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A
O5'
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1
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A
O5'
DC
1
1
1.00
1
O
8.69
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A
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DC
1
ATOM
A
C5'
DC
1
1
1.00
1
C
13.82
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A
C4'
DC
1
ATOM
A
C4'
DC
1
1
1.00
1
C
20.49
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A
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DC
1
ATOM
A
O4'
DC
1
1
1.00
1
O
17.46
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A
C3'
DC
1
ATOM
A
C3'
DC
1
1
1.00
1
C
18.23
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A
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DC
1
ATOM
A
O3'
DC
1
1
1.00
1
O
21.24
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A
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DC
1
ATOM
A
C2'
DC
1
1
1.00
1
C
14.09
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A
C1'
DC
1
ATOM
A
C1'
DC
1
1
1.00
1
C
12.05
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A
N1
DC
1
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A
N1
DC
1
1
1.00
1
N
4.87
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A
C2
DC
1
ATOM
A
C2
DC
1
1
1.00
1
C
11.19
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A
O2
DC
1
ATOM
A
O2
DC
1
1
1.00
1
O
4.72
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A
N3
DC
1
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A
N3
DC
1
1
1.00
1
N
1.77
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A
C4
DC
1
ATOM
A
C4
DC
1
1
1.00
1
C
8.34
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A
N4
DC
1
ATOM
A
N4
DC
1
1
1.00
1
N
8.00
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A
C5
DC
1
ATOM
A
C5
DC
1
1
1.00
1
C
6.94
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A
C6
DC
1
ATOM
A
C6
DC
1
1
1.00
1
C
20.08
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A
P
DG
2
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A
P
DG
1
2
1.00
1
P
20.87
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A
OP1
DG
2
ATOM
A
OP1
DG
1
2
1.00
1
O
25.95
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A
OP2
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2
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A
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DG
1
2
1.00
1
O
19.12
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2
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DG
1
2
1.00
1
O
12.41
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A
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2
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A
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DG
1
2
1.00
1
C
14.68
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A
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2
ATOM
A
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DG
1
2
1.00
1
C
13.38
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2
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DG
1
2
1.00
1
O
9.37
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A
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2
ATOM
A
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DG
1
2
1.00
1
C
17.12
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A
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2
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DG
1
2
1.00
1
O
10.88
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A
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2
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A
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DG
