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O
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O
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O
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O
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O
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O
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2
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C
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N1
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N1
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2
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N
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2
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C
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2
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O
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N3
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2
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N
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2
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2
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O
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2
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2
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C
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P
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P
C
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3
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P
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OP1
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OP1
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3
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O
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OP2
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3
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O
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3
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O
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C
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3
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C
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O4'
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O
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C
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3
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O
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1
3
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1
C
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O2'
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3
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O
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3
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3
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C
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N1
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N1
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3
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1
N
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C2
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3
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C
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O2
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O2
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3
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O
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N3
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N3
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3
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N
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C4
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3
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N4
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N4
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N
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C5
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C6
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OP1
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C
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O4'
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O4'
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O
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C
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O3'
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5
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O
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C2'
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C2'
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5
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C
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O2'
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O2'
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O
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C1'
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N1
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N
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O2
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5
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O
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N3
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5
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1
N
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N4
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5
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N
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O
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O
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C
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O
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C
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O
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6
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C
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6
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O
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C
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6
1.00
1
N
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6
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C
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6
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1
N
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6
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C
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6
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C
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6
1.00
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O
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N1
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6
1.00
1
N
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6
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C
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6
1.00
1
N
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ATOM
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N3
G
1
6
1.00
1
N
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C4
G
6
ATOM
A
C4
G
1
6
1.00
1
C
18.10
-13.399
-4.547
0.995
A
O
HOH
7
HETATM
B
O
HOH
2
1.03
1
O
19.59
-11.068
-6.112
0.483
A
O
HOH
8
HETATM
B
O
HOH
2
0.92
1
O
17.46
-9.671
-3.363
3.260
A
O
HOH
9
HETATM
B
O
HOH
2
1.09
1
O
27.43
-11.648
-1.587
6.346
A
O
HOH
10
HETATM
B
O
HOH
2
1.19
1
O
25.21
-9.631
0.172
5.680
A
O
HOH
11
HETATM
B
O
HOH
2
1.00
1
O
17.74
-11.737
2.486
8.017
A
O
HOH
12
HETATM
B
O
HOH
2
0.93
1
O
34.27
-10.913
5.380
5.841
A
O
HOH
13
HETATM
B
O
HOH
2
0.56
1
O
15.54
-9.961
-9.804
7.809
A
O
HOH
14
HETATM
B
O
HOH
2
0.86
1
O
35.79
-12.370
-2.605
3.003
A
O
HOH
15
HETATM
B
O
HOH
2
1.01
1
O
22.66
-14.006
0.525
9.186
A
O
HOH
16
HETATM
B
O
HOH
2
0.49
1
O
21.62
-5.444
-1.220
13.259
A
O
HOH
17
HETATM
B
O
HOH
2
0.85
1
O
16.38
-4.101
4.813
8.026
A
O
HOH
18
HETATM
B
O
HOH
2
0.65
1
O
24.01
-3.814
3.171
12.078
A
O
HOH
19
HETATM
B
O
HOH
2
0.95
1
O
17.70
-9.629
-12.867
-1.932
A
O
HOH
20
HETATM
B
O
HOH
2
0.56
1
O
31.62
-6.653
8.395
16.037
A
O
HOH
21
HETATM
B
O
HOH
2
1.07
1
O
18.02
-14.393
2.876
10.576
A
O
HOH
22
HETATM
B
O
HOH
2
0.34
1
O
31.12
-14.633
2.691
15.115
A
O
HOH
23
HETATM
B
O
HOH
2
0.90
1
O
28.60
-16.269
0.042
1.781
A
O
HOH
24
HETATM
B
O
HOH
2
0.86
1
O
38.75
-14.551
-1.172
3.724
A
O
HOH
25
HETATM
B
O
HOH
2
0.67
1
O
35.84
-13.733
-7.666
-1.692
A
O
HOH
26
HETATM
B
O
HOH
2
0.99
1
O
35.66
-15.378
-9.081
-3.649
A
O
HOH
27
HETATM
B
O
HOH
2
0.86
1
O
19.33
-5.405
3.614
14.506
A
O
HOH
28
HETATM
B
O
HOH
2
0.59
1
O
24.60
-6.368
-5.548
10.106
A
O
HOH
29
HETATM
B
O
HOH
2
0.87
1
O
31.01
-21.401
-10.131
1.169
A
O
HOH
30
HETATM
B
O
HOH
2
0.88
1
O
28.15
-20.311
-11.969
-1.479
A
O
HOH
31
HETATM
B
O
HOH
2
0.61
1
O
28.13
-20.075
-9.534
3.707
A
O
HOH
32
HETATM
B
O
HOH
2
0.80
1
O
22.41
-15.241
-11.955
4.617
A
O
HOH
33
HETATM
B
O
HOH
2
0.57
1
O
30.71
-12.213
-11.204
9.818
A
O
HOH
34
HETATM
B
O
HOH
2
0.70
1
O
37.82
-22.847
-7.848
3.855
A
O
HOH
35
HETATM
B
O
HOH
2
0.63
1
O
26.77
-4.040
3.116
5.400
A
O
HOH
36
HETATM
B
O
HOH
2
0.64
1
O
49.73
-13.528
0.086
5.787
A
O
HOH
37
HETATM
B
O
HOH
2
0.64
1
O
24.05
-8.589
-11.089
