1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Nagaswamy, U.
Gao, X.
Martinis, S.A.
Fox, G.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 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
29
5129
5139
10.1093/nar/29.24.5129
11812846
NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop.
2001
10.2210/pdb1k5i/pdb
pdb_00001k5i
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
CUCAA pentaloop
7369.440
5'-R(P*GP*GP*AP*CP*CP*CP*GP*GP*GP*CP*UP*CP*AP*AP*CP*CP*UP*GP*GP*GP*UP*CP*C)-3'
16S ribosomal RNA fragment (612-628)
1
syn
polymer
no
no
GGACCCGGGCUCAACCUGGGUCC
GGACCCGGGCUCAACCUGGGUCC
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
-3.953
1
19
A
1
A
23
-1.621
A_G1:C23_A
1
8.611
-0.299
-0.129
-0.085
-3.776
1
19
A
2
A
22
-1.219
A_G2:C22_A
2
7.528
-0.307
-0.091
-0.084
-2.702
1
20
A
3
A
21
-2.124
A_A3:U21_A
3
8.127
0.093
0.127
-0.013
0.877
1
19
A
4
A
20
-1.192
A_C4:G20_A
4
8.094
0.344
0.006
-0.091
1.915
1
19
A
5
A
19
-1.136
A_C5:G19_A
5
10.684
0.308
-0.032
-0.092
6.199
1
19
A
6
A
18
-1.546
A_C6:G18_A
6
7.586
0.271
-0.206
-0.084
-0.231
1
28
A
7
A
17
-1.200
A_G7:U17_A
7
5.464
-1.607
0.102
-0.367
3.320
1
19
A
8
A
16
-1.174
A_G8:C16_A
8
8.383
-0.755
0.065
-0.224
1.772
1
19
A
9
A
15
-1.212
A_G9:C15_A
9
6.379
-0.726
0.045
-0.213
19.804
1
A
10
A
14
27.471
A_C10:A14_A
10
48.509
3.137
0.511
-0.611
2.688
33.003
A
A
1
2
18.214
A
A
23
22
3.355
10.186
0.105
-1.686
AA_G1G2:C22C23_AA
1
-0.921
1.648
31.421
-4.606
-0.333
2.952
35.463
A
A
2
3
12.735
A
A
22
21
3.362
7.697
-0.044
-1.588
AA_G2A3:U21C22_AA
2
-1.436
2.376
34.615
-3.710
-0.133
2.726
32.446
A
A
3
4
14.657
A
A
21
20
3.232
8.106
-0.011
-1.670
AA_A3C4:G20U21_AA
3
0.948
-1.715
31.430
-4.308
0.175
2.673
32.165
A
A
4
5
18.339
A
A
20
19
3.359
10.000
-0.061
-1.732
AA_C4C5:G19G20_AA
4
0.811
-1.487
30.600
-4.819
0.248
2.653
30.472
A
A
5
6
16.309
A
A
19
18
3.247
8.458
-0.125
-1.682
AA_C5C6:G18G19_AA
5
2.006
-3.869
29.234
-4.756
0.607
2.111
27.327
A
A
6
7
29.337
A
A
18
17
3.516
13.241
-0.020
-1.968
AA_C6G7:U17G18_AA
6
-3.964
8.782
23.631
-7.213
-0.869
2.675
36.355
A
A
7
8
14.841
A
A
17
16
3.157
9.157
-0.212
-1.613
AA_G7G8:C16U17_AA
7
-2.906
4.710
35.104
-3.745
-0.028
2.892
32.197
A
A
8
9
15.889
A
A
16
15
3.462
8.705
-0.044
-1.695
AA_G8G9:C15C16_AA
8
-1.258
2.297
31.003
-4.595
-0.142
2.988
41.508
A
A
9
10
7.006
A
A
15
14
3.361
4.899
0.437
-1.116
AA_G9C10:A14C15_AA
9
-11.069
15.829
39.779
-2.093
-1.787
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2001-10-17
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
RCSB
Y
RCSB
2001-10-10
REL
The oligonucleotide was synthesized by T7 run-off transcription.
sample
structures with the lowest energy
33
10
2D NOESY
DQF-COSY
1H-31P HETCOR
COSY-35
TOCSY
10 mM Sodium Phosphate
6.5
ambient
298
K
A total of 300 structures were calculated using distance geometry utilizing 123 experimentally derived distance restraints for the loop and 918 (258-experimental distances, 660-A form distances) distance restraints for the stem region and 143 dihedral angle restraints. Additionally, 50 distance restraints were used to maintain the Watson-Crick geometry of the base pairs in the stem region. Final refinement resulted in 10 lowest energy structures.
