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1
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1
1
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16.33
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1
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1
1
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16.33
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1
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1
1
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1
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17.03
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1
1
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20.53
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1
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1
1
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26.22
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1
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1
1
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22.12
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1
1
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13.81
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1
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1
1
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9.30
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1
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1
1
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1
N
11.32
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A
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1
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1
1
1.00
1
C
15.50
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A
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1
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1
1
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1
N
12.26
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1
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1
1
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1
C
15.09
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1
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1
1
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1
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12.47
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1
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1
1
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O
12.23
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A
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1
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1
1
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1
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11.62
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A
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1
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1
1
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1
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8.93
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1
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1
1
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6.23
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1
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1
1
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12.50
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1
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1
1
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1
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27.57
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2
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1
2
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28.30
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2
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1
2
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20.33
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2
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15.55
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2
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17.04
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2
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16.71
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2
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36.44
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2
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12.71
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2
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10.85
6.895
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2
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1
2
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13.97
6.966
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2
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1
2
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16.12
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2
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2
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6.28
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2
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1
2
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8.33
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2
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2
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16.07
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3.41
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2
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9.33
6.240
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2
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1
2
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6.33
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2
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1
2
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11.38
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2
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9.10
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2
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35.95
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3
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3
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35.97
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3
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1
3
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32.85
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3
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9.143
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3
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3
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11.584
0.380
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3
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3
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3
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11.374
2.394
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3
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10.365
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0.349
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3
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24.90
9.261
9.511
0.169
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3
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18.74
9.500
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1
3
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17.19
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3
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1
3
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22.97
9.006
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3
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1
3
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O
16.14
9.561
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1
3
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17.55
9.917
6.567
-2.712
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3
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1
3
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15.35
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5.598
-3.600
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3
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1
3
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16.34
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-3.083
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3
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1
3
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14.49
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-2.136
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3
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1
3
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39.51
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4
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1
4
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37.31
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4
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1
4
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O
33.41
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4
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4
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33.56
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4
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10.582
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4
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30.53
11.504
8.437
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4
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4
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32.53
11.622
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4
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33.57
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4
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42.58
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4
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4
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31.37