1
2
1.00
1
C
13.06
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A
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2
ATOM
A
C1'
DG
1
2
1.00
1
C
11.11
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18.363
18.610
A
N9
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2
ATOM
A
N9
DG
1
2
1.00
1
N
9.82
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18.811
18.520
A
C8
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2
ATOM
A
C8
DG
1
2
1.00
1
C
11.29
-16.296
17.851
18.351
A
N7
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2
ATOM
A
N7
DG
1
2
1.00
1
N
10.56
-15.540
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18.309
A
C5
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2
ATOM
A
C5
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1
2
1.00
1
C
7.53
-15.873
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18.161
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2
ATOM
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C6
DG
1
2
1.00
1
C
7.69
-17.015
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O6
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2
ATOM
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O6
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1
2
1.00
1
O
10.01
-14.835
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18.166
A
N1
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2
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A
N1
DG
1
2
1.00
1
N
3.01
-13.559
14.832
18.319
A
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2
ATOM
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DG
1
2
1.00
1
C
4.22
-12.577
13.856
18.272
A
N2
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2
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A
N2
DG
1
2
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1
N
8.25
-13.162
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A
N3
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2
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A
N3
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1
2
1.00
1
N
6.34
-14.194
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A
C4
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2
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A
C4
DG
1
2
1.00
1
C
17.10
-10.042
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A
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3
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A
P
DA
1
3
1.00
1
P
26.98
-9.614
23.358
17.611
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3
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A
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DA
1
3
1.00
1
O
21.98
-10.730
22.488
15.776
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3
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1
3
1.00
1
O
14.71
-8.713
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16.665
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3
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DA
1
3
1.00
1
O
18.49
-7.700
20.437
17.479
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3
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A
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DA
1
3
1.00
1
C
13.46
-7.566
19.052
16.850
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3
ATOM
A
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DA
1
3
1.00
1
C
19.10
-8.886
18.514
16.998
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3
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A
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DA
1
3
1.00
1
O
9.72
-7.317
19.116
15.348
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3
