18.10
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A
O5'
DG
1
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A
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DG
1
1
1.00
1
O
18.87
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A
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1
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A
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DG
1
1
1.00
1
C
16.81
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-8.706
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A
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1
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A
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DG
1
1
1.00
1
C
14.95
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-11.107
A
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1
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A
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DG
1
1
1.00
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O
16.45
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-9.099
-8.994
A
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1
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A
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DG
1
1
1.00
1
C
17.65
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A
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1
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1
1
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O
15.90
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-8.895
A
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1
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A
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1
1
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1
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14.66
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A
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1
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A
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DG
1
1
1.00
1
C
14.19
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A
N9
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1
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A
N9
DG
1
1
1.00
1
N
14.37
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A
C8
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1
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A
C8
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1
1
1.00
1
C
14.55
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-11.637
A
N7
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1
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A
N7
DG
1
1
1.00
1
N
13.59
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A
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1
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A
C5
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1
1
1.00
1
C
14.02
0.357
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A
C6
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1
ATOM
A
C6
DG
1
1
1.00
1
C
14.94
1.480
-13.683
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A
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1
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A
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1
1
1.00
1
O
14.11
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A
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1
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A
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1
1
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1
N
15.12
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-14.576
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A
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1
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A
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1
1
1.00
1
C
17.00
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-8.850
A
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1
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A
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1
1
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1
N
15.39
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-13.565
-9.693
A
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1
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A
N3
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1
1
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1
N
13.98
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A
C4
