1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Rudisser, S.
Tinoco Jr., I.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
J.Mol.Biol.
JMOBAK
0070
0022-2836
295
1211
1232
10.1006/jmbi.1999.3421
10653698
Solution structure of Cobalt(III)hexammine complexed to the GAAA tetraloop, and metal-ion binding to G.A mismatches.
2000
10.2210/pdb1f9l/pdb
pdb_00001f9l
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
7175.371
5'-R(*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*AP*AP*AP*GP*AP*UP*GP*GP*CP*GP*CP*CP*)-3'
P5ABC DOMAIN
1
syn
polymer
no
no
GGCGAAGUCGAAAGAUGGCGCC
GGCGAAGUCGAAAGAUGGCGCC
A
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
29.668
1
19
A
1
A
22
-5.981
A_G1:C22_A
1
20.355
-0.014
-0.317
-0.146
2.523
1
19
A
2
A
21
7.136
A_G2:C21_A
2
26.162
-0.430
0.676
-0.396
10.066
1
19
A
3
A
20
3.509
A_C3:G20_A
3
-17.715
0.197
-0.837
-0.282
-3.547
1
19
A
4
A
19
-18.929
A_G4:C19_A
4
-17.763
0.382
0.881
-0.427
-6.105
8
A
5
A
18
-23.184
A_A5:G18_A
5
0.510
0.043
-0.872
1.123
1.811
8
A
6
A
17
-22.412
A_A6:G17_A
6
-5.291
0.107
-0.538
1.247
-4.341
28
A
7
A
16
-5.401
A_G7:U16_A
7
-9.111
-2.147
-0.501
-0.370
2.072
1
20
A
8
A
15
-6.032
A_U8:A15_A
8
-0.802
0.097
-0.353
-0.044
20.290
1
19
A
9
A
14
-3.456
A_C9:G14_A
9
-5.584
0.064
0.008
-0.172
31.387
A
10
A
13
-63.956
A_G10:A13_A
10
7.842
7.104
-1.176
-5.355
5.217
25.467
A
A
1
2
-14.160
A
A
22
21
6.124
-6.023
1.065
-0.598
AA_G1G2:C21C22_AA
1
-9.796
23.029
22.761
1.811
-7.569
1.951
40.145
A
A
2
3
24.399
A
A
21
20
2.908
16.037
0.743
-2.087
AA_G2C3:G20C21_AA
2
12.339
-18.774
34.855
-4.503
0.044
4.548
33.340
A
A
3
4
-1.565
A
A
20
19
3.945
-0.888
-2.712
-1.585
AA_C3G4:C19G20_AA
3
-8.779
15.477
32.183
-2.567
2.797
3.973
28.140
A
A
4
5
-11.115
A
A
19
18
3.555
-5.245
0.983
-2.023
AA_G4A5:G18C19_AA
4
10.529
-22.315
25.609
-2.676
0.958
2.439
26.968
A
A
5
6
17.100
A
A
18
17
3.154
7.862
-0.188
-2.046
AA_A5A6:G17G18_AA
5
-0.764
1.663
25.806
-6.144
0.232
3.268
31.738
A
A
6
7
19.893
A
A
17
16
3.763
10.676
1.859
-0.705
AA_A6G7:U16G17_AA
6
-0.917
1.709
29.918
-3.462
-3.586
2.467
36.531
A
A
7
8
17.416
A
A
16
15
3.088
10.754
-1.236
-2.032
AA_G7U8:A15U16_AA
7
-2.931
4.747
34.844
-4.535
1.620
3.523
32.981
A
A
8
9
-33.885
A
A
15
14
3.623
-18.192
0.224
-0.932
AA_U8C9:G14A15_AA
8
-2.490
4.638
27.515
2.063
-0.902
3.156
66.936
A
A
9
10
12.322
A
A
14
13
4.196
13.447
-3.903
-1.230
AA_C9G10:A13G14_AA
9
13.186
-12.084
64.530
-1.722
4.134
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-07-26
1
1
2008-01-08
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
2009-07-28
SPRSDE
Solution structure of the 22-nucleotide without Cobalt(III)hexammine
RCSB
Y
RCSB
2000-07-11
REL
REL
The RNA was enzymatically synthesized from a synthetic RNA template using T7 RNA polymerase
sample
The structure of the complex was determined using 7 NOE constraints between Cobalt(III)Hexammine and the GAAA tetraloop.