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A
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DA
1
3
1.00
1
C
18.44
-6.066
18.470
15.094
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3
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DA
1
3
1.00
1
O
14.74
-8.453
18.335
14.708
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3
ATOM
A
C2'
DA
1
3
1.00
1
C
14.51
-9.071
17.613
15.893
A
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DA
3
ATOM
A
C1'
DA
1
3
1.00
1
C
14.85
-10.476
17.339
15.618
A
N9
DA
3
ATOM
A
N9
DA
1
3
1.00
1
N
11.82
-11.522
18.207
15.528
A
C8
DA
3
ATOM
A
C8
DA
1
3
1.00
1
C
10.78
-12.655
17.613
15.274
A
N7
DA
3
ATOM
A
N7
DA
1
3
1.00
1
N
8.04
-12.348
16.256
15.221
A
C5
DA
3
ATOM
A
C5
DA
1
3
1.00
1
C
9.80
-13.069
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14.994
A
C6
DA
3
ATOM
A
C6
DA
1
3
1.00
1
C
9.68
-14.365
14.975
14.793
A
N6
DA
3
ATOM
A
N6
DA
1
3
1.00
1
N
5.76
-12.381
13.872
14.989
A
N1
DA
3
ATOM
A
N1
DA
1
3
1.00
1
N
10.84
-11.080
13.794
15.237
A
C2
DA
3
ATOM
A
C2
DA
1
3
1.00
1
C
11.86
-10.350
14.877
15.454
A
N3
DA
3
ATOM
A
N3
DA
1
3
1.00
1
N
12.98
-10.991
16.055
15.433
A
C4
DA
3
ATOM
A
C4
DA
1
3
1.00
1
C
17.51
-5.397
17.904
13.826
A
P
DT
4
ATOM
A
P
DT
1
4
1.00
1
P
21.02
-3.858
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14.090
A
OP1
DT
4
ATOM
A
OP1
DT
1
4
1.00
1
O
21.97
-5.674
18.965
12.810
A
OP2
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4
ATOM
A
OP2
DT
1
4
1.00
1
O
18.91
-6.150
16.687
13.292
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O5'
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4
ATOM
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O5'
DT
1
4
1.00
1
O
23.53
-6.217
15.448
14.016
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C5'
DT
4
ATOM
A
C5'
DT
1
4
1.00
1
C
17.44
-6.514
14.278
13.122
A
C4'
DT
4
ATOM
A
C4'
DT
1
4
1.00
1
C
21.32
-7.893
14.029
13.054
A
O4'
DT
4
ATOM
A
O4'
DT
1
4
1.00
1
O
17.72
-6.060
14.340
11.663
A
C3'
DT
4
ATOM
A
C3'
DT
1
4
1.00
1
C
19.94
-5.624
13.011
11.282
A
O3'
DT
4
ATOM
A
O3'
DT
1
4
1.00
1
O
13.67
-7.345
14.695
10.934
A
C2'
DT
4
ATOM
A
C2'
DT
1
4
1.00
1
C
16.63
-8.358
13.777
11.695
A
C1'
DT
4
ATOM
A
C1'
DT
1
4
1.00
1
C
15.46
-9.695
14.387
11.631
A
N1
DT
4
ATOM
A
N1
DT
1
4
1.00
1
N
10.43
-10.856
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11.631
A
C2
DT
4
ATOM
A
C2
DT
1
4
1.00
1
C
21.45
-11.083
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11.579
A
O2
DT
4
ATOM
A
O2
DT
1
4
1.00
1
O
14.05
-12.003
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11.663
A
N3
DT
4
ATOM
A
N3
DT
1
4
1.00
1
N
12.17
-12.015
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A
C4
DT
4
ATOM
A
C4
DT
1
4
1.00
1
C
13.54
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11.753
A
O4
DT
4
ATOM
A
O4
DT
1
4
1.00
1
O
13.56
-10.828
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A
C5
DT
4
ATOM
A
C5
DT
1
4
1.00
1
C
11.81
-10.865
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A
C7
DT
4
ATOM
A
C7
DT
1
4
1.00
1
C
10.76
-9.712
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11.748
A
C6
DT
4
ATOM
A
C6
DT
1
4
1.00
1
C
19.54
-4.592
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10.040
A
P
DC
5
ATOM
A
P
DC
1
5
1.00
1
P
16.66
-4.110
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A
OP1
DC
5
ATOM
A
OP1
DC
1
5
1.00
1
O
22.88
-4.091
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A
OP2
DC
5
ATOM
A
OP2
DC
1
5
1.00
1
O
22.73
-5.492
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8.713
A
O5'
DC
5
ATOM
A
O5'
DC
1
5
1.00
1
O
21.14
-5.582
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8.184
A
C5'
DC
5
ATOM
A
C5'
DC
1
5
1.00
1
C
15.19
-7.006