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1
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A
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1
1
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1
C
18.56
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-6.645
A
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2
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A
P
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1
2
1.00
1
P
20.02
-4.047
-7.003
-5.751
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2
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1
2
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O
19.55
-1.831
-7.414
-7.190
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2
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2
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O
17.54
-2.825
-9.337
-5.865
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2
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2
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O
13.91
-0.754
-12.608
-6.337
A
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A
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1
2
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1
N
16.57
-0.674
-11.418
-6.945
A
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2
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A
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1
2
1.00
1
C
14.34
0.208
-13.601
-6.472
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2
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A
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1
2
1.00
1
C
16.14
0.112
-14.660
-5.810
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2
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A
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1
2
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O
14.52
1.256
-13.313
-7.226
A
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2
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A
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1
2
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1
N
13.84
1.408
-12.147
-7.907
A
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2
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A
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1
2
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14.86
2.402
-12.029
-8.618
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2
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1
2
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O
16.07
0.379
-11.107
-7.744
A
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2
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1
2
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1
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17.05
0.566
-9.808
-8.451
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2
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A
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1
2
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16.96
-1.658
-12.749
-3.968
A
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2
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A
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2
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18.99
-3.863
-9.969
-5.206
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2
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2
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18.04
-3.417
-11.324
-4.678
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2
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2
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16.61
-3.019
-12.113
-5.824
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2
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2
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15.91
-1.909
-12.962
-5.484
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2
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17.41
-2.158
-11.311
-3.884
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2
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A
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2
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22.72
-2.753
-13.951
-2.813
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2
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A
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1
2
0.80
1
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19.28
-1.614
-15.553
-3.155
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2
