1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Fedoroff, O.Y.
Ge, Y.
Reid, B.R.
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 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA 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
269
225
239
10.1006/jmbi.1997.1024
9191067
Solution structure of r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1 (+)-strand synthesis.
1997
10.2210/pdb1nxr/pdb
pdb_00001nxr
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
2362.568
DNA (5'-D(*CP*AP*GP*TP*CP*CP*TP*C)-3')
1
syn
polymer
2605.625
RNA (5'-R(*GP*AP*GP*GP*AP*CP*UP*G)-3')
1
syn
polymer
RNA/DNA HYBRID
RNA/DNA HYBRID
no
no
(DC)(DA)(DG)(DT)(DC)(DC)(DT)(DC)
CAGTCCTC
A
polydeoxyribonucleotide
no
no
GAGGACUG
GAGGACUG
B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1.412
1
19
A
1
B
8
1.763
A_DC1:G8_B
1
-19.267
0.708
-0.293
-0.234
-2.791
1
20
A
2
B
7
4.568
A_DA2:U7_B
2
-11.516
0.127
0.100
0.018
1.733
1
19
A
3
B
6
-1.847
A_DG3:C6_B
3
-20.679
0.292
0.041
-0.060
9.764
1
20
A
4
B
5
2.588
A_DT4:A5_B
4
-16.186
0.442
-0.064
0.012
3.525
1
19
A
5
B
4
-2.180
A_DC5:G4_B
5
-15.350
-0.375
0.126
-0.033
8.707
1
19
A
6
B
3
-0.682
A_DC6:G3_B
6
-4.878
0.786
-0.142
-0.199
13.482
1
20
A
7
B
2
1.099
A_DT7:A2_B
7
-8.307
0.582
-0.416
-0.117
-4.400
1
19
A
8
B
1
3.844
A_DC8:G1_B
8
-21.630
-0.274
-0.327
-0.036
2.389
35.256
A
A
1
2
23.705
B
B
8
7
3.228
13.970
0.007
-1.499
AA_DC1DA2:U7G8_BB
1
2.918
-4.951
32.323
-4.339
0.378
3.085
30.982
A
A
2
3
6.119
B
B
7
6
3.188
3.255
-0.555
-1.264
AA_DA2DG3:C6U7_BB
2
-3.733
7.017
30.593
-2.971
0.344
2.920
32.346
A
A
3
4
1.819
B
B
6
5
2.987
1.013
0.300
-1.762
AA_DG3DT4:A5C6_BB
3
-1.138
2.044
32.311
-3.324
-0.720
2.625
27.626
A
A
4
5
13.582
B
B
5
4
3.153
6.378
-0.534
-2.139
AA_DT4DC5:G4A5_BB
4
-6.018
12.816
26.223
-5.886
-0.209
2.762
33.448
A
A
5
6
11.256
B
B
4
3
3.191
6.440
0.062
-1.992
AA_DC5DC6:G3G4_BB
5
0.145
-0.254
32.839
-4.438
-0.086
2.768
26.692
A
A
6
7
7.853
B
B
3
2
3.025
3.614
0.108
-1.747
AA_DC6DT7:A2G3_BB
6
1.066
-2.316
26.429
-4.622
0.014
1.865
38.671
A
A
7
8
31.159
B
B
2
1
3.322
19.699
0.312
-2.090
AA_DT7DC8:G1A2_BB
7
3.554
-5.621
33.258
-5.235
-0.096
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1997-07-07
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
Y
BNL
1997-02-21
REL
REL
RMSD
20
18
NOESY 120
180
240
300 MS : DQF-COSY
E.COSY
7.0
298
K
DISTANCE GEOMETRY, : RESTRAINED MOLECULAR : DYNAMICS
BIOSYM TECHNOLOGIES
refinement
DISCOVER, WITH AMBER FORCE FIELD
FIELD
structure solution
BIOSYM
750
Bruker
DMX-750
C
1
n
1
DC
1
A
A
2
n
2
DA
2
A
G
3
n
3
DG
3
A
T
4
n
4
DT
4
A
C
5
n
5
DC
5
A
C
6
n
6
DC
6
A
T
7
n
7
DT
7
A
C
8
n
8
DC
8
A
G
1
n
1
G
1
B
A
2
n
2
A
2
B
G
3
n
3
G
3
B
G
4
n
4
G
4
B
A
5
n
5
A
5
B
C
6
n
6
C
6
B
U
7
n
7
U
7
B
G
8
n
8
G
8
B
author_defined_assembly
2
dimeric
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
DC
6
0.062
SIDE CHAIN
1
B
G
1
0.066
SIDE CHAIN
1
B
U
7
0.093
SIDE CHAIN
2
A
DC
6
0.060
SIDE CHAIN
2
B
U
7
0.095
SIDE CHAIN
3
A
DC
6
0.061
SIDE CHAIN
3
B
G
1
0.069
SIDE CHAIN
3
B
U
7
0.097
SIDE CHAIN
4
A
DC
6
0.072
SIDE CHAIN
4
B
U
7
0.100
SIDE CHAIN
5
A
DC
6
0.060
SIDE CHAIN
5
B
U
7
0.111
SIDE CHAIN
6
A
DC
6
0.056
SIDE CHAIN
6
B
G
1
0.064
SIDE CHAIN
6
B
U
7
0.098
SIDE CHAIN
7
A
DC
6
0.065
SIDE CHAIN
7
A
DT
7
0.065
SIDE CHAIN
7
B
G
1
0.065
SIDE CHAIN
7
B
U
7
0.095
SIDE CHAIN
8
B
U
7
0.094
SIDE CHAIN
9
A
DC
6
0.057
SIDE CHAIN
9
B
G
1
0.069
SIDE CHAIN
9
B
U
7
0.099
SIDE CHAIN
10
A
DG
3
0.064
SIDE CHAIN
10
B
U
7
0.105
SIDE CHAIN
11
A
DC
6
0.067
SIDE CHAIN
11
B
G
1
0.074
SIDE CHAIN
11
B
U
7
0.094
SIDE CHAIN
12
A
DC
6
0.064
SIDE CHAIN
12
B
U
7
0.093
SIDE CHAIN
13
A
DC
6
0.065
SIDE CHAIN
13
B
U
7
0.089
SIDE CHAIN
14
A
DC
6
0.066
SIDE CHAIN
14
B
U
7
0.094
SIDE CHAIN
15
A
DC
6
0.064
SIDE CHAIN
15
B
U
7
0.089
SIDE CHAIN
16
A
DC
6
0.071
SIDE CHAIN
16
B
U
7
0.090
SIDE CHAIN
17
B
U
7
0.088
SIDE CHAIN
18
A
DC
6
0.064
SIDE CHAIN
18
B
U
7
0.088
SIDE CHAIN
1
3.88
0.30
108.30
112.18
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
4.96
0.30
108.30
113.26
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
3.97
0.30
108.30
112.27
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
5.62
0.30
108.30
113.92
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
4.04
0.30
108.30
112.34
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
1
3.57
0.30
108.30
111.87
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
3.59
0.30
108.30
111.89
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
5.97
0.70
108.50
114.47
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
1
5.93
0.70
108.50
114.43
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
1
6.38
0.70
108.50