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4
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26.40
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4
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4
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16.59
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4
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1
4
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18.63
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4
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1
4
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16.21
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4
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1
4
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7.42
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-0.292
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4
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1
4
1.00
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10.49
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4
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1
4
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16.57
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4
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1
4
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O
2.00
12.784
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4
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1
4
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5.89
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4
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1
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5.35
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4
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1
4
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7.80
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4
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8.33
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4
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1
4
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C
47.01
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5
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1
5
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P
52.64
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5
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1
5
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O
44.52
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5
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1
5
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O
41.71
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5
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40.60
13.323
5.459
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5
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1
5
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38.37
14.013
4.259
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5
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1
5
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36.12
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4.402
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5
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O
37.53
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5
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5
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44.86
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5
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1
5
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O
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5
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1
5
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29.15
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1
5
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C
25.34
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3.936
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5
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A
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1
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N
22.58
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2.756
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5
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1
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C
28.49
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5
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1
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O
22.01
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5
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1
5
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21.09
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6.024
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5
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1
5
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C
18.87
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6.576
0.371
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5
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1
5
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14.76
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2.745
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5
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1
5
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21.18
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6.186
3.904
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5
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1
5
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C
51.81
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2.105
8.795
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6
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1
6
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57.73
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1.086
9.704
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6
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1
6
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O
50.64
17.442
3.279
9.369
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6
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1
6
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47.07
17.693
1.312
7.810
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6
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6
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45.33
17.668
1.587
6.404
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6
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6
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39.78
18.072
0.356
5.628
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6
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1
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36.75
18.016
0.730
4.237
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6
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1
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40.35
19.519
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5.886
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6
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1
6
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46.40
19.718
-1.407
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6
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1
6
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36.69
20.277
0.838
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6
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1
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28.95
19.317
1.017
3.753
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6
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1
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20.03
19.312
2.391
3.260
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6
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1
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21.50
19.371
2.602
1.891
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6
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1
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21.59
19.362
1.619
1.138
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6
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1
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O
18.29
19.433
3.862
1.415
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6
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1
6
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19.91
19.427
4.886
2.263
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6
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1
6
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23.81
19.515
6.109
1.746
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6
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1
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20.39
19.335
4.699
3.674
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6
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1
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18.50
19.275
3.443
4.125
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6
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1
6
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56.77
23.373
5.014
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7
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B
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1
1
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46.25
22.133
4.560
-8.660
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B
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DG
1
1
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42.25
21.687
3.265
-8.022
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ATOM
B
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1
1
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44.02
21.636
3.431
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ATOM
B
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1
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44.64
20.283
2.835