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A
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1
2
0.80
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22.36
-2.469
-10.904
-2.502
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2
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A
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1
2
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O
28.37
-1.435
-10.096
-1.543
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3
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P
DG
1
3
1.00
1
P
36.95
-1.976
-9.718
-0.244
A
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3
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A
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1
3
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O
31.36
-0.775
-9.074
-2.259
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3
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1
3
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O
29.59
-0.079
-11.033
-1.410
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3
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1
3
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O
28.55
-0.028
-11.989
-0.545
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3
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A
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1
3
1.00
1
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23.83
1.080
-12.983
-0.869
A
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3
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1
3
1.00
1
C
19.59
0.991
-13.468
-2.265
A
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3
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1
3
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O
20.03
2.568
-12.653
-0.745
A
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3
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A
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1
3
1.00
1
C
19.30
2.942
-12.556
0.735
A
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3
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DG
1
3
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1
O
17.86
3.128
-13.921
-1.410
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3
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A
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DG
1
3
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1
C
19.26
2.243
-14.032
-2.660
A
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3
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A
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DG
1
3
1.00
1
C
17.78
2.809
-13.212
-3.718
A
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3
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A
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DG
1
3
1.00
1
N
16.82
2.462
-11.973
-4.191
A
C8
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3
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A
C8
DG
1
3
1.00
1
C
17.70
3.214
-11.578
-5.202
A
N7
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3
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A
N7
DG
1
3
1.00
1
N
14.59
4.171
-12.625
-5.357
A
C5
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3
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A
C5
DG
1
3
1.00
1
C
12.95
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-12.782
-6.298
A
C6
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3
ATOM
A
C6
DG
1
3
1.00
1
C
15.11
5.590
-11.976
-7.116
A
O6
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3
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A
O6
DG
1
3
1.00
1
O
14.10
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-13.998
-6.096
A
N1
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3
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A
N1
DG
1
3
1.00
1
N
13.39
5.603
-14.908
-5.184
A
C2
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3
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A
C2
DG
1
3
1.00
1
C
15.25
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-16.045
-5.177
A
N2
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3
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A
N2
DG
1
3
1.00
1
N
15.07
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-14.784
-4.334
A
N3
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3
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A
N3
DG
1
3
1.00
1
N
15.46
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-13.620
-4.511
A
C4
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3
