80.61
9.529
69.761
48.578
C
O5'
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1
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A
O5'
DC
1
1
1.00
1
O
88.06
9.244
70.973
47.862
C
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DC
1
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A
C5'
DC
1
1
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1
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89.95
7.809
70.961
47.393
C
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1
ATOM
A
C4'
DC
1
1
1.00
1
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89.28
7.561
72.000
46.415
C
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1
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A
O4'
DC
1
1
1.00
1
O
94.09
7.389
69.662
46.706
C
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DC
1
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A
C3'
DC
1
1
1.00
1
C
99.21
6.082
69.301
47.123
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1
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A
O3'
DC
1
1
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1
O
90.80
7.477
69.982
45.233
C
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DC
1
ATOM
A
C2'
DC
1
1
1.00
1
C
84.74
7.030
71.435
45.217
C
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DC
1
ATOM
A
C1'
DC
1
1
1.00
1
C
78.44
7.520
72.242
44.089
C
N1
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1
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A
N1
DC
1
1
1.00
1
N
75.45
6.583
72.691
43.153
C
C2
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1
ATOM
A
C2
DC
1
1
1.00
1
C
84.21
5.395
72.380
43.337
C
O2
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1
ATOM
A
O2
DC
1
1
1.00
1
O
75.75
7.007
73.435
42.108
C
N3
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1
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A
N3
DC
1
1
1.00
1
N
73.23
8.297
73.746
41.956
C
C4
DC
1
ATOM
A
C4
DC
1
1
1.00
1
C
51.76
8.655
74.487
40.900
C
N4
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1
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A
N4
DC
1
1
1.00
1
N
68.48
9.273
73.301
42.892
C
C5
DC
1
ATOM
A
C5
DC
1
1
1.00
1
C
74.56
8.837
72.565
43.923
C
C6
DC
1
ATOM
A
C6
DC
1
1
1.00
1
C
97.08
5.638
67.760
47.265
C
P
DG
2
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A
P
DG
1
2
1.00
1
P
103.65
5.788
67.326
48.682
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OP1
DG
2
ATOM
A
OP1
DG
1
2
1.00
1
O
101.10
6.286
66.948
46.202
C
OP2
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2
ATOM
A
OP2
DG
1
2
1.00
1
O
89.97
4.077
67.856
46.954
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2
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DG
1
2
1.00