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7
ATOM
B
C3'
DG
1
1
1.00
1
C
49.40
20.247
1.401
-8.444
B
O3'
DG
7
ATOM
B
O3'
DG
1
1
1.00
1
O
42.79
19.414
3.376
-7.324
B
C2'
DG
7
ATOM
B
C2'
DG
1
1
1.00
1
C
37.42
20.317
3.196
-6.116
B
C1'
DG
7
ATOM
B
C1'
DG
1
1
1.00
1
C
27.07
20.069
4.108
-5.005
B
N9
DG
7
ATOM
B
N9
DG
1
1
1.00
1
N
20.63
19.966
5.475
-5.058
B
C8
DG
7
ATOM
B
C8
DG
1
1
1.00
1
C
21.77
19.772
6.018
-3.884
B
N7
DG
7
ATOM
B
N7
DG
1
1
1.00
1
N
10.16
19.741
4.944
-3.005
B
C5
DG
7
ATOM
B
C5
DG
1
1
1.00
1
C
18.53
19.567
4.914
-1.605
B
C6
DG
7
ATOM
B
C6
DG
1
1
1.00
1
C
22.77
19.422
5.865
-0.822
B
O6
DG
7
ATOM
B
O6
DG
1
1
1.00
1
O
12.43
19.586
3.612
-1.114
B
N1
DG
7
ATOM
B
N1
DG
1
1
1.00
1
N
15.02
19.765
2.490
-1.877
B
C2
DG
7
ATOM
B
C2
DG
1
1
1.00
1
C
15.20
19.754
1.323
-1.221
B
N2
DG
7
ATOM
B
N2
DG
1
1
1.00
1
N
16.77
19.942
2.506
-3.186
B
N3
DG
7
ATOM
B
N3
DG
1
1
1.00
1
N
19.58
19.914
3.759
-3.680
B
C4
DG
7
ATOM
B
C4
DG
1
1
1.00
1
C
48.68
18.974
0.631
-9.049
B
P
DG
8
ATOM
B
P
DG
1
2
1.00
1
P
49.16
19.474
-0.453
-9.936
B
OP1
DG
8
ATOM
B
OP1
DG
1
2
1.00
1
O
49.40
18.033
1.650
-9.583
B
OP2
DG
8
ATOM
B
OP2
DG
1
2
1.00
1
O
41.70
18.338
-0.064
-7.769
B
O5'
DG
8
ATOM
B
O5'
DG
1
2
1.00
1
O
39.74
19.188
-0.651
-6.780
B
C5'
DG
8
ATOM
B
C5'
DG
1
2
1.00
1
C
39.99
18.355
-1.417
-5.781
B
C4'
DG
8
ATOM
B
C4'
DG
1
2
1.00
1
C
45.96
18.056
-0.574
-4.644
B
O4'
DG
8
ATOM
B
O4'
DG
1
2
1.00
1
O
39.68
17.008
-1.830
-6.366
B
C3'
DG
8
ATOM
B
C3'
DG
1
2
1.00
1
C
44.64
16.625
-3.064
-5.735
B
O3'
DG
8
ATOM
B
O3'
DG
1
2
1.00
1
O
39.13
16.108
-0.674
-5.968
B
C2'
DG
8
ATOM
B
C2'
DG
1
2
1.00
1
C
36.76
16.678
-0.211
-4.635
B
C1'
DG
8
ATOM
B
C1'
DG
1
2
1.00
1
C
26.47
16.596
1.225
-4.371
B
N9
DG
8
ATOM
B
N9
DG
1
2
1.00
1
N
24.48
16.693
2.250
-5.282
B
C8
DG
8
ATOM
B
C8
DG
1
2
1.00
1
C
26.18
16.623
3.434
-4.731
B
N7
DG
8
ATOM
B
N7
DG
1
2
1.00
1
N
19.94
16.467
3.177
-3.376
B
C5
DG
8
ATOM
B
C5
DG
1
2
1.00
1
C
20.91
16.342
4.074
-2.271
B
C6
DG
8
ATOM
B
C6
DG
1
2
1.00
1
C
21.12
16.368
5.314
-2.264
B
O6
DG
8
ATOM
B
O6
DG
1
2
1.00
1
O
16.13
16.186
3.387
-1.076
B
N1
DG
8
ATOM
B
N1
DG
1
2
1.00
1
N
18.90
16.157
2.019
-0.959
B
C2
DG
8
ATOM
B
C2
DG
1
2
1.00
1
C
18.94
15.956
1.545
0.276
B
N2
DG
8
ATOM
B
N2
DG
1
2
1.00
1
N
13.77
16.297
1.176
-1.970
B
N3
DG
8
ATOM
B
N3
DG
1
2
1.00
1
N
19.03
16.437
1.819
-3.140
B
C4
DG
8
ATOM
B
C4
DG
1
2
1.00
1
C
44.37
15.216
-3.754
-6.081
B
P
DC
9
ATOM
B
P
DC
1
3
1.00
1
P
47.58
15.416
-5.213
-5.902
B
OP1
DC
9
ATOM
B
OP1
DC
1
3
1.00
1
O
39.84
14.672
-3.232
-7.365
B
OP2
DC
9
ATOM
B
OP2
DC
1
3
1.00
1
O
40.12
14.276
-3.266
-4.893
B
O5'
DC
9
ATOM
B
O5'
DC
1
3
1.00
1
O
33.07
14.724
-3.345
-3.532
B
C5'
DC
9
ATOM
B
C5'
DC
1
3
1.00
1
C
29.51
13.612
-2.933
-2.595
B
C4'
DC
9
ATOM
B
C4'
DC
1
3
1.00
1
C
29.59
13.664
-1.516
-2.320
B
O4'
DC
9
ATOM
B
O4'
DC
1
3
1.00
1
O
32.97
12.208
-3.191
-3.139
B
C3'
DC
9
ATOM
B
C3'
DC
1
3
1.00
1
C
40.73
11.384
-3.395
-1.987
B
O3'
DC
9
ATOM
B
O3'
DC
1
3
1.00
1
O
24.93
11.846
-1.840
-3.728
B
C2'
DC
9
ATOM
B
C2'
DC
1
3
1.00
1
C
18.03
12.411
-0.943
-2.649
B
C1'
DC
9
ATOM
B
C1'
DC
1
3
1.00
1
C
8.15
12.638
0.444
-3.040
B
N1
DC
9
ATOM
B
N1
DC
1
3
1.00
1
N
13.97
12.680
1.414
-2.041
B
C2
DC
9
ATOM
B
C2
DC
1
3
1.00
1
C
14.50
12.519
1.055
-0.854
B
O2
DC
9
ATOM
B
O2
DC
1
3
1.00
1
O
6.11
12.893
2.706
-2.384
B
N3
DC
9
ATOM
B
N3
DC
1
3
1.00
1
N
7.55
13.062
3.024
-3.667
B
C4
DC
9
ATOM
B
C4
DC
1
3
1.00
1
C
9.93
13.279
4.296
-3.976
B
N4
DC
9
ATOM
B
N4
DC
1
3
1.00
1
N
4.90
13.018
2.050
-4.699
B
C5
DC
9
ATOM
B
C5
DC
1
3
1.00
1
C
6.04
12.805
0.784
-4.345
B
C6
DC
9
ATOM
B
C6
DC
1
3
1.00
1
C
43.27
10.356
-4.626
-1.927
B
P
DG
10
ATOM
B
P
DG
1
4
1.00
1
P
44.18
11.148
-5.880
-1.808
B
OP1
DG
10
ATOM
B
OP1
DG
1
4
1.00
1
O
43.69
9.346
-4.487
-3.005
B
OP2
DG
10
ATOM
B
OP2
DG
1
4
1.00
1
O
38.97
9.670
-4.366
-0.520
B
O5'
DG
10
ATOM
B
O5'
DG
1
4
1.00
1
O
34.26
10.504
-4.119
0.621
B
C5'
DG
10
ATOM
B
C5'
DG
1
4
1.00
1
C
28.78
9.873
-3.083
1.518
B
C4'
DG
10
ATOM
B
C4'
DG
1
4
1.00
1
C
31.50
10.046
-1.768
0.952
B
O4'
DG
10
ATOM
B
O4'
DG
1
4
1.00
1
O
29.12
8.371
-3.280
1.683
B
C3'
DG
10
ATOM
B
C3'
DG
1
4
1.00
1
C
34.90
8.082
-2.998
3.051
B
O3'
DG
10
ATOM
B
O3'
DG
1
4
1.00
1
O
28.14
7.769
-2.235
0.763
B
C2'
DG
10
ATOM
B
C2'
DG
1
4
1.00
1
C
19.68
8.797
-1.122
0.802
B
C1'
DG
10
ATOM
B
C1'
DG
1
4
1.00
1
C
11.79
8.869
-0.328
-0.416
B
N9
DG
10
ATOM
B
N9
DG
1
4
1.00
1
N
15.93
8.858
-0.795
-1.704
B
C8
DG
10
ATOM
B
C8
DG
1
4
1.00
1
C
17.05
8.951
0.158
-2.594
B
N7
DG
10
ATOM
B
N7
DG
1
4
1.00
1
N
13.38
9.022
1.325
-1.843
B
C5
DG
10
ATOM
B
C5
DG
1
4
1.00
1
C
13.37
9.128
2.686
-2.251
B
C6
DG
10
ATOM
B
C6
DG
1
4
1.00
1
C
19.22
9.171
3.152
-3.394
B
O6
DG
10
ATOM
B
O6
DG
1
4
1.00
1
O
5.60
9.176
3.546
-1.165
B
N1
DG
10
ATOM
B
N1
DG
1
4
1.00
1
N
10.60
9.122
3.155
0.142
B
C2
DG
10
ATOM
B
C2
DG
1
4
1.00
1
C
16.20
9.179
4.140
1.045
B
N2
DG
10
ATOM
B
N2
DG
1
4
1.00
1
N
15.15
9.017
1.897
0.541
B
N3
DG
10
ATOM
B
N3
DG
1
4
1.00
1
N
13.26
8.974
1.041
-0.499
B
C4
DG
10
ATOM
B
C4
DG
1
4
1.00
1
C
41.60
6.637
-3.347
3.645
B
P
DC
11
ATOM
B
P
DC
1
5
1.00
1
P
39.72
6.860
-3.865
5.019
B
OP1
DC
11
ATOM
B
OP1
DC
1
5
1.00
1
O
35.45
5.878
-4.160
2.651
B
OP2
DC
11
ATOM
B
OP2
DC
1
5
1.00
1
O
39.77
5.960
-1.915
3.771
B
O5'
DC
11
ATOM
B
O5'
DC
1