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A
C4
DG
1
3
1.00
1
C
19.82
4.236
-11.778
1.151
A
P
DG
4
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A
P
DG
1
4
1.00
1
P
22.33
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-11.829
2.679
A
OP1
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4
ATOM
A
OP1
DG
1
4
1.00
1
O
22.01
4.407
-10.530
0.447
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4
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DG
1
4
1.00
1
O
19.09
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-12.750
0.607
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4
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DG
1
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1.00
1
O
18.52
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-14.001
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4
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DG
1
4
1.00
1
C
19.72
6.727
-14.793
0.402
A
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4
ATOM
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C4'
DG
1
4
1.00
1
C
17.10
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-14.857
-1.055
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4
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A
O4'
DG
1
4
1.00
1
O
18.86
8.005
-14.064
0.360
A
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4
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DG
1
4
1.00
1
C
20.17
8.665
-14.476
1.571
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4
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1
4
1.00
1
O
18.46
8.771
-14.687
-0.800
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4
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DG
1
4
1.00
1
C
16.17
7.645
-14.766
-1.822
A
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4
ATOM
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C1'
DG
1
4
1.00
1
C
15.13
7.523
-13.556
-2.615
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N9
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4
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A
N9
DG
1
4
1.00
1
N
15.53
6.695
-12.498
-2.444
A
C8
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4
ATOM
A
C8
DG
1
4
1.00
1
C
15.06
6.801
-11.524
-3.307
A
N7
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4
ATOM
A
N7
DG
1
4
1.00
1
N
15.12
7.843
-11.982
-4.128
A
C5
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4
ATOM
A
C5
DG
1
4
1.00
1
C
14.69
8.432
-11.419
-5.324
A
C6
DG
4
ATOM
A
C6
DG
1
4
1.00
1
C
15.65
8.140
-10.387
-5.904
A
O6
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4
ATOM
A
O6
DG
1
4
1.00
1
O
14.13
9.402
-12.266
-5.828
A
N1
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4
ATOM
A
N1
DG
1
4
1.00
1
N
12.61
9.810
-13.445
-5.278
A
C2
DG
4
ATOM
A
C2
DG
1
4
1.00
1
C
13.71
10.785
-14.123
-5.861
A
N2
DG
4
ATOM
A
N2
DG
1
4
1.00
1
N
14.33
9.219
-14.002
-4.205
A
N3
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4
ATOM
A
N3
DG
1
4
1.00
1
N
13.89
8.247
-13.233
-3.728
A
C4
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4
ATOM
A
C4
DG
1
4
1.00
1
C
22.76
9.469
-13.519
2.511
A
P
DC
5
ATOM
A
P
DC
1
5
1.00
1
P
28.93
9.433
-14.216
3.853
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OP1
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5
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A
OP1
DC
1
5
1.00
1
O
20.83
9.300
-12.241
2.228
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OP2
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5
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A
OP2
DC
1
5
1.00
1
O
26.52
10.943
-14.054
2.137
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5
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DC
1
5
1.00
1
O
19.56
11.927
-13.310
1.813
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5
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A
C5'
DC
1
5
1.00
1
C
18.70
12.708
-13.969
0.701
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5
ATOM
A
C4'
DC
1
5
1.00
1
C
17.32
11.864
-14.127
-0.476
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5
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A
O4'
DC
1
5
1.00
1
O
16.34
13.803
-13.034
0.287
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5
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A
C3'
DC
1
5
1.00
1
C
17.38
15.035
-13.323
1.052
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5
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O3'
DC
1
5
1.00
1
O
15.96
13.958
-13.281
-1.189
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5
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A
C2'
DC
1
5
1.00
