29.10
29.002
19.538
-5.666
A
O5'
DG
1
ATOM
A
O5'
DG
1
1
1.00
1
O
27.31
28.768
18.211
-5.166
A
C5'
DG
1
ATOM
A
C5'
DG
1
1
1.00
1
C
28.25
29.997
17.521
-4.508
A
C4'
DG
1
ATOM
A
C4'
DG
1
1
1.00
1
C
26.07
31.191
17.607
-5.311
A
O4'
DG
1
ATOM
A
O4'
DG
1
1
1.00
1
O
28.35
30.426
18.233
-3.285
A
C3'
DG
1
ATOM
A
C3'
DG
1
1
1.00
1
C
32.50
29.786
17.826
-2.113
A
O3'
DG
1
ATOM
A
O3'
DG
1
1
1.00
1
O
27.29
31.902
17.823
-3.143
A
C2'
DG
1
ATOM
A
C2'
DG
1
1
1.00
1
C
27.21
32.322
17.837
-4.606
A
C1'
DG
1
ATOM
A
C1'
DG
1
1
1.00
1
C
26.18
32.759
19.153
-5.011
A
N9
DG
1
ATOM
A
N9
DG
1
1
1.00
1
N
26.73
32.049
20.021
-5.825
A
C8
DG
1
ATOM
A
C8
DG
1
1
1.00
1
C
26.17
32.748
21.024
-6.241
A
N7
DG
1
ATOM
A
N7
DG
1
1
1.00
1
N
24.99
33.941
20.879
-5.506
A
C5
DG
1
ATOM
A
C5
DG
1
1
1.00
1
C
25.56
35.174
21.693
-5.462
A
C6
DG
1
ATOM
A
C6
DG
1
1
1.00
1
C
26.72
35.515
22.763
-5.986
A
O6
DG
1
ATOM
A
O6
DG
1
1
1.00
1
O
28.37
36.121
21.068
-4.655
A
N1
DG
1
ATOM
A
N1
DG
1
1
1.00
1
N
27.77
35.945
19.892
-4.000
A
C2
DG
1
ATOM
A
C2
DG
1
1
1.00
1
C
30.49
37.002
19.551
-3.349
A
N2
DG
1
ATOM
A
N2
DG
1
1
1.00
1
N
26.54
34.860
19.185
-3.986
A
N3
DG
1
ATOM
A
N3
DG
1
1
1.00
1
N
24.63
33.920
19.728
-4.762
A
C4
DG
1
ATOM
A
C4
DG
1
1
1.00
1
C
35.73
29.403
18.896
-0.872
A
P
DC
2
ATOM
A
P
DC
1
2
1.00
1
P
36.79
28.409
18.106
-0.088
A
OP1
DC
2
ATOM
A
OP1
DC
1
2
1.00
1
O
32.95
29.014
20.215
-1.474
A
OP2
DC
2
ATOM
A
OP2
DC
1
2
1.00
1
O
31.57
30.567
19.213
0.040
A
O5'
DC
2
ATOM
A
O5'
DC
1
2
1.00
1
O
33.41
31.295
18.286
0.600
A
C5'
DC
2
ATOM
A
C5'
DC
1
2
1.00
1
C
31.91
32.703
18.731
0.877
A
C4'
DC
2
ATOM
A
C4'
DC
1
2
1.00
1
C
31.64
33.383
18.904
-0.410
A
O4'
DC
2
ATOM
A
O4'
DC
1
2
1.00
1
O
33.72
32.915
20.048
1.601
A
C3'
DC
2
ATOM
A
C3'
DC
1
2
1.00
1
C
38.80
32.971
19.977
3.082
A
O3'
DC
2
ATOM
A
O3'
DC
1
2
1.00
1
O
32.83
34.369
20.318
1.229
A
C2'
DC
2
ATOM
A
C2'
DC
1
2
1.00
1
C
31.03
34.474
19.854
-0.246
A
C1'
DC
2
ATOM
A
C1'
DC
1
2
1.00
1
C
28.11
34.123
21.104
-1.010
A
N1
DC
2
ATOM
A
N1
DC
1
2
1.00
1
N
28.55
35.069
21.955
-1.319
A
C2
DC
2
ATOM
A
C2
DC
1
2
1.00
1
C
33.12
36.175
21.804
-0.786
A
O2
DC
2
ATOM
A
O2
DC
1
2
1.00
1
O
26.56
34.892
22.942
-2.223
A
N3
DC
2
ATOM
A
N3
DC
1
2
1.00
1
N
29.26
33.682
23.155
-2.758
A
C4
DC
2
ATOM
A
C4
DC
1
2
1.00
1
C
27.25
33.478
24.259
-3.560
A
N4
DC
2
ATOM
A
N4
DC
1
2
1.00
1
N
28.28
32.576
22.280
-2.491
A
C5
DC
2
ATOM
A
C5
DC
1
2
1.00
1