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7.724
A
C4'
DC
5
ATOM
A
C4'
DC
1
5
1.00
1
C
19.73
-7.904
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8.512
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O4'
DC
5
ATOM
A
O4'
DC
1
5
1.00
1
O
13.56
-7.289
11.819
6.313
A
C3'
DC
5
ATOM
A
C3'
DC
1
5
1.00
1
C
18.23
-7.941
10.644
5.689
A
O3'
DC
5
ATOM
A
O3'
DC
1
5
1.00
1
O
15.85
-8.304
12.921
6.413
A
C2'
DC
5
ATOM
A
C2'
DC
1
5
1.00
1
C
14.82
-9.001
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7.761
A
C1'
DC
5
ATOM
A
C1'
DC
1
5
1.00
1
C
10.26
-9.827
13.895
8.036
A
N1
DC
5
ATOM
A
N1
DC
1
5
1.00
1
N
5.49
-11.234
13.822
8.116
A
C2
DC
5
ATOM
A
C2
DC
1
5
1.00
1
C
14.31
-11.905
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8.105
A
O2
DC
5
ATOM
A
O2
DC
1
5
1.00
1
O
10.40
-11.942
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8.306
A
N3
DC
5
ATOM
A
N3
DC
1
5
1.00
1
N
5.32
-11.343
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8.343
A
C4
DC
5
ATOM
A
C4
DC
1
5
1.00
1
C
10.77
-11.942
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8.496
A
N4
DC
5
ATOM
A
N4
DC
1
5
1.00
1
N
11.30
-9.930
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8.221
A
C5
DC
5
ATOM
A
C5
DC
1
5
1.00
1
C
9.80
-9.247
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8.005
A
C6
DC
5
ATOM
A
C6
DC
1
5
1.00
1
C
14.85
-6.975
9.994
4.589
A
P
DG
6
ATOM
A
P
DG
1
6
1.00
1
P
20.41
-6.074
9.253
5.440
A
OP1
DG
6
ATOM
A
OP1
DG
1
6
1.00
1
O
19.56
-6.701
10.795
3.484
A
OP2
DG
6
ATOM
A
OP2
DG
1
6
1.00
1
O
12.03
-8.013
9.057
3.981
A
O5'
DG
6
ATOM
A
O5'
DG
1
6
1.00
1
O
18.00
-9.270
8.926
4.711
A
C5'
DG
6
ATOM
A
C5'
DG
1
6
1.00
1
C
12.50
-9.997
8.187
3.606
A
C4'
DG
6
ATOM
A
C4'
DG
1
6
1.00
1
C
16.23
-10.954
8.998
2.987
A
O4'
DG
6
ATOM
A
O4'
DG
1
6
1.00
1
O
16.51
-9.105
7.653
2.464
A
C3'
DG
6
ATOM
A
C3'
DG
1
6
1.00
1
C
18.28
-9.720
6.475
1.893
A
O3'
DG
6
ATOM
A
O3'
DG
1
6
1.00
1
O
13.54
-9.194
8.710
1.385
A
C2'
DG
6
ATOM
A
C2'
DG
1
6
1.00
1
C
6.98
-10.593
9.228
1.623
A
C1'
DG
6
ATOM
A
C1'
DG
1
6
1.00
1
C
7.48
-10.616
10.691
1.539
A
N9
DG
6
ATOM
A
N9
DG
1
6
1.00
1
N
6.52
-9.533
11.575
1.570
A
C8
DG
6
ATOM
A
C8
DG
1
6
1.00
1
C
4.24
-9.874
12.823
1.570
A
N7
DG
6
ATOM
A
N7
DG
1
6
1.00
1
N
6.57
-11.262
12.818
1.554
A
C5
DG
6
ATOM
A
C5
DG
1
6
1.00
1
C
4.06
-12.236
13.819
1.523
A
C6
DG
6
ATOM
A
C6
DG
1
6
1.00
1
C
9.11
-12.037
15.050
1.512
A
O6
DG
6
ATOM
A
O6
DG
1
6
1.00
1
O
11.50
-13.576
13.349
1.523
A
N1
DG
6
ATOM
A
N1
DG
1
6
1.00
1
N
3.53
-13.853
12.043
1.517
A
C2
DG
6
ATOM
A
C2
DG
1
6
1.00
1
C
6.86
-15.090
11.463
1.507
A
N2
DG
6
ATOM
A
N2
DG
1
6
1.00
1
N
7.72
-12.960
11.021
1.565
A
N3
DG
6
ATOM
A
N3
DG
1
6
1.00
1
N
6.27
-11.693
11.494
1.565
A
C4
DG
6
ATOM
A
C4
DG
1
6
1.00
1
C
12.73
-12.667
18.363
4.959
A
C1
DM1
7
HETATM
B
C1
DM1
2
1.00
1
C
12.67
-11.469
19.122
4.927
A
C2
DM1
7
HETATM
B
C2
DM1
2
1.00
1
C
12.75
-10.179
18.481
4.848
A
C3
DM1
7
HETATM
B
C3
DM1
2
1.00
1
C
13.11
-10.196
17.096
4.790
A
C4
DM1
7
HETATM
B
C4
DM1
2
1.00
1
C
15.64
-9.040
16.449
4.758
A
O4
DM1
7
HETATM
B
O4
DM1
2
1.00
1
O
12.38
-11.421
16.360
4.832
A
C5
DM1
7
HETATM
B
C5
DM1
2
1.00
1
C
12.54
-11.421
14.950
4.790
A
C6
DM1
7
HETATM
B
C6
DM1
2
1.00
1
C
15.10
-10.232
14.264
4.700
A
O6
DM1
7
HETATM
B
O6
DM1
2
1.00
1
O
10.91
-12.611
14.214
4.816
A
C7
DM1
7
HETATM
B
C7
DM1
2
1.00
1
C
10.43
-12.639
12.801
4.779
A
C8
DM1
7
HETATM
B
C8
DM1
2
1.00
1
C
18.94
-11.410
12.101
4.705
A
O8
DM1
7
HETATM
B
O8
DM1
2
1.00
1
O
14.70
-13.850
12.079
4.859
A
C9
DM1
7
HETATM
B
C9
DM1
2
1.00
1
C
18.19
-13.761
10.590
4.790
A
C10
DM1
7
HETATM
B
C10
DM1
2
1.00
1
C
18.87
-13.030
10.112
5.911
A
O10
DM1
7
HETATM
B
O10
DM1
2
1.00
1
O
16.52
-15.126
9.855
4.742
A
C11
DM1
7
HETATM
B
C11
DM1
2
1.00
1
C
17.42
-16.270
10.669