1
C
16.54
12.509
-13.526
-1.629
A
C1'
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5
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A
C1'
DC
1
5
1.00
1
C
15.10
11.813
-12.302
-2.051
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N1
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5
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A
N1
DC
1
5
1.00
1
N
13.12
12.105
-11.733
-3.299
A
C2
DC
5
ATOM
A
C2
DC
1
5
1.00
1
C
14.49
12.959
-12.243
-3.937
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O2
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5
ATOM
A
O2
DC
1
5
1.00
1
O
13.72
11.459
-10.651
-3.695
A
N3
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5
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A
N3
DC
1
5
1.00
1
N
12.84
10.508
-10.116
-2.971
A
C4
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5
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A
C4
DC
1
5
1.00
1
C
15.20
9.882
-9.062
-3.435
A
N4
DC
5
ATOM
A
N4
DC
1
5
1.00
1
N
14.78
10.152
-10.641
-1.668
A
C5
DC
5
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A
C5
DC
1
5
1.00
1
C
15.30
10.832
-11.711
-1.258
A
C6
DC
5
ATOM
A
C6
DC
1
5
1.00
1
C
17.91
16.017
-12.246
1.483
A
P
DC
6
ATOM
A
P
DC
1
6
1.00
1
P
21.37
17.068
-12.937
2.281
A
OP1
DC
6
ATOM
A
OP1
DC
1
6
1.00
1
O
17.71
15.325
-11.210
2.029
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OP2
DC
6
ATOM
A
OP2
DC
1
6
1.00
1
O
16.54
16.717
-11.769
0.090
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O5'
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6
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O5'
DC
1
6
1.00
1
O
15.59
17.582
-12.589
-0.508
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C5'
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6
ATOM
A
C5'
DC
1
6
1.00
1
C
15.58
17.979
-11.894
-1.795
A
C4'
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6
ATOM
A
C4'
DC
1
6
1.00
1
C
16.11
16.877
-11.762
-2.745
A
O4'
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6
ATOM
A
O4'
DC
1
6
1.00
1
O
15.35
18.478
-10.467
-1.694
A
C3'
DC
6
ATOM
A
C3'
DC
1
6
1.00
1
C
17.46
19.852
-10.470
-1.293
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O3'
DC
6
ATOM
A
O3'
DC
1
6
1.00
1
O
15.75
18.394
-9.974
-3.161
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C2'
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6
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A
C2'
DC
1
6
1.00
1
C
14.96
17.014
-10.566
-3.556
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C1'
DC
6
ATOM
A
C1'
DC
1
6
1.00
1
C
12.35
15.868
-9.691
-3.242
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N1
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6
ATOM
A
N1
DC
1
6
1.00
1
N
13.68
15.562
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-4.188
A
C2
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6
ATOM
A
C2
DC
1
6
1.00
1
C
14.74
16.333
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-5.134
A
O2
DC
6
ATOM
A
O2
DC
1
6
1.00
1
O
12.39
14.474
-7.960
-4.017
A
N3
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6
ATOM
A
N3
DC
1
6
1.00
1
N
13.75
13.693
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-2.944
A
C4
DC
6
ATOM
A
C4
DC
1
6
1.00
1
C
15.62
12.617
-7.354
-2.811
A
N4
DC
6
ATOM
A
N4
DC
1
6
1.00
1
N
13.97
14.034
-9.121
-1.953
A
C5
DC
6
ATOM
A
C5
DC
1
6
1.00
1
C
13.16
15.097
-9.868
-2.143
A
C6
DC
6
ATOM
A
C6
DC
1
6
1.00
1
C
17.15
20.439
-9.204
-0.493
A
P
DA
7
ATOM
A
P
DA
1
7
1.00
1
P
19.50
21.777
-9.679
0.056
A
OP1
DA
7
ATOM
A
OP1
DA
1
7
1.00
1
O
16.95
19.466
-8.633
0.393
A
OP2
DA
7
ATOM
A
OP2
DA
1
7
1.00
1
O
15.18
20.627
-8.138
-1.648
A
O5'
DA
7
ATOM
A
O5'
DA
1
7
1.00
1
O
16.24
21.552
-8.405
-2.712
A
C5'
DA
7
ATOM
A
C5'
DA
1
7
1.00
1
C
15.95
21.450
-7.234
-3.720
A
C4'
DA
7
ATOM
A
C4'
DA
1
7
1.00
1
C
14.91
20.127
-7.203
-4.322
A
O4'
DA
7
ATOM
A
O4'
DA
1
7
1.00
1
O
15.17
21.576
-5.823
-3.114
A
C3'
DA
7
ATOM
A
C3'
DA
1
7
1.00
1
C
17.18
23.020
-5.528
-3.002
A
O3'
DA
7
ATOM
A
O3'
DA
1
7
1.00
1
O
14.11
20.902
-4.936
-4.098
A
C2'
DA
7
ATOM
A
C2'
DA
1
7
1.00
1
C
14.12
19.705
-5.840
-4.486
A
C1'
DA
7
ATOM
A
C1'
DA
1
7
1.00
1
C
13.02
18.468
-5.667
-3.751
A
N9
DA
7
ATOM
A
N9
DA
1
7
1.00
1
N
13.11
17.968
-6.345
-2.715
A
C8
DA
7
ATOM
A
C8
DA
1
7
1.00
1
C
12.12
16.767
-5.975
-2.339
A
N7
DA
7
ATOM
A
N7
DA
1
7
1.00
1
N
12.68
16.455
-4.959
-3.253
A
C5
DA
7
ATOM
A
C5
DA
1
7
1.00
1
C
13.17
15.304
-4.135
-3.422
A
C6
DA
7
ATOM
A
C6
DA
1
7
1.00
1
C
13.03
14.201
-4.274
-2.644
A
N6
DA
7
ATOM
A
N6
DA
1
7
1.00
1
N
13.87
15.372
-3.239
-4.411
A
N1
DA
7
ATOM
A
N1
DA
1
7
1.00
1
N
12.30
16.471
-3.130
-5.154
A
C2
DA
7
ATOM
A
C2
DA
1
7
1.00
1
C
12.92
17.542
-3.853
-5.088
A