C
29.49
32.837
21.279
-1.531
A
C6
DC
2
ATOM
A
C6
DC
1
2
1.00
1
C
39.73
32.387
21.256
4.025
A
P
DG
3
ATOM
A
P
DG
1
3
1.00
1
P
40.98
31.863
20.300
5.069
A
OP1
DG
3
ATOM
A
OP1
DG
1
3
1.00
1
O
39.39
31.329
21.963
3.424
A
OP2
DG
3
ATOM
A
OP2
DG
1
3
1.00
1
O
38.30
33.699
22.085
4.201
A
O5'
DG
3
ATOM
A
O5'
DG
1
3
1.00
1
O
36.47
34.824
21.574
4.646
A
C5'
DG
3
ATOM
A
C5'
DG
1
3
1.00
1
C
36.52
35.946
22.571
4.572
A
C4'
DG
3
ATOM
A
C4'
DG
1
3
1.00
1
C
38.24
36.143
22.657
3.157
A
O4'
DG
3
ATOM
A
O4'
DG
1
3
1.00
1
O
38.17
35.814
24.047
4.959
A
C3'
DG
3
ATOM
A
C3'
DG
1
3
1.00
1
C
38.83
36.265
24.393
6.295
A
O3'
DG
3
ATOM
A
O3'
DG
1
3
1.00
1
O
35.73
36.823
24.729
4.065
A
C2'
DG
3
ATOM
A
C2'
DG
1
3
1.00
1
C
35.37
36.798
23.845
2.761
A
C1'
DG
3
ATOM
A
C1'
DG
1
3
1.00
1
C
30.85
35.832
24.553
1.888
A
N9
DG
3
ATOM
A
N9
DG
1
3
1.00
1
N
28.74
34.514
24.204
1.632
A
C8
DG
3
ATOM
A
C8
DG
1
3
1.00
1
C
27.54
34.054
24.827
0.660
A
N7
DG
3
ATOM
A
N7
DG
1
3
1.00
1
N
26.60
35.030
25.757
0.370
A
C5
DG
3
ATOM
A
C5
DG
1
3
1.00
1
C
22.91
35.030
26.894
-0.569
A
C6
DG
3
ATOM
A
C6
DG
1
3
1.00
1
C
24.28
34.194
27.174
-1.368
A
O6
DG
3
ATOM
A
O6
DG
1
3
1.00
1
O
19.33
36.111
27.616
-0.409
A
N1
DG
3
ATOM
A
N1
DG
1
3
1.00
1
N
21.66
37.134
27.406
0.502
A
C2
DG
3
ATOM
A
C2
DG
1
3
1.00
1
C
22.50
38.064
28.194
0.453
A
N2
DG
3
ATOM
A
N2
DG
1
3
1.00
1
N
23.78
37.193
26.434
1.359
A
N3
DG
3
ATOM
A
N3
DG
1
3
1.00
1
N
26.90
36.108
25.617
1.200
A
C4
DG
3
ATOM
A
C4
DG
1
3
1.00
1
C
41.04
35.451
25.592
7.038
A
P
DC
4
ATOM
A
P
DC
1
4
1.00
1
P
40.06
36.091
25.406
8.384
A
OP1
DC
4
ATOM
A
OP1
DC
1
4
1.00
1
O
38.33
33.987
25.422
6.884
A
OP2
DC
4
ATOM
A
OP2
DC
1
4
1.00
1
O
36.12
36.183
26.909
6.511
A
O5'
DC
4
ATOM
A
O5'
DC
1
4
1.00
1
O
31.66
37.514
27.073
6.685
A
C5'
DC
4
ATOM
A
C5'
DC
1
4
1.00
1
C
31.19
37.953
28.380
6.085
A
C4'
DC
4
ATOM
A
C4'
DC
1
4
1.00
1
C
31.22
37.898
28.351
4.627
A
O4'
DC
4
ATOM
A
O4'
DC
1
4
1.00
1
O
29.12
36.907
29.456
6.437
A
C3'
DC
4
ATOM
A
C3'
DC
1
4
1.00
1
C
31.60
37.393
30.146
7.677
A
O3'
DC
4
ATOM
A
O3'
DC
1
4
1.00
1
O
27.40
37.176
30.443
5.317
A
C2'
DC
4
ATOM
A
C2'
DC
1
4
1.00
1
C
27.48
37.447
29.556
4.131
A
C1'
DC
4
ATOM
A
C1'
DC
1
4
1.00
1
C
24.46
36.165
29.272
3.384
A
N1
DC
4
ATOM
A
N1
DC
1
4
1.00
1
N
20.59
35.835
30.140
2.401
A
C2
DC
4
ATOM
A
C2
DC
1
4
1.00
1
C
22.37
36.591
31.087
2.266
A
O2
DC
4
ATOM
A
O2
DC
1
4
1.00
1
O
21.11
34.686
29.981