5.483
A
C12
DM1
7
HETATM
B
C12
DM1
2
1.00
1
C
15.66
-15.996
10.490
6.873
A
O12
DM1
7
HETATM
B
O12
DM1
2
1.00
1
O
18.95
-17.605
9.958
5.266
A
C13
DM1
7
HETATM
B
C13
DM1
2
1.00
1
C
18.71
-18.030
10.104
4.013
A
O13
DM1
7
HETATM
B
O13
DM1
2
1.00
1
O
19.75
-18.075
8.623
5.826
A
C14
DM1
7
HETATM
B
C14
DM1
2
1.00
1
C
16.32
-16.352
12.118
4.949
A
C15
DM1
7
HETATM
B
C15
DM1
2
1.00
1
C
16.41
-14.997
12.759
4.970
A
C16
DM1
7
HETATM
B
C16
DM1
2
1.00
1
C
12.31
-15.036
14.177
4.964
A
C17
DM1
7
HETATM
B
C17
DM1
2
1.00
1
C
14.72
-16.228
14.785
5.049
A
O17
DM1
7
HETATM
B
O17
DM1
2
1.00
1
O
13.47
-13.850
14.888
4.912
A
C18
DM1
7
HETATM
B
C18
DM1
2
1.00
1
C
12.25
-13.853
16.343
4.970
A
C19
DM1
7
HETATM
B
C19
DM1
2
1.00
1
C
16.51
-14.961
16.875
5.033
A
O19
DM1
7
HETATM
B
O19
DM1
2
1.00
1
O
12.07
-12.613
16.981
4.927
A
C20
DM1
7
HETATM
B
C20
DM1
2
1.00
1
C
16.58
-7.703
17.037
4.716
A
C21
DM1
7
HETATM
B
C21
DM1
2
1.00
1
C
18.06
-12.090
9.253
6.307
A
C1'
DM1
7
HETATM
B
C1'
DM1
2
1.00
1
C
21.89
-11.240
9.720
7.508
A
C2'
DM1
7
HETATM
B
C2'
DM1
2
1.00
1
C
23.51
-12.286
9.846
8.697
A
C3'
DM1
7
HETATM
B
C3'
DM1
2
1.00
1
C
21.68
-11.696
10.344
9.903
A
N3'
DM1
7
HETATM
B
N3'
DM1
2
1.00
1
N
26.18
-13.055
8.450
8.956
A
C4'
DM1
7
HETATM
B
C4'
DM1
2
1.00
1
C
23.29
-12.015
7.465
9.347
A
O4'
DM1
7
HETATM
B
O4'
DM1
2
1.00
1
O
25.34
-12.812
7.585
7.566
A
C5'
DM1
7
HETATM
B
C5'
DM1
2
1.00
1
C
23.07
-12.846
8.039
6.403
A
O5'
DM1
7
HETATM
B
O5'
DM1
2
1.00
1
O
18.53
-14.267
6.866
7.856
A
C6'
DM1
7
HETATM
B
C6'
DM1
2
1.00
1
C
0.035740
0.000000
0.000000
0.000000
0.035740
0.000000
0.000000
0.000000
0.018914
0.00000
0.00000
0.00000
Moore, M.H.
Hunter, W.N.
Langlois D'Estaintot, B.
Kennard, O.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
27.980
27.980
52.870
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
C27 H29 N O10
527.520
DAUNOMYCIN
DAUNORUBICIN
non-polymer
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
Y
108
N
C
Y
109
N
C
Y
110
N
C
Y
111
N
C
N
112
N
O
Y
113
N
C
N
114
N
C
N
115
N
O
Y
116
N
C
Y
117
N
C
N
118
N
O
Y
119
N
C
N
120
S
C
N
121
N
O
N
122
N
C
N
123
S
C
N
124
N
O
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
C
Y
129
N
C
Y
130
N
C
N
131
N
O
Y
132
N
C
N
133
N
C
N
134
N
O
Y
135
N
C
N
136
N
C
N
137
R
C
N
138
N
C
N
139
S
C
N
140
N
N
N
141
S
C
N
142
N
O
N
143
S
C
N
144
N
O
N
145
N
C
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
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
O
N
176
N
P
N
177
N
O
N
178
N
O
N
179
N
O
N
180
N
C
N
181
R
C
N
182
N
O
N
183
S
C
N
184
N
O
N
185
N
C
N
186
R
C
N
187
N
N
N
188
N
C
N
189
N
O
N
190
N
N
N
191
N
C
N
192
N
O
N
193
N
C
N
194
N
C
N
195
N
C
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
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
Y
113
N
doub
Y
114
N
sing
N
115
N
sing
Y
116
N
sing
N
117
N
sing
Y
118
N
doub
N
119
N
sing
N
120
N
sing
Y
121
N
sing
N
122
N
sing
N
123
N
sing
Y
124
N
doub
N
125
N
doub
N
126
N
sing
Y
127
N
doub
Y
128
N
sing
N
129
N
sing
Y
130
N
sing
N
131
N
sing
N
132
N
sing
Y
133
N
doub
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
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
sing
Y
153
N
sing
N
154
N
sing
Y
155
N
doub
N
156
N
sing
N
157
N
sing
N
158
N
doub
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
sing
N
180
N
sing
N
181
N
sing
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
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
doub
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
doub
N
214
N
sing
N
215
N
sing
N
216
N
doub
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
206
693
705
10.1016/0022-2836(89)90577-9
2738914
DNA-drug interactions. The crystal structure of d(CGATCG) complexed with daunomycin.
