57
0.40
106.40
103.83
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
7
3.67
0.50
113.80
117.47
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
7
3.92
0.50
113.80
117.72
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
7
3.84
0.50
113.80
117.64
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
7
4.59
0.50
113.10
117.69
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
7
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
7
4.47
0.50
113.10
117.57
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
7
-2.64
0.40
106.40
103.76
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
7
3.79
0.50
113.80
117.59
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
7
4.68
0.50
113.10
117.78
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
7
-2.79
0.40
106.40
103.61
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
7
3.77
0.50
113.80
117.57
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
7
3.69
0.50
113.80
117.49
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
8
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
8
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
8
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
8
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
8
4.69
0.50
113.10
117.79
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
8
-2.58
0.40
106.40
103.82
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
8
3.65
0.50
113.80
117.45
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
8
3.70
0.50
113.80
117.50
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
8
3.64
0.50
113.80
117.44
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
8
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
8
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
8
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
8
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
8
3.84
0.50
113.80
117.64
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
8
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
8
-2.69
0.40
106.40
103.71
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
8
3.70
0.50
113.80
117.50
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
8
3.79
0.50
113.80
117.59
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
9
4.57
0.50
113.10
117.67
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
9
-2.73
0.40
106.40
103.67
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
9
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
9
-2.64
0.40
106.40
103.76
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
9
4.66
0.50
113.10
117.76
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
9
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
9
3.49
0.50
113.80
117.29
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
9
3.80
0.50
113.80
117.60
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
9
3.73
0.50
113.80
117.53
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
9
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
9
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
9
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
9
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
9
3.89
0.50
113.80
117.69
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
9
4.59
0.50
113.10
117.69
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
9
-2.62
0.40
106.40
103.78
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
9
3.75
0.50
113.80
117.55
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
9
3.71
0.50
113.80
117.51
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
10
4.60
0.50
113.10
117.70
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
10
-2.63
0.40
106.40
103.77
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
10
4.51
0.50
113.10
117.61
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
10
-2.63
0.40
106.40
103.77
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
10
4.63
0.50
113.10
117.73
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
10
-2.50
0.40
106.40
103.90
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
10
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
10
3.95
0.50
113.80
117.75
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
10
-2.43
0.40
105.80
103.37
A
A
A
C8
N9
C4
A
A
A
14
14
14
N
10
3.75
0.50
113.80
117.55
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
10
4.49
0.50
113.10
117.59
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
10
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
10
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
10
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
10
3.75
0.50
113.80
117.55
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
10
4.45
0.50
113.10
117.55
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
10
-2.57
0.40
106.40
103.83
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
10
3.79
0.50
113.80
117.59
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
10
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
11
4.51
0.50
113.10
117.61
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
11
-2.64
0.40
106.40
103.76
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
11
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
11
-2.64
0.40
106.40
103.76
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
11
4.61
0.50
113.10
117.71
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
11
-2.53
0.40
106.40
103.87
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
11
3.72
0.50
113.80
117.52
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