1.629
A
N3
DC
4
ATOM
A
N3
DC
1
4
1.00
1
N
22.19
33.866
28.978
1.962
A
C4
DC
4
ATOM
A
C4
DC
1
4
1.00
1
C
22.32
32.664
28.814
1.287
A
N4
DC
4
ATOM
A
N4
DC
1
4
1.00
1
N
21.40
34.180
28.063
3.042
A
C5
DC
4
ATOM
A
C5
DC
1
4
1.00
1
C
22.69
35.367
28.249
3.691
A
C6
DC
4
ATOM
A
C6
DC
1
4
1.00
1
C
30.29
36.455
31.152
8.392
A
P
DG
5
ATOM
A
P
DG
1
5
1.00
1
P
34.80
37.153
31.316
9.594
A
OP1
DG
5
ATOM
A
OP1
DG
1
5
1.00
1
O
31.93
35.060
30.819
8.567
A
OP2
DG
5
ATOM
A
OP2
DG
1
5
1.00
1
O
28.60
36.699
32.348
7.497
A
O5'
DG
5
ATOM
A
O5'
DG
1
5
1.00
1
O
24.45
35.658
33.285
7.378
A
C5'
DG
5
ATOM
A
C5'
DG
1
5
1.00
1
C
25.02
36.113
34.208
6.300
A
C4'
DG
5
ATOM
A
C4'
DG
1
5
1.00
1
C
24.06
36.087
33.444
5.013
A
O4'
DG
5
ATOM
A
O4'
DG
1
5
1.00
1
O
26.34
35.215
35.376
6.023
A
C3'
DG
5
ATOM
A
C3'
DG
1
5
1.00
1
C
27.71
35.582
36.512
6.830
A
O3'
DG
5
ATOM
A
O3'
DG
1
5
1.00
1
O
22.49
35.434
35.712
4.530
A
C2'
DG
5
ATOM
A
C2'
DG
1
5
1.00
1
C
22.65
35.616
34.303
3.974
A
C1'
DG
5
ATOM
A
C1'
DG
1
5
1.00
1
C
19.71
34.318
33.708
3.523
A
N9
DG
5
ATOM
A
N9
DG
1
5
1.00
1
N
16.61
33.759
32.554
4.050
A
C8
DG
5
ATOM
A
C8
DG
1
5
1.00
1
C
17.77
32.752
32.140
3.398
A
N7
DG
5
ATOM
A
N7
DG
1
5
1.00
1
N
19.61
32.623
33.049
2.342
A
C5
DG
5
ATOM
A
C5
DG
1
5
1.00
1
C
19.87
31.616
33.155
1.279
A
C6
DG
5
ATOM
A
C6
DG
1
5
1.00
1
C
22.58
30.549
32.448
1.147
A
O6
DG
5
ATOM
A
O6
DG
1
5
1.00
1
O
20.02
31.838
34.318
0.447
A
N1
DG
5
ATOM
A
N1
DG
1
5
1.00
1
N
20.39
32.912
35.222
0.619
A
C2
DG
5
ATOM
A
C2
DG
1
5
1.00
1
C
19.15
32.995
36.234
-0.355
A
N2
DG
5
ATOM
A
N2
DG
1
5
1.00
1
N
20.69
33.791
35.143
1.598
A
N3
DG
5
ATOM
A
N3
DG
1
5
1.00
1
N
19.59
33.562
34.080
2.462
A
C4
DG
5
ATOM
A
C4
DG
1
5
1.00
1
C
21.84
31.753
37.844
2.829
A
N1
5CM
6
HETATM
A
N1
5CM
1
6
1.00
1
N
21.35
30.804
37.569
1.950
A
C2
5CM
6
HETATM
A
C2
5CM
1
6
1.00
1
C
21.31
29.960
36.485
2.124
A
N3
5CM
6
HETATM
A
N3
5CM
1
6
1.00
1
N
22.85
30.067
35.712
3.206
A
C4
5CM
6
HETATM
A
C4
5CM
1
6
1.00
1
C
20.91
31.028
36.006
4.230
A
C5
5CM
6
HETATM
A
C5
5CM
1
6
1.00
1
C
22.08
31.090
35.138
5.486
A
C5A
5CM
6
HETATM
A
C5A
5CM
1
6
1.00
1
C
23.29
31.828
37.117
4.005
A
C6
5CM
6
HETATM
A
C6
5CM
1
6
1.00
1
C
25.49
30.703
38.292
0.982
A
O2
5CM
6
HETATM
A
O2
5CM
1
6
1.00
1
O
22.21
29.244
34.629
3.385
A
N4
5CM
6
HETATM
A
N4
5CM
1
6
1.00
1
N
25.13
32.744
38.866
2.492
A
C1'
5CM
6
HETATM
A
C1'
5CM
1
6
1.00
1
C
24.69
32.103
40.185
