0.036364
0.000000
0.000000
0.000000
0.022609
0.000000
0.000000
0.000000
0.022417
0.00000
0.00000
0.00000
Egli, M.
Usman, N.
Rich, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
27.500
44.230
44.610
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
H2 O
18.015
WATER
non-polymer
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
N
C
N
12
R
C
Y
13
N
N
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
N
18
N
N
Y
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
N
23
N
H
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
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
56
N
C
N
57
N
H
N
58
N
H
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
O
N
72
N
P
N
73
N
O
N
74
N
O
N
75
N
O
N
76
N
C
N
77
R
C
N
78
N
O
N
79
S
C
N
80
N
O
N
81
N
C
N
82
R
C
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
N
Y
93
N
C
N
94
N
H
N
95
N
H
N
96
N
H
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
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
N
C
N
119
R
C
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
C
N
129
N
H
N
130
N
H
N
131
N
H
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
O
N
145
N
P
N
146
N
O
N
147
N
O
N
148
N
O
N
149
N
C
N
150
R
C
N
151
N
O
N
152
S
C
N
153
N
O
N
154
R
C
N
155
N
O
N
156
R
C
Y
157
N
N
Y
158
N
C
Y
159
N
N
Y
160
N
C
N
161
N
C
N
162
N
O
N
163
N
N
N
164
N
C
N
165
N
N
N
166
N
N
Y
167
N
C
N
168
N
H
N
169
N
H
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
O
N
183
N
H
N
184
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
Y
24
N
sing
Y
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
sing
Y
30
N
doub
N
31
N
sing
Y
32
N
doub
N
33
N
sing
N
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
doub
N
42
N
sing
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
doub
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
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
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
N
116
N
sing
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
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
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
Y
174
N
sing
Y
175
N
sing
Y
176
N
doub
N
177
N
sing
Y
178
N
sing
N
179
N
sing
Y
180
N
doub
N
181
N
doub
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
doub
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
32
3221
3237
10.1021/bi00064a004
7681688
Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes.
1993
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
20
6695
6699