1
O
86.60
3.348
66.847
46.293
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DG
2
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DG
1
2
1.00
1
C
94.54
3.153
67.094
44.835
C
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2
ATOM
A
C4'
DG
1
2
1.00
1
C
101.47
3.752
68.318
44.317
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2
ATOM
A
O4'
DG
1
2
1.00
1
O
104.39
3.840
66.073
43.922
C
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DG
2
ATOM
A
C3'
DG
1
2
1.00
1
C
108.00
3.301
64.769
44.059
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2
ATOM
A
O3'
DG
1
2
1.00
1
O
105.42
3.578
66.718
42.581
C
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2
ATOM
A
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DG
1
2
1.00
1
C
96.47
3.756
68.209
42.893
C
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2
ATOM
A
C1'
DG
1
2
1.00
1
C
78.58
4.991
68.705
42.296
C
N9
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2
ATOM
A
N9
DG
1
2
1.00
1
N
77.81
6.292
68.389
42.601
C
C8
DG
2
ATOM
A
C8
DG
1
2
1.00
1
C
70.92
7.170
69.022
41.864
C
N7
DG
2
ATOM
A
N7
DG
1
2
1.00
1
N
64.60
6.404
69.812
41.012
C
C5
DG
2
ATOM
A
C5
DG
1
2
1.00
1
C
62.35
6.784
70.718
39.988
C
C6
DG
2
ATOM
A
C6
DG
1
2
1.00
1
C
68.35
7.911
71.045
39.584
C
O6
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2
ATOM
A
O6
DG
1
2
1.00
1
O
52.15
5.682
71.303
39.377
C
N1
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2
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A
N1
DG
1
2
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1
N
56.99
4.376
71.041
39.717
C
C2
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2
ATOM
A
C2
DG
1
2
1.00
1
C
47.82
3.444
71.706
39.012
C
N2
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2
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A
N2
DG
1
2
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1
N
59.46
4.007
70.202
40.666
C
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2
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A
N3
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1
2
1.00
1
N
64.36
5.063
69.624
41.270
C
C4
DG
2
ATOM
A
C4
DG
1
2
1.00
1
C
102.24
1.930
64.462
43.263
C
P
DT
3
ATOM
A
P
DT
1
3
1.00
1
P
103.75
1.081
65.686
43.316
C
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3
ATOM
A
OP1
DT
1
3
1.00
1
O
106.07
1.381
63.159
43.714
C
OP2
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3
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A
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DT
1
3
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1
O
95.34
2.440
64.299
41.758
C
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DT
3
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A