3.099
A
C2'
5CM
6
HETATM
A
C2'
5CM
1
6
1.00
1
C
28.16
32.818
40.170
4.500
A
C3'
5CM
6
HETATM
A
C3'
5CM
1
6
1.00
1
C
28.28
34.183
39.559
4.214
A
C4'
5CM
6
HETATM
A
C4'
5CM
1
6
1.00
1
C
26.64
33.913
38.554
3.231
A
O4'
5CM
6
HETATM
A
O4'
5CM
1
6
1.00
1
O
31.23
32.806
41.602
4.896
A
O3'
5CM
6
HETATM
A
O3'
5CM
1
6
1.00
1
O
29.01
34.822
38.982
5.427
A
C5'
5CM
6
HETATM
A
C5'
5CM
1
6
1.00
1
C
26.75
33.957
38.412
6.180
A
O5'
5CM
6
HETATM
A
O5'
5CM
1
6
1.00
1
O
29.72
34.409
37.429
7.369
A
P
5CM
6
HETATM
A
P
5CM
1
6
1.00
1
P
32.33
35.219
38.405
8.260
A
OP1
5CM
6
HETATM
A
OP1
5CM
1
6
1.00
1
O
27.15
33.286
36.884
7.857
A
OP2
5CM
6
HETATM
A
OP2
5CM
1
6
1.00
1
O
32.23
31.482
42.084
5.811
A
P
DG
7
ATOM
A
P
DG
1
7
1.00
1
P
35.30
32.028
43.521
6.376
A
OP1
DG
7
ATOM
A
OP1
DG
1
7
1.00
1
O
33.50
30.781
41.058
6.621
A
OP2
DG
7
ATOM
A
OP2
DG
1
7
1.00
1
O
29.77
30.354
42.261
4.666
A
O5'
DG
7
ATOM
A
O5'
DG
1
7
1.00
1
O
29.08
30.534
43.095
3.513
A
C5'
DG
7
ATOM
A
C5'
DG
1
7
1.00
1
C
31.42
29.273
43.007
2.646
A
C4'
DG
7
ATOM
A
C4'
DG
1
7
1.00
1
C
28.96
29.162
41.623
2.209
A
O4'
DG
7
ATOM
A
O4'
DG
1
7
1.00
1
O
31.10
27.974
43.199
3.384
A
C3'
DG
7
ATOM
A
C3'
DG
1
7
1.00
1
C
35.30
27.420
44.413
3.238
A
O3'
DG
7
ATOM
A
O3'
DG
1
7
1.00
1
O
28.64
26.999
42.296
2.619
A
C2'
DG
7
ATOM
A
C2'
DG
1
7
1.00
1
C
27.65
27.887
41.299
1.974
A
C1'
DG
7
ATOM
A
C1'
DG
1
7
1.00
1
C
25.27
27.694
40.031
2.690
A
N9
DG
7
ATOM
A
N9
DG
1
7
1.00
1
N
23.03
28.469
39.472
3.657
A
C8
DG
7
ATOM
A
C8
DG
1
7
1.00
1
C
23.39
28.048
38.297
4.039
A
N7
DG
7
ATOM
A
N7
DG
1
7
1.00
1
N
23.83
26.857
38.062
3.383
A
C5
DG
7
ATOM
A
C5
DG
1
7
1.00
1
C
22.61
25.870
36.960
3.417
A
C6
DG
7
ATOM
A
C6
DG
1
7
1.00
1
C
24.41
25.832
35.972
4.105
A
O6
DG
7
ATOM
A
O6
DG
1
7
1.00
1
O
22.54
24.935
37.102
2.396
A
N1
DG
7
ATOM
A
N1
DG
1
7
1.00
1
N
21.39
24.837
38.223
1.674
A
C2
DG
7
ATOM
A
C2
DG
1
7
1.00
1
C
22.46
23.758
38.268
0.859
A
N2
DG
7
ATOM
A
N2
DG
1
7
1.00
1
N
21.83
25.644
39.281
1.764
A
N3
DG
7
ATOM
A
N3
DG
1
7
1.00
1
N
24.75
26.583
39.145
2.528
A
C4
DG
7
ATOM
A
C4
DG
1
7
1.00
1
C
30.97
22.684
40.903
3.635
A
N1
5CM
8
HETATM
A
N1
5CM
1
8
1.00
1
N
28.98
22.085
39.701
3.684
A
C2
5CM
8
HETATM
A
C2
5CM
1
8
1.00
1
C
28.92
22.641
38.754
4.450
A
N3
5CM
8
HETATM
A
N3
5CM
1
8
1.00
1
N
25.80
23.666
39.053
5.231
A
C4
5CM
8
HETATM
A
C4
5CM
1
8
1.00
1
C
27.01
24.245
40.339
5.231
A
C5
5CM
8
HETATM
A
C5
5CM
1