9.666
A
O
HOH
38
HETATM
B
O
HOH
2
0.43
1
O
29.70
-12.015
9.665
10.566
A
O
HOH
39
HETATM
B
O
HOH
2
0.98
1
O
23.13
-9.754
8.515
6.672
A
O
HOH
40
HETATM
B
O
HOH
2
0.54
1
O
25.35
-15.270
-2.424
7.302
A
O
HOH
41
HETATM
B
O
HOH
2
0.39
1
O
22.27
-15.272
-11.261
7.304
A
O
HOH
42
HETATM
B
O
HOH
2
0.48
1
O
37.61
-15.275
-0.088
7.307
A
O
HOH
43
HETATM
B
O
HOH
2
0.34
1
O
26.36
-15.269
2.301
7.303
A
O
HOH
44
HETATM
B
O
HOH
2
0.47
1
O
0.032680
0.000000
0.000000
0.000000
0.029412
0.000000
0.000000
0.000000
0.034247
0.00000
0.00000
0.00000
Wahl, M.C.
Rao, S.T.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
30.600
34.000
29.200
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
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
3
24
31
10.1038/nsb0196-24
8548450
The structure of r(UUCGCG) has a 5'-UU-overhang exhibiting Hoogsteen-like trans U.U base pairs.
1996
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
2
56
62
Structure of an RNA Double Helix Including Uracil-Uracil Base Pairs in an Internal Loop
1995
10.2210/pdb1osu/pdb
pdb_00001osu
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
277.00
1
AREA DETECTOR
SIEMENS
SINGLE WAVELENGTH
M
x-ray
1
1.0
ROTATING ANODE
MACSCIENCE
1868.149
RNA (5'-R(*UP*UP*CP*GP*CP*G)-3')
1
syn
polymer
18.015
water
38
nat
water
no
no
UUCGCG
UUCGCG
A
polyribonucleotide
n
n
n
n
n
n
2.03
39.49
VAPOR DIFFUSION, HANGING DROP
7.00
pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
277.00
WATER
1
ISOPROPANOL
1
MG2+
1
SPERMINE
1
6.334
1
19
A
3
A
6
-1.846
A_C3:G6_A
1
-17.141
0.107
-0.086
-0.183
-3.214
1
19
A
4
A
5
-0.084
A_G4:C5_A
2
-17.233
-0.236
-0.107
-0.104
3.214
1
19
A
5
A
4
-0.084
A_C5:G4_A
3
-17.233
0.236
-0.107
-0.104
-6.334
1
19
A
6
A
3
-1.846
A_G6:C3_A
4
-17.141
-0.107
-0.086
-0.183
2.248
35.141
A
A
3
4
28.811
A
A
6
5
3.414
16.727
-0.252
-1.684
AA_C3G4:C5G6_AA
1
-1.187
2.045
30.994
-5.099
0.254
3.003
33.070
A
A
4
5
9.928
A
A
5
4
3.207
5.625
0.000
-0.969
AA_G4C5:G4C5_AA
2
0.000
0.000
32.601
-2.612
0.000
2.248
35.141
A
A
5
6
28.811
A
A
4
3
3.414
16.727
0.252
-1.684
AA_C5G6:C3G4_AA
3
1.187
-2.045
30.994
-5.099
-0.254
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
1
0
1996-04-04
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
BNL
Y
NDB
1995-11-08
REL
REL
HOH
water
HOH
7
2
HOH
HOH
7
A
HOH
8
2
HOH
HOH
8
A
HOH
9
2
HOH
HOH
9
A
HOH
10
2
HOH
HOH
10
A
HOH
11
2
HOH
HOH
11
A
HOH
12
2
HOH
HOH
12
A
HOH
13
2
HOH
HOH
13
A
HOH
14
2
HOH
HOH
14
A
HOH
15
2
HOH
HOH
15
A
HOH
16
2
HOH
HOH
16
A
HOH
17
2
HOH
HOH
17
A
HOH
18
2
HOH
HOH
18
A
HOH
19
2
HOH
HOH
19
A
HOH
20
2
HOH
HOH
20
A
HOH
21
2
HOH
HOH
21
A
HOH
22
2
HOH
HOH
22
A
HOH
23
2
HOH
HOH
23
A
HOH
24
2
HOH
HOH
24
A
HOH
25
2
HOH
HOH
25
A
HOH
26
2
HOH
HOH
26
A
HOH
27
2
HOH
HOH
27
A
HOH
28
2
HOH
HOH
28
A
HOH
29
2
HOH
HOH
29
A
HOH
30
2
HOH
HOH
30
A
HOH
31
2
HOH
HOH
31
A
HOH
32
2
HOH
HOH
32
A
HOH
33
2
HOH
HOH
33
A
HOH
34
2
HOH
HOH
34
A
HOH
35
2
HOH
HOH
35
A
HOH
36
2
HOH
HOH
36
A
HOH
37
2
HOH
HOH
37
A
HOH
38
2
HOH
HOH
38
A
HOH
39
2
HOH
HOH
39
A
HOH
40
2
HOH
HOH
40
A
HOH
41
2
HOH
HOH
41
A
HOH
42
2
HOH
HOH
42
A
HOH
43
2
HOH
HOH
43
A
HOH
44
2
HOH
HOH
44
A
U
1
n
1
U
1
A
U
2
n
2
U
2
A
C
3
n
3
C
3
A
G
4
n
4
G
4
A
C
5
n
5
C
5
A
G
6
n
6
G
6
A
author_defined_assembly
3
trimeric
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_455
-x-1,-y,z+1/2
crystal symmetry operation
-30.6000000000
0.0000000000
14.6000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_556
x,-y,-z+1
crystal symmetry operation
0.0000000000
0.0000000000
29.2000000000
1
A
HOH
41
B
HOH
1
A
HOH
42
B
HOH
1
A
HOH
43
B
HOH
1
A
HOH
44
B
HOH
0.1610000
0.1610000
1.400
8.000
2991
86.400
1
2.000
TR
isotropic
TR
isotropic
1.400
8.000
38
161
0
123
0
0.012
1.70
fix
ref
1.400
8.000
1OSU
2991
2.000
1
refinement
X-PLOR
STRUCTURE OF THE RNA HEXAMER, R(UUCGCG), WITH A 5'-UU-OVERHANG EXHIBITING HOOGSTEEN-LIKE TRANS U-U BASE PAIRS
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
6
A
N1
G
6
3_455
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
6
A
O6
G
6
3_455
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
6
A
N2
G
6
3_455
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
A
C
5
A
N3
C
5
3_455
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
A
C
5
A
O2
C
5
3_455
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
A
C
5
A
N4
C
5
3_455
hydrog
WATSON-CRICK
A
C
5
A
N3
C
5
1_555
A
G
4
A
N1
G
4
3_455
hydrog
WATSON-CRICK
A
C
5
A
N4
C
5
1_555
A
G
4
A
O6
G
4
3_455
hydrog
WATSON-CRICK
A
C
5
A
O2
C
5
1_555
A
G
4
A
N2
G
4
3_455
hydrog
WATSON-CRICK
A
G
6
A
N1
G
6
1_555
A
C
3
A
N3
C
3
3_455
hydrog
WATSON-CRICK
A
G
6
A
N2
G
6
1_555
A
C
3
A
O2
C
3
3_455
hydrog
WATSON-CRICK
A
G
6
A
O6
G
6
1_555
A
C
3
A
N4
C
3
3_455
RNA
A-RNA, DOUBLE HELIX, NICKED, 5'-UU-OVERHANG, MISMATCHED, RNA
1OSU
PDB
1
1OSU
1
6
1OSU
1
6
1OSU
A
1
1
6
20
C 2 2 21