In addition, the same constraints as for the 22-nucleotide hairpin without Cobalt(III)hexammine were used.
For RNA without Cobalt(III)Hexammine see entry 1EOR.
structures with the least restraint violations
50
1
2D NOESY
200 mM NaCl
5.6
ambient
283
K
356 NOE constraints, 16 sugar pucker constraints, 93 torsion angle constraints, 7 constraints between Cobalt(III)Hexammine and the GAAA tetraloop
restrained molecular dynamics,
1
minimized average structure
2.8 mM RNA, 10 mM sodium Phosphate, 200 mM NaCl, 0.1 mM EDTA pH 5.6,
3.4 mM Cobalt(III)Hexammine
90% H2O/10% D2O
Brunger
structure solution
X-PLOR
3.1
MSI
data analysis
Felix
95
Brunger
refinement
X-PLOR
3.1
600
Bruker
AMX
500
Bruker
DRX
G
1
n
1
G
1
A
G
2
n
2
G
2
A
C
3
n
3
C
3
A
G
4
n
4
G
4
A
A
5
n
5
A
5
A
A
6
n
6
A
6
A
G
7
n
7
G
7
A
U
8
n
8
U
8
A
C
9
n
9
C
9
A
G
10
n
10
G
10
A
A
11
n
11
A
11
A
A
12
n
12
A
12
A
A
13
n
13
A
13
A
G
14
n
14
G
14
A
A
15
n
15
A
15
A
U
16
n
16
U
16
A
G
17
n
17
G
17
A
G
18
n
18
G
18
A
C
19
n
19
C
19
A
G
20
n
20
G
20
A
C
21
n
21
C
21
A
C
22
n
22
C
22
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
H61
O6
A
G
6
17
1.51
1
A
A
H61
O6
A
G
5
18
1.55
minimized average
Solution Structure of a 22-Nucleotide Hairpin Similar to the P5ABC Region of a Group I Ribozyme with Cobalt(III)hexammine Complexed to the GAAA Tetraloop
1
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
A
C
22
A
N3
C
22
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
A
C
22
A
O2
C
22
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
A
C
22
A
N4
C
22
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
C
21
A
N3
C
21
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
C
21
A
O2
C
21
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
C
21
A
N4
C
21
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
A
G
20
A
N1
G
20
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
A
G
20
A
O6
G
20
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
A
G
20
A
N2
G
20
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
A
C
19
A
N3
C
19
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
A
C
19
A
O2
C
19
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
A
C
19
A
N4
C
19
1_555
hydrog
TYPE_8_PAIR
A
A
5
A
N1
A
5
1_555
A
G
18
A
N1
G
18
1_555
hydrog
TYPE_8_PAIR
A
A
5
A
N6
A
5
1_555
A
G
18
A
O6
G
18
1_555
hydrog
TYPE_8_PAIR
A
A
6
A
N1
A
6
1_555
A
G
17
A
N1
G
17
1_555
hydrog
TYPE_8_PAIR
A
A
6
A
N6
A
6
1_555
A
G
17
A
O6
G
17
1_555
hydrog
TYPE_28_PAIR
A
G
7
A
N1
G
7
1_555
A
U
16
A
O2
U
16
1_555
hydrog
TYPE_28_PAIR
A
G
7
A
O6
G
7
1_555
A
U
16
A
N3
U
16
1_555
hydrog
WATSON-CRICK
A
U
8
A
N3
U
8
1_555
A
A
15
A
N1
A
15
1_555
hydrog
WATSON-CRICK
A
U
8
A
O4
U
8
1_555
A
A
15
A
N6
A
15
1_555
hydrog
WATSON-CRICK
A
C
9
A
N3
C
9
1_555
A
G
14
A
N1
G
14
1_555
hydrog
WATSON-CRICK
A
C
9
A
N4
C
9
1_555
A
G
14
A
O6
G
14
1_555
hydrog
WATSON-CRICK
A
C
9
A
O2
C
9
1_555
A
G
14
A
N2
G
14
1_555
hydrog
G-A MISPAIR
A
G
10
A
N2
G
10
1_555
A
A
13
A
N7
A
13
1_555
RNA
GA mismatches, GAAA tetraloop, metal-ion binding, Cobalt(III)hexammine, hairpin, P5abc, group I intron, RNA
1F9L
PDB
1
1F9L
1
22
1F9L
1
22
1F9L
A
1
1
22
1
P 1