0.021891
0.012639
0.000000
0.000000
0.025278
0.000000
0.000000
0.000000
0.016681
0.00000
0.00000
0.00000
Shi, K.
Wahl, M.C.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
18
90.00
90.00
120.00
45.68
45.68
59.95
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
H2 O
18.015
WATER
non-polymer
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
N
14
N
N
N
15
N
C
N
16
N
O
N
17
N
N
N
18
N
C
N
19
N
N
N
20
N
C
N
21
N
C
N
22
N
H
N
23
N
H
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
O
N
37
N
P
N
38
N
O
N
39
N
O
N
40
N
O
N
41
N
C
N
42
R
C
N
43
N
O
N
44
S
C
N
45
N
O
N
46
R
C
N
47
N
O
N
48
R
C
Y
49
N
N
Y
50
N
C
Y
51
N
N
Y
52
N
C
N
53
N
C
N
54
N
O
N
55
N
N
N
56
N
C
N
57
N
N
N
58
N
N
Y
59
N
C
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
H
N
74
N
O
N
75
N
H
N
76
N
H
N
77
N
O
N
78
N
P
N
79
N
O
N
80
N
O
N
81
N
O
N
82
N
C
N
83
R
C
N
84
N
O
N
85
S
C
N
86
N
O
N
87
R
C
N
88
N
O
N
89
R
C
N
90
N
N
N
91
N
C
N
92
N
O
N
93
N
N
N
94
N
C
N
95
N
O
N
96
N
C
N
97
N
C
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
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
N
25
N
sing
N
26
N
sing
N
27
N
doub
N
28
N
sing
N
29
N
doub
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
doub
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
doub
N
40
N
sing
N
41
N
sing
N
42
N
sing
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
Y
61
N
sing
Y
62
N
sing
Y
63
N
doub
N
64
N
sing
Y
65
N
sing
N
66
N
sing
Y
67
N
doub
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
sing
N
79
N
sing
N
80
N
sing
N
81
N
doub
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
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
doub
N
112
N
sing
N
113
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
27
2196
2201
10.1093/nar/27.10.2196
10219093
Crystal structure of an RNA duplex r(G GCGC CC)2 with non-adjacent G*U base pairs.
1999
10.2210/pdb438d/pdb
pdb_0000438d
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
IMAGE PLATE
RIGAKU RAXIS IIC
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
2862.759
RNA (5'-R(*GP*GP*GP*CP*GP*CP*UP*CP*C)-3')
2
syn
polymer
18.015
water
34
nat
water
no
no
GGGCGCUCC
GGGCGCUCC
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
n
1
2.10
41.50
2.237
1
19
A
1
B
17
0.549
A_G1:C17_B
1
-10.793
-0.309
0.360
-0.397
5.547
28
A
2
B
16
-1.165
A_G2:U16_B
2
-17.948
-2.237
0.432
-0.576
7.931
1
A
3
B
15
5.587
A_G3:C15_B
3
-16.257
-0.011
0.910
0.045
5.101
1
19
A
4
B
14
0.005
A_C4:G14_B
4
-17.511
-0.014
-0.118
-0.218
-7.503
1
19
A
5
B
13
1.236
A_G5:C13_B
5
-15.725
-0.164
0.120
-0.242
-8.876
1
19
A
6
B
12
-1.099
A_C6:G12_B
6
-13.067