8
1.00
1
C
24.76
25.471
40.619
5.979
A
C5A
5CM
8
HETATM
A
C5A
5CM
1
8
1.00
1
C
27.29
23.659
41.225
4.480
A
C6
5CM
8
HETATM
A
C6
5CM
1
8
1.00
1
C
25.44
20.981
39.497
3.013
A
O2
5CM
8
HETATM
A
O2
5CM
1
8
1.00
1
O
24.77
24.096
38.085
5.914
A
N4
5CM
8
HETATM
A
N4
5CM
1
8
1.00
1
N
35.35
22.165
41.881
2.523
A
C1'
5CM
8
HETATM
A
C1'
5CM
1
8
1.00
1
C
36.44
21.200
42.875
3.191
A
C2'
5CM
8
HETATM
A
C2'
5CM
1
8
1.00
1
C
41.62
21.870
44.270
3.082
A
C3'
5CM
8
HETATM
A
C3'
5CM
1
8
1.00
1
C
37.56
23.277
44.067
2.431
A
C4'
5CM
8
HETATM
A
C4'
5CM
1
8
1.00
1
C
39.63
23.221
42.684
2.038
A
O4'
5CM
8
HETATM
A
O4'
5CM
1
8
1.00
1
O
44.72
20.751
44.374
2.044
A
O3'
5CM
8
HETATM
A
O3'
5CM
1
8
1.00
1
O
38.57
24.343
43.791
3.416
A
C5'
5CM
8
HETATM
A
C5'
5CM
1
8
1.00
1
C
37.51
24.999
44.930
3.692
A
O5'
5CM
8
HETATM
A
O5'
5CM
1
8
1.00
1
O
38.61
26.406
44.894
4.340
A
P
5CM
8
HETATM
A
P
5CM
1
8
1.00
1
P
38.13
26.679
46.384
4.358
A
OP1
5CM
8
HETATM
A
OP1
5CM
1
8
1.00
1
O
37.35
25.482
44.155
5.148
A
OP2
5CM
8
HETATM
A
OP2
5CM
1
8
1.00
1
O
22.69
36.084
36.854
1.226
A
O
HOH
101
HETATM
B
O
HOH
2
1.00
1
O
26.51
28.577
37.337
6.645
A
O
HOH
102
HETATM
B
O
HOH
2
1.00
1
O
43.91
31.533
24.907
-0.209
A
O
HOH
103
HETATM
B
O
HOH
2
1.00
1
O
37.62
31.601
27.011
-1.859
A
O
HOH
104
HETATM
B
O
HOH
2
1.00
1
O
35.41
31.084
30.140
4.269
A
O
HOH
105
HETATM
B
O
HOH
2
1.00
1
O
39.76
29.582
30.168
2.034
A
O
HOH
106
HETATM
B
O
HOH
2
1.00
1
O
44.57
30.775
38.529
7.500
A
O
HOH
107
HETATM
B
O
HOH
2
1.00
1
O
57.44
29.385
35.099
8.927
A
O
HOH
108
HETATM
B
O
HOH
2
1.00
1
O
53.46
28.579
31.993
5.327
A
O
HOH
109
HETATM
B
O
HOH
2
1.00
1
O
43.21
30.844
26.880
2.027
A
O
HOH
110
HETATM
B
O
HOH
2
1.00
1
O
38.08
26.980
34.892
6.084
A
O
HOH
111
HETATM
B
O
HOH
2
1.00
1
O
46.94
26.118
38.047
7.984
A
O
HOH
112
HETATM
B
O
HOH
2
1.00
1
O
38.18
34.337
24.830
-7.317
A
O
HOH
113
HETATM
B
O
HOH
2
1.00
1
O
42.28
31.563
23.212
-7.594
A
O
HOH
114
HETATM
B
O
HOH
2
1.00
1
O
35.09
37.154
38.734
2.506
A
O
HOH
115
HETATM
B
O
HOH
2
1.00
1
O
52.09
36.034
41.335
2.112
A
O
HOH
116
HETATM
B
O
HOH
2
1.00
1
O
48.64
24.568
41.198
-0.265
A
O
HOH
117
HETATM
B
O
HOH
2
1.00
1
O
53.51
29.556
37.812
10.692
A
O
HOH
118
HETATM
B
O
HOH
2
1.00
1
O
43.99
38.418
38.771
4.699
A
O
HOH
119
HETATM
B
O
HOH
2
1.00
1
O
0.023191
0.000000
0.000000
0.000000
0.023191
0.000000
0.000000
0.000000
0.040371
0.00000
0.00000
0.00000
Shi, K.
