1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kennedy, S.D.
Turner, D.H.
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 H14 N3 O8 P
323.197
n
ISOCYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
n
ISOGUANOSINE-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
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
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
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
R
C
N
49
N
O
N
50
R
C
N
51
N
N
N
52
N
C
N
53
N
O
N
54
N
N
N
55
N
C
N
56
N
N
N
57
N
C
N
58
N
C
N
59
N
H
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
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
R
C
N
84
N
O
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
N
Y
96
N
C
N
97
N
H
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
111
N
P
N
112
N
O
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
O
N
117
R
C
N
118
R
C
N
119
S
C
N
120
R
C
N
121
N
C
N
122
N
O
N
123
N
O
N
124
N
N
N
125
N
C
N
126
N
N
N
127
N
C
N
128
N
O
N
129
N
N
N
130
N
C
N
131
N
C
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
P
N
147
N
O
N
148
N
O
N
149
N
O
N
150
N
O
N
151
N
O
N
152
R
C
N
153
R
C
N
154
S
C
N
155
R
C
N
156
N
C
N
157
N
O
N
158
N
O
N
159
N
N
N
160
N
O
N
161
N
C
N
162
N
C
N
163
N
N
N
164
N
C
N
165
N
N
N
166
N
C
N
167
N
N
N
168
N
C
N
169
N
N
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
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
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
doub
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
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
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
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
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
Y
100
N
sing
Y
101
N
sing
Y
102
N
doub
N
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
146
N
doub
N
147
N
sing
N
148
N
sing
N
149
N
doub
N
150
N
sing
N
151
N
sing
N
152
N
doub
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
doub
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
doub
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
doub
N
189
N
sing
N
190
N
sing
N
191
N
sing
US
J.Phys.Chem.B
JPCBFK
1278
1089-5647
111
6718
6727
10.1021/jp068732m
17411085
Stacking Effects on Local Structure in RNA: Changes in the Structure of Tandem GA Pairs when Flanking GC Pairs are Replaced by isoG-isoC Pairs
2007
10.2210/pdb2o83/pdb
pdb_00002o83
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
2909.823
5'-R(*GP*GP*(IC)P*GP*AP*(IG)P*CP*CP*A)-3'
2
syn
polymer
no
yes
GG(IC)GA(IG)CCA
GGCGAGCCA
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
n
-9.306
1
19
A
1
B
8
-1.883
A_G1:C8_B
1
-19.706
-0.562
0.032
-0.201
-14.242
1
19
A
2
B
7
-1.683
A_G2:C7_B
2
-18.965
-0.190
0.060
-0.092
-9.534
A
3
B
6
-4.400
A_IC3:IG6_B
3
-9.752
-0.292
0.430
0.018
-0.818
8
A
4
B
5
-17.408
A_G4:A5_B
4
-9.988
-0.088
-0.090
1.619
2.564
8
A
5
B
4
-17.385
A_A5:G4_B
5
-10.317
0.090
-0.091
1.620
10.280
A
6
B
3
-4.509
A_IG6:IC3_B
6
-10.932
0.315
0.479
0.011
15.130
1
19
A
7
B
2
-1.806
A_C7:G2_B
7
-20.980
0.203
0.069
-0.101
10.568
1
19
A
8
B
1
-1.901
A_C8:G1_B
8
-21.283
0.548
0.042
-0.195
3.085
36.933
A
A
1
2
9.548
B
B
8
7
3.341
6.023
0.102
-1.365
AA_G1G2:C7C8_BB
1
0.863
-1.368
36.446
-2.959
-0.046
3.180
33.130
A
A
2
3
-0.879
B
B
7
6
3.152
-0.501
0.096
-1.834
AA_G2IC3:IG6C7_BB
2
0.489
-0.858
33.123
-3.135
-0.088
2.839
32.024
A
A
3
4
1.692
B
B
6
5
3.066
0.929
-0.869
-1.534
AA_IC3G4:A5IG6_BB
3
5.350
-9.743
31.572
-2.933
2.452
3.075
26.049
A
A
4
5
4.715
B
B
5
4
3.215
2.123
0.037
-1.622
AA_G4A5:G4A5_BB
4
0.099
-0.221
25.964
-4.159
-0.056
2.787
31.978
A
A
5
6
3.100
B
B
4
3
3.056
1.699
0.815
-1.618
AA_A5IG6:IC3G4_BB
5
-5.530
10.091
31.464
-3.213
-2.380
3.185
33.343
A
A
6
7
-1.489
B
B
3
2
3.138
-0.854
-0.217
-1.817
AA_IG6C7:G2IC3_BB
6
-0.464
0.808
33.329
-3.030
0.303
3.093
37.532
A
A
7
8
10.099
B
B
2
1
3.339
6.467
-0.151
-1.211
AA_C7C8:G1G2_BB
7
-0.544
0.850
36.987
-2.719
0.164
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Data collection
1
0
2007-07-10
1
1
2008-05-01
1
2
2011-07-13
1
3
2022-03-16
1
4
2023-12-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
GC(IG)GA(IC)GCA
RCSB
Y
RCSB
2006-12-11
REL
REL
structures with the least restraint violations,structures with the lowest energy
20
18
2D NOESY
2D TOCSY
DQF-COSY
7.1
278
K
simulated annealing, molecular dynamics
1
lowest energy
80 mM NaCl, 10 mM sodium phosphate, 0.5 mM Na2EDTA, pH 7.1, 0.7mM RNA duplex concentration, 90% H2O, 10% D2O
90% H2O/10% D2O
Varian
collection
VNMR
6.1C
Delagio, F.
