1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Popovic, M.
Greenbaum, N.L.
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 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
R
C
N
49
N
O
N
50
R
C
N
51
N
N
N
52
N
C
N
53
N
O
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
C
N
58
N
C
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
R
C
N
84
N
O
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
96
N
C
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
O
N
112
N
P
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
O
N
119
S
C
N
120
N
O
N
121
R
C
N
122
N
O
N
123
R
C
N
124
N
N
N
125
N
C
N
126
N
O
N
127
N
N
N
128
N
C
N
129
N
O
N
130
N
C
N
131
N
C
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
doub
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
doub
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
UK
Rna
RNARFU
2122
1355-8382
20
24
35
10.1261/rna.039701.113
24243113
Role of helical constraints of the EBS1-IBS1 duplex of a group II intron on demarcation of the 5' splice site.
2014
10.2210/pdb2m12/pdb
pdb_00002m12
10.13018/BMR18838
7443.480
RNA (5'-R(*GP*GP*GP*UP*GP*UP*AP*UP*UP*GP*GP*AP*AP*AP*UP*GP*AP*GP*CP*AP*CP*CP*C)-3')
1
syn
polymer
no
no
GGGUGUAUUGGAAAUGAGCACCC
GGGUGUAUUGGAAAUGAGCACCC
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
RNA stem loop
16.713
1
19
A
1
A
23
-4.772
A_G1:C23_A
1
23.023
-0.134
-0.298
-0.234
4.243
1
19
A
2
A
22
-4.313
A_G2:C22_A
2
-11.576
-0.042
0.646
-0.248
-0.079
1
19
A
3
A
21
-2.005
A_G3:C21_A
3
-9.923
-0.101
0.110
-0.183
0.585
1
20
A
4
A
20
-4.059
A_U4:A20_A
4
-9.636
-0.041
-0.221
-0.072
-2.248
1
19
A
5
A
19
-2.907
A_G5:C19_A
5
-8.696
-0.041
0.184
-0.175
-8.467
1
28
A
6
A
18
-4.437
A_U6:G18_A
6
0.196
1.997
0.421
-0.391
-17.049
1
A
9
A
17
22.952
A_U9:A17_A
7
3.242
1.283
1.912
-0.672
-5.962
A
11
A
13
-8.194
A_G11:A13_A
8
-31.384
4.473
-2.491
-1.821
3.485
32.786
A
A
1
2
17.700
A
A
23
22
4.029
9.676
-0.737
-1.361
AA_G1G2:C22C23_AA
1
-10.413
19.048
29.621
-4.427
-0.862
3.086
31.591
A
A
2
3
15.982
A
A
22
21
3.649
8.594
0.051
-1.622
AA_G2G3:C21C22_AA
2
1.314
-2.443
30.400
-4.652
0.161
2.752
31.632
A
A
3
4
18.380
A
A
21
20
3.410
9.857
-0.104
-1.606
AA_G3U4:A20C21_AA
3
1.334
-2.488
30.066
-4.709
0.430
2.778
31.544
A
A
4
5
19.803
A
A
20
19
3.516
10.561
0.140
-1.616
AA_U4G5:C19A20_AA
4
-1.935
3.629
29.705
-4.923
-0.614
3.546
37.497
A
A
5
6
18.641
A
A
19
18
4.234
11.776
0.449
-1.678
AA_G5U6:G18C19_AA
5
3.632
-5.750
35.483
-4.499
-0.116
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_nmr_spectrometer
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Database references
Data collection
Database references
Other
Data collection
Database references
1
0
2013-10-23
1
1
2014-02-05
1
2
2023-06-14
1
3
2024-05-15
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_database_2.pdbx_DOI
BMRB
Y
RCSB
2012-11-13
REL
REL
REL
REL
287
130
26
99
structures with the least restraint violations
100
10
2D 1H-1H NOESY
2D 1H-1H TOCSY
2D DQF-COSY
2D 1H-15N HSQC
2D 1H-13C HSQC
2D 1H-13C HSQC aliphatic
2D 1H-13C HSQC aromatic
3D 1H-15N NOESY
3D HCCH-COSY
3D HCCH-TOCSY
2D 1H-1H NOESY
0.03-0.9
mM
60
mM
0.3-0.9
mM
60
mM
0.3-0.5
mM
[U-100% 13C; U-100% 15N]
60
mM
0.3-0.5
mM
[U-100% 13C; U-100% 15N]
60
mM
0.06
6.4
ambient
277
K
0.06
6.4
ambient
303
K