Large Scale Chemical Synthesis, Purification and Crystallization of RNA-DNA Chimeras
1992
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
89
534
538
Crystal Structure of an Okazaki Fragment at 2 Angstroms Resolution
1992
10.2210/pdb1d87/pdb
pdb_00001d87
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
273.00
1
DIFFRACTOMETER
RIGAKU AFC-5R
x-ray
1
1.0
ROTATING ANODE
3061.005
DNA/RNA (5'-R(*GP*)-D(*CP*GP*TP*AP*TP*AP*CP*GP*C)-3')
2
syn
polymer
18.015
water
110
nat
water
no
no
G(DC)(DG)(DT)(DA)(DT)(DA)(DC)(DG)(DC)
GCGTATACGC
A,B
polydeoxyribonucleotide/polyribonucleotide hybrid
n
n
n
n
n
n
n
n
n
n
2.22
44.49
VAPOR DIFFUSION, SITTING DROP
6.00
pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 291.00K
291.00
WATER
1
NA CACODYLATE
1
MGCL2
1
SPERMINE
1
WATER
2
MPD
2
-3.059
1
19
A
1
B
20
-2.373
A_G1:DC20_B
1
-19.256
0.517
-0.139
-0.253
0.437
1
19
A
2
B
19
2.997
A_DC2:DG19_B
2
-16.241
0.044
0.006
-0.043
-13.184
1
19
A
3
B
18
-3.372
A_DG3:DC18_B
3
-11.151
0.354
-0.448
-0.078
4.287
1
20
A
4
B
17
-1.750
A_DT4:DA17_B
4
-16.958
-1.095
-0.551
-0.219
4.207
1
20
A
5
B
16
-15.461
A_DA5:DT16_B
5
-10.276
1.331
0.683
0.076
9.419
1
20
A
6
B
15
-4.498
A_DT6:DA15_B
6
6.512
-1.205
0.014
-0.001
-9.066
1
20
A
7
B
14
-0.148
A_DA7:DT14_B
7
-27.165
0.693
-0.928
-0.123
8.246
1
19
A
8
B
13
-4.451
A_DC8:DG13_B
8
-10.975
1.386
-0.420
-0.815
-11.369
1
19
A
9
B
12
3.164
A_DG9:DC12_B
9
-17.203
-0.472
0.090
-0.030
-3.416
1
19
A
10
B
11
0.118
A_DC10:G11_B
10
17.271
0.137
0.548
-0.282
2.576
29.852
A
A
1
2
17.220
B
B
20
19
3.214
8.741
1.255
-1.488
AA_G1DC2:DG19DC20_BB
1
-1.720
3.389
28.521
-4.535
-2.761
4.141
29.196
A
A
2
3
-1.423
B
B
19
18
4.125
-0.717
-0.271
-1.195
AA_DC2DG3:DC18DG19_BB
2
1.053
-2.089
29.169
-2.173
0.826
2.037
36.071
A
A
3
4
13.861
B
B
18
17
2.644
8.499
-0.994
-2.006
AA_DG3DT4:DA17DC18_BB
3
2.711
-4.422
34.985
-4.115
1.885
2.652
38.033
A
A
4
5
24.197
B
B
17
16
3.663
15.287
0.544
-1.521
AA_DT4DA5:DT16DA17_BB
4
-5.948
9.414
34.433
-4.313
-1.604
2.251
23.653
A
A
5
6
19.859
B
B
16
15
3.307
7.895
0.344
-2.562
AA_DA5DT6:DA15DT16_BB
5
6.000
-15.091
21.501
-8.592
0.940
2.938
42.122
A
A
6
7
29.039
B
B
15
14
3.828
19.970
0.870
-1.203
AA_DT6DA7:DT14DA15_BB
6
7.887
-11.469
36.454
-3.978
-0.300
2.553
35.041
A
A
7
8
7.371
B
B
14
13
2.803
4.427
0.818
-1.933
AA_DA7DC8:DG13DT14_BB
7
0.373
-0.621
34.767
-3.757
-1.313
3.547
23.246
A
A
8
9
10.635
B
B
13
12
3.826
4.262
0.096
-1.201
AA_DC8DG9:DC12DG13_BB
8
0.163
-0.408
22.856
-4.649
-0.173
3.228
40.230
A
A
9
10
12.560
B
B
12
11
3.407
8.507
-0.900
-1.084