0.608
0.209
-0.538
-3.665
28
A
7
B
11
-0.517
A_U7:G11_B
7
-19.935
2.617
0.333
-0.866
9.074
1
19
A
8
B
10
0.575
A_C8:G10_B
8
-13.056
0.548
0.001
-0.151
2.260
28.070
A
A
1
2
17.953
B
B
17
16
3.025
8.556
0.119
-1.986
AA_G1G2:U16C17_BB
1
-3.137
6.581
26.578
-5.770
-0.860
2.727
43.513
A
A
2
3
11.776
B
B
16
15
3.085
8.655
0.051
-1.441
AA_G2G3:C15U16_BB
2
-5.462
7.431
42.349
-2.698
-0.545
2.388
35.122
A
A
3
4
22.306
B
B
15
14
3.328
12.999
-0.261
-1.474
AA_G3C4:G14C15_BB
3
9.164
-15.726
31.416
-4.243
1.703
2.375
35.063
A
A
4
5
27.147
B
B
14
13
3.529
15.797
0.571
-1.767
AA_C4G5:C13G14_BB
4
-1.124
1.932
31.383
-5.200
-1.109
3.257
35.357
A
A
5
6
5.771
B
B
13
12
3.402
3.497
-0.411
-1.553
AA_G5C6:G12C13_BB
5
-2.347
3.872
35.114
-3.085
0.323
2.957
40.038
A
A
6
7
8.286
B
B
12
11
3.166
5.655
-0.117
-1.292
AA_C6U7:G11G12_BB
6
1.209
-1.771
39.635
-2.497
0.301
2.708
28.381
A
A
7
8
4.967
B
B
11
10
2.886
2.412
0.106
-1.433
AA_U7C8:G10G11_BB
7
6.430
-13.241
27.554
-3.406
1.069
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
1
0
1999-05-12
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-28
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
NDB
Y
NDB
1998-12-28
REL
REL
HOH
water
HOH
101
2
HOH
HOH
101
A
HOH
102
2
HOH
HOH
102
A
HOH
103
2
HOH
HOH
103
A
HOH
104
2
HOH
HOH
104
A
HOH
110
2
HOH
HOH
110
A
HOH
112
2
HOH
HOH
112
A
HOH
113
2
HOH
HOH
113
A
HOH
114
2
HOH
HOH
114
A
HOH
115
2
HOH
HOH
115
A
HOH
119
2
HOH
HOH
119
A
HOH
121
2
HOH
HOH
121
A
HOH
122
2
HOH
HOH
122
A
HOH
124
2
HOH
HOH
124
A
HOH
125
2
HOH
HOH
125
A
HOH
126
2
HOH
HOH
126
A
HOH
127
2
HOH
HOH
127
A
HOH
201
2
HOH
HOH
201
A
HOH
203
2
HOH
HOH
203
A
HOH
205
2
HOH
HOH
205
A
HOH
105
2
HOH
HOH
105
B
HOH
106
2
HOH
HOH
106
B
HOH
107
2
HOH
HOH
107
B
HOH
108
2
HOH
HOH
108
B
HOH
109
2
HOH
HOH
109
B
HOH
111
2
HOH
HOH
111
B
HOH
116
2
HOH
HOH
116
B
HOH
117
2
HOH
HOH
117
B
HOH
118
2
HOH
HOH
118
B
HOH
120
2
HOH
HOH
120
B
HOH
123
2
HOH
HOH
123
B
HOH
128
2
HOH
HOH
128
B
HOH
129
2
HOH
HOH
129
B
HOH
130
2
HOH
HOH
130
B
HOH
202
2
HOH
HOH
202
B
G
1
n
1
G
1
A
G
2
n
2
G
2
A
G
3
n
3
G
3
A
C
4
n
4
C
4
A
G
5
n
5
G
5
A
C
6
n
6
C
6
A
U
7
n
7
U
7
A
C
8
n
8
C
8
A
C
9
n
9
C
9
A
G
10
n
1
G
10
B
G
11
n
2
G
11
B
G
12
n
3
G
12
B
C
13
n
4
C
13
B
G
14
n
5
G
14
B
C
15
n
6
C
15
B
U
16
n
7
U
16
B
C
17
n
8
C
17
B
C
18
n
9
C
18
B
author_defined_assembly
2
dimeric
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
HOH
201
C
HOH
1
A
HOH
203
C
HOH
1
A
HOH
205
C
HOH
1
B
HOH
202
D
HOH
1
A
C5'
C
9
A
C5'
C
9
1
Y
1
A
C4'
C
9
A
C4'
C
9
1
Y
1
A
O4'
C
9
A
O4'
C
9
1
Y
1
A
C3'
C
9
A
C3'
C
9
1
Y
1
A
O3'
C
9
A
O3'
C
9
1
Y
1
A
C2'
C
9
A
C2'
C
9
1
Y
1