1989
10.2210/pdb1da0/pdb
pdb_00001da0
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
277.00
1
DIFFRACTOMETER
SYNTEX P21
x-ray
1
1.0
1809.217
DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
1
syn
polymer
527.520
DAUNOMYCIN
1
syn
non-polymer
no
no
(DC)(DG)(DA)(DT)(DC)(DG)
CGATCG
A
polydeoxyribonucleotide
n
n
n
n
n
n
2.86
56.99
VAPOR DIFFUSION
6.50
pH 6.50, VAPOR DIFFUSION, temperature 293.00K
293.00
WATER
1
MPD
1
MG ACETATE
1
SPERMINE_HCL
1
NA CACODYLATE
1
WATER
2
MPD
2
5.455
1
19
A
1
A
6
-2.537
A_DC1:DG6_A
1
0.849
0.080
-0.022
-0.467
-11.065
1
22
A
2
A
5
6.550
A_DG2:DC5_A
2
-0.030
0.014
-0.201
-0.398
-7.237
1
20
A
3
A
4
-3.874
A_DA3:DT4_A
3
-4.173
-0.601
-0.015
-0.443
7.237
1
20
A
4
A
3
-3.874
A_DT4:DA3_A
4
-4.173
0.601
-0.015
-0.443
11.065
1
22
A
5
A
2
6.550
A_DC5:DG2_A
5
-0.030
-0.014
-0.201
-0.398
-5.455
1
19
A
6
A
1
-2.537
A_DG6:DC1_A
6
0.849
-0.080
-0.022
-0.467
6.687
33.393
A
A
1
2
-7.241
A
A
6
5
6.901
-4.150
1.370
1.205
AA_DC1DG2:DC5DG6_AA
1
-0.454
0.791
33.139
3.530
-2.540
3.479
25.229
A
A
2
3
-3.146
A
A
5
4
3.316
-1.371
-1.788
0.199
AA_DG2DA3:DT4DC5_AA
2
-2.853
6.549
25.033
0.874
3.225
2.937
43.962
A
A
3
4
8.073
A
A
4
3
3.108
6.026
0.000
-1.107
AA_DA3DT4:DA3DT4_AA
3
0.000
0.000
43.567
-2.008
0.000
3.479
25.229
A
A
4
5
-3.146
A
A
3
2
3.316
-1.371
1.788
0.199
AA_DT4DC5:DG2DA3_AA
4
2.853
-6.549
25.033
0.874
-3.225
6.687
33.393
A
A
5
6
-7.241
A
A
2
1
6.901
-4.150
-1.370
1.205
AA_DC5DG6:DC1DG2_AA
5
0.454
-0.791
33.139
3.530
2.540
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
NDB
1992-10-17
REL
DM1
DAUNOMYCIN
DM1
7
2
DM1
DM1
7
A
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
A
3
n
3
DA
3
A
T
4
n
4
DT
4
A
C
5
n
5
DC
5
A
G
6
n
6
DG
6
A
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
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
8_555
-y,-x,-z+1/2
crystal symmetry operation
0.0000000000
0.0000000000
26.4350000000
1
A
C5'
DM1
7
WRONG HAND
1
14.85
1.10
109.80
124.65
A
A
A
C5'
C4'
O4'
DC
DC
DC
1
1
1
N
1
6.49
0.70
110.30
116.79
A
A
A
C1'
O4'
C4'
DC
DC
DC
1
1
1
N
1
6.91
0.30
108.30
115.21
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
3.38
0.50
119.90
123.28
A
A
A
C2
N3
C4
DC
DC
DC
1
1
1
N
1
3.57
0.50
121.00
124.57
A
A
A
C5
C6
N1
DC
DC
DC
1
1
1
N
1
-5.69
0.70
118.00
112.31
A
A
A
N3
C4
N4
DC
DC
DC
1
1
1
N
1
6.23
0.70
120.20
126.43
A
A
A
C5
C4
N4
DC
DC
DC
1
1
1
N
1
11.98
1.90
104.00
115.98
A
A
A
O3'
P
O5'
DC
DG
DG