AA_DG9DC10:G11DC12_BB
9
-9.201
13.586
38.306
-2.580
0.222
chem_comp_atom
chem_comp_bond
database_2
struct_keywords
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Structure summary
1
0
1993-07-15
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_keywords.text
BNL
Y
NDB
1992-08-28
REL
HOH
water
HOH
21
2
HOH
HOH
21
A
HOH
22
2
HOH
HOH
22
A
HOH
23
2
HOH
HOH
23
A
HOH
24
2
HOH
HOH
24
A
HOH
25
2
HOH
HOH
25
A
HOH
26
2
HOH
HOH
26
A
HOH
29
2
HOH
HOH
29
A
HOH
30
2
HOH
HOH
30
A
HOH
31
2
HOH
HOH
31
A
HOH
34
2
HOH
HOH
34
A
HOH
35
2
HOH
HOH
35
A
HOH
36
2
HOH
HOH
36
A
HOH
38
2
HOH
HOH
38
A
HOH
39
2
HOH
HOH
39
A
HOH
40
2
HOH
HOH
40
A
HOH
44
2
HOH
HOH
44
A
HOH
46
2
HOH
HOH
46
A
HOH
47
2
HOH
HOH
47
A
HOH
48
2
HOH
HOH
48
A
HOH
49
2
HOH
HOH
49
A
HOH
51
2
HOH
HOH
51
A
HOH
60
2
HOH
HOH
60
A
HOH
62
2
HOH
HOH
62
A
HOH
63
2
HOH
HOH
63
A
HOH
66
2
HOH
HOH
66
A
HOH
69
2
HOH
HOH
69
A
HOH
71
2
HOH
HOH
71
A
HOH
73
2
HOH
HOH
73
A
HOH
74
2
HOH
HOH
74
A
HOH
75
2
HOH
HOH
75
A
HOH
76
2
HOH
HOH
76
A
HOH
77
2
HOH
HOH
77
A
HOH
78
2
HOH
HOH
78
A
HOH
79
2
HOH
HOH
79
A
HOH
80
2
HOH
HOH
80
A
HOH
81
2
HOH
HOH
81
A
HOH
82
2
HOH
HOH
82
A
HOH
83
2
HOH
HOH
83
A
HOH
84
2
HOH
HOH
84
A
HOH
88
2
HOH
HOH
88
A
HOH
93
2
HOH
HOH
93
A
HOH
95
2
HOH
HOH
95
A
HOH
96
2
HOH
HOH
96
A
HOH
97
2
HOH
HOH
97
A
HOH
98
2
HOH
HOH
98
A
HOH
99
2
HOH
HOH
99
A
HOH
101
2
HOH
HOH
101
A
HOH
110
2
HOH
HOH
110
A
HOH
111
2
HOH
HOH
111
A
HOH
112
2
HOH
HOH
112
A
HOH
113
2
HOH
HOH
113
A
HOH
114
2
HOH
HOH
114
A
HOH
115
2
HOH
HOH
115
A
HOH
116
2
HOH
HOH
116
A
HOH
119
2
HOH
HOH
119
A
HOH
121
2
HOH
HOH
121
A
HOH
122
2
HOH
HOH
122
A
HOH
123
2
HOH
HOH
123
A
HOH
124
2
HOH
HOH
124
A
HOH
126
2
HOH
HOH
126
A
HOH
130
2
HOH
HOH
130
A
HOH
27
2
HOH
HOH
27
B
HOH
28
2
HOH
HOH
28
B
HOH
32
2
HOH
HOH
32
B
HOH
33
2
HOH
HOH
33
B
HOH
37
2
HOH
HOH
37
B
HOH
41
2
HOH
HOH
41
B
HOH
42
2
HOH
HOH
42
B
HOH
43
2
HOH
HOH
43
B
HOH
45
2
HOH
HOH
45
B
HOH
50
2
HOH
HOH
50
B
HOH
52
2
HOH
HOH
52
B
HOH
53
2
HOH
HOH
53
B
HOH
54
2
HOH
HOH
54
B
HOH
55
2
HOH
HOH
55
B
HOH
56
2
HOH
HOH
56
B
HOH
57
2
HOH
HOH
57
B
HOH
58
2
HOH
HOH
58
B
HOH
59
2
HOH
HOH
59
B
HOH
61
2
HOH
HOH
61
B
HOH
64
2
HOH
HOH
64
B
HOH
65
2
HOH
HOH
65
B
HOH
67
2
HOH
HOH
67
B
HOH
68
2
HOH
HOH
68
B
HOH
70
2
HOH
HOH
70
B
HOH
72
2
HOH
HOH
72
B
HOH
85
2
HOH
HOH
85
B
HOH
86
2
HOH
HOH
86
B
HOH
87
2
HOH
HOH
87
B
HOH
89
2
HOH
HOH
89
B
HOH
90
2
HOH
HOH
90
B
HOH
91
2
HOH
HOH
91
B
HOH
92
2
HOH
HOH
92
B
HOH
94
2
HOH
HOH
94
B
HOH
100
2
HOH
HOH
100
B
HOH
102
2
HOH
HOH
102
B
HOH
103
2
HOH
HOH
103
B
HOH
104
2
HOH
HOH
104
B
HOH
105
2
HOH
HOH