Pan, B.
Tippin, D.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90
90
90
43.12
43.12
24.77
C10 H16 N3 O7 P
321.224
n
5-METHYL-2'-DEOXY-CYTIDINE-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
N
1
N
N
N
2
N
C
N
3
N
N
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
O
N
9
N
N
N
10
R
C
N
11
N
C
N
12
S
C
N
13
R
C
N
14
N
O
N
15
N
O
N
16
N
C
N
17
N
O
N
18
N
P
N
19
N
O
N
20
N
O
N
21
N
O
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
H
N
36
N
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
N
C
N
49
R
C
N
50
N
N
N
51
N
C
N
52
N
O
N
53
N
N
N
54
N
C
N
55
N
N
N
56
N
C
N
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
P
N
74
N
O
N
75
N
O
N
76
N
O
N
77
N
C
N
78
R
C
N
79
N
O
N
80
S
C
N
81
N
O
N
82
N
C
N
83
R
C
Y
84
N
N
Y
85
N
C
Y
86
N
N
Y
87
N
C
N
88
N
C
N
89
N
O
N
90
N
N
N
91
N
C
N
92
N
N
N
93
N
N
Y
94
N
C
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
O
N
110
N
H
N
111
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
N
6
N
doub
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
doub
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
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
doub
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
doub
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
60
61
65
10.1107/S0907444903021899
14684893
Structures of d(Gm5)CGm5CGCGC) and d(GCGCGm5CGm5C): effects of methylation on alternating DNA octamers.
2004
10.2210/pdb1r41/pdb
pdb_00001r41
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
RIGAKU RAXIS IIC
GRAPHITE
SINGLE WAVELENGTH
M
x-ray
1
1.54
1.0
1.54
ROTATING ANODE
RIGAKU RU200
2456.647
5'-D(*GP*CP*GP*CP*GP*(5CM)P*GP*(5CM))-3'
1
syn
polymer
18.015
water
19
nat
water
no
yes
(DG)(DC)(DG)(DC)(DG)(5CM)(DG)(5CM)
GCGCGCGC
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
1
2.26
45.46
VAPOR DIFFUSION, HANGING DROP
6.0
cacodylate, magnesium chloride, spermine tetrachloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
cacodylate
1
magnesium chloride
1
spermine tetrachloride
1
H2O
1
cacodylate
2
magnesium chloride
2
spermine tetrachloride
2
H2O
2
-6.963
1
19
A
1
A
8
0.930
A_DG1:5CM8_A
1
-6.098
-0.263
-0.235
0.007
9.535
1
19
A
2
A
7
2.739
A_DC2:DG7_A
2
-6.994
0.305
-0.206
-0.002
-8.137
1
19
A
3
A
6
1.618
A_DG3:5CM6_A
3
-13.235
-0.073
-0.302
-0.127
-4.720
1
19
A
4
A
5
2.653
A_DC4:DG5_A
4
-3.291
0.295
0.094
-0.126
4.720
1
19
A
5
A
4
2.653
A_DG5:DC4_A
5
-3.291
-0.295
0.094
-0.126
8.137
1
19
A
6
A
3
1.618
A_5CM6:DG3_A
6
-13.235
0.073
-0.302
-0.127
-9.535
1
19
A
7
A
2
2.739
A_DG7:DC2_A
7
-6.994
-0.305
-0.206
-0.002
6.963
1
19
A
8
A
1
0.930
A_5CM8:DG1_A
8
-6.098
0.263
-0.235
0.007
2.977
35.032
A
A
1
2
3.202
A
A
8
7
3.064
1.926
0.443
-1.172
AA_DG1DC2:DG75CM8_AA
1
-1.498
2.491
34.950
-2.215
-0.944
2.721
33.107
A
A
2
3
24.793
A
A
7
6
3.691
13.718
-0.307
-1.567
AA_DC2DG3:5CM6DG7_AA
2
1.655
-2.991
30.159
-5.131
0.826
3.304
37.541
A
A
3
4
-0.770
A
A
6
5
3.305
-0.495
0.104
-1.400