O5'
DT
1
3
1.00
1
O
87.19
1.523
64.142
40.690
C
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DT
3
ATOM
A
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DT
1
3
1.00
1
C
80.30
1.241
65.421
39.941
C
C4'
DT
3
ATOM
A
C4'
DT
1
3
1.00
1
C
81.85
2.308
66.373
40.103
C
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DT
3
ATOM
A
O4'
DT
1
3
1.00
1
O
83.11
1.086
65.189
38.438
C
C3'
DT
3
ATOM
A
C3'
DT
1
3
1.00
1
C
86.71
-0.292
65.337
38.067
C
O3'
DT
3
ATOM
A
O3'
DT
1
3
1.00
1
O
73.67
1.978
66.195
37.767
C
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DT
3
ATOM
A
C2'
DT
1
3
1.00
1
C
72.53
2.552
67.044
38.875
C
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DT
3
ATOM
A
C1'
DT
1
3
1.00
1
C
54.94
4.011
67.228
38.780
C
N1
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3
ATOM
A
N1
DT
1
3
1.00
1
N
64.22
4.526
68.196
37.955
C
C2
DT
3
ATOM
A
C2
DT
1
3
1.00
1
C
69.76
3.862
68.958
37.261
C
O2
DT
3
ATOM
A
O2
DT
1
3
1.00
1
O
60.59
5.901
68.262
37.956
C
N3
DT
3
ATOM
A
N3
DT
1
3
1.00
1
N
58.12
6.765
67.470
38.686
C
C4
DT
3
ATOM
A
C4
DT
1
3
1.00
1
C
72.36
7.979
67.639
38.592
C
O4
DT
3
ATOM
A
O4
DT
1
3
1.00
1
O
48.16
6.142
66.477
39.527
C
C5
DT
3
ATOM
A
C5
DT
1
3
1.00
1
C
60.39
7.006
65.580
40.348
C
C7
DT
3
ATOM
A
C7
DT
1
3
1.00
1
C
44.92
4.808
66.397
39.538
C
C6
DT
3
ATOM
A
C6
DT
1
3
1.00
1
C
80.92
-0.915
66.809
37.915
C
P
DA
4
ATOM
A
P
DA
1
4
1.00
1
P
68.35
-0.398
67.650
39.030
C
OP1
DA
4
ATOM
A
OP1
DA
1
4
1.00
1
O
83.39
-2.374
66.716
37.676
C
OP2
DA
4
ATOM
A
OP2
DA
1
4
1.00
1
O
88.73
-0.266
67.335
36.549
C
O5'
DA
4
ATOM
A
O5'
DA
1
4
1.00
1
O
82.63
-0.948
68.218
35.672
C
C5'
DA
4
ATOM
A
C5'
DA
1
4
1.00
1
C
73.99
-0.443
68.145
34.250
C
C4'
DA
4
ATOM
A
C4'
DA
1
4
1.00
1
C
78.87
0.685
67.253
34.125
C
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DA
4
ATOM
A
O4'
DA
1
4
1.00
1
O
73.69
-1.478
67.612
33.261
C
C3'
DA
4
ATOM
A
C3'
DA
1
4
1.00
1
C
79.28
-1.538
68.466
32.121
C
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DA
4
ATOM
A
O3'
DA
1
4
1.00
1
O
74.90
-1.022
66.211
32.920
C
C2'
DA
4
ATOM
A
C2'
DA
1
4
1.00
1
C
71.17
0.476
66.292
33.079
C
C1'
DA
4
ATOM
A
C1'
DA
1
4
1.00
1
C
70.68
1.189
65.101
33.544
C
N9
DA
4
ATOM
A
N9
DA
1
4
1.00
1
N
67.48
1.206
64.560
34.811
C
C8
DA
4
ATOM
A
C8
DA
1
4
1.00
1
C
63.05
1.945
63.479
34.927
C
N7
DA
4
ATOM
A
N7
DA
1
4
1.00
1
N
67.43
2.453
63.292
33.646
C
C5
DA
4
ATOM
A
C5
DA
1
4
1.00
1
C
69.03
3.307
62.329
33.087
C
C6
DA
4
ATOM
A
C6
DA
1
4
1.00
1
C
81.68
3.841
61.306
33.756
C
N6
DA
4
ATOM
A
N6
DA
1
4
1.00
1
N
71.75
3.618
62.436
31.774
C
N1
DA
4
ATOM
A
N1
DA
1
4
1.00
1
N
68.35
3.099
63.450
31.074
C
C2
DA
4
ATOM
A
C2
DA
1
4
1.00
1
C
72.97
2.285
64.419
31.479
C
N3
DA
4
ATOM
A
N3
DA
1
4
1.00
1
N
73.52
1.997