105
B
HOH
106
2
HOH
HOH
106
B
HOH
107
2
HOH
HOH
107
B
HOH
108
2
HOH
HOH
108
B
HOH
109
2
HOH
HOH
109
B
HOH
117
2
HOH
HOH
117
B
HOH
118
2
HOH
HOH
118
B
HOH
120
2
HOH
HOH
120
B
HOH
125
2
HOH
HOH
125
B
HOH
127
2
HOH
HOH
127
B
HOH
128
2
HOH
HOH
128
B
HOH
129
2
HOH
HOH
129
B
G
1
n
1
G
1
A
C
2
n
2
DC
2
A
G
3
n
3
DG
3
A
T
4
n
4
DT
4
A
A
5
n
5
DA
5
A
T
6
n
6
DT
6
A
A
7
n
7
DA
7
A
C
8
n
8
DC
8
A
G
9
n
9
DG
9
A
C
10
n
10
DC
10
A
G
11
n
1
G
11
B
C
12
n
2
DC
12
B
G
13
n
3
DG
13
B
T
14
n
4
DT
14
B
A
15
n
5
DA
15
B
T
16
n
6
DT
16
B
A
17
n
7
DA
17
B
C
18
n
8
DC
18
B
G
19
n
9
DG
19
B
C
20
n
10
DC
20
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
-5.75
0.60
125.10
119.35
A
A
A
C6
N1
C2
G
G
G
1
1
1
N
1
5.01
0.60
123.90
128.91
A
A
A
N1
C2
N3
G
G
G
1
1
1
N
1
5.42
0.50
111.50
116.92
A
A
A
C5
C6
N1
G
G
G
1
1
1
N
1
-8.88
0.70
119.90
111.02
A
A
A
N3
C2
N2
G
G
G
1
1
1
N
1
-5.79
0.60
128.60
122.81
A
A
A
C5
C6
O6
G
G
G
1
1
1
N
1
-9.98
0.90
105.70
95.72
A
A
A
O5'
P
OP1
DC
DC
DC
2
2
2
N
1
-5.14
0.80
109.40
104.26
A
A
A
O5'
C5'
C4'
DC
DC
DC
2
2
2
N
1
-9.81
1.60
120.90
111.09
A
A
A
P
O5'
C5'
DC
DC
DC
2
2
2
N
1
-4.36
0.40
104.50
100.14
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
1
4.83
0.50
119.90
124.73
A
A
A
C2
N3
C4
DC
DC
DC
2
2
2
N
1
-5.06
0.40
121.90
116.84
A
A
A
N3
C4
C5
DC
DC
DC
2
2
2
N
1
3.21
0.50
121.00
124.21
A
A
A
C5
C6
N1
DC
DC
DC
2
2
2
N
1
5.79
0.60
118.90
124.69
A
A
A
N1
C2
O2
DC
DC
DC
2
2
2
N
1
4.81
0.70
120.20
125.01
A
A
A
C5
C4
N4
DC
DC
DC
2
2
2
N
1
7.92
1.20
119.70
127.62
A
A
A
C3'
O3'
P
DC
DC
DG
2
2
3
Y
1
-9.14
0.90
105.70
96.56
A
A
A
O5'
P
OP1
DG
DG
DG
3
3
3
N
1
-2.84
0.40
104.50
101.66
A
A
A
O4'
C4'
C3'
DG
DG
DG
3
3
3
N
1
-5.81
0.60
125.10
119.29
A
A
A
C6
N1
C2
DG
DG
DG
3
3
3
N
1
4.93
0.60
123.90
128.83
A
A
A
N1
C2
N3
DG
DG
DG
3
3
3
N
1
5.98
0.50
111.50
117.48
A
A
A
C5
C6
N1
DG
DG
DG
3
3
3
N
1
-7.84
0.70
119.90
112.06
A
A
A
N3
C2
N2
DG
DG
DG
3
3
3
N
1
-5.65
0.60
128.60
122.95
A
A
A
C5
C6
O6
DG
DG
DG
3
3
3
N
1
-9.95
0.90
105.70
95.75
A
A
A
O5'
P
OP2
DT
DT
DT
4
4
4
N
1
-6.07
0.80
109.40
103.33
A
A
A
O5'
C5'
C4'
DT
DT
DT
4
4
4
N
1
-11.87
1.60
120.90
109.03
A
A
A
P
O5'
C5'
DT
DT
DT
4
4
4
N
1
-4.71
0.40
104.50
99.79
A
A
A
O4'
C4'
C3'
DT
DT
DT
4
4
4
N
1
-4.81
0.70
102.20
97.39
A
A
A
C4'
C3'
C2'
DT
DT
DT
4
4
4
N
1
5.43
0.60
119.00
124.43
A
A
A
C4
C5
C7
DT
DT
DT
4
4
4
N
1
-6.56
0.60
122.90
116.34
A
A
A
C6
C5
C7
DT
DT
DT
4
4
4
N
1
-6.48
0.90
105.70
99.22
A
A
A
O5'
P
OP1
DA
DA
DA
5
5
5
N
1
-2.93
0.40
104.50
101.57
A
A
A
O4'
C4'
C3'
DA
DA
DA
5
5
5
N
1
-5.41
0.70
102.20