1
2
2
Y
1
-6.40
0.80
102.40
96.00
A
A
A
C3'
C2'
C1'
DG
DG
DG
2
2
2
N
1
3.02
0.30
108.30
111.32
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
-5.01
0.60
125.10
120.09
A
A
A
C6
N1
C2
DG
DG
DG
2
2
2
N
1
5.66
0.50
111.50
117.16
A
A
A
C5
C6
N1
DG
DG
DG
2
2
2
N
1
3.05
0.40
106.40
109.45
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
14.28
1.20
119.70
133.98
A
A
A
C3'
O3'
P
DG
DG
DA
2
2
3
Y
1
7.86
1.10
110.50
118.36
A
A
A
O3'
P
OP1
DG
DA
DA
2
3
3
Y
1
-24.51
1.50
119.60
95.09
A
A
A
OP1
P
OP2
DA
DA
DA
3
3
3
N
1
-6.33
0.80
109.40
103.07
A
A
A
O5'
C5'
C4'
DA
DA
DA
3
3
3
N
1
13.08
1.60
120.90
133.98
A
A
A
P
O5'
C5'
DA
DA
DA
3
3
3
N
1
4.46
0.30
108.30
112.76
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
1
3.87
0.60
118.60
122.47
A
A
A
C6
N1
C2
DA
DA
DA
3
3
3
N
1
-7.75
0.50
129.30
121.55
A
A
A
N1
C2
N3
DA
DA
DA
3
3
3
N
1
6.29
0.50
110.60
116.89
A
A
A
C2
N3
C4
DA
DA
DA
3
3
3
N
1
-3.06
0.50
117.00
113.94
A
A
A
C4
C5
C6
DA
DA
DA
3
3
3
N
1
-3.66
0.60
118.60
114.94
A
A
A
N1
C6
N6
DA
DA
DA
3
3
3
N
1
14.04
1.20
119.70
133.74
A
A
A
C3'
O3'
P
DA
DA
DT
3
3
4
Y
1
-10.93
1.50
119.60
108.67
A
A
A
OP1
P
OP2
DT
DT
DT
4
4
4
N
1
10.58
1.20
110.70
121.28
A
A
A
O5'
P
OP1
DT
DT
DT
4
4
4
N
1
-7.54
0.80
105.90
98.36
A
A
A
O4'
C1'
C2'
DT
DT
DT
4
4
4
N
1
-5.78
0.60
127.20
121.42
A
A
A
C2
N3
C4
DT
DT
DT
4
4
4
N
1
7.28
0.60
115.20
122.48
A
A
A
N3
C4
C5
DT
DT
DT
4
4
4
N
1
9.94
0.80
123.10
133.04
A
A
A
N1
C2
O2
DT
DT
DT
4
4
4
N
1
-12.31
0.60
122.30
109.99
A
A
A
N3
C2
O2
DT
DT
DT
4
4
4
N
1
-6.03
0.60
119.90
113.87
A
A
A
N3
C4
O4
DT
DT
DT
4
4
4
N
1
20.76
1.50
119.60
140.36
A
A
A
OP1
P
OP2
DC
DC
DC
5
5
5
N
1
-8.38
0.80
109.40
101.02
A
A
A
O5'
C5'
C4'
DC
DC
DC
5
5
5
N
1
-5.93
0.80
105.90
99.97
A
A
A
O4'
C1'
C2'
DC
DC
DC
5
5
5
N
1
22.89
0.30
108.30
131.19
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
6.43
0.60
118.90
125.33
A
A
A
N1
C2
O2
DC
DC
DC
5
5
5
N
1
-6.24
0.70
121.90
115.66
A
A
A
N3
C2
O2
DC
DC
DC
5
5
5
N
1
8.48
0.70
118.00
126.48
A
A
A
N3
C4
N4
DC
DC
DC
5
5
5
N
1
-6.61
0.70
120.20
113.59
A
A
A
C5
C4
N4
DC
DC
DC
5
5
5
N
1
-9.48
1.20
119.70
110.22
A
A
A
C3'
O3'
P
DC
DC
DG
5
5
6
Y
1
10.21
1.50
119.60
129.81
A
A
A
OP1
P
OP2
DG
DG
DG
6
6
6
N
1
-5.85
0.90
105.70
99.85
A
A
A
O5'
P
OP2
DG
DG
DG
6
6
6
N
1
-14.11
0.80
109.40
95.29
A
A
A
O5'
C5'
C4'
DG
DG
DG
6
6
6
N
1
-5.80
0.70
108.00
102.20
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
-3.80
0.60
125.10
121.30
A