11
3.86
0.50
113.80
117.66
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
11
3.72
0.50
113.80
117.52
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
11
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
11
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
11
4.50
0.50
113.10
117.60
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
11
-2.57
0.40
106.40
103.83
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
11
3.80
0.50
113.80
117.60
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
11
4.48
0.50
113.10
117.58
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
11
-2.50
0.40
106.40
103.90
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
11
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
11
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
12
4.48
0.50
113.10
117.58
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
12
-2.63
0.40
106.40
103.77
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
12
4.58
0.50
113.10
117.68
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
12
-2.74
0.40
106.40
103.66
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
12
4.60
0.50
113.10
117.70
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
12
-2.47
0.40
106.40
103.93
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
12
3.99
0.50
113.80
117.79
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
12
-2.67
0.40
105.80
103.13
A
A
A
C8
N9
C4
A
A
A
12
12
12
N
12
3.85
0.50
113.80
117.65
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
12
3.74
0.50
113.80
117.54
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
12
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
12
-2.64
0.40
106.40
103.76
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
12
4.64
0.50
113.10
117.74
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
12
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
12
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
12
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
12
-2.62
0.40
106.40
103.78
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
12
3.82
0.50
113.80
117.62
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
12
3.73
0.50
113.80
117.53
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
13
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
13
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
13
4.46
0.50
113.10
117.56
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
13
-2.56
0.40
106.40
103.84
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
13
4.67
0.50
113.10
117.77
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
13
-2.60
0.40
106.40
103.80
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
13
3.70
0.50
113.80
117.50
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
13
3.82
0.50
113.80
117.62
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
13
3.84
0.50
113.80
117.64
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
13
4.58
0.50
113.10
117.68
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
13
-2.69
0.40
106.40
103.71
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
13
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
13
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
13
3.83
0.50
113.80
117.63
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
13
4.63
0.50
113.10
117.73
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
13
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
13
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
13
3.78
0.50
113.80
117.58
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
14
4.57
0.50
113.10
117.67
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
14
-2.64
0.40
106.40
103.76
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
14
4.48
0.50
113.10
117.58
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
14
-2.61
0.40
106.40
103.79
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
14
4.68
0.50
113.10
117.78
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
14
-2.51
0.40
106.40
103.89
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
14
3.63
0.50
113.80
117.43
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
14
3.63
0.50
113.80
117.43
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
14
3.73
0.50
113.80
117.53
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
14
4.73
0.50
113.10
117.83
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
14
-2.83
0.40
106.40
103.57
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
14
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
14
-2.74
0.40
106.40
103.66
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
14
3.85
0.50
113.80
117.65
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
14
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
14
-2.65
0.40
106.40
103.75
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
14
3.82
0.50
113.80
117.62
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
14
3.83
0.50
113.80
117.63
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
15
4.52
0.50
113.10
117.62
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
15
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
15
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
15
-2.61
0.40
106.40
103.79
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
15
4.48
0.50
113.10
117.58
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
15
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
15
3.88
0.50
113.80
117.68
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