96.79
A
A
A
C4'
C3'
C2'
DA
DA
DA
5
5
5
N
1
-6.37
0.80
102.40
96.03
A
A
A
C3'
C2'
C1'
DA
DA
DA
5
5
5
N
1
11.28
1.20
119.70
130.98
A
A
A
C3'
O3'
P
DA
DA
DT
5
5
6
Y
1
-8.31
0.90
105.70
97.39
A
A
A
O5'
P
OP1
DT
DT
DT
6
6
6
N
1
-4.64
0.60
122.90
118.26
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
1
-7.74
0.90
105.70
97.96
A
A
A
O5'
P
OP1
DA
DA
DA
7
7
7
N
1
-14.22
1.60
120.90
106.68
A
A
A
P
O5'
C5'
DA
DA
DA
7
7
7
N
1
-5.90
0.70
102.20
96.30
A
A
A
C4'
C3'
C2'
DA
DA
DA
7
7
7
N
1
-4.95
0.80
105.90
100.95
A
A
A
O4'
C1'
C2'
DA
DA
DA
7
7
7
N
1
4.93
0.30
108.30
113.23
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
1
31.71
1.20
119.70
151.41
A
A
A
C3'
O3'
P
DA
DA
DC
7
7
8
Y
1
11.91
1.90
104.00
115.91
A
A
A
O3'
P
O5'
DA
DC
DC
7
8
8
Y
1
-7.74
0.90
105.70
97.96
A
A
A
O5'
P
OP1
DC
DC
DC
8
8
8
N
1
-4.02
0.40
104.50
100.48
A
A
A
O4'
C4'
C3'
DC
DC
DC
8
8
8
N
1
7.67
1.20
115.70
123.37
A
A
A
C5'
C4'
C3'
DC
DC
DC
8
8
8
N
1
-4.67
0.70
108.00
103.33
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
5.24
0.50
119.90
125.14
A
A
A
C2
N3
C4
DC
DC
DC
8
8
8
N
1
-4.50
0.40
121.90
117.40
A
A
A
N3
C4
C5
DC
DC
DC
8
8
8
N
1
4.99
0.60
118.90
123.89
A
A
A
N1
C2
O2
DC
DC
DC
8
8
8
N
1
11.82
1.90
104.00
115.82
A
A
A
O3'
P
O5'
DC
DG
DG
8
9
9
Y
1
-9.57
0.80
109.40
99.83
A
A
A
O5'
C5'
C4'
DG
DG
DG
9
9
9
N
1
-4.54
0.40
104.50
99.96
A
A
A
O4'
C4'
C3'
DG
DG
DG
9
9
9
N
1
-7.11
0.70
102.20
95.09
A
A
A
C4'
C3'
C2'
DG
DG
DG
9
9
9
N
1
5.50
0.30
108.30
113.80
A
A
A
O4'
C1'
N9
DG
DG
DG
9
9
9
N
1
-5.67
0.60
125.10
119.43
A
A
A
C6
N1
C2
DG
DG
DG
9
9
9
N
1
5.54
0.60
123.90
129.44
A
A
A
N1
C2
N3
DG
DG
DG
9
9
9
N
1
-3.16
0.50
111.90
108.74
A
A
A
C2
N3
C4
DG
DG
DG
9
9
9
N
1
5.58
0.50
111.50
117.08
A
A
A
C5
C6
N1
DG
DG
DG
9
9
9
N
1
-10.92
0.70
119.90
108.98
A
A
A
N3
C2
N2
DG
DG
DG
9
9
9
N
1
10.27
1.20
119.70
129.97
A
A
A
C3'
O3'
P
DG
DG
DC
9
9
10
Y
1
-6.91
0.90
105.70
98.79
A
A
A
O5'
P
OP1
DC
DC
DC
10
10
10
N
1
4.63
0.50
119.90
124.53
A
A
A
C2
N3
C4
DC
DC
DC
10
10
10
N
1
-4.39
0.40
121.90
117.51
A
A
A
N3
C4
C5
DC
DC
DC
10
10
10
N
1
4.38
0.50
121.00
125.38
A
A
A
C5
C6
N1
DC
DC
DC
10
10
10
N
1
6.64
0.60
118.90
125.54
A
A
A
N1
C2
O2
DC
DC
DC
10
10
10
N
1
-5.76
0.60
125.10
119.34
B
B
B
C6
N1
C2
G
G
G
11
11
11
N
1
4.83
0.60
123.90
128.73
B
B
B
N1
C2
N3
G
G
G
11
11
11
N
1
5.84
0.50
111.50
117.34
B
B
B
C5
C6
N1
G
G
G
11
11
11
N
1
-8.06
0.70
119.90
111.84
B
B
B
N3
C2
N2
G
G
G
11
11
11
N
1
-5.75
0.60
128.60
122.85
B
B
B
C5
C6
O6
G
G
G
11
11
11
N
1
8.07
1.20
119.70
127.77
B
B
B
C3'
O3'
P
G
G
DC
11
11
12
Y
1
-9.05
0.90