5
1.00
1
O
36.78
6.699
-0.826
4.333
B
C5'
DC
11
ATOM
B
C5'
DC
1
5
1.00
1
C
33.68
6.012
0.484
4.027
B
C4'
DC
11
ATOM
B
C4'
DC
1
5
1.00
1
C
32.06
6.340
0.918
2.692
B
O4'
DC
11
ATOM
B
O4'
DC
1
5
1.00
1
O
32.99
4.486
0.410
4.087
B
C3'
DC
11
ATOM
B
C3'
DC
1
5
1.00
1
C
39.60
4.027
1.318
5.093
B
O3'
DC
11
ATOM
B
O3'
DC
1
5
1.00
1
O
33.92
4.026
0.891
2.722
B
C2'
DC
11
ATOM
B
C2'
DC
1
5
1.00
1
C
24.36
5.235
1.626
2.178
B
C1'
DC
11
ATOM
B
C1'
DC
1
5
1.00
1
C
21.06
5.342
1.623
0.713
B
N1
DC
11
ATOM
B
N1
DC
1
5
1.00
1
N
14.91
5.511
2.836
0.047
B
C2
DC
11
ATOM
B
C2
DC
1
5
1.00
1
C
18.38
5.574
3.878
0.712
B
O2
DC
11
ATOM
B
O2
DC
1
5
1.00
1
O
10.24
5.602
2.841
-1.296
B
N3
DC
11
ATOM
B
N3
DC
1
5
1.00
1
N
11.98
5.527
1.692
-1.972
B
C4
DC
11
ATOM
B
C4
DC
1
5
1.00
1
C
13.91
5.594
1.736
-3.309
B
N4
DC
11
ATOM
B
N4
DC
1
5
1.00
1
N
3.87
5.372
0.444
-1.316
B
C5
DC
11
ATOM
B
C5
DC
1
5
1.00
1
C
11.38
5.280
0.453
0.014
B
C6
DC
11
ATOM
B
C6
DC
1
5
1.00
1
C
41.38
2.539
1.172
5.677
B
P
DC
12
ATOM
B
P
DC
1
6
1.00
1
P
43.41
2.652
1.130
7.157
B
OP1
DC
12
ATOM
B
OP1
DC
1
6
1.00
1
O
42.97
1.826
0.083
4.954
B
OP2
DC
12
ATOM
B
OP2
DC
1
6
1.00
1
O
40.23
1.877
2.563
5.290
B
O5'
DC
12
ATOM
B
O5'
DC
1
6
1.00
1
O
31.82
2.469
3.786
5.750
B
C5'
DC
12
ATOM
B
C5'
DC
1
6
1.00
1
C
21.97
2.094
4.916
4.822
B
C4'
DC
12
ATOM
B
C4'
DC
1
6
1.00
1
C
19.50
2.641
4.628
3.527
B
O4'
DC
12
ATOM
B
O4'
DC
1
6
1.00
1
O
15.59
0.594
5.041
4.603
B
C3'
DC
12
ATOM
B
C3'
DC
1
6
1.00
1
C
23.29
0.125
5.939
5.611
B
O3'
DC
12
ATOM
B
O3'
DC
1
6
1.00
1
O
11.53
0.488
5.495
3.158
B
C2'
DC
12
ATOM
B
C2'
DC
1
6
1.00
1
C
7.60
1.869
5.298
2.554
B
C1'
DC
12
ATOM
B
C1'
DC
1
6
1.00
1
C
4.54
1.918
4.490
1.333
B
N1
DC
12
ATOM
B
N1
DC
1
6
1.00
1
N
4.61
2.117
5.130
0.128
B
C2
DC
12
ATOM
B
C2
DC
1
6
1.00
1
C
14.37
2.195
6.364
0.119
B
O2
DC
12
ATOM
B
O2
DC
1
6
1.00
1
O
5.10
2.216
4.404
-1.001
B
N3
DC
12
ATOM
B
N3
DC
1
6
1.00
1
N
4.60
2.102
3.081
-0.950
B
C4
DC
12
ATOM
B
C4
DC
1
6
1.00
1
C
6.34
2.219
2.415
-2.091
B
N4
DC
12
ATOM
B
N4
DC
1
6
1.00
1
N
3.77
1.868
2.393
0.269
B
C5
DC
12
ATOM
B
C5
DC
1
6
1.00
1
C
7.19
1.786
3.133
1.381
B
C6
DC
12
ATOM
B
C6
DC
1
6
1.00
1
C
63.10
15.197
8.674
-3.814
A
MG
MG
13
HETATM
C
MG
MG
2
1.00
1
MG
5.31
3.533
3.534
-7.911
A
CO
NCO
14
HETATM
D
CO
NCO
3
0.50
1
CO
9.38
3.138
1.834
-8.689
A
N1
NCO
14
HETATM
D
N1
NCO
3
1.00
1
N
8.11
3.982
2.526
-6.346
A
N2
NCO
14
HETATM
D
N2
NCO
3
1.00
1
N
59.32
9.870
9.870
-7.910
A
O
HOH
15
HETATM
E
O
HOH
4
0.50
1
O
55.46
16.653
9.105
0.302
A
O
HOH
20
HETATM
E
O
HOH
4
1.00
1
O
57.99
0.442
6.358
-9.085
A
O
HOH
22
HETATM
E
O
HOH
4
1.00
1
O
54.51
3.559
10.301
-2.436
A
O
HOH
24
HETATM
E
O
HOH
4
1.00
1
O
61.62
11.558
4.365
3.684
A
O
HOH
25
HETATM
E
O
HOH
4
1.00
1
O
66.01
19.804
-0.545
0.970
A
O
HOH
26
HETATM
E
O
HOH
4
1.00
1
O
64.92
13.844
9.800
-2.819
A
O
HOH
28
HETATM
E
O
HOH
4
1.00
1
O
68.18
13.738
7.368
-4.296
A
O
HOH
32
HETATM
E
O
HOH
4
1.00
1
O
95.18
5.242
-1.335
-4.314
B
O
HOH
16
HETATM
F
O
HOH
4
1.00
1
O
52.56
8.046
-1.409
-4.511
B
O
HOH
17
HETATM
F
O
HOH
4
1.00
1
O
45.30
1.585
-0.522
-1.910
B
O
HOH
18
HETATM
F
O
HOH
4
1.00
1
O
37.91
19.419
7.889
-2.437
B
O
HOH
19
HETATM
F
O
HOH
4
1.00
1
O
41.21
2.965
-2.965
7.920
B
O
HOH
21
HETATM
F
O
HOH
4
0.50
1
O
56.55
0.901
8.544
1.281
B
O
HOH
23
HETATM
F
O
HOH
4
1.00
1
O
63.07
16.538
7.542
-4.817
B
O
HOH
27
HETATM
F
O
HOH
4
1.00
1
O
64.54
15.581
7.643
-2.114
B
O
HOH
29
HETATM
F
O
HOH
4
1.00
1
O
64.42
14.825
9.703
-5.502
B
O
HOH
30
HETATM
F
O
HOH
4
1.00
1
O
65.39
16.649
9.982
-3.335
B
O
HOH
31
HETATM
F
O
HOH
4
1.00
1
O
0.023480
0.000000
0.000000
0.000000
0.023480
0.000000
0.000000
0.000000
0.015798
0.00000
0.00000
0.00000
Vargason, J.M.
Eichman, B.F.
Ho, P.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
42.590
42.590
63.300
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
H2 O
18.015
WATER
non-polymer
Mg 2
24.305
MAGNESIUM ION
non-polymer
Co H18 N6 3
161.116
COBALT HEXAMMINE(III)
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
N
13
N
N
N
14
N
C
N
15
N
O
N
16
N
N
N
17
N
C
N
18
N
N
N
19
N
C
N
20
N
C
N
21
N
H
N
22
N
H
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
O
N
36
N
P
N
37
N
O
N
38
N
O
N
39
N
O
N
40
N
C
N
41
R
C
N
42
N
O
N
43
S
C
N
44
N
O
N
45
N
C
N
46
R
C
Y
47
N
N
Y
48
N
C
Y
49
N
N
Y
50
N
C
N
51
N
C
N
52
N
O
N
53
N
N
N
54
N
C
N
55
N
N
N
56
N
N
Y
57
N
C
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
H
N
72
N
O
N
73
N
H
N
74
N
H
N
75
N
MG
N
76
N
CO
N
77
N
N
N
78
N
N
N
79
N
N
N
80
N
N
N
81
N
N
N
82
N
N
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
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
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
N
25
N
sing
N
26
N
doub
N
27
N
sing
N
28
N
doub
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
doub
N
39
N
sing
N
40
N
sing
N
41
N
sing
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
Y
59
N
sing
Y
60
N
sing
Y
61
N
doub
N
62
N
sing
Y
63
N
sing
N
64
N
sing
Y
65
N
doub
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
sing
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
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
7
758
761
10.1038/78985
10966645
The extended and eccentric E-DNA structure induced by cytosine methylation or bromination.
