1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Chou, S.-H.
Cheng, J.-W.
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 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
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
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
228
138
155
10.1016/0022-2836(92)90497-8
1447778
Solution structure of [d(ATGAGCGAATA)]2. Adjacent G:A mismatches stabilized by cross-strand base-stacking and BII phosphate groups.
1992
10.2210/pdb1d69/pdb
pdb_00001d69
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3406.261
DNA (5'-D(P*AP*TP*GP*AP*GP*CP*GP*AP*AP*TP*A)-3')
2
syn
polymer
no
no
(DA)(DT)(DG)(DA)(DG)(DC)(DG)(DA)(DA)(DT)(DA)
ATGAGCGAATA
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
1.621
1
20
A
1
B
20
-1.081
A_DA1:DT20_B
1
-3.147
0.088
0.072
-0.064
-2.284
1
20
A
2
B
19
1.076
A_DT2:DA19_B
2
4.627
0.170
0.504
-0.142
27.759
A
3
B
18
-10.674
A_DG3:DA18_B
3
10.833
6.760
0.779
-4.529
-28.853
10
11
A
4
B
17
-15.876
A_DA4:DG17_B
4
-0.406
-6.841
0.112
-4.327
-0.979
1
19
A
5
B
16
-0.364
A_DG5:DC16_B
5
4.490
0.121
-0.557
-0.154
1.022
1
19
A
6
B
15
-0.362
A_DC6:DG15_B
6
4.488
-0.122
-0.557
-0.154
28.898
10
11
A
7
B
14
-15.841
A_DG7:DA14_B
7
-0.432
6.841
0.114
-4.326
-27.825
A
8
B
13
-10.662
A_DA8:DG13_B
8
10.775
-6.761
0.775
-4.527
2.214
1
20
A
9
B
12
1.056
A_DA9:DT12_B
9
4.668
-0.169
0.500
-0.143
-1.647
1
20
A
10
B
11
-1.121
A_DT10:DA11_B
10
-3.080
-0.088
0.068
-0.064
3.270
31.859
A
A
1
2
8.132
B
B
20
19
3.493
4.450
0.031
-1.388
AA_DA1DT2:DA19DT20_BB
1
-0.847
1.549
31.544
-3.371
-0.217
3.350
63.652
A
A
2
3
1.904
B
B
19
18
3.337
2.007
0.009
0.668
AA_DT2DG3:DA18DA19_BB
2
-3.247
3.080
63.549
0.544
-0.153
3.659
-12.473
A
A
3
4
12.366
B
B
18
17
4.123
-2.656
-0.394
-1.797
AA_DG3DA4:DG17DA18_BB
3
1.865
8.685
-12.045
12.137
0.903
3.281
60.410
A
A
4
5
-0.078
B
B
17
16
3.271
-0.079
0.279
1.229
AA_DA4DG5:DC16DG17_BB
4
4.602
-4.577
60.251
1.225
-0.052
2.433
32.273
A
A
5
6
24.226
B
B
16
15
3.011
13.097
-0.001
-0.833
AA_DG5DC6:DG15DC16_BB
5
-0.037
0.068
29.561
-3.525
-0.004
3.283
60.404
A
A
6
7
-0.005
B
B
15
14
3.271
-0.005
-0.279
1.229
AA_DC6DG7:DA14DG15_BB
6
-4.610
4.586
60.244
1.222
0.052
3.680
-12.465
A
A
7
8
11.894
B
B
14
13
4.123
-2.554
0.393
-1.799
AA_DG7DA8:DG13DA14_BB
7
-1.867
-8.695
-12.058
12.015
-0.917
3.351
63.624
A
A
8
9
1.944
B
B
13
12
3.337
2.048
-0.004
0.664
AA_DA8DA9:DT12DG13_BB
8
3.224
-3.060
63.522
0.539
0.147
3.266
31.838
A
A
9
10
8.188
B
B
12
11
3.492
4.477
-0.030
-1.391
AA_DA9DT10:DA11DT12_BB
9
0.873
-1.597
31.518
-3.384
0.220
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
Data collection
1
0
1993-04-15
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
1
4
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
Y
BNL
1992-04-15
REL
CHEMICALLY SYNTHESIZED
sample
THE 3' OVERHANGING ADENOSINE RESIDUES WERE NOT INCLUDED IN THE BACK-CALCULATION AND NO COORDINATES ARE PRESENTED FOR THEM IN THIS ENTRY.