105.70
96.65
B
B
B
O5'
P
OP1
DC
DC
DC
12
12
12
N
1
4.73
0.50
119.90
124.63
B
B
B
C2
N3
C4
DC
DC
DC
12
12
12
N
1
-5.54
0.40
121.90
116.36
B
B
B
N3
C4
C5
DC
DC
DC
12
12
12
N
1
4.96
0.60
118.90
123.86
B
B
B
N1
C2
O2
DC
DC
DC
12
12
12
N
1
5.67
0.70
120.20
125.87
B
B
B
C5
C4
N4
DC
DC
DC
12
12
12
N
1
-11.02
0.40
104.50
93.48
B
B
B
O4'
C4'
C3'
DG
DG
DG
13
13
13
N
1
6.62
1.10
109.80
116.42
B
B
B
C5'
C4'
O4'
DG
DG
DG
13
13
13
N
1
-5.96
0.60
125.10
119.14
B
B
B
C6
N1
C2
DG
DG
DG
13
13
13
N
1
5.83
0.60
123.90
129.73
B
B
B
N1
C2
N3
DG
DG
DG
13
13
13
N
1
5.62
0.50
111.50
117.12
B
B
B
C5
C6
N1
DG
DG
DG
13
13
13
N
1
-7.93
0.70
119.90
111.97
B
B
B
N3
C2
N2
DG
DG
DG
13
13
13
N
1
-4.87
0.60
128.60
123.73
B
B
B
C5
C6
O6
DG
DG
DG
13
13
13
N
1
-10.27
1.20
119.70
109.43
B
B
B
C3'
O3'
P
DG
DG
DT
13
13
14
Y
1
-2.74
0.40
104.50
101.76
B
B
B
O4'
C4'
C3'
DT
DT
DT
14
14
14
N
1
-5.14
0.80
102.40
97.26
B
B
B
C3'
C2'
C1'
DT
DT
DT
14
14
14
N
1
3.47
0.30
108.30
111.77
B
B
B
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
3.74
0.60
119.00
122.74
B
B
B
C4
C5
C7
DT
DT
DT
14
14
14
N
1
-3.76
0.60
122.90
119.14
B
B
B
C6
C5
C7
DT
DT
DT
14
14
14
N
1
13.14
1.20
119.70
132.84
B
B
B
C3'
O3'
P
DT
DT
DA
14
14
15
Y
1
-8.73
0.90
105.70
96.97
B
B
B
O5'
P
OP1
DA
DA
DA
15
15
15
N
1
-12.25
1.60
120.90
108.65
B
B
B
P
O5'
C5'
DA
DA
DA
15
15
15
N
1
4.18
0.30
108.30
112.48
B
B
B
O4'
C1'
N9
DA
DA
DA
15
15
15
N
1
-8.45
0.90
105.70
97.25
B
B
B
O5'
P
OP1
DT
DT
DT
16
16
16
N
1
-10.74
1.60
120.90
110.16
B
B
B
P
O5'
C5'
DT
DT
DT
16
16
16
N
1
-6.80
0.40
104.50
97.70
B
B
B
O4'
C4'
C3'
DT
DT
DT
16
16
16
N
1
8.97
1.20
115.70
124.67
B
B
B
C5'
C4'
C3'
DT
DT
DT
16
16
16
N
1
-5.90
0.70
102.20
96.30
B
B
B
C4'
C3'
C2'
DT
DT
DT
16
16
16
N
1
-4.08
0.60
127.20
123.12
B
B
B
C2
N3
C4
DT
DT
DT
16
16
16
N
1
-8.13
0.90
105.70
97.57
B
B
B
O5'
P
OP2
DA
DA
DA
17
17
17
N
1
-10.06
0.90
105.70
95.64
B
B
B
O5'
P
OP1
DC
DC
DC
18
18
18
N
1
5.10
0.50
119.90
125.00
B
B
B
C2
N3
C4
DC
DC
DC
18
18
18
N
1
-4.91
0.40
121.90
116.99
B
B
B
N3
C4
C5
DC
DC
DC
18
18
18
N
1
3.93
0.50
121.00
124.93
B
B
B
C5
C6
N1
DC
DC
DC
18
18
18
N
1
6.84
0.60
118.90
125.74
B
B
B
N1
C2
O2
DC
DC
DC
18
18
18
N
1
-6.81
0.90
105.70
98.89
B
B
B
O5'
P
OP2
DG
DG
DG
19
19
19
N
1
-14.80
1.60
120.90
106.10
B
B
B
P
O5'
C5'
DG
DG
DG
19
19
19
N
1
7.50
1.10
109.80
117.30
B
B
B
C5'
C4'
O4'
DG
DG
DG
19
19
19
N
1
1.82
0.30
108.30
110.12
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
1
-5.37
0.60
125.10
119.73
B
B
B
C6
N1
C2
DG
DG
DG
19
19
19
N
1
5.77
0.60
123.90
129.67
B
B
B
N1
C2
N3