114.88
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
1
6.14
0.70
108.50
114.64
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
1
6.72
0.70
108.50
115.22
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
2
6.14
0.30
108.30
114.44
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
2
1.94
0.30
108.30
110.24
A
A
A
O4'
C1'
N9
DA
DA
DA
2
2
2
N
2
5.04
0.30
108.30
113.34
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
2
4.08
0.30
108.30
112.38
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
2
5.77
0.30
108.30
114.07
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
2
4.09
0.30
108.30
112.39
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
2
3.51
0.30
108.30
111.81
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
2
3.51
0.30
108.30
111.81
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
2
6.31
0.70
108.50
114.81
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
2
5.76
0.70
108.50
114.26
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
2
6.18
0.70
108.50
114.68
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
2
6.39
0.70
108.50
114.89
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
2
6.92
0.70
108.50
115.42
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
3
4.94
0.30
108.30
113.24
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
3
5.13
0.30
108.30
113.43
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
3
4.06
0.30
108.30
112.36
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
3
5.72
0.30
108.30
114.02
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
3
4.05
0.30
108.30
112.35
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
3
3.54
0.30
108.30
111.84
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
3
3.58
0.30
108.30
111.88
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
3
6.13
0.70
108.50
114.63
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
3
5.80
0.70
108.50
114.30
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
3
6.01
0.70
108.50
114.51
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
3
6.19
0.70
108.50
114.69
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
3
6.85
0.70
108.50
115.35
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
4
5.73
0.30
108.30
114.03
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
4
5.03
0.30
108.30
113.33
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
4
4.06
0.30
108.30
112.36
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
4
5.71
0.30
108.30
114.01
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
4
4.07
0.30
108.30
112.37
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
4
2.93
0.30
108.30
111.23
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
4
3.43
0.30
108.30
111.73
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
4
6.90
0.70
108.50
115.40
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
4
5.78
0.70
108.50
114.28
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
4
6.29
0.70
108.50
114.79
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
4
6.35
0.70
108.50
114.85
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
4
6.69
0.70
108.50
115.19
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
5
6.02
0.30
108.30
114.32
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
5
1.96
0.30
108.30
110.26
A
A
A
O4'
C1'
N9
DA
DA
DA
2
2
2
N
5
5.17
0.30
108.30
113.47
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
5
4.27
0.30
108.30
112.57
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
5
5.82
0.30
108.30
114.12
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
5
4.21
0.30
108.30
112.51
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
5
3.42
0.30
108.30
111.72
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
5
3.60
0.30
108.30
111.90
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
5
6.55
0.70
108.50
115.05
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
5
5.85
0.70
108.50
114.35
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
5
6.07
0.70
108.50
114.57
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
5
6.20
0.70
108.50
114.70
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
5
6.64
0.70
108.50
115.14
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
6
5.96
0.30
108.30
114.26
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
6
1.85
0.30
108.30
110.15
A
A
A
O4'
C1'
N9
DA
DA
DA
2
2
2
N
6
5.09
0.30
108.30
113.39
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
6
4.08
0.30
108.30
112.38
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
6
5.78
0.30
108.30
114.08
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
6
4.16
0.30
108.30
112.46