A
A
C6
N1
C2
DG
DG
DG
6
6
6
N
1
3.38
0.50
111.50
114.88
A
A
A
C5
C6
N1
DG
DG
DG
6
6
6
N
1
-2.57
0.40
110.80
108.23
A
A
A
C4
C5
N7
DG
DG
DG
6
6
6
N
1
3.26
0.40
105.40
108.66
A
A
A
N9
C4
C5
DG
DG
DG
6
6
6
N
1
3.61
0.60
130.40
134.01
A
A
A
C6
C5
N7
DG
DG
DG
6
6
6
N
1
10.90
0.90
116.20
127.10
A
A
A
N1
C2
N2
DG
DG
DG
6
6
6
N
1
-13.87
0.70
119.90
106.03
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
1
A
A
O3'
P
DC
DG
1
2
-0.082
0.012
1.607
1.525
Y
1
A
A
C2
N3
DG
DG
2
2
0.058
0.008
1.323
1.381
N
1
A
A
C8
N9
DG
DG
2
2
-0.056
0.007
1.374
1.318
N
1
A
A
O3'
P
DG
DA
2
3
-0.127
0.012
1.607
1.480
Y
1
A
A
P
OP1
DA
DA
3
3
0.143
0.017
1.485
1.628
N
1
A
A
P
O5'
DT
DT
4
4
-0.066
0.010
1.593
1.527
N
1
A
A
P
O5'
DG
DG
6
6
-0.068
0.010
1.593
1.525
N
1
A
A
N2
O2
DG
DC
2
5
1.96
1_555
8_555
0.2500000
1.500
10.000
1845
1
5.000
TR
isotropic
1.500
10.000
0
158
38
120
0
fix
1.500
1DA0
3529
2801
2.000
0.0900000
1
refinement
NUCLSQ
DNA-DRUG INTERACTIONS: THE CRYSTAL STRUCTURE OF D(CGATCG) COMPLEXED WITH DAUNOMYCIN
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
6
A
N1
DG
6
8_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
6
A
O6
DG
6
8_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
6
A
N2
DG
6
8_555
hydrog
REVERSED WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
A
DC
5
A
O2
DC
5
8_555
hydrog
REVERSED WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
A
DC
5
A
N3
DC
5
8_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
A
DT
4
A
N3
DT
4
8_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
A
DT
4
A
O4
DT
4
8_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
A
DA
3
A
N1
DA
3
8_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
A
DA
3
A
N6
DA
3
8_555
hydrog
REVERSED WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
A
DG
2
A
N2
DG
2
8_555
hydrog
REVERSED WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
A
DG
2
A
N1
DG
2
8_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
A
DC
1
A
N3
DC
1
8_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
A
DC
1
A
O2
DC
1
8_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
A
DC
1
A
N4
DC
1
8_555
DNA
RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA
1DA0
PDB
1
1DA0
1
6
1DA0
1
6
1DA0
A
1
1
6
BINDING SITE FOR RESIDUE DM1 A 7
A
DM1
7
Software
6
A
DC
1
A
DC
1
6
8_555
A
DG
2
A
DG
2
6
8_555
A
DA
3
A
DA
3
6
8_555
A
DT
4
A
DT
4
6
1_555
A
DC
5
A
DC
5
6
1_555
A
DG
6
A
DG
6
6
1_555
92
P 41 21 2