64.284
32.787
C
C4
DA
4
ATOM
A
C4
DA
1
4
1.00
1
C
81.27
-2.699
68.193
31.041
C
P
DC
5
ATOM
A
P
DC
1
5
1.00
1
P
85.90
-2.915
69.385
30.180
C
OP1
DC
5
ATOM
A
OP1
DC
1
5
1.00
1
O
90.66
-3.876
67.635
31.773
C
OP2
DC
5
ATOM
A
OP2
DC
1
5
1.00
1
O
79.03
-2.088
67.037
30.124
C
O5'
DC
5
ATOM
A
O5'
DC
1
5
1.00
1
O
72.12
-0.723
67.024
29.736
C
C5'
DC
5
ATOM
A
C5'
DC
1
5
1.00
1
C
78.47
-0.501
66.215
28.489
C
C4'
DC
5
ATOM
A
C4'
DC
1
5
1.00
1
C
86.82
0.121
64.947
28.838
C
O4'
DC
5
ATOM
A
O4'
DC
1
5
1.00
1
O
82.31
-1.723
65.762
27.695
C
C3'
DC
5
ATOM
A
C3'
DC
1
5
1.00
1
C
84.52
-1.367
65.458
26.370
C
O3'
DC
5
ATOM
A
O3'
DC
1
5
1.00
1
O
74.57
-2.162
64.567
28.521
C
C2'
DC
5
ATOM
A
C2'
DC
1
5
1.00
1
C
76.00
-0.815
63.874
28.657
C
C1'
DC
5
ATOM
A
C1'
DC
1
5
1.00
1
C
66.07
-0.617
62.969
29.798
C
N1
DC
5
ATOM
A
N1
DC
1
5
1.00
1
N
59.52
0.225
61.865
29.625
C
C2
DC
5
ATOM
A
C2
DC
1
5
1.00
1
C
60.07
0.780
61.666
28.535
C
O2
DC
5
ATOM
A
O2
DC
1
5
1.00
1
O
64.84
0.434
61.011
30.648
C
N3
DC
5
ATOM
A
N3
DC
1
5
1.00
1
N
65.84
-0.166
61.233
31.817
C
C4
DC
5
ATOM
A
C4
DC
1
5
1.00
1
C
87.34
0.097
60.338
32.775
C
N4
DC
5
ATOM
A
N4
DC
1
5
1.00
1
N
61.58
-1.029
62.343
32.027
C
C5
DC
5
ATOM
A
C5
DC
1
5
1.00
1
C
64.52
-1.229
63.186
31.004
C
C6
DC
5
ATOM
A
C6
DC
1
5
1.00
1
C
84.81
-2.170
65.771
25.027
C
P
DG
6
ATOM
A
P
DG
1
6
1.00
1
P
82.70
-1.306
66.479
24.037
C
OP1
DG
6
ATOM
A
OP1
DG
1
6
1.00
1
O
79.61
-3.500
66.357
25.343
C
OP2
DG
6
ATOM
A
OP2
DG
1
6
1.00
1
O
87.91
-2.400
64.301
24.411
C
O5'
DG
6
ATOM
A
O5'
DG
1
6
1.00
1
O
89.55
-1.300
63.386
24.408
C
C5'
DG
6
ATOM
A
C5'
DG
1
6
1.00
1
C
89.60
-1.750
61.963
24.217
C
C4'
DG
6
ATOM
A
C4'
DG
1
6
1.00
1
C
76.84
-1.549
61.180
25.434
C
O4'
DG
6
ATOM
A
O4'
DG
1
6
1.00
1
O
90.67
-3.230
61.807
23.889
C
C3'
DG
6
ATOM
A
C3'
DG
1
6
1.00
1
C
103.17
-3.497
60.665
23.097
C
O3'
DG
6
ATOM
A
O3'
DG
1
6
1.00
1
O
84.10
-3.836
61.698
25.275
C
C2'
DG
6
ATOM
A
C2'
DG
1
6
1.00
1
C
74.75
-2.825
60.690
25.844
C
C1'
DG
6
ATOM
A
C1'
DG
1
6
1.00
1
C
63.75
-2.877
60.572
27.290
C
N9
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6
ATOM
A
N9
DG
1
6
1.00
1
N
61.33
-3.545
61.295
28.239
C
C8
DG
6
ATOM
A
C8
DG
1
6
1.00
1
C
64.19
-3.327
60.866
29.455
C
N7
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6
ATOM
A
N7
DG
1
6
1.00
1
N
62.14
-2.459
59.791
29.299
C
C5
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6
ATOM
A
C5
DG
1
6
1.00
1
C
59.37
-1.847
58.903
30.213
C
C6
DG
6
ATOM
A
C6
DG
1
6
1.00
1
C
64.94
-1.929
58.852
31.445
C
O6
DG
6
ATOM
A
O6
DG
1
6
1.00
1
O
65.29
-1.042
57.969
29.576
C
N1
DG
6
ATOM
A
N1
DG
1
6
1.00
1
N
71.52
-0.829
57.871
28.227
C
C2
DG
6
ATOM
A
C2
DG
1
6
1.00
1
C
79.13
-0.016
56.900
27.790
C
N2
DG
6
ATOM
A
N2
DG
1
6
1.00
1
N
76.56
-1.390