2000
10.2210/pdb1f69/pdb
pdb_00001f69
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298
1
IMAGE PLATE
1999-01-27
RIGAKU RAXIS IV
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU300
1810.205
DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
2
syn
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
161.116
COBALT HEXAMMINE(III)
1
syn
non-polymer
18.015
water
18
nat
water
no
no
(DG)(DG)(DC)(DG)(DC)(DC)
GGCGCC
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
1
3.76
67.33
VAPOR DIFFUSION, SITTING DROP
6.0
MGCL2, CO(NH3)6, SPERMINE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
MGCL2
1
CO(NH3)6
1
SPERMINE
1
SODIUM CACODYLATE
1
MGCL2
2
1.550
1
19
A
1
B
12
-0.671
A_DG1:DC12_B
1
-4.824
0.012
0.244
-0.407
3.872
1
19
A
2
B
11
-2.851
A_DG2:DC11_B
2
-1.000
0.323
0.254
-0.445
-0.524
1
19
A
3
B
10
-3.903
A_DC3:DG10_B
3
-14.341
-0.229
0.308
-0.320
1.145
1
19
A
4
B
9
-5.938
A_DG4:DC9_B
4
0.981
0.208
-0.262
-0.527
3.336
1
19
A
5
B
8
-0.854
A_DC5:DG8_B
5
-9.321
-0.223
0.108
-0.013
2.696
1
19
A
6
B
7
0.813
A_DC6:DG7_B
6
-6.631
0.643
0.109
-0.616
3.297
32.095
A
A
1
2
9.767
B
B
12
11
3.341
5.375
0.410
0.065
AA_DG1DG2:DC11DC12_BB
1
-0.737
1.339
31.645
-0.869
-0.877
3.562
33.943
A
A
2
3
-6.541
B
B
11
10
3.521
-3.809
-0.806
-0.196
AA_DG2DC3:DG10DC11_BB
2
-2.037
3.499
33.675
0.328
1.026
3.581
39.508
A
A
3
4
3.390
B
B
10
9
3.511
2.284
0.407
0.942
AA_DC3DG4:DC9DG10_BB
3
5.527
-8.205
39.071
1.101
0.107
3.352
31.216
A
A
4
5
1.289
B
B
9
8
3.333
0.692
-0.331
0.258
AA_DG4DC5:DG8DC9_BB
4
-4.231
7.886
30.928
0.345
-0.209
3.277
41.383
A
A
5
6
9.109
B
B
8
7
3.315
6.412
0.444
-0.109
AA_DC5DC6:DG7DG8_BB
5
1.674
-2.378
40.872
-0.850
-0.446
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-08-28
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr2_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
B-DNA HEXAMER GGCGCC WITH SPERMINE
A-DNA HEXAMER GGCGM5CC
E-DNA HEXAMER GGCGM5CC
E-DNA HEXAMER GGCGBR5CC
RCSB
Y
RCSB
2000-06-20
REL
REL
MG
MAGNESIUM ION
NCO
COBALT HEXAMMINE(III)
HOH
water
MO6
13
2
MG
MG
13
A
NCO
14
3
NCO
NCO
14
A
HOH
15
4
HOH
HOH
15
A
HOH
20
4
HOH
HOH
20
A
HOH
22
4
HOH
HOH
22
A
HOH
24
4
HOH
HOH
24
A
HOH
25
4
HOH
HOH
25
A
HOH
26
4
HOH
HOH
26
A
MO6
13
4
HOH
HOH
28
A
MO6
13
4
HOH
HOH
32
A
HOH
16
4
HOH
HOH
16
B
HOH
17
4
HOH
HOH
17
B
HOH
18
4
HOH
HOH
18
B
HOH
19
4
HOH
HOH
19
B
HOH
21
4
HOH
HOH
21
B
HOH
23
4
HOH
HOH
23
B
MO6
13
4
HOH
HOH
27
B
MO6
13
4
HOH
HOH
29
B
MO6
13
4
HOH
HOH
30
B
MO6
13
4
HOH
HOH
31
B
G
1
n
1
DG
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
C
5
n
5
DC
5
A
C
6
n
6
DC
6
A
G
7
n
1
DG
7
B
G
8
n
2
DG
8
B
C
9
n
3
DC
9
B
G
10
n
4
DG
10
B
C
11
n
5
DC
11
B
C
12
n
6
DC
12
B
author_defined_assembly
2
dimeric
A
DG
1
A
N7
DG
1
1_555
A
NCO
14
D
CO
NCO
1_555
A
NCO
14
D
N1
NCO
1_555
164.8
A
DG
1
A
N7
DG
1
1_555
A
NCO
14
D
CO
NCO
1_555
A
NCO
14
D
N2
NCO
1_555
90.5
A
NCO
14
D
N1
NCO
1_555
A
NCO
14
D
CO
NCO
1_555
A
NCO
14
D
N2
NCO
1_555
85.0
A
DG
1
A
N7
DG
1
1_555
A
NCO
14
D
CO
NCO
1_555
A
DG
1
A
N7
DG
1
7_554
108.7
A
NCO
14
D
N1
NCO
1_555
A
NCO
14
D
CO
NCO
1_555
A
DG
1
A
N7
DG
1
7_554
86.4
A
NCO
14
D
N2
NCO
1_555
A
NCO
14
D
CO
NCO
1_555
A
DG
1
A
N7
DG
1
7_554
103.4
A
HOH
28
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
A
HOH
32
E
O
HOH
1_555
89.7
A
HOH
28
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
27
F
O
HOH
1_555
179.6
A
HOH
32
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
27
F
O
HOH
1_555
89.9
A
HOH
28
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
29
F
O
HOH
1_555
89.8
A
HOH
32