AA_DG3DC4:DG55CM6_AA
3
-3.127
4.864
37.412
-2.109
-0.575
2.288
20.872
A
A
4
5
17.237
A
A
5
4
3.054
6.154
0.000
-2.170
AA_DC4DG5:DC4DG5_AA
4
0.000
0.000
19.953
-8.190
0.000
3.304
37.541
A
A
5
6
-0.770
A
A
4
3
3.305
-0.495
-0.104
-1.400
AA_DG55CM6:DG3DC4_AA
5
3.127
-4.864
37.412
-2.109
0.575
2.721
33.107
A
A
6
7
24.793
A
A
3
2
3.691
13.718
0.307
-1.567
AA_5CM6DG7:DC2DG3_AA
6
-1.655
2.991
30.159
-5.131
-0.826
2.977
35.032
A
A
7
8
3.202
A
A
2
1
3.064
1.926
-0.443
-1.172
AA_DG75CM8:DG1DC2_AA
7
1.498
-2.491
34.950
-2.215
0.944
chem_comp_atom
chem_comp_bond
database_2
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2003-12-23
1
1
2008-04-29
1
2
2011-07-13
1
3
2024-02-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
Crystal structures of d(Gm5CGm5CGCGC) and d(GCGCGm5CGm5C): Effects of methylation on alternating DNA octamers
RCSB
Y
RCSB
2003-10-03
REL
REL
HOH
water
DNA Synthesizer
sample
WAT
101
2
HOH
HOH
101
A
WAT
102
2
HOH
HOH
102
A
WAT
103
2
HOH
HOH
103
A
WAT
104
2
HOH
HOH
104
A
WAT
105
2
HOH
HOH
105
A
WAT
106
2
HOH
HOH
106
A
WAT
107
2
HOH
HOH
107
A
WAT
108
2
HOH
HOH
108
A
WAT
109
2
HOH
HOH
109
A
WAT
110
2
HOH
HOH
110
A
WAT
111
2
HOH
HOH
111
A
WAT
112
2
HOH
HOH
112
A
WAT
113
2
HOH
HOH
113
A
WAT
114
2
HOH
HOH
114
A
WAT
115
2
HOH
HOH
115
A
WAT
116
2
HOH
HOH
116
A
WAT
117
2
HOH
HOH
117
A
WAT
118
2
HOH
HOH
118
A
WAT
119
2
HOH
HOH
119
A
GUA
1
n
1
DG
1
A
CYT
2
n
2
DC
2
A
GUA
3
n
3
DG
3
A
CYT
4
n
4
DC
4
A
GUA
5
n
5
DG
5
A
CYM
6
n
6
5CM
6
A
GUA
7
n
7
DG
7
A
CYM
8
n
8
5CM
8
A
author_defined_assembly
2
dimeric
A
5CM
6
A
5CM
6
DC
A
5CM
8
A
5CM
8
DC
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
7_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1
A
DG
1
0.055
SIDE CHAIN
1
A
DC
2
0.071
SIDE CHAIN
1
A
DG
3
0.099
SIDE CHAIN
1
-3.45
0.40
104.50
101.05
A
A
A
O4'
C4'
C3'
DG
DG
DG
1
1
1
N
1
5.22
0.60
128.60
133.82
A
A
A
C5
C6
O6
DG
DG
DG
1
1
1
N
1
-13.68
2.20
105.20
91.52
A
A
A
O3'
P
OP1
DC
DG
DG
2
3
3
Y
1
12.65
1.20
110.70
123.35
A
A
A
O5'
P
OP1
DG
DG
DG
3
3
3
N
1
-2.74
0.40
104.50
101.76
A
A
A
O4'
C4'
C3'
DG
DG
DG
3
3
3
N
1
8.53
1.20
115.70
124.23
A
A
A
C5'
C4'
C3'
DG
DG
DG
3
3
3
N
1
10.19
1.20
110.70
120.89
A
A
A
O5'
P
OP2
DC
DC
DC
4
4
4
N
1
8.87
1.10
110.50
119.37
A
A
A
O3'
P
OP2
DC
DG
DG
4
5
5
Y
1
-5.04
0.80
109.40
104.36
A
A
A
O5'
C5'
C4'
DG
DG
DG
5
5
5
N
1
10.11
1.10
110.50
120.61
A
A
A
O3'
P
OP2
DG
5CM
5CM
5
6
6
Y
1
7.63
1.10
110.50
118.13
A
A
A
O3'
P
OP2
5CM
DG
DG
6
7
7
Y
1
-8.07
0.90
105.70
97.63
A
A
A
O5'
P
OP2
DG
DG
DG
7
7
7
N
1
-2.82
0.40
104.50
101.68
A
A
A
O4'
C4'
C3'
DG
DG
DG
7
7
7
N
1
20.28
1.10
110.50
130.78
A
A
A
O3'
P
OP2
DG
5CM
5CM
7
8
8
Y
1
A
A
C5'
C4'
DG
DG
1
1
0.043
0.007
1.512
1.555
N
1
A
A
N9
C4
DG
DG
1
1
-0.056
0.008
1.375
1.319
N
1
A
A
O3'
P
DG
DC
1
2
0.076
0.012
1.607
1.683
Y
1
A
A
P
O5'
DC
DC
2
2
-0.081
0.010
1.593
1.512
N
1
A
A
N1
C2
DC
DC
2
2
-0.088
0.010
1.397
1.309
N
1
A
A
C5
C6
DC
DC
2
2
0.072
0.008
1.339
1.411
N
1
A
A
O3'
P
DC
DG
2
3
0.086