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
6
3.17
0.30
108.30
111.47
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
6
3.57
0.30
108.30
111.87
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
6
6.13
0.70
108.50
114.63
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
6
5.75
0.70
108.50
114.25
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
6
6.02
0.70
108.50
114.52
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
6
6.21
0.70
108.50
114.71
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
6
6.67
0.70
108.50
115.17
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
7
4.86
0.30
108.30
113.16
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
7
5.06
0.30
108.30
113.36
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
7
3.97
0.30
108.30
112.27
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
7
6.08
0.30
108.30
114.38
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
7
3.65
0.30
108.30
111.95
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
7
3.49
0.30
108.30
111.79
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
7
3.45
0.30
108.30
111.75
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
7
6.18
0.70
108.50
114.68
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
7
6.24
0.70
108.50
114.74
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
7
6.02
0.70
108.50
114.52
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
7
6.40
0.70
108.50
114.90
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
7
6.93
0.70
108.50
115.43
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
8
3.48
0.30
108.30
111.78
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
8
4.89
0.30
108.30
113.19
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
8
4.18
0.30
108.30
112.48
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
8
6.07
0.30
108.30
114.37
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
8
3.64
0.30
108.30
111.94
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
8
3.06
0.30
108.30
111.36
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
8
3.10
0.30
108.30
111.40
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
8
5.94
0.70
108.50
114.44
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
8
5.97
0.70
108.50
114.47
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
8
5.93
0.70
108.50
114.43
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
8
6.36
0.70
108.50
114.86
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
8
6.96
0.70
108.50
115.46
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
9
3.48
0.30
108.30
111.78
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
9
4.81
0.30
108.30
113.11
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
9
3.81
0.30
108.30
112.11
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
9
6.12
0.30
108.30
114.42
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
9
3.62
0.30
108.30
111.92
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
9
3.43
0.30
108.30
111.73
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
9
3.31
0.30
108.30
111.61
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
9
6.13
0.70
108.50
114.63
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
9
5.78
0.70
108.50
114.28
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
9
6.28
0.70
108.50
114.78
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
9
6.17
0.70
108.50
114.67
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
9
6.70
0.70
108.50
115.20
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
10
4.76
0.30
108.30
113.06
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
10
5.17
0.30
108.30
113.47
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
10
4.04
0.30
108.30
112.34
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
10
6.00
0.30
108.30
114.30
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
10
3.46
0.30
108.30
111.76
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
10
2.91
0.30
108.30
111.21
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
10
2.89
0.30
108.30
111.19
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
10
6.40
0.70
108.50
114.90
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
10
5.55
0.70
108.50
114.05
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
10
6.07
0.70
108.50
114.57
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
10
6.28
0.70
108.50
114.78
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
10
6.94
0.70
108.50
115.44
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
11
6.01
0.30
108.30
114.31
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
11
2.09
0.30
108.30
110.39
A
A
A
O4'
C1'
N9
DA
DA
DA
2
2
2
N
11
5.12
0.30
108.30
