1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Znosko, B.M.
Kennedy, S.D.
Wille, P.C.
Krugh, T.R.
Turner, D.H.
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
US
Biochemistry
BICHAW
0033
0006-2960
43
15822
15837
10.1021/bi049256y
15595837
Structural Features and Thermodynamics of the J4/5 Loop from the Candida albicans and Candida dubliniensis Group I Introns.
2004
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
3648.282
5'-R(*GP*AP*GP*GP*AP*AP*GP*GP*CP*GP*A)-3'
1
syn
polymer
3405.034
5'-R(*UP*CP*GP*UP*UP*AP*AP*UP*CP*UP*C)-3'
1
syn
polymer
no
no
GAGGAAGGCGA
GAGGAAGGCGA
A
polyribonucleotide
no
no
UCGUUAAUCUC
UCGUUAAUCUC
B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-22.809
1
19
A
1
B
21
-0.467
A_G1:C21_B
1
-10.764
-0.445
-0.737
-0.077
-19.421
1
20
A
2
B
20
-0.293
A_A2:U20_B
2
-5.777
0.198
-0.391
0.096
-2.562
1
19
A
3
B
19
0.162
A_G3:C19_B
3
-4.666
-0.403
-0.134
-0.083
1.716
1
28
A
4
B
18
-1.528
A_G4:U18_B
4
-20.242
-1.967
0.328
-0.386
3.621
10
A
5
B
17
-14.589
A_A5:A17_B
5
-16.119
6.483
-0.073
-4.541
-7.921
10
A
6
B
16
-13.754
A_A6:A16_B
6
4.069
-6.487
0.034
-4.215
-0.482
28
A
7
B
15
4.948
A_G7:U15_B
7
-13.869
-2.659
-0.297
-0.442
4.245
1
28
A
8
B
14
1.831
A_G8:U14_B
8
-13.558
-2.218
0.243
-0.328
7.907
1
19
A
9
B
13
0.458
A_C9:G13_B
9
-19.629
0.243
0.001
-0.068
-1.428
1
19
A
10
B
12
0.009
A_G10:C12_B
10
-17.927
-0.443
-0.016
-0.108
-4.994
1
20
A
11
B
B
11
-1.655
A_A11:U11B_B
11
-23.613
0.182
-0.368
0.008
2.825
35.197
A
A
1
2
15.245
B
B
21
20
3.218
9.119
0.364
-1.121
AA_G1A2:U20C21_BB
1
-0.745
1.245
34.023
-3.130
-0.706
2.891
27.681
A
A
2
3
4.337
B
B
20
19
2.992
2.073
0.413
-1.421
AA_A2G3:C19U20_BB
2
0.890
-1.862
27.591
-3.423
-0.669
1.699
25.291
A
A
3
4
22.197
B
B
19
18
2.949
9.438
0.422
-2.507
AA_G3G4:U18C19_BB
3
-4.405
10.360
23.078
-7.767
-1.917
3.565
70.036
A
A
4
5
-2.184
B
B
18
17
3.527
-2.506
-2.085
-0.865
AA_G4A5:A17U18_BB
4
-0.514
0.448
69.995
-0.658
1.797
3.651
-16.983
A
A
5
6
-4.749
B
B
17
16
3.581
1.398
0.203
-1.455
AA_A5A6:A16A17_BB
5
1.697
5.763
-16.841
3.923
1.906
2.950
43.759
A
A
6
7
8.064
B
B
16
15
3.157
5.993
2.311
-1.447
AA_A6G7:U15A16_BB
6
0.190
-0.255
43.366
-2.478
-3.083
3.275
30.637
A
A
7
8
-2.039
B
B
15
14
3.244
-1.070
-0.152
-1.846
AA_G7G8:U14U15_BB
7
-5.935
11.302
30.052
-3.281
-0.890
3.247
41.811
A
A
8
9
-0.162
B
B
14
13
3.244
-0.115
-0.374
-1.503
AA_G8C9:G13U14_BB
8
0.069
-0.097
41.810
-2.093
0.531
2.356
35.250
A
A
9
10
27.270
B
B
13
12
3.329
15.939
-0.571
-1.497
AA_C9G10:C12G13_BB
9
-2.150
3.679
31.471
-4.655
0.648
3.091
37.360
A
A
10
11
13.450
B
B
B
12
11
3.338
8.542
-0.411
-0.654
AA_G10A11:U11BC12_BB
10
1.549
-2.439
36.372
-2.144
0.845
repository
Initial release
Version format compliance
Version format compliance
1
0
2004-12-28
1
1
2008-04-30
1
2
2011-07-13
RCSB
Y
RCSB
2004-06-25
REL
REL
closest to average
50
1
2D NOESY
2D NOESY
80 mM NaCl, 3 mM cobalt hexamine
6.1
ambient
298
K
80 mM NaCl, 3 mM cobalt hexamine
6.1
ambient
298
K
The structures are based on a total of 217 NMR-derived interproton distance restraints (108 intranucleotide and 109 internucleotide). Hydrogn bond restraints were used for the six WC pairs and for the G8-U14 wobble pair. On the basis of NMR data that is consistent with the formation of tandem sheared AA pairs, two artificial hydrogen bonding restraints were used between each sheared AA pair.