0.012
1.607
1.693
Y
1
A
A
C6
N1
DG
DG
3
3
-0.081
0.007
1.391
1.310
N
1
A
A
N7
C8
DG
DG
3
3
-0.062
0.006
1.305
1.243
N
1
A
A
N9
C4
DG
DG
3
3
-0.078
0.008
1.375
1.297
N
1
A
A
C2
N2
DG
DG
3
3
-0.121
0.010
1.341
1.220
N
1
A
A
P
O5'
DG
DG
5
5
-0.079
0.010
1.593
1.514
N
1
A
A
C6
N1
DG
DG
5
5
0.056
0.007
1.391
1.447
N
1
A
A
C2
N2
DG
DG
5
5
0.066
0.010
1.341
1.407
N
1
A
A
O3'
P
5CM
DG
6
7
0.073
0.012
1.607
1.680
Y
1
A
A
P
OP1
DG
DG
7
7
0.153
0.017
1.485
1.638
N
1
A
A
O4'
C1'
DG
DG
7
7
-0.082
0.012
1.418
1.336
N
1
A
A
O3'
C3'
DG
DG
7
7
-0.077
0.006
1.419
1.342
N
1
A
A
N3
C4
DG
DG
7
7
-0.132
0.007
1.350
1.218
N
1
A
A
C5
C6
DG
DG
7
7
0.061
0.010
1.419
1.480
N
1
A
A
N9
C4
DG
DG
7
7
0.055
0.008
1.375
1.430
N
0.198
0.183
0.204
0.183
1.9
10
RANDOM
1
0
Molecular Placement
Engh & Huber
1.9
10
19
182
0
163
0
1.80
19.23
1R41
2192
1
Crystal structures of d(Gm5CGm5CGCGC) and d(GCGCGm5CGm5C): Effects of methylation on alternating DNA octamers
1
N
N
2
N
N
covale
1.583
both
A
DG
5
A
O3'
DG
5
1_555
A
5CM
6
A
P
5CM
6
1_555
covale
1.680
both
A
5CM
6
A
O3'
5CM
6
1_555
A
DG
7
A
P
DG
7
1_555
covale
1.573
both
A
DG
7
A
O3'
DG
7
1_555
A
5CM
8
A
P
5CM
8
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
A
5CM
8
A
N3
5CM
8
7_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
A
5CM
8
A
O2
5CM
8
7_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
A
5CM
8
A
N4
5CM
8
7_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
A
DG
7
A
N1
DG
7
7_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
A
DG
7
A
O6
DG
7
7_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
A
DG
7
A
N2
DG
7
7_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
A
5CM
6
A
N3
5CM
6
7_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
A
5CM
6
A
O2
5CM
6
7_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
A
5CM
6
A
N4
5CM
6
7_555
hydrog
WATSON-CRICK
A
DC
4
A
N3
DC
4
1_555
A
DG
5
A
N1
DG
5
7_555
hydrog
WATSON-CRICK
A
DC
4
A
N4
DC
4
1_555
A
DG
5
A
O6
DG
5
7_555
hydrog
WATSON-CRICK
A
DC
4
A
O2
DC
4
1_555
A
DG
5
A
N2
DG
5
7_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
A
DC
4
A
N3
DC
4
7_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
A
DC
4
A
O2
DC
4
7_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
A
DC
4
A
N4
DC
4
7_555
hydrog
WATSON-CRICK
A
5CM
6
A
N3
5CM
6
1_555
A
DG
3
A
N1
DG
3
7_555
hydrog
WATSON-CRICK
A
5CM
6
A
N4
5CM
6
1_555
A
DG
3
A
O6
DG
3
7_555
hydrog
WATSON-CRICK
A
5CM
6
A
O2
5CM
6
1_555
A
DG
3
A
N2
DG
3
7_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
A
DC
2
A
N3
DC
2
7_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
A
DC
2
A
O2
DC
2
7_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
A
DC
2
A
N4
DC
2
7_555
hydrog
WATSON-CRICK
A
5CM
8
A
N3
5CM
8
1_555
A
DG
1
A
N1
DG
1
7_555
hydrog
WATSON-CRICK
A
5CM
8
A
N4
5CM
8
1_555
A
DG
1
A
O6
DG
1
7_555
hydrog
WATSON-CRICK
A
5CM
8
A
O2
5CM
8
1_555
A
DG
1
A
N2
DG
1
7_555
DNA
DNA
1R41
PDB
1
1R41
1
8
1R41
1
8
1R41
A
1
1
8
96
P 43 21 2