1
A
1
n
1
DA
1
A
T
2
n
2
DT
2
A
G
3
n
3
DG
3
A
A
4
n
4
DA
4
A
G
5
n
5
DG
5
A
C
6
n
6
DC
6
A
G
7
n
7
DG
7
A
A
8
n
8
DA
8
A
A
9
n
9
DA
9
A
T
10
n
10
DT
10
A
n
11
11
A
A
11
n
1
DA
11
B
T
12
n
2
DT
12
B
G
13
n
3
DG
13
B
A
14
n
4
DA
14
B
G
15
n
5
DG
15
B
C
16
n
6
DC
16
B
G
17
n
7
DG
17
B
A
18
n
8
DA
18
B
A
19
n
9
DA
19
B
T
20
n
10
DT
20
B
n
11
21
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
DA
11
A
DA
11
1
Y
1
B
DA
21
B
DA
11
1
Y
1
-10.00
1.50
119.60
109.60
A
A
A
OP1
P
OP2
DA
DA
DA
1
1
1
N
1
16.56
1.20
119.70
136.26
A
A
A
C3'
O3'
P
DA
DA
DT
1
1
2
Y
1
3.71
0.60
114.60
118.31
A
A
A
N1
C2
N3
DT
DT
DT
2
2
2
N
1
-4.40
0.60
127.20
122.80
A
A
A
C2
N3
C4
DT
DT
DT
2
2
2
N
1
-3.74
0.60
123.70
119.96
A
A
A
C5
C6
N1
DT
DT
DT
2
2
2
N
1
-5.53
0.70
108.00
102.47
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
4.43
0.70
110.30
114.73
A
A
A
C1'
O4'
C4'
DA
DA
DA
4
4
4
N
1
7.71
0.30
108.30
116.01
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
6.65
1.10
109.80
116.45
A
A
A
C5'
C4'
O4'
DG
DG
DG
5
5
5
N
1
-6.91
0.70
108.00
101.09
A
A
A
O4'
C1'
N9
DG
DG
DG
5
5
5
N
1
15.02
1.20
119.70
134.72
A
A
A
C3'
O3'
P
DG
DG
DC
5
5
6
Y
1
10.45
1.20
119.70
130.15
A
A
A
C3'
O3'
P
DG
DG
DA
7
7
8
Y
1
7.67
0.30
108.30
115.97
A
A
A
O4'
C1'
N9
DA
DA
DA
8
8
8
N
1
11.59
1.20
119.70
131.29
A
A
A
C3'
O3'
P
DA
DA
DA
8
8
9
Y
1
7.54
1.10
109.80
117.34
A
A
A
C5'
C4'
O4'
DA
DA
DA
9
9
9
N
1
-8.29
0.70
108.00
99.71
A
A
A
O4'
C1'
N9
DA
DA
DA
9
9
9
N
1
11.22
1.20
119.70
130.92
A
A
A
C3'
O3'
P
DA
DA
DT
9
9
10
Y
1
-6.17
0.70
108.00
101.83
A
A
A
O4'
C1'
N1
DT
DT
DT
10
10
10
N
1
-4.40
0.60
127.20
122.80
A
A
A
C2
N3
C4
DT
DT
DT
10
10
10
N
1
-3.78
0.60
123.70
119.92
A
A
A
C5
C6
N1
DT
DT
DT
10
10
10
N
1
-10.10
1.50
119.60
109.50
B
B
B
OP1
P
OP2
DA
DA
DA
11
11
11
N
1
16.50
1.20
119.70
136.20
B
B
B
C3'
O3'
P
DA
DA
DT
11
11
12
Y
1
3.75
0.60
114.60
118.35
B
B
B
N1
C2
N3
DT
DT
DT
12
12
12
N
1
-4.39
0.60
127.20
122.81
B
B
B
C2
N3
C4
DT
DT
DT
12
12
12
N
1
-3.80
0.60
123.70
119.90
B
B
B
C5
C6
N1
DT
DT
DT
12
12
12
N
1
-5.52
0.70
108.00
102.48
B
B
B
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
4.30
0.70
110.30
114.60
B
B
B
C1'
O4'
C4'
DA
DA
DA
14
14
14
N
1
7.68
0.30
108.30
115.98
B
B
B
O4'
C1'
N9
DA
DA
DA
14
14
14
N
1
6.63
1.10
109.80
116.43
B
B
B
C5'
C4'
O4'
DG
DG
DG
15
15
15
N
1
-6.93
0.70
108.00
101.07
B
B
B
O4'
C1'
N9
DG
DG
DG
15
15
15
N
1
15.05
1.20
119.70
134.75
B
B
B
C3'
O3'
P
DG
DG
DC
15
15
16
Y
1
10.45
1.20
119.70
130.15
B
B
B
C3'
O3'
P
DG
DG
DA
17
17
18
Y
1
7.70
0.30
108.30
116.00
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
11.74
1.20
119.70
131.44
B
B
B
C3'
O3'
P
DA
DA
DA
18
18
19
Y
1
7.52
1.10
109.80
117.32
B
B
B
C5'
C4'
O4'
DA
DA
DA
19
19
19
N
1
-8.30
0.70
108.00
99.70
B
B
B
O4'
C1'
N9
DA
DA
DA
19
19
19
N
1
11.29
1.20
119.70
130.99
B
B
B
C3'
O3'
P
DA
DA
DT
19
19
20
Y
1
-6.10
0.70
108.00
101.90
B
B
B