113.42
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
11
3.91
0.30
108.30
112.21
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
11
5.91
0.30
108.30
114.21
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
11
3.51
0.30
108.30
111.81
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
11
3.12
0.30
108.30
111.42
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
11
3.19
0.30
108.30
111.49
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
11
6.27
0.70
108.50
114.77
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
11
5.65
0.70
108.50
114.15
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
11
5.78
0.70
108.50
114.28
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
11
6.19
0.70
108.50
114.69
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
11
6.89
0.70
108.50
115.39
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
12
3.64
0.30
108.30
111.94
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
12
4.89
0.30
108.30
113.19
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
12
3.62
0.30
108.30
111.92
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
12
5.65
0.30
108.30
113.95
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
12
3.43
0.30
108.30
111.73
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
12
2.65
0.30
108.30
110.95
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
12
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
12
6.62
0.70
108.50
115.12
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
12
5.25
0.70
108.50
113.75
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
12
6.06
0.70
108.50
114.56
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
12
6.36
0.70
108.50
114.86
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
12
7.07
0.70
108.50
115.57
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
13
6.01
0.30
108.30
114.31
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
13
4.98
0.30
108.30
113.28
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
13
3.65
0.30
108.30
111.95
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
13
5.72
0.30
108.30
114.02
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
13
3.43
0.30
108.30
111.73
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
13
2.64
0.30
108.30
110.94
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
13
2.68
0.30
108.30
110.98
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
13
6.59
0.70
108.50
115.09
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
13
5.07
0.70
108.50
113.57
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
13
6.02
0.70
108.50
114.52
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
13
6.36
0.70
108.50
114.86
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
13
6.85
0.70
108.50
115.35
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
14
6.03
0.30
108.30
114.33
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
14
4.94
0.30
108.30
113.24
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
14
3.57
0.30
108.30
111.87
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
14
5.62
0.30
108.30
113.92
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
14
3.37
0.30
108.30
111.67
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
14
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
14
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
14
6.81
0.70
108.50
115.31
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
14
5.11
0.70
108.50
113.61
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
14
6.29
0.70
108.50
114.79
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
14
6.31
0.70
108.50
114.81
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
14
6.99
0.70
108.50
115.49
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
15
5.96
0.30
108.30
114.26
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
15
4.95
0.30
108.30
113.25
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
15
3.61
0.30
108.30
111.91
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
15
5.67
0.30
108.30
113.97
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
15
3.34
0.30
108.30
111.64
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
15
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
15
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
15
-4.71
0.70
109.70
104.99
B
B
B
C1'
O4'
C4'
G
G
G
1
1
1
N
15
8.08
0.70
108.50
116.58
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
15
5.13
0.70
108.50
113.63
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
15
6.25
0.70
108.50
114.75
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
15
6.23
0.70
108.50
114.73
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