Distance Geometry, Simulated Annealing, Restrained Molecular Dynamics
0.8 mM RNA; 10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5
90% H2O/10% D2O
10 mM Sodium Phosphate; 0.1 mM EDTA; pH 6.5
99.99 % D2O
Brunger
refinement
X-PLOR
3.1
600
Bruker
AMX
G
1
n
1
G
1
A
G
2
n
2
G
2
A
A
3
n
3
A
3
A
C
4
n
4
C
4
A
C
5
n
5
C
5
A
C
6
n
6
C
6
A
G
7
n
7
G
7
A
G
8
n
8
G
8
A
G
9
n
9
G
9
A
C
10
n
10
C
10
A
U
11
n
11
U
11
A
C
12
n
12
C
12
A
A
13
n
13
A
13
A
A
14
n
14
A
14
A
C
15
n
15
C
15
A
C
16
n
16
C
16
A
U
17
n
17
U
17
A
G
18
n
18
G
18
A
G
19
n
19
G
19
A
G
20
n
20
G
20
A
U
21
n
21
U
21
A
C
22
n
22
C
22
A
C
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
NMR Structure of a Ribosomal RNA Hairpin Containing a Conserved CUCAA Pentaloop
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
A
3
A
N1
A
3
1_555
A
U
21
A
N3
U
21
1_555
hydrog
WATSON-CRICK
A
A
3
A
N6
A
3
1_555
A
U
21
A
O4
U
21
1_555
hydrog
WATSON-CRICK
A
C
4
A
N3
C
4
1_555
A
G
20
A
N1
G
20
1_555
hydrog
WATSON-CRICK
A
C
4
A
N4
C
4
1_555
A
G
20
A
O6
G
20
1_555
hydrog
WATSON-CRICK
A
C
4
A
O2
C
4
1_555
A
G
20
A
N2
G
20
1_555
hydrog
WATSON-CRICK
A
C
5
A
N3
C
5
1_555
A
G
19
A
N1
G
19
1_555
hydrog
WATSON-CRICK
A
C
5
A
N4
C
5
1_555
A
G
19
A
O6
G
19
1_555
hydrog
WATSON-CRICK
A
C
5
A
O2
C
5
1_555
A
G
19
A
N2
G
19
1_555
hydrog
WATSON-CRICK
A
C
6
A
N3
C
6
1_555
A
G
18
A
N1
G
18
1_555
hydrog
WATSON-CRICK
A
C
6
A
N4
C
6
1_555
A
G
18
A
O6
G
18
1_555
hydrog
WATSON-CRICK
A
C
6
A
O2
C
6
1_555
A
G
18
A
N2
G
18
1_555
hydrog
TYPE_28_PAIR
A
G
7
A
N1
G
7
1_555
A
U
17
A
O2
U
17
1_555
hydrog
TYPE_28_PAIR
A
G
7
A
O6
G
7
1_555
A
U
17
A
N3
U
17
1_555
hydrog
WATSON-CRICK
A
G
8
A
N1
G
8
1_555
A
C
16
A
N3
C
16
1_555
hydrog
WATSON-CRICK
A
G
8
A
N2
G
8
1_555
A
C
16
A
O2
C
16
1_555
hydrog
WATSON-CRICK
A
G
8
A
O6
G
8
1_555
A
C
16
A
N4
C
16
1_555
hydrog
WATSON-CRICK
A
G
9
A
N1
G
9
1_555
A
C
15
A
N3
C
15
1_555
hydrog
WATSON-CRICK
A
G
9
A
N2
G
9
1_555
A
C
15
A
O2
C
15
1_555
hydrog
WATSON-CRICK
A
G
9
A
O6
G
9
1_555
A
C
15
A
N4
C
15
1_555
hydrog
C-A MISPAIR
A
C
10
A
O2
C
10
1_555
A
A
13
A
N6
A
13
1_555
hydrog
C-A MISPAIR
A
C
10
A
O2
C
10
1_555
A
A
14
A
N6
A
14
1_555
RNA
CUCAA pentaloop, RNA hairpin, non standard base-base interaction, RNA
1K5I
PDB
1
1K5I
1
23
1K5I
1
23
1K5I
A
1
1
23