DG
DG
DG
19
19
19
N
1
-3.31
0.50
111.90
108.59
B
B
B
C2
N3
C4
DG
DG
DG
19
19
19
N
1
5.37
0.50
111.50
116.87
B
B
B
C5
C6
N1
DG
DG
DG
19
19
19
N
1
-9.02
0.70
119.90
110.88
B
B
B
N3
C2
N2
DG
DG
DG
19
19
19
N
1
-4.18
0.60
128.60
124.42
B
B
B
C5
C6
O6
DG
DG
DG
19
19
19
N
1
-8.52
0.90
105.70
97.18
B
B
B
O5'
P
OP2
DC
DC
DC
20
20
20
N
1
-5.04
0.80
105.90
100.86
B
B
B
O4'
C1'
C2'
DC
DC
DC
20
20
20
N
1
9.68
1.40
114.30
123.98
B
B
B
N1
C1'
C2'
DC
DC
DC
20
20
20
N
1
-2.57
0.40
120.30
117.73
B
B
B
C6
N1
C2
DC
DC
DC
20
20
20
N
1
5.98
0.50
119.90
125.88
B
B
B
C2
N3
C4
DC
DC
DC
20
20
20
N
1
-5.31
0.40
121.90
116.59
B
B
B
N3
C4
C5
DC
DC
DC
20
20
20
N
1
5.55
0.50
121.00
126.55
B
B
B
C5
C6
N1
DC
DC
DC
20
20
20
N
1
4.72
0.60
118.90
123.62
B
B
B
N1
C2
O2
DC
DC
DC
20
20
20
N
1
4.53
0.70
118.00
122.53
B
B
B
N3
C4
N4
DC
DC
DC
20
20
20
N
1
A
A
C6
N1
G
G
1
1
-0.056
0.007
1.391
1.335
N
1
A
A
C2
N2
G
G
1
1
-0.104
0.010
1.341
1.237
N
1
A
A
O3'
C3'
DC
DC
2
2
-0.050
0.006
1.419
1.369
N
1
A
A
N3
C4
DC
DC
2
2
0.047
0.007
1.335
1.382
N
1
A
A
O3'
C3'
DG
DG
3
3
-0.068
0.006
1.419
1.351
N
1
A
A
C6
N1
DG
DG
3
3
-0.059
0.007
1.391
1.332
N
1
A
A
C2
N2
DG
DG
3
3
-0.092
0.010
1.341
1.249
N
1
A
A
C4'
C3'
DT
DT
4
4
0.070
0.010
1.529
1.599
N
1
A
A
C2'
C1'
DT
DT
4
4
0.064
0.010
1.519
1.583
N
1
A
A
O3'
C3'
DT
DT
4
4
-0.083
0.006
1.419
1.336
N
1
A
A
O3'
C3'
DA
DA
5
5
-0.072
0.006
1.419
1.347
N
1
A
A
P
O5'
DA
DA
7
7
0.071
0.010
1.593
1.664
N
1
A
A
C4'
C3'
DA
DA
7
7
0.065
0.010
1.529
1.594
N
1
A
A
C2'
C1'
DA
DA
7
7
0.127
0.010
1.519
1.646
N
1
A
A
O3'
C3'
DA
DA
7
7
-0.085
0.006
1.419
1.334
N
1
A
A
O3'
C3'
DC
DC
8
8
-0.051
0.006
1.419
1.368
N
1
A
A
C2'
C1'
DG
DG
9
9
0.082
0.010
1.519
1.601
N
1
A
A
O3'
C3'
DG
DG
9
9
-0.042
0.006
1.419
1.377
N
1
A
A
C6
N1
DG
DG
9
9
-0.049
0.007
1.391
1.342
N
1
A
A
C2
N2
DG
DG
9
9
-0.113
0.010
1.341
1.228
N
1
A
A
N3
C4
DC
DC
10
10
0.049
0.007
1.335
1.384
N
1
B
B
C6
N1
G
G
11
11
-0.059
0.007
1.391
1.332
N
1
B
B
C2
N2
G
G
11
11
-0.108
0.010
1.341
1.233
N
1
B
B
P
O5'
DC
DC
12
12
0.067
0.010
1.593
1.660
N
1
B
B
C3'
C2'
DC
DC
12
12
-0.066
0.008
1.516
1.450
N
1
B
B
N3
C4
DC
DC
12
12
0.052
0.007
1.335
1.387
N
1
B
B
C6
N1
DG
DG
13
13
-0.059
0.007
1.391
1.332
N
1
B
B
C2
N2
DG
DG
13
13
-0.110
0.010
1.341
1.231
N
1
B
B
O3'
C3'
DT
DT
14
14
-0.090
0.006
1.419
1.329
N
1
B
B
N3
C4
DC
DC
18
18
0.048
0.007
1.335
1.383
N
1
B
B
C3'
C2'
DG
DG
19
19
-0.050
0.008
1.516
1.466
N
1
B
B
O4'
C4'
DG
DG
19
19
-0.066
0.010
1.446
1.380
N
1
B
B
C6
N1
DG
DG
19
19
-0.056
0.007
1.391
1.335
N
1
B
B
C2
N2
DG
DG
19
19
-0.114