58.689
27.359
C
N3
DG
6
ATOM
A
N3
DG
1
6
1.00
1
N
66.32
-2.175
59.601
27.969
C
C4
DG
6
ATOM
A
C4
DG
1
6
1.00
1
C
88.78
1.698
75.572
47.551
C
FE
FE2
101
HETATM
B
FE
FE2
2
0.33
1
FE
95.00
8.216
82.089
41.033
C
FE
FE2
102
HETATM
C
FE
FE2
2
0.33
1
FE
70.95
5.093
68.781
29.717
C
FE
FE2
201
HETATM
D
FE
FE2
2
0.33
1
FE
92.03
11.692
62.182
36.316
C
FE
FE2
202
HETATM
E
FE
FE2
2
0.33
1
FE
98.57
0.317
76.253
48.799
C
N11
5PM
111
HETATM
F
N11
5PM
3
1.00
1
N
73.57
0.897
76.896
46.388
C
N12
5PM
111
HETATM
F
N12
5PM
3
1.00
1
N
109.77
7.375
80.448
40.307
C
N13
5PM
111
HETATM
F
N13
5PM
3
1.00
1
N
137.31
9.732
81.406
39.964
C
N14
5PM
111
HETATM
F
N14
5PM
3
1.00
1
N
108.79
0.067
75.872
50.048
C
C1A
5PM
111
HETATM
F
C1A
5PM
3
1.00
1
C
116.43
-0.941
76.441
50.831
C
C1B
5PM
111
HETATM
F
C1B
5PM
3
1.00
1
C
117.59
-1.707
77.410
50.307
C
C1C
5PM
111
HETATM
F
C1C
5PM
3
1.00
1
C
109.44
-1.467
77.813
49.008
C
C1D
5PM
111
HETATM
F
C1D
5PM
3
1.00
1
C
94.03
-0.458
77.222
48.287
C
C1E
5PM
111
HETATM
F
C1E
5PM
3
1.00
1
C
78.64
-0.082
77.548
46.926
C
C1F
5PM
111
HETATM
F
C1F
5PM
3
1.00
1
C
73.90
1.198
77.283
45.022
C
C1G
5PM
111
HETATM
F
C1G
5PM
3
1.00
1
C
70.68
0.939
76.417
43.983
C
C1H
5PM
111
HETATM
F
C1H
5PM
3
1.00
1
C
70.61
1.254
76.787
42.672
C
C1I
5PM
111
HETATM
F
C1I
5PM
3
1.00
1
C
68.71
1.798
78.016
42.394
C
C1J
5PM
111
HETATM
F
C1J
5PM
3
1.00
1
C
60.95
2.058
78.869
43.470
C
C1K
5PM
111
HETATM
F
C1K
5PM
3
1.00
1
C
65.48
1.774
78.507
44.778
C
C1L
5PM
111
HETATM
F
C1L
5PM
3
1.00
1
C
72.93
2.001
78.488
40.976
C
S1M
5PM
111
HETATM
F
S1M
5PM
3
1.00
1
S
75.86
3.416
78.998
40.812
C
C1N
5PM
111
HETATM
F
C1N
5PM
3
1.00
1
C
69.62
3.683
80.162
40.145
C
C1O
5PM
111
HETATM
F
C1O
5PM
3
1.00
1
C
76.62
4.957
80.650
39.959
C
C1P
5PM
111
HETATM
F
C1P
5PM
3
1.00
1
C
94.89
6.006
79.983
40.505
C
C1Q
5PM
111
HETATM
F
C1Q
5PM
3
1.00
1
C
92.25
5.765
78.833
41.166
C
C1R
5PM
111
HETATM
F
C1R
5PM
3
1.00
1
C
86.34
4.495
78.337
41.314
C
C1S
5PM
111
HETATM
F
C1S
5PM
3
1.00
1
C
123.24
8.118
79.746
39.534
C
C1T
5PM
111
HETATM
F
C1T
5PM
3
1.00
1
C
133.33
9.468
80.221
39.318
C
C1U
5PM
111
HETATM
F
C1U
5PM
3
1.00
1
C
139.31
10.421
79.557
38.548
C
C1V
5PM
111
HETATM
F
C1V
5PM
3
1.00
1
C
143.09
11.668
80.127
38.419
C
C1W
5PM
111
HETATM
F
C1W
5PM
3
1.00
1
C
143.77
11.912
81.321
39.079
C
C1X
5PM
111
HETATM
F
C1X
5PM
3
1.00
1
C
140.76
10.945
81.934
39.833
C
C1Y
5PM
111
HETATM
F
C1Y
5PM
3
1.00
1
C
58.70
4.186
67.990
28.134
C
N11
5PM
211
HETATM
G
N11
5PM
3
1.00
1
N
62.28
4.400
67.150
30.548
C
N12
5PM
211
HETATM
G
N12
5PM
3
1.00
1
N
70.60
10.551
63.528
37.235
C
N13
5PM
211
HETATM
G
N13
5PM
3
1.00
1
N
83.41
13.015
62.879
37.597
C
N14
5PM
211
HETATM
G
N14
5PM
3
1.00
1
N
63.71
4.109
68.475
26.896
C
C1A
5PM
211
HETATM
G
C1A
5PM
3