15
3.70
0.50
113.80
117.50
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
15
3.66
0.50
113.80
117.46
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
15
4.60
0.50
113.10
117.70
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
15
-2.70
0.40
106.40
103.70
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
15
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
15
-2.68
0.40
106.40
103.72
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
15
3.80
0.50
113.80
117.60
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
15
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
15
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
15
3.70
0.50
113.80
117.50
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
15
3.81
0.50
113.80
117.61
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
16
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
16
-2.69
0.40
106.40
103.71
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
16
4.60
0.50
113.10
117.70
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
16
-2.69
0.40
106.40
103.71
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
16
4.64
0.50
113.10
117.74
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
16
-2.45
0.40
106.40
103.95
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
16
4.11
0.50
113.80
117.91
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
16
-2.78
0.40
105.80
103.02
A
A
A
C8
N9
C4
A
A
A
12
12
12
N
16
3.98
0.50
113.80
117.78
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
16
3.72
0.50
113.80
117.52
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
16
4.53
0.50
113.10
117.63
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
16
-2.69
0.40
106.40
103.71
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
16
4.47
0.50
113.10
117.57
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
16
-2.55
0.40
106.40
103.85
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
16
3.78
0.50
113.80
117.58
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
16
4.61
0.50
113.10
117.71
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
16
-2.76
0.40
106.40
103.64
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
16
3.71
0.50
113.80
117.51
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
16
3.60
0.50
113.80
117.40
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
17
4.49
0.50
113.10
117.59
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
17
-2.59
0.40
106.40
103.81
A
A
A
C8
N9
C4
G
G
G
1
1
1
N
17
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
G
G
G
2
2
2
N
17
-2.66
0.40
106.40
103.74
A
A
A
C8
N9
C4
G
G
G
2
2
2
N
17
4.69
0.50
113.10
117.79
A
A
A
N7
C8
N9
G
G
G
10
10
10
N
17
-2.41
0.40
106.40
103.99
A
A
A
C8
N9
C4
G
G
G
10
10
10
N
17
4.33
0.50
113.80
118.13
A
A
A
N7
C8
N9
A
A
A
12
12
12
N
17
-2.96
0.40
105.80
102.84
A
A
A
C8
N9
C4
A
A
A
12
12
12
N
17
3.85
0.50
113.80
117.65
A
A
A
N7
C8
N9
A
A
A
14
14
14
N
17
3.68
0.50
113.80
117.48
A
A
A
N7
C8
N9
A
A
A
15
15
15
N
17
4.61
0.50
113.10
117.71
A
A
A
N7
C8
N9
G
G
G
16
16
16
N
17
-2.73
0.40
106.40
103.67
A
A
A
C8
N9
C4
G
G
G
16
16
16
N
17
4.58
0.50
113.10
117.68
A
A
A
N7
C8
N9
G
G
G
17
17
17
N
17
-2.67
0.40
106.40
103.73
A
A
A
C8
N9
C4
G
G
G
17
17
17
N
17
3.92
0.50
113.80
117.72
A
A
A
N7
C8
N9
A
A
A
18
18
18
N
17
4.61
0.50
113.10
117.71
A
A
A
N7
C8
N9
G
G
G
20
20
20
N
17
-2.69
0.40
106.40
103.71
A
A
A
C8
N9
C4
G
G
G
20
20
20
N
17
3.59
0.50
113.80
117.39
A
A
A
N7
C8
N9
A
A
A
21
21
21
N
17
3.74
0.50
113.80
117.54
A
A
A
N7
C8
N9
A
A
A
22
22
22
N
Solution structure of the S. cerevisiae U6 Intramolecular stem-loop containing an SP phosphorothioate at nucleotide U80
1
N
N
covale
1.610
both
A
A
18
A
O3'
A
18
1_555
A
SSU
19
A
P
SSU
19
1_555
covale
1.611
both
A
SSU
19
A
O3'
SSU
19
1_555
A
G
20
A
P
G
20
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
24
A
N3
C
24
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
24
A
O2
C
24
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
24
A
N4
C
24
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
23
A
N3
C
23
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
23
A
O2
C
23
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
23
A
N4
C
23
1_555
hydrog
WATSON-CRICK
A
U
3
A
N3
U
3
1_555
A
A
22
A
N1
A
22
1_555
hydrog
WATSON-CRICK
A
U
3
A
O4
U
3
1_555
A
A
22
A
N6
A
22
1_555
hydrog
WATSON-CRICK
A
U
4
A
N3
U
4
1_555
A
A
21
A
N1
A
21
1_555
hydrog
WATSON-CRICK
A
U
4
A
O4
U
4
1_555
A
A
21
A
N6
A
21
1_555
hydrog
WATSON-CRICK
A
C
5
A
N3
C
5
1_555
A
G
20
A
N1
G
20
1_555
hydrog
WATSON-CRICK
A
C
5
A
N4
C
5
1_555
A
G
20
A
O6
G
20
1_555
hydrog
WATSON-CRICK
A
C
5
A
O2
C
5
1_555
A
G
20
A
N2
G
20
1_555
hydrog
C-A MISPAIR
A
C
6
A
N3
C
6
1_555
A
A
18
A
N6
A
18
1_555
hydrog
WATSON-CRICK
A
C
7
A
N3
C
7
1_555
A
G
17
A
N1
G
17
1_555
hydrog
WATSON-CRICK
A
C
7
A
N4
C
7
1_555
A
G
17
A
O6
G
17
1_555
hydrog
WATSON-CRICK
A
C
7
A
O2
C
7
1_555
A
G
17
A
N2
G
17
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
A
G
16
A
N1
G
16
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
A
G
16
A
O6
G
16
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
A
G
16
A
N2
G
16
1_555
hydrog
WATSON-CRICK
A
U
9
A
N3
U
9
1_555
A
A
15
A
N1
A
15
1_555
hydrog
WATSON-CRICK
A
U
9
A
O4
U
9
1_555
A
A
15
A
N6
A
15
1_555
hydrog
TYPE_11_PAIR
A
G
10
A
N2
G
10
1_555
A
A
14
A
N7
A
14
1_555
hydrog
TYPE_11_PAIR
A
G
10
A
N3
G
10
1_555
A
A
14
A
N6
A
14
1_555
RNA
U6 RNA, stem-loop, phosphorothioate, Sp phosphorothioate, residual dipolar coupling, RDC, RNA
1NZ1
PDB
1
1NZ1
1
24
1NZ1
1
24
1NZ1
A
1
1
24