N3
DA
7
ATOM
A
N3
DA
1
7
1.00
1
N
12.38
17.490
-4.800
-4.152
A
C4
DA
7
ATOM
A
C4
DA
1
7
1.00
1
C
18.01
23.540
-4.495
-1.912
A
P
DC
8
ATOM
A
P
DC
1
8
1.00
1
P
18.30
25.037
-4.500
-2.119
A
OP1
DC
8
ATOM
A
OP1
DC
1
8
1.00
1
O
22.28
22.991
-4.820
-0.579
A
OP2
DC
8
ATOM
A
OP2
DC
1
8
1.00
1
O
16.81
22.979
-3.140
-2.238
A
O5'
DC
8
ATOM
A
O5'
DC
1
8
1.00
1
O
16.49
23.381
-2.549
-3.435
A
C5'
DC
8
ATOM
A
C5'
DC
1
8
1.00
1
C
17.71
22.729
-1.180
-3.737
A
C4'
DC
8
ATOM
A
C4'
DC
1
8
1.00
1
C
18.13
21.276
-1.436
-3.850
A
O4'
DC
8
ATOM
A
O4'
DC
1
8
1.00
1
O
19.39
22.971
-0.238
-2.532
A
C3'
DC
8
ATOM
A
C3'
DC
1
8
1.00
1
C
24.39
23.168
0.969
-3.129
A
O3'
DC
8
ATOM
A
O3'
DC
1
8
1.00
1
O
20.62
21.612
-0.254
-1.787
A
C2'
DC
8
ATOM
A
C2'
DC
1
8
1.00
1
C
16.97
20.566
-0.604
-2.880
A
C1'
DC
8
ATOM
A
C1'
DC
1
8
1.00
1
C
13.86
19.432
-1.358
-2.242
A
N1
DC
8
ATOM
A
N1
DC
1
8
1.00
1
N
14.04
18.131
-0.838
-2.628
A
C2
DC
8
ATOM
A
C2
DC
1
8
1.00
1
C
17.10
17.923
0.124
-3.420
A
O2
DC
8
ATOM
A
O2
DC
1
8
1.00
1
O
12.40
17.114
-1.435
-1.925
A
N3
DC
8
ATOM
A
N3
DC
1
8
1.00
1
N
3.99
17.309
-2.390
-1.152
A
C4
DC
8
ATOM
A
C4
DC
1
8
1.00
1
C
13.44
16.265
-2.832
-0.558
A
N4
DC
8
ATOM
A
N4
DC
1
8
1.00
1
N
10.66
18.553
-2.914
-1.016
A
C5
DC
8
ATOM
A
C5
DC
1
8
1.00
1
C
5.25
19.651
-2.360
-1.401
A
C6
DC
8
ATOM
A
C6
DC
1
8
1.00
1
C
32.01
1.541
-10.136
-12.606
A
PT
PT
101
HETATM
B
PT
PT
2
0.25
1
PT
31.85
5.814
-9.458
-3.218
A
PT
PT
102
HETATM
C
PT
PT
2
0.25
1
PT
28.29
3.473
-9.073
-6.018
A
O
HOH
201
HETATM
D
O
HOH
3
1.00
1
O
23.76
-1.119
-6.188
-9.414
A
O
HOH
202
HETATM
D
O
HOH
3
1.00
1
O
24.95
-5.013
-4.651
-6.791
A
O
HOH
203
HETATM
D
O
HOH
3
1.00
1
O
17.14
14.722
-14.250
-4.681
A
O
HOH
204
HETATM
D
O
HOH
3
1.00
1
O
20.39
26.107
-4.460
-4.538
A
O
HOH
205
HETATM
D
O
HOH
3
1.00
1
O
21.84
16.851
-15.284
-3.334
A
O
HOH
206
HETATM
D
O
HOH
3
1.00
1
O
33.82
0.419
-7.520
-5.525
A
O
HOH
207
HETATM
D
O
HOH
3
1.00
1
O
30.78
18.113
-15.745
1.184
A
O
HOH
208
HETATM
D
O
HOH
3
1.00
1
O
20.75
19.901
-2.494
-6.268
A
O
HOH
209
HETATM
D
O
HOH
3
1.00
1
O
24.93
-0.236
-17.390
-5.897
A
O
HOH
210
HETATM
D
O
HOH
3
1.00
1
O
25.02
4.258
-16.867
-2.538
A
O
HOH
211
HETATM
D
O
HOH
3
1.00
1
O
25.56
19.210
-14.209
-4.104
A
O
HOH
212
HETATM
D
O
HOH
3
1.00
1
O
27.25
19.564
3.112
-2.335
A
O
HOH
213
HETATM
D
O
HOH
3
1.00
1
O
25.57
11.070
-7.373
-0.356
A
O
HOH
214
HETATM
D
O
HOH
3
1.00
1
O
24.56
15.379
-6.553
-0.004
A
O
HOH
215
HETATM
D
O
HOH
3
1.00
1
O
29.85
13.320
-5.535
-0.032
A
O
HOH
216
HETATM
D
O
HOH
3
1.00
1
O
26.13
19.203
-5.964
0.893
A
O
HOH
217
HETATM
D
O
HOH
3
1.00
1
O
25.85
21.155
-4.481
1.088
A
O
HOH
218
HETATM
D
O
HOH
3
1.00
1
O
35.55
-3.623
-3.696
-10.689
A
O
HOH
219
HETATM
D
O
HOH
3
1.00
1
O
32.59
-3.765
-16.680
-5.811
A
O
HOH
220
HETATM
D
O
HOH
3
1.00
1
O
36.06
14.490
-16.508
3.048
A
O
HOH
221
HETATM
D
O
HOH
3
1.00
1
O
0.023603
0.000000
0.000000
0.000000
0.023603
0.000000
0.000000
0.000000
0.041570
0.00000
0.00000
0.00000
Zhang, W.
Coronado, G.
Huang, Z.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
42.368
42.368
24.056
C11 H17 N2 O8 P Se
415.195
n
5-METHYL-2'-SE-METHYL-2'-SELENOURIDINE 5'-(DIHYDROGEN PHOSPHATE)
DNA linking
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
non-polymer
Pt 2
195.078
PLATINUM (II) ION
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
N
N
7
N
C
N
8
N
C
N
9
N
O
N
10
N
N
N
11
N
C
N
12
N
O
N
13
N
C
N
14
N
C
N
15
R
C
N
16
N
C
N
17
R
C
N
18
N
O
N
19
R
C
N
20
R
C
N
21
N
SE
N
22
N
C
N
23
N
O
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
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
O
N
42
N
P
N
43
N
O
N
44
N
O
N
45
N
O
N
46
N
C
N
47
R
C
N
48
N
O
N
49
S
C
N
50
N
O
N
51
N
C
N
52
R
C
Y
53
N
N
Y
54
N
C
Y
55
N
N
Y
56
N
C
Y
57
N
C
N
58
N
N
Y
59
N
N
Y
60
N
C
Y
61
N
N
Y
62
N
C
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
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
O
N
78
N
P
N
79
N
O
N
80
N
O
N
81
N
O
N
82
N
C
N
83
R
C
N
84
N
O
N
85
S
C
N
86
N
O
N
87
N
C
N
88
R
C
N
89
N
N
N
90
N
C
N
91
N
O
N
92
N
N
N
93
N
C
N
94
N
N
N
95
N
C
N
96
N
C
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
H
N
109
N
H
N
110
N
H
N
111
N
O
N
112
N
P
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
O
N
119
S
C
N
120
N
O
N
121
N
C
N
122
R
C
Y
123
N
N
Y
124
N
C
Y
125
N
N
Y
126
N
C
N
127
N
C
N
128
N
O
N
129
N
N
N
130
N
C
N
131
N
N
N
132
N
N
Y
133
N
C
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
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
O
N
149
N
H
N
150
N
H
N
151
N
PT
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
doub
N
12
N
sing
N
13
N
doub
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
doub
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