A
O2'
C
9
A
O2'
C
9
1
Y
1
A
C1'
C
9
A
C1'
C
9
1
Y
1
A
N1
C
9
A
N1
C
9
1
Y
1
A
C2
C
9
A
C2
C
9
1
Y
1
A
O2
C
9
A
O2
C
9
1
Y
1
A
N3
C
9
A
N3
C
9
1
Y
1
A
C4
C
9
A
C4
C
9
1
Y
1
A
N4
C
9
A
N4
C
9
1
Y
1
A
C5
C
9
A
C5
C
9
1
Y
1
A
C6
C
9
A
C6
C
9
1
Y
1
A
OP1
C
9
A
OP1
C
9
0
Y
1
A
OP2
C
9
A
OP2
C
9
0
Y
1
A
O5'
C
9
A
O5'
C
9
0
Y
1
B
C5'
C
18
B
C5'
C
9
1
Y
1
B
C4'
C
18
B
C4'
C
9
1
Y
1
B
O4'
C
18
B
O4'
C
9
1
Y
1
B
C3'
C
18
B
C3'
C
9
1
Y
1
B
O3'
C
18
B
O3'
C
9
1
Y
1
B
C2'
C
18
B
C2'
C
9
1
Y
1
B
O2'
C
18
B
O2'
C
9
1
Y
1
B
C1'
C
18
B
C1'
C
9
1
Y
1
B
N1
C
18
B
N1
C
9
1
Y
1
B
C2
C
18
B
C2
C
9
1
Y
1
B
O2
C
18
B
O2
C
9
1
Y
1
B
N3
C
18
B
N3
C
9
1
Y
1
B
C4
C
18
B
C4
C
9
1
Y
1
B
N4
C
18
B
N4
C
9
1
Y
1
B
C5
C
18
B
C5
C
9
1
Y
1
B
C6
C
18
B
C6
C
9
1
Y
1
B
OP1
C
18
B
OP1
C
9
0
Y
1
B
OP2
C
18
B
OP2
C
9
0
Y
1
B
O5'
C
18
B
O5'
C
9
0
Y
1
B
C
15
0.061
SIDE CHAIN
1
A
A
C5
C6
G
G
3
3
-0.062
0.010
1.419
1.357
N
0.2400000
0.1860000
0.1860000
2.50
10.0
1521
1403
83.8
RANDOM
1
THROUGHOUT
2.0
2.50
10.0
34
380
0
346
0
2.50
10.0
438D
1521
1403
2.0
0.0430000
1
37
83.8
refinement
X-PLOR
3.1
STRUCTURE OF AN RNA DUPLEX R(GGGCGCUCC)2 WITH NON-ADJACENT G.U BASE PAIRS
1
N
N
1
N
N
2
N
N
2
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
17
B
N3
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
17
B
O2
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
17
B
N4
C
8
1_555
hydrog
TYPE_28_PAIR
A
G
2
A
N1
G
2
1_555
B
U
16
B
O2
U
7
1_555
hydrog
TYPE_28_PAIR
A
G
2
A
O6
G
2
1_555
B
U
16
B
N3
U
7
1_555
hydrog
G-C PAIR
A
G
3
A
N1
G
3
1_555
B
C
15
B
N3
C
6
1_555
hydrog
WATSON-CRICK
A
C
4
A
N3
C
4
1_555
B
G
14
B
N1
G
5
1_555
hydrog
WATSON-CRICK
A
C
4
A
N4
C
4
1_555
B
G
14
B
O6
G
5
1_555
hydrog
WATSON-CRICK
A
C
4
A
O2
C
4
1_555
B
G
14
B
N2
G
5
1_555
hydrog
WATSON-CRICK
A
G
5
A
N1
G
5
1_555
B
C
13
B
N3
C
4
1_555
hydrog
WATSON-CRICK
A
G
5
A
N2
G
5
1_555
B
C
13
B
O2
C
4
1_555
hydrog
WATSON-CRICK
A
G
5
A
O6
G
5
1_555
B
C
13
B
N4
C
4
1_555
hydrog
WATSON-CRICK
A
C
6
A
N3
C
6
1_555
B
G
12
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
C
6
A
N4
C
6
1_555
B
G
12
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
C
6
A
O2
C
6
1_555
B
G
12
B
N2
G
3
1_555
hydrog
TYPE_28_PAIR
A
U
7
A
N3
U
7
1_555
B
G
11
B
O6
G
2
1_555
hydrog
TYPE_28_PAIR
A
U
7
A
O2
U
7
1_555
B
G
11
B
N1
G
2
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
B
G
10
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
B
G
10
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
B
G
10
B
N2
G
1
1_555
RNA
A-RNA, DOUBLE HELIX, MISMATCHED, RNA
438D
PDB
1
438D
1
9
438D
1
9
438D
A
1
1
9
10
18
438D
10
18
438D
B
1
1
9
146
hexagonal
H 3