torsion angle dynamics
1
fewest violations
0.03-0.9 mM ID3, 60 mM sodium chloride, 90% H2O/10% D2O
90% H2O/10% D2O
0.3-0.9 mM ID3, 60 mM sodium chloride, 100% D2O
100% D2O
0.3-0.5 mM [U-100% 13C; U-100% 15N] ID3, 60 mM sodium chloride, 90% H2O/10% D2O
90% H2O/10% D2O
0.3-0.5 mM [U-100% 13C; U-100% 15N] ID3, 60 mM potassium chloride, 100% D2O
100% D2O
CCPN
chemical shift assignment
CCPN
Bruker Biospin
collection
TopSpin
Bruker Biospin
processing
TopSpin
Goddard
chemical shift assignment
Sparky
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
Schwieters, Kuszewski, Tjandra and Clore
structure solution
X-PLOR NIH
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR NIH
600
Bruker
AVANCE
Bruker Avance
GUA
1
n
1
G
1
A
GUA
2
n
2
G
2
A
GUA
3
n
3
G
3
A
URA
4
n
4
U
4
A
GUA
5
n
5
G
5
A
URA
6
n
6
U
6
A
ADE
7
n
7
A
7
A
URA
8
n
8
U
8
A
URA
9
n
9
U
9
A
GUA
10
n
10
G
10
A
GUA
11
n
11
G
11
A
ADE
12
n
12
A
12
A
ADE
13
n
13
A
13
A
ADE
14
n
14
A
14
A
URA
15
n
15
U
15
A
GUA
16
n
16
G
16
A
ADE
17
n
17
A
17
A
GUA
18
n
18
G
18
A
CYT
19
n
19
C
19
A
ADE
20
n
20
A
20
A
CYT
21
n
21
C
21
A
CYT
22
n
22
C
22
A
CYT
23
n
23
C
23
A
author_defined_assembly
1
monomeric
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
O2'
H8
G
G
1
2
1.50
1
A
A
O2'
H6
A
U
14
15
1.58
2
A
A
O2'
H5''
U
U
8
9
1.57
2
A
A
H1'
O4
G
U
11
15
1.57
3
A
A
HO2'
O5'
U
G
15
16
1.52
4
A
A
H4'
OP1
G
G
10
11
1.59
5
A
A
HO2'
O5'
U
G
15
16
1.51
5
A
A
HO2'
O5'
A
U
7
8
1.53
6
A
A
O2'
H8
G
G
1
2
1.48
6
A
A
HO2'
O5'
G
G
1
2
1.54
7
A
A
O2'
H8
G
G
1
2
1.47
7
A
A
O2'
H5'
U
G
15
16
1.53
7
A
A
HO2'
O5'
G
G
1
2
1.54
7
A
A
HO2'
O5'
A
G
17
18
1.55
8
A
A
HO2'
O4'
U
G
15
16
1.46
9
A
A
HO2'
OP1
U
G
9
10
1.36
9
A
A
HO2'
O5'
A
U
14
15
1.53
9
A
A
HO2'
O5'
U
U
8
9
1.59
10
A
A
HO2'
O4'
A
U
14
15
1.29
10
A
A
O2'
H8
G
G
1
2
1.53
10
A
A
HO2'
O5'
U
G
15
16
1.54
10
A
A
H1'
OP1
G
A
10
12
1.58
fewest violations, model3
Solution structure of the ID3 stem loop of domain 1 of the ai5gamma group II intron
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
23
A
N3
C
23
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
23
A
O2
C
23
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
23
A
N4
C
23
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
22
A
N3
C
22
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
22
A
O2
C
22
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
22
A
N4
C
22
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
3
1_555
A
C
21
A
N3
C
21
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
3
1_555
A
C
21
A
O2
C
21
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
3
1_555
A
C
21
A
N4
C
21
1_555
hydrog
WATSON-CRICK
A
U
4
A
N3
U
4
1_555
A
A
20
A
N1
A
20
1_555
hydrog
WATSON-CRICK
A
U
4
A
O4
U
4
1_555
A
A
20
A
N6
A
20
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
A
C
19
A
N3
C
19
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
A
C
19
A
O2
C
19
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
A
C
19
A
N4
C
19
1_555
hydrog
TYPE_28_PAIR
A
U
6
A
N3
U
6
1_555
A
G
18
A
O6
G
18
1_555
hydrog
TYPE_28_PAIR
A
U
6
A
O2
U
6
1_555
A
G
18
A
N1
G
18
1_555
hydrog
U-A PAIR
A
U
9
A
N3
U
9
1_555
A
A
17
A
N1
A
17
1_555
hydrog
G-A MISPAIR
A
G
11
A
N3
G
11
1_555
A
A
13
A
N6
A
13
1_555
RNA
EBS1, stem loop, ID3, RNA
2M12
PDB
1
2M12
1
23
2M12
1
23
2M12
A
1
1
23