molecular dynamics
1
closest to the average
~~2 mM RNA, 80 mM NaCl, 3 mM KH2PO4, 7 mM K2HPO4, 0.5 mM Na2EDTA, 3 mM cobalt hexamine, pH=6.1, 90% H2O, 10% D2O
90% H2O/10% D2O
~~2 mM RNA, 80 mM NaCl, 3 mM KH2PO4, 7 mM K2HPO4, 0.5 mM Na2EDTA, 3 mM cobalt hexamine, pH=6.1, 100% D2O
100% D2O
Varian
collection
VNMR
5.2
Felix
data analysis
FELIX
2000
Insight
structure solution
DISCOVER
95.0
Insight
refinement
DISCOVER
95.0
500
Varian
INOVA
G
1
n
1
G
1
A
A
2
n
2
A
2
A
G
3
n
3
G
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
G
8
n
8
G
8
A
C
9
n
9
C
9
A
G
10
n
10
G
10
A
A
11
n
11
A
11
A
U
11
n
1
B
U
11
B
C
12
n
2
C
12
B
G
13
n
3
G
13
B
U
14
n
4
U
14
B
U
15
n
5
U
15
B
A
16
n
6
A
16
B
A
17
n
7
A
17
B
U
18
n
8
U
18
B
C
19
n
9
C
19
B
U
20
n
10
U
20
B
C
21
n
11
C
21
B
1
A
A
6
0.073
SIDE CHAIN
1
A
G
10
0.082
SIDE CHAIN
B
1
B
U
11
0.087
SIDE CHAIN
1
B
A
16
0.065
SIDE CHAIN
1
B
A
17
0.060
SIDE CHAIN
1
B
U
18
0.080
SIDE CHAIN
1
B
C
19
0.075
SIDE CHAIN
1
B
U
20
0.074
SIDE CHAIN
1
4.56
0.70
108.50
113.06
A
A
A
O4'
C1'
N1
C
C
C
9
9
9
N
1
4.46
0.70
108.50
112.96
B
B
B
O4'
C1'
N1
C
C
C
12
12
12
N
1
4.24
0.70
108.50
112.74
B
B
B
O4'
C1'
N9
G
G
G
13
13
13
N
1
5.30
0.70
108.50
113.80
B
B
B
O4'
C1'
N1
U
U
U
14
14
14
N
1
5.56
0.70
108.50
114.06
B
B
B
O4'
C1'
N1
U
U
U
15
15
15
N
1
4.51
0.70
108.50
113.01
B
B
B
O4'
C1'
N1
C
C
C
19
19
19
N
1
4.31
0.70
108.50
112.81
B
B
B
O4'
C1'
N1
U
U
U
20
20
20
N
5'-R(*GP*AP*GP*GP*AP*AP*GP*GP*CP*GP*A)-3'
J4/5 Loop from the Candida albicans and Candida dubliniensis Group I Introns
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
21
B
N3
C
11
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
21
B
O2
C
11
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
21
B
N4
C
11
1_555
hydrog
WATSON-CRICK
A
A
2
A
N1
A
2
1_555
B
U
20
B
N3
U
10
1_555
hydrog
WATSON-CRICK
A
A
2
A
N6
A
2
1_555
B
U
20
B
O4
U
10
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
3
1_555
B
C
19
B
N3
C
9
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
3
1_555
B
C
19
B
O2
C
9
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
3
1_555
B
C
19
B
N4
C
9
1_555
hydrog
TYPE_28_PAIR
A
G
4
A
N1
G
4
1_555
B
U
18
B
O2
U
8
1_555
hydrog
TYPE_28_PAIR
A
G
4
A
O6
G
4
1_555
B
U
18
B
N3
U
8
1_555
hydrog
A-A MISPAIR
A
A
5
A
N3
A
5
1_555
B
A
17
B
N6
A
7
1_555
hydrog
A-A MISPAIR
A
A
6
A
N6
A
6
1_555
B
A
16
B
N3
A
6
1_555
hydrog
TYPE_28_PAIR
A
G
7
A
N1
G
7
1_555
B
U
15
B
O2
U
5
1_555
hydrog
TYPE_28_PAIR
A
G
7
A
O6
G
7
1_555
B
U
15
B
N3
U
5
1_555
hydrog
TYPE_28_PAIR
A
G
8
A
N1
G
8
1_555
B
U
14
B
O2
U
4
1_555
hydrog
TYPE_28_PAIR
A
G
8
A
O6
G
8
1_555
B
U
14
B
N3
U
4
1_555
hydrog
WATSON-CRICK
A
C
9
A
N3
C
9
1_555
B
G
13
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
C
9
A
N4
C
9
1_555
B
G
13
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
C
9
A
O2
C
9
1_555
B
G
13
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
G
10
A
N1
G
10
1_555
B
C
12
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
G
10
A
N2
G
10
1_555
B
C
12
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
G
10
A
O6
G
10
1_555
B
C
12
B
N4
C
2
1_555
hydrog
WATSON-CRICK
B
A
A
11
A
N1
A
11
1_555
B
U
11
B
N3
U
1
1_555
hydrog
WATSON-CRICK
B
A
A
11
A
N6
A
11
1_555
B
U
11
B
O4
U
1
1_555
RNA
RNA, internal loop, tandem mismatch, GU pairs, AA pairs
1TUT
PDB
1
1TUT
1TUT
PDB
2
1TUT
1
11
1TUT
1
11
1TUT
A
1
1
11
11
21
1TUT
11
21
1TUT
B
B
2
1
11
1
P 1