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
doub
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
sing
Y
65
N
sing
Y
66
N
sing
Y
67
N
doub
N
68
N
sing
Y
69
N
sing
Y
70
N
sing
Y
71
N
doub
N
72
N
sing
Y
73
N
doub
N
74
N
sing
N
75
N
sing
Y
76
N
sing
Y
77
N
doub
N
78
N
sing
Y
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
doub
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
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
doub
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
Y
138
N
sing
Y
139
N
sing
Y
140
N
doub
N
141
N
sing
Y
142
N
sing
N
143
N
sing
Y
144
N
doub
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
doub
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
TO BE PUBLISHED
0353
dna octamer d(GTseGTACAC) partially crosslinked with two platinums
10.2210/pdb4i1g/pdb
pdb_00004i1g
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
200
1
CCD
2012-09-27
CUSTOM-MADE
SINGLE WAVELENGTH
M
x-ray
1
0.97
1.0
12.3.1
ALS
0.97
SYNCHROTRON
ALS BEAMLINE 12.3.1
DNA Octamer d(GTseGTACAC)
2520.592
DNA (5'-D(*GP*(2ST)P*GP*GP*CP*CP*AP*C)-3')
1
syn
polymer
195.078
PLATINUM (II) ION
2
syn
non-polymer
18.015
water
21
nat
water
no
yes
(DG)(2ST)(DG)(DG)(DC)(DC)(DA)(DC)
GTGGCCAC
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
1
1.97
42.56
VAPOR DIFFUSION, HANGING DROP
6.0
10% MPD, 40 mM Sodium codylate trihydrate, 12 mM Spermine tetrahydrochloride, 80 mM Strontium chloride , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
298.0
-23.734
1
19
A
1
A
8
-1.086
A_DG1:DC8_A
1
-9.429
-0.257
-0.456
-0.007
-8.686
1
20
A
2
A
7
0.047
A_2ST2:DA7_A
2
-10.785
-0.075
0.144
-0.060
-5.325
1
19
A
3
A
6
-2.138
A_DG3:DC6_A
3
-10.360
-0.184
0.046
-0.205
-6.908
1
19
A
4
A
5
-0.011
A_DG4:DC5_A
4
-15.356
-0.121
0.078
-0.120
6.907
1
19
A
5
A
4
-0.011
A_DC5:DG4_A
5
-15.356
0.121
0.078
-0.120
5.325
1
19
A
6
A
3
-2.138
A_DC6:DG3_A
6
-10.360
0.184
0.046
-0.205
8.686
1
20
A
7
A
2
0.047
A_DA7:2ST2_A
7
-10.785
0.075
0.144
-0.060
23.734
1
19
A
8
A
1
-1.086
A_DC8:DG1_A
8
-9.429
0.257
-0.456
-0.007
2.578
32.378
A
A
1
2
19.110
A
A
8
7
3.055
10.458
0.076
-0.951
AA_DG12ST2:DA7DC8_AA
1
-3.125
5.710
30.529
-3.344
-0.625
2.486
29.831
A
A
2
3
20.416
A
A
7
6
3.124
10.289
0.611
-1.465
AA_2ST2DG3:DC6DA7_AA
2
2.646
-5.250
27.916
-4.747
-0.698
3.027
35.984
A
A
3
4
8.887
A
A
6
5
3.281
5.467
0.418
-1.622
AA_DG3DG4:DC5DC6_AA
3
2.332
-3.792
35.506
-3.382
-0.355
2.784
29.306
A
A
4
5
10.423
A
A
5
4
2.986
5.246
0.000
-0.886
AA_DG4DC5:DG4DC5_AA
4
0.000
0.000
28.842
-2.759
0.000
3.027
35.984
A
A
5
6
8.887
A
A
4
3
3.281
5.467
-0.418
-1.622
AA_DC5DC6:DG3DG4_AA
5
-2.332
3.792
35.506
-3.382
0.355
2.486
29.831
A
A
6
7
20.416
A
A
3
2
3.124
10.289
-0.611
-1.465
AA_DC6DA7:2ST2DG3_AA
6
-2.646
5.250
27.916
-4.747
0.698
2.578
32.378
A
A
7
8
19.110
A
A
2
1
3.055
10.458
-0.076
-0.951
AA_DA7DC8:DG12ST2_AA
7
3.125
-5.710
30.529
-3.344
0.625
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_site
repository
Initial release
Data collection
Database references
Derived calculations
Refinement description
1
0
2012-12-05
1
1
2023-09-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2012-11-20
REL
REL
PT
PLATINUM (II) ION
HOH
water
32630
synthetic
synthetic construct
sample
1DNS
PDB
experimental model
PT
1
2
PT
PT
101
A
PT
2
2
PT
PT
102
A
HOH
1
3
HOH
HOH
201
A
HOH
3
3
HOH
HOH
202
A
HOH
4
3
HOH
HOH
203
A
HOH
5
3
HOH
HOH
204
A
HOH
6
3
HOH
HOH
205
A
HOH
7
3
HOH
HOH
206
A
HOH
8
3
HOH
HOH
207
A
HOH
9
3
HOH
HOH
208
A
HOH
10
3
HOH
HOH
209
A
HOH
13
3
HOH
HOH
210
A
HOH
14
3
HOH
HOH
211
A
HOH
18
3
HOH
HOH
212
A
HOH
32
3
HOH
HOH
213
A
HOH
35
3
HOH
HOH
214
A
HOH
42
3
HOH
HOH
215
A
HOH
43
3
HOH
HOH
216
A
HOH
45
3
HOH
HOH
217
A
HOH
46
3
HOH
HOH
218
A
HOH
49
3
HOH
HOH
219
A
HOH
71
3
HOH
HOH
220
A
HOH
73
3
HOH
HOH
221
A
DG
1
n
1
DG
1
A
2ST
2
n
2
2ST
2
A
DG
3
n
3
DG
3
A
DG
4
n
4
DG
4
A
DC
5
n
5
DC
5
A
DC
6
n
6
DC
6
A
DA
7
n
7
DA
7
A
DC
8
n
8
DC
8
A
author_and_software_defined_assembly
PISA
2
dimeric
2450
-61
2880
A
2ST
2
A
2ST
2
DT
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_554
-y,-x,-z-1/2
crystal symmetry operation
0.0000000000
0.0000000000
-12.0280000000
1
A
DC
8
0.067
SIDE CHAIN
1
-4.27
0.50
113.10
108.83
A
A
A
N7
C8
N9
DG
DG
DG
1
1
1
N
1
2.74
0.40
106.40
109.14
A
A
A
C8
N9
C4
DG
DG
DG
1
1
1
N
1
-11.82
0.90
105.70
93.88
A
A
A
O5'
P
OP2
DG
DG
DG
3
3
3
N
1
-2.63
0.40
104.50
101.87
A
A
A
O4'
C4'
C3'
DG
DG
DG
3
3
3
N
1
7.65
1.20
115.70
123.35
A
A
A
C5'
C4'
C3'
DG
DG
DG
3
3
3
N
1
-3.71
0.40
104.50
100.79
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
1
3.62
0.50
113.10
116.72
A
A
A
N7
C8
N9
DG
DG
DG
4
4
4
N
1
9.70
1.50
119.60
129.30
A
A
A
OP1
P
OP2
DC