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
-4.40
0.60
127.20
122.80
B
B
B
C2
N3
C4
DT
DT
DT
20
20
20
N
1
-3.78
0.60
123.70
119.92
B
B
B
C5
C6
N1
DT
DT
DT
20
20
20
N
1
A
A
P
OP2
DA
DA
1
1
0.118
0.017
1.485
1.603
N
1
A
A
P
OP3
DA
DA
1
1
-0.121
0.012
1.607
1.486
N
1
A
A
C5
C6
DT
DT
2
2
0.054
0.007
1.339
1.393
N
1
A
A
O3'
C3'
DG
DG
3
3
-0.047
0.006
1.419
1.372
N
1
A
A
O4'
C1'
DA
DA
4
4
-0.105
0.012
1.418
1.313
N
1
A
A
C3'
C2'
DG
DG
5
5
0.090
0.012
1.518
1.608
N
1
A
A
O3'
C3'
DG
DG
7
7
-0.053
0.006
1.419
1.366
N
1
A
A
O4'
C1'
DA
DA
8
8
-0.112
0.012
1.418
1.306
N
1
A
A
O3'
C3'
DA
DA
9
9
-0.046
0.006
1.419
1.373
N
1
A
A
C5
C6
DT
DT
10
10
0.052
0.007
1.339
1.391
N
1
B
B
P
OP2
DA
DA
11
11
0.119
0.017
1.485
1.604
N
1
B
B
P
OP3
DA
DA
11
11
-0.121
0.012
1.607
1.486
N
1
B
B
C5
C6
DT
DT
12
12
0.055
0.007
1.339
1.394
N
1
B
B
O3'
C3'
DG
DG
13
13
-0.046
0.006
1.419
1.373
N
1
B
B
O4'
C1'
DA
DA
14
14
-0.105
0.012
1.418
1.313
N
1
B
B
C3'
C2'
DG
DG
15
15
0.091
0.012
1.518
1.609
N
1
B
B
O3'
C3'
DG
DG
17
17
-0.052
0.006
1.419
1.367
N
1
B
B
O4'
C1'
DA
DA
18
18
-0.113
0.012
1.418
1.305
N
1
B
B
O3'
C3'
DA
DA
19
19
-0.046
0.006
1.419
1.373
N
1
B
B
C5
C6
DT
DT
20
20
0.053
0.007
1.339
1.392
N
SOLUTION STRUCTURE OF [D(ATGAGCGAATA)]2: ADJACENT G:A MISMATCHES STABILIZED BY CROSS-STRAND BASE-STACKING AND BII PHOSPHATE GROUPS
1
N
N
1
N
N
hydrog
WATSON-CRICK
A
DA
1
A
N1
DA
1
1_555
B
DT
20
B
N3
DT
10
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N6
DA
1
1_555
B
DT
20
B
O4
DT
10
1_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
B
DA
19
B
N1
DA
9
1_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
B
DA
19
B
N6
DA
9
1_555
hydrog
DG-DA MISPAIR
A
DG
3
A
N2
DG
3
1_555
B
DA
18
B
N7
DA
8
1_555
hydrog
TYPE_11_PAIR
A
DA
4
A
N6
DA
4
1_555
B
DG
17
B
N3
DG
7
1_555
hydrog
TYPE_11_PAIR
A
DA
4
A
N7
DA
4
1_555
B
DG
17
B
N2
DG
7
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
B
DC
16
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
B
DC
16
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
B
DC
16
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
B
DG
15
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
B
DG
15
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
B
DG
15
B
N2
DG
5
1_555
hydrog
TYPE_11_PAIR
A
DG
7
A
N2
DG
7
1_555
B
DA
14
B
N7
DA
4
1_555
hydrog
TYPE_11_PAIR
A
DG
7
A
N3
DG
7
1_555
B
DA
14
B
N6
DA
4
1_555
hydrog
DA-DG MISPAIR
A
DA
8
A
N7
DA
8
1_555
B
DG
13
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DA
9
A
N1
DA
9
1_555
B
DT
12
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
9
A
N6
DA
9
1_555
B
DT
12
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DT
10
A
N3
DT
10
1_555
B
DA
11
B
N1
DA
1
1_555
hydrog
WATSON-CRICK
A
DT
10
A
O4
DT
10
1_555
B
DA
11
B
N6
DA
1
1_555
DNA
DNA, DOUBLE HELIX, SHEARED HYDROGEN BONDING
1D69
PDB
1
1D69
1
11
1D69
1
11
1D69
A
1
1
11
11
21
1D69
11
21
1D69
B
1
1
11
1
P 1