0.010
1.341
1.227
N
1
A
B
O
O
HOH
HOH
34
127
1.52
1_555
1_655
1
A
B
O
O
HOH
HOH
35
117
1.65
1_555
1_655
1
A
B
O
O
HOH
HOH
24
52
1.75
1_555
1_655
1
A
B
O
O
HOH
HOH
63
104
1.81
1_555
4_565
1
A
B
O2
N2
DT
G
4
11
1.98
1_555
2_664
1
A
B
O
O
HOH
HOH
35
54
2.15
1_555
1_655
0.1780000
2.250
1592
1
2.000
TR
isotropic
TR
isotropic
2.250
110
516
0
406
0
0.020
0.010
0.140
fix
fix
2.250
1D87
1592
2.000
1
refinement
PROLSQ
(MODIFIED BY G.J.QUIGLEY)
refinement
MODIFIED
BY G.J.QUIGLEY
CONFORMATIONAL INFLUENCE OF THE RIBOSE 2'-HYDROXYL GROUP: CRYSTAL STRUCTURES OF DNA-RNA CHIMERIC DUPLEXES
1
N
N
1
N
N
2
N
N
2
N
N
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
DC
20
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
DC
20
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
DC
20
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
19
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
19
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
19
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
DC
18
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
18
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
18
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
DA
17
B
N1
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
DA
17
B
N6
DA
7
1_555
hydrog
DT-DC MISPAIR
A
DT
4
A
N3
DT
4
1_555
B
DC
18
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
16
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
16
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
15
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
15
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
B
DT
14
B
N3
DT
4
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
B
DT
14
B
O4
DT
4
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
13
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
13
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
13
B
N2
DG
3
1_555
hydrog
DC-DT MISPAIR
A
DC
8
A
O2
DC
8
1_555
B
DT
14
B
N3
DT
4
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
B
DC
12
B
N3
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
B
DC
12
B
O2
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
B
DC
12
B
N4
DC
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
G
11
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
G
11
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
G
11
B
N2
G
1
1_555
DNA-RNA HYBRID
A-DNA/RNA, DOUBLE HELIX, DNA-RNA HYBRID COMPLEX, DNA-RNA HYBRID
1D87
PDB
1
1D87
1
10
1D87
1
10
1D87
A
1
1
10
11
20
1D87
11
20
1D87
B
1
1
10
19
P 21 21 21