DC
DC
5
5
5
N
1
-11.42
0.90
105.70
94.28
A
A
A
O5'
P
OP1
DC
DC
DC
5
5
5
N
1
2.95
0.30
108.30
111.25
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
-2.57
0.40
104.50
101.93
A
A
A
O4'
C4'
C3'
DC
DC
DC
6
6
6
N
1
-2.62
0.40
121.90
119.28
A
A
A
N3
C4
C5
DC
DC
DC
6
6
6
N
1
3.02
0.50
110.60
113.62
A
A
A
C2
N3
C4
DA
DA
DA
7
7
7
N
1
3.70
0.60
118.60
122.30
A
A
A
N1
C6
N6
DA
DA
DA
7
7
7
N
1
2.95
0.30
108.30
111.25
A
A
A
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
5.61
0.40
120.30
125.91
A
A
A
C6
N1
C2
DC
DC
DC
8
8
8
N
1
-7.39
0.70
119.20
111.81
A
A
A
N1
C2
N3
DC
DC
DC
8
8
8
N
1
8.42
0.50
117.40
125.82
A
A
A
C4
C5
C6
DC
DC
DC
8
8
8
N
1
-9.07
0.50
121.00
111.93
A
A
A
C5
C6
N1
DC
DC
DC
8
8
8
N
1
7.00
0.60
118.90
125.90
A
A
A
N1
C2
O2
DC
DC
DC
8
8
8
N
1
4.41
0.70
120.20
124.61
A
A
A
C5
C4
N4
DC
DC
DC
8
8
8
N
1
A
A
N1
C2
DG
DG
1
1
-0.055
0.008
1.373
1.318
N
1
A
A
N7
C8
DG
DG
1
1
0.064
0.006
1.305
1.369
N
1
A
A
P
O5'
DG
DG
3
3
0.061
0.010
1.593
1.654
N
1
A
A
O3'
C3'
DG
DG
3
3
0.095
0.013
1.435
1.530
N
1
A
A
N1
C2
DG
DG
3
3
-0.048
0.008
1.373
1.325
N
1
A
A
C4
C5
DG
DG
3
3
-0.046
0.007
1.379
1.333
N
1
A
A
C5
N7
DG
DG
3
3
0.039
0.006
1.388
1.427
N
1
A
A
C5'
C4'
DG
DG
4
4
0.044
0.007
1.512
1.556
N
1
A
A
P
OP2
DC
DC
5
5
-0.165
0.017
1.485
1.320
N
1
A
A
C2
O2
DC
DC
5
5
-0.058
0.009
1.240
1.182
N
1
A
A
O3'
P
DC
DC
5
6
-0.087
0.012
1.607
1.520
Y
1
A
A
P
OP2
DC
DC
6
6
-0.125
0.017
1.485
1.360
N
1
A
A
P
O5'
DC
DC
8
8
-0.091
0.010
1.593
1.502
N
1
A
A
O3'
C3'
DC
DC
8
8
-0.058
0.006
1.419
1.361
N
1
A
A
C4
N4
DC
DC
8
8
-0.055
0.009
1.335
1.280
N
1
A
A
N1
C6
DC
DC
8
8
-0.041
0.006
1.367
1.326
N
1
A
A
N3
C4
DC
DC
8
8
-0.091
0.007
1.335
1.244
N
1
A
A
C4
C5
DC
DC
8
8
-0.068
0.008
1.425
1.357
N
1
A
A
C5
C6
DC
DC
8
8
-0.050
0.008
1.339
1.289
N
18.517
0.01
0.00
0.00
0.01
0.00
-0.01
0.957
0.948
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.21729
0.20908
0.20947
0.20947
1.25
15.90
279
6256
5900
4.5
96.34
0.948
0.039
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.052
0.051
0.80
0.80
1.40
1DNS
MAXIMUM LIKELIHOOD
MASK
1.25
15.90
21
186
2
163
0
0.040
0.021
180
3.373
3.000
271
0.487
0.200
32
0.034
0.020
84
2.297
3.000
180
2.753
4.500
271
0.536
0.363
1.283
17
373
20
86.67
1.25
15.90
4I1G
6256
5900
0.094
0.090
1
25.6
11.7
94.3
data collection
HKL-2000
phasing
PHASES
refinement
REFMAC
5.5.0110
data reduction
HKL-2000
data scaling
HKL-2000
dna octamer d(GTseGTACAC) partially crosslinked with two platinums
1
N
N
2
N
N
2
N
N
3
N
N
covale
1.595
both
A
DG
1
A
O3'
DG
1
1_555
A
2ST
2
A
P
2ST
2
1_555
covale
1.625
both
A
2ST
2
A
O3'
2ST
2
1_555
A
DG
3
A
P
DG
3
1_555
metalc
2.422
A
DG
1
A
N7
DG
1
1_555
A
PT
101
B
PT
PT
1_555
metalc
2.291
A
DG
4
A
N7
DG
4
1_555
A
PT
102
C
PT
PT
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
A
DC
8
A
N3
DC
8
8_554
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
A
DC
8
A
O2
DC
8
8_554
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
A
DC
8
A
N4
DC
8
8_554
hydrog
WATSON-CRICK
A
2ST
2
A
N3
2ST
2
1_555
A
DA
7
A
N1
DA
7
8_554
hydrog
WATSON-CRICK
A
2ST
2
A
O4
2ST
2
1_555
A
DA
7
A
N6
DA
7
8_554
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
A
DC
6
A
N3
DC
6
8_554
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
A
DC
6
A
O2
DC
6
8_554
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
A
DC
6
A
N4
DC
6
8_554
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
A
DC
5
A
N3
DC
5
8_554
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
A
DC
5
A
O2
DC
5
8_554
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
A
DC
5
A
N4
DC
5
8_554
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
A
DG
4
A
N1
DG
4
8_554
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
A
DG
4
A
O6
DG
4
8_554
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
A
DG
4
A
N2
DG
4
8_554
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
A
DG
3
A
N1
DG
3
8_554
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
A
DG
3
A
O6
DG
3
8_554
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
A
DG
3
A
N2
DG
3
8_554
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
A
2ST
2
A
N3
2ST
2
8_554
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
A
2ST
2
A
O4
2ST
2
8_554
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
A
DG
1
A
N1
DG
1
8_554
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
A
DG
1
A
O6
DG
1
8_554
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
A
DG
1
A
N2
DG
1
8_554
DNA
platinum crosslink, selenium, DNA
4I1G
PDB
1
4I1G
1
8
4I1G
1
8
4I1G
A
1
1
8
BINDING SITE FOR RESIDUE PT A 101
A
PT
101
Software
1
BINDING SITE FOR RESIDUE PT A 102
A
PT
102
Software
1
A
DG
1
A
DG
1
1
1_555
A
DG
4
A
DG
4
1
1_555
96
P 43 21 2