processing
NMRPipe
2.3
Goddard, T.D.; Kneller, D.G.
data analysis
Sparky
3.11
Molecular Simulations, Inc.
structure solution
Discover
I2000
Molecular Simulations, Inc.
refinement
Discover
I2000
600
Varian
INOVA
500
Varian
INOVA
G
1
n
1
G
1
A
G
2
n
2
G
2
A
IC
3
n
3
IC
3
A
G
4
n
4
G
4
A
A
5
n
5
A
5
A
IG
6
n
6
IG
6
A
C
7
n
7
C
7
A
C
8
n
8
C
8
A
A
9
n
9
A
9
A
G
1
n
1
G
1
B
G
2
n
2
G
2
B
IC
3
n
3
IC
3
B
G
4
n
4
G
4
B
A
5
n
5
A
5
B
IG
6
n
6
IG
6
B
C
7
n
7
C
7
B
C
8
n
8
C
8
B
A
9
n
9
A
9
B
author_defined_assembly
2
dimeric
A
IC
3
ISOCYTIDINE-5'-MONOPHOSPHATE
A
IC
3
C
A
IG
6
ISOGUANOSINE-5'-MONOPHOSPHATE
A
IG
6
G
B
IC
3
ISOCYTIDINE-5'-MONOPHOSPHATE
B
IC
3
C
B
IG
6
ISOGUANOSINE-5'-MONOPHOSPHATE
B
IG
6
G
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
C
7
0.067
SIDE CHAIN
1
B
C
7
0.065
SIDE CHAIN
3
A
C
7
0.067
SIDE CHAIN
3
B
C
7
0.065
SIDE CHAIN
5
A
C
7
0.066
SIDE CHAIN
6
B
C
7
0.062
SIDE CHAIN
7
B
C
7
0.059
SIDE CHAIN
8
B
C
7
0.066
SIDE CHAIN
9
A
C
7
0.064
SIDE CHAIN
9
B
C
7
0.062
SIDE CHAIN
10
A
C
7
0.067
SIDE CHAIN
10
B
C
7
0.065
SIDE CHAIN
11
A
C
7
0.068
SIDE CHAIN
11
B
C
7
0.063
SIDE CHAIN
12
A
C
7
0.065
SIDE CHAIN
12
B
C
7
0.062
SIDE CHAIN
13
A
C
7
0.068
SIDE CHAIN
14
A
C
7
0.065
SIDE CHAIN
14
B
C
7
0.066
SIDE CHAIN
15
A
C
7
0.066
SIDE CHAIN
17
B
C
7
0.064
SIDE CHAIN
1
4.22
0.70
108.50
112.72
A
A
A
O4'
C1'
N9
A
A
A
5
5
5
N
1
4.20
0.70
108.50
112.70
A
A
A
O4'
C1'
N1
C
C
C
7
7
7
N
2
4.25
0.70
108.50
112.75
A
A
A
O4'
C1'
N1
C
C
C
7
7
7
N
2
4.85
0.70
108.50
113.35
A
A
A
O4'
C1'
N1
C
C
C
8
8
8
N
2
4.37
0.70
108.50
112.87
B
B
B
O4'
C1'
N9
G
G
G
2
2
2
N
3
4.28
0.70
108.50
112.78
A
A
A
O4'
C1'
N9
A
A
A
5
5
5
N
4
4.93
0.70
108.50
113.43
A
A
A
O4'
C1'
N1
C
C
C
8
8
8
N
4
4.31
0.70
108.50
112.81
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
5
4.25
0.70
108.50
112.75
A
A
A
O4'
C1'
N9
A
A
A
5
5
5
N
5
4.47
0.70
108.50
112.97
B
B
B
O4'
C1'
N1
C
C
C
8
8
8
N
6
4.23
0.70
108.50
112.73
A
A
A
O4'
C1'
N9
A
A
A
5
5
5
N
6
4.21
0.70
108.50
112.71
A
A
A
O4'
C1'
N1
C
C
C
7
7
7
N
6
4.85
0.70
108.50
113.35
A
A
A
O4'
C1'
N1
C
C
C
8
8
8
N
7
4.97
0.70
108.50
113.47
A
A
A
O4'
C1'
N1
C
C
C
8
8
8
N
8
4.22
0.70
108.50
112.72
A
A
A
O4'
C1'
N9
A
A
A
5
5
5
N
8
4.20
0.70
108.50
112.70
A
A
A
O4'
C1'
N1
C
C
C
7
7
7
N
8
4.48
0.70
108.50
112.98
A
A
A
O4'
C1'
N1
C
C
C
8
8
8
N
9
4.24
0.70
108.50
112.74
A
A
A
O4'
C1'
N9
A
A
A
5
5
5
N
10
4.21
0.70
108.50
112.71
A
A
A
O4'
C1'
N1
C
C
C
7
7
7
N
10
4.36
0.70
108.50
112.86
B
B
B
O4'
C1'
N1
C
C
C
8
8
8
N
11
4.30
0.70
108.50
112.80
A
A
A
O4'
C1'
N9
A
A
A
5
5
5
N
13
4.24
0.70
108.50
112.74
A
A
A
O4'
C1'
N9
A
A
A
5
5
5
N
13
4.56