15
6.77
0.70
108.50
115.27
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
16
6.03
0.30
108.30
114.33
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
16
4.95
0.30
108.30
113.25
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
16
3.70
0.30
108.30
112.00
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
16
5.67
0.30
108.30
113.97
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
16
3.35
0.30
108.30
111.65
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
16
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
16
2.94
0.30
108.30
111.24
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
16
6.64
0.70
108.50
115.14
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
16
5.10
0.70
108.50
113.60
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
16
6.20
0.70
108.50
114.70
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
16
6.30
0.70
108.50
114.80
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
16
6.89
0.70
108.50
115.39
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
17
6.11
0.30
108.30
114.41
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
17
4.90
0.30
108.30
113.20
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
17
3.63
0.30
108.30
111.93
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
17
5.67
0.30
108.30
113.97
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
17
3.48
0.30
108.30
111.78
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
17
2.89
0.30
108.30
111.19
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
17
2.81
0.30
108.30
111.11
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
17
6.71
0.70
108.50
115.21
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
17
5.07
0.70
108.50
113.57
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
17
6.19
0.70
108.50
114.69
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
17
6.28
0.70
108.50
114.78
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
17
6.85
0.70
108.50
115.35
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
18
3.63
0.30
108.30
111.93
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
18
4.91
0.30
108.30
113.21
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
18
3.72
0.30
108.30
112.02
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
18
5.72
0.30
108.30
114.02
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
18
3.41
0.30
108.30
111.71
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
18
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
18
2.74
0.30
108.30
111.04
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
18
4.85
0.80
101.50
106.35
B
B
B
C3'
C2'
C1'
G
G
G
1
1
1
N
18
6.36
0.70
108.50
114.86
B
B
B
O4'
C1'
N9
G
G
G
1
1
1
N
18
5.08
0.70
108.50
113.58
B
B
B
O4'
C1'
N9
G
G
G
3
3
3
N
18
6.09
0.70
108.50
114.59
B
B
B
O4'
C1'
N9
G
G
G
4
4
4
N
18
6.24
0.70
108.50
114.74
B
B
B
O4'
C1'
N9
A
A
A
5
5
5
N
18
6.93
0.70
108.50
115.43
B
B
B
O4'
C1'
N1
C
C
C
6
6
6
N
refinement
AMBER
HIV-1 POLYPURINE HYBRID, R(GAGGACUG):D(CAGTCCTC), NMR, 18 STRUCTURES
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
G
8
B
N1
G
8
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
G
8
B
O6
G
8
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
G
8
B
N2
G
8
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N1
DA
2
1_555
B
U
7
B
N3
U
7
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N6
DA
2
1_555
B
U
7
B
O4
U
7
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
C
6
B
N3
C
6
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
C
6
B
O2
C
6
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
C
6
B
N4
C
6
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
A
5
B
N1
A
5
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
A
5
B
N6
A
5
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
G
4
B
N1
G
4
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
G
4
B
O6
G
4
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
G
4
B
N2
G
4
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
B
G
3
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
B
G
3
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
B
G
3
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
A
2
B
N1
A
2
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
A
2
B
N6
A
2
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
G
1
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
G
1
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
G
1
B
N2
G
1
1_555
DNA-RNA HYBRID
HIV-1 POLYPURINE HYBRID, RNA/DNA HYBRID, RNASE H, REVERSE TRANSCRIPTASE, DNA-RNA COMPLEX, DNA-RNA HYBRID
1NXR
PDB
1
1NXR
1NXR
PDB
2
1NXR
1
8
1NXR
1
8
1NXR
A
1
1
8
1
8
1NXR
1
8
1NXR
B
2
1
8
1
P 1