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
29
F
O
HOH
1_555
90.5
B
HOH
27
F
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
29
F
O
HOH
1_555
90.3
A
HOH
28
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
30
F
O
HOH
1_555
90.2
A
HOH
32
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
30
F
O
HOH
1_555
89.8
B
HOH
27
F
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
30
F
O
HOH
1_555
89.6
B
HOH
29
F
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
30
F
O
HOH
1_555
179.7
A
HOH
28
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
31
F
O
HOH
1_555
90.2
A
HOH
32
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
31
F
O
HOH
1_555
179.8
B
HOH
27
F
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
31
F
O
HOH
1_555
90.2
B
HOH
29
F
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
31
F
O
HOH
1_555
89.7
B
HOH
30
F
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
31
F
O
HOH
1_555
90.0
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
NCO
14
D
NCO
1
A
HOH
15
E
HOH
1
B
HOH
21
F
HOH
0.2790000
0.2050000
0.2136000
0.2134000
2.6
8.0
214
1938
1937
11.
RANDOM
1
THROUGHOUT
2.0
MOLECULAR REPLACEMENT, REAL SPACE TRANSLATION/ROTATION/RIGID BODY SEARCH USING A CUSTOM X-PLOR 3.851 SCRIPT
PARKINSON ET AL.
2.6
8.0
12
262
10
240
0
0.005
1.1
42.5
2.6
500
1F69
2026
2026
0.0
0.0
0.0610000
1
27.0
9.5
99.9
0.2510000
2.60
2.72
9.7
99.9
model building
X-PLOR
refinement
X-PLOR
3.851
data reduction
d*TREK
data scaling
d*TREK
phasing
X-PLOR
CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
metalc
1.944
A
DG
1
A
N7
DG
1
1_555
A
NCO
14
D
CO
NCO
1_555
metalc
1.947
A
DG
1
A
N7
DG
1
7_554
A
NCO
14
D
CO
NCO
1_555
metalc
2.022
A
MG
13
C
MG
MG
1_555
A
HOH
28
E
O
HOH
1_555
metalc
2.017
A
MG
13
C
MG
MG
1_555
A
HOH
32
E
O
HOH
1_555
metalc
2.021
A
MG
13
C
MG
MG
1_555
B
HOH
27
F
O
HOH
1_555
metalc
2.025
A
MG
13
C
MG
MG
1_555
B
HOH
29
F
O
HOH
1_555
metalc
2.012
A
MG
13
C
MG
MG
1_555
B
HOH
30
F
O
HOH
1_555
metalc
2.012
A
MG
13
C
MG
MG
1_555
B
HOH
31
F
O
HOH
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
B
DC
12
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
B
DC
12
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
B
DC
12
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
11
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
11
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
11
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
10
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
10
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
10
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
9
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
9
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
9
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
8
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
8
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
8
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
B
DG
7
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
B
DG
7
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
B
DG
7
B
N2
DG
1
1_555
DNA
B-DNA, E-DNA, DOUBLE HELIX, DNA
1F69
PDB
1
1F69
1
6
1F69
1
6
1F69
A
1
1
6
7
12
1F69
7
12
1F69
B
1
1
6
BINDING SITE FOR RESIDUE MG A 13
A
MG
13
Software
7
BINDING SITE FOR RESIDUE NCO A 14
A
NCO
14
Software
4
A
DG
4
A
DG
4
7
1_555
A
HOH
28
E
HOH
7
1_555
A
HOH
32
E
HOH
7
1_555
B
HOH
27
F
HOH
7
1_555
B
HOH
29
F
HOH
7
1_555
B
HOH
30
F
HOH
7
1_555
B
HOH
31
F
HOH
7
1_555
A
DG
1
A
DG
1
4
7_554
A
DG
1
A
DG
1
4
1_555
A
DG
2
A
DG
2
4
1_555
B
DC
11
B
DC
5
4
1_555
91
tetragonal
P 41 2 2