0.70
108.50
113.06
B
B
B
O4'
C1'
N1
C
C
C
8
8
8
N
14
4.30
0.70
108.50
112.80
A
A
A
O4'
C1'
N9
A
A
A
5
5
5
N
15
4.33
0.70
108.50
112.83
A
A
A
O4'
C1'
N9
A
A
A
5
5
5
N
15
4.57
0.70
108.50
113.07
B
B
B
O4'
C1'
N1
C
C
C
8
8
8
N
16
4.21
0.70
108.50
112.71
A
A
A
O4'
C1'
N9
A
A
A
5
5
5
N
16
5.00
0.70
108.50
113.50
A
A
A
O4'
C1'
N1
C
C
C
8
8
8
N
16
4.69
0.70
108.50
113.19
B
B
B
O4'
C1'
N1
C
C
C
8
8
8
N
17
4.23
0.70
108.50
112.73
A
A
A
O4'
C1'
N9
A
A
A
5
5
5
N
17
4.24
0.70
108.50
112.74
A
A
A
O4'
C1'
N1
C
C
C
7
7
7
N
17
4.49
0.70
108.50
112.99
A
A
A
O4'
C1'
N1
C
C
C
8
8
8
N
18
4.92
0.70
108.50
113.42
A
A
A
O4'
C1'
N1
C
C
C
8
8
8
N
18
4.63
0.70
108.50
113.13
B
B
B
O4'
C1'
N1
C
C
C
8
8
8
N
The Structure of Tandem GA RNA Pairs When Flanking Pairs are isoG-isoC Pairs
1
N
N
1
N
N
covale
1.615
both
A
G
2
A
O3'
G
2
1_555
A
IC
3
A
P
IC
3
1_555
covale
1.613
both
A
IC
3
A
O3'
IC
3
1_555
A
G
4
A
P
G
4
1_555
covale
1.617
both
A
A
5
A
O3'
A
5
1_555
A
IG
6
A
P
IG
6
1_555
covale
1.612
both
A
IG
6
A
O3'
IG
6
1_555
A
C
7
A
P
C
7
1_555
covale
1.615
both
B
G
2
B
O3'
G
2
1_555
B
IC
3
B
P
IC
3
1_555
covale
1.613
both
B
IC
3
B
O3'
IC
3
1_555
B
G
4
B
P
G
4
1_555
covale
1.618
both
B
A
5
B
O3'
A
5
1_555
B
IG
6
B
P
IG
6
1_555
covale
1.614
both
B
IG
6
B
O3'
IG
6
1_555
B
C
7
B
P
C
7
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
8
B
N3
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
8
B
O2
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
8
B
N4
C
8
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
B
C
7
B
N3
C
7
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
B
C
7
B
O2
C
7
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
B
C
7
B
N4
C
7
1_555
hydrog
IC-IG PAIR
A
IC
3
A
N3
IC
3
1_555
B
IG
6
B
N1
IG
6
1_555
hydrog
TYPE_8_PAIR
A
G
4
A
N1
G
4
1_555
B
A
5
B
N1
A
5
1_555
hydrog
TYPE_8_PAIR
A
G
4
A
O6
G
4
1_555
B
A
5
B
N6
A
5
1_555
hydrog
TYPE_8_PAIR
A
A
5
A
N1
A
5
1_555
B
G
4
B
N1
G
4
1_555
hydrog
TYPE_8_PAIR
A
A
5
A
N6
A
5
1_555
B
G
4
B
O6
G
4
1_555
hydrog
IG-IC PAIR
A
IG
6
A
N1
IG
6
1_555
B
IC
3
B
N3
IC
3
1_555
hydrog
WATSON-CRICK
A
C
7
A
N3
C
7
1_555
B
G
2
B
N1
G
2
1_555
hydrog
WATSON-CRICK
A
C
7
A
N4
C
7
1_555
B
G
2
B
O6
G
2
1_555
hydrog
WATSON-CRICK
A
C
7
A
O2
C
7
1_555
B
G
2
B
N2
G
2
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
B
G
1
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
B
G
1
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
B
G
1
B
N2
G
1
1_555
RNA
RNA, Thermodynamics, secondary structure prediction, imino GA pair, isoguanosine, isocytidine
2O83
PDB
1
2O83
1
9
2O83
1
9
2O83
A
1
1
9
1
9
2O83
1
9
2O83
B
1
1
9