1.00
1
C
46.00
3.452
67.841
25.834
C
C1B
5PM
211
HETATM
G
C1B
5PM
3
1.00
1
C
48.64
2.847
66.672
26.092
C
C1C
5PM
211
HETATM
G
C1C
5PM
3
1.00
1
C
55.25
2.905
66.151
27.368
C
C1D
5PM
211
HETATM
G
C1D
5PM
3
1.00
1
C
56.63
3.588
66.815
28.360
C
C1E
5PM
211
HETATM
G
C1E
5PM
3
1.00
1
C
58.47
3.733
66.401
29.742
C
C1F
5PM
211
HETATM
G
C1F
5PM
3
1.00
1
C
65.44
4.542
66.679
31.918
C
C1G
5PM
211
HETATM
G
C1G
5PM
3
1.00
1
C
55.57
3.869
67.224
32.987
C
C1H
5PM
211
HETATM
G
C1H
5PM
3
1.00
1
C
52.23
4.038
66.696
34.276
C
C1I
5PM
211
HETATM
G
C1I
5PM
3
1.00
1
C
66.51
4.912
65.663
34.525
C
C1J
5PM
211
HETATM
G
C1J
5PM
3
1.00
1
C
58.39
5.586
65.111
33.423
C
C1K
5PM
211
HETATM
G
C1K
5PM
3
1.00
1
C
57.69
5.401
65.618
32.141
C
C1L
5PM
211
HETATM
G
C1L
5PM
3
1.00
1
C
68.59
5.165
65.105
35.908
C
S1M
5PM
211
HETATM
G
S1M
5PM
3
1.00
1
S
70.18
6.566
64.654
36.268
C
C1N
5PM
211
HETATM
G
C1N
5PM
3
1.00
1
C
70.93
6.839
63.424
36.815
C
C1O
5PM
211
HETATM
G
C1O
5PM
3
1.00
1
C
73.63
8.127
63.044
37.164
C
C1P
5PM
211
HETATM
G
C1P
5PM
3
1.00
1
C
72.27
9.170
63.881
36.936
C
C1Q
5PM
211
HETATM
G
C1Q
5PM
3
1.00
1
C
70.15
8.926
65.084
36.362
C
C1R
5PM
211
HETATM
G
C1R
5PM
3
1.00
1
C
70.27
7.641
65.461
36.053
C
C1S
5PM
211
HETATM
G
C1S
5PM
3
1.00
1
C
75.48
11.153
64.232
38.116
C
C1T
5PM
211
HETATM
G
C1T
5PM
3
1.00
1
C
84.73
12.536
63.907
38.378
C
C1U
5PM
211
HETATM
G
C1U
5PM
3
1.00
1
C
97.30
13.328
64.543
39.333
C
C1V
5PM
211
HETATM
G
C1V
5PM
3
1.00
1
C
100.25
14.638
64.138
39.486
C
C1W
5PM
211
HETATM
G
C1W
5PM
3
1.00
1
C
98.70
15.100
63.117
38.668
C
C1X
5PM
211
HETATM
G
C1X
5PM
3
1.00
1
C
89.95
14.285
62.521
37.739
C
C1Y
5PM
211
HETATM
G
C1Y
5PM
3
1.00
1
C
0.020305
0.000000
0.000000
0.000000
0.020305
0.000000
0.000000
0.000000
0.020305
0.000000
0.000000
0.000000
Boer, D.R.
Uson, I.
Coll, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
90.00
49.249
49.249
49.249
C24 H18 N4 S
394.492
4,4'-sulfanediylbis{N-[(1E)-pyridin-2-ylmethylidene]aniline}
1,1-Bis(N-(4-phenyl)-2-pyridylcarboxaldimine)thioether
non-polymer
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
Fe 2
55.845
FE (II) ION
non-polymer
Y
1
N
N
N
2
N
N
N
3
N
N
Y
4
N
N
Y
5
N
C
Y
6
N
C
Y
7
N
C
Y
8
N
C
Y
9
N
C
N
10
N
C
Y
11
N
C
Y
12
N
C
Y
13
N
C
Y
14
N
C
Y
15
N
C
Y
16
N
C
N
17
N
S
Y
18
N
C
Y
19
N
C
Y
20
N
C
Y
21
N
C
Y
22
N
C
Y
23
N
C
N
24
N
C
Y
25
N
C
Y
26
N
C
Y
27
N
C
Y
28
N
C
Y
29
N
C
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
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
O
N
49
N
P
N
50
N
O
N
51
N
O
N
52
N
O
N
53
N
C
N
54
R
C
N
55
N
O
N
56
S
C
N
57
N
O
N
58
N
C
N
59
R
C
Y
60
N
N
Y
61
N
C
Y
62
N
N
Y
63
N
C
Y
64
N
C
N
65
N
N
Y
66
N
N
Y
67
N
C
Y
68
N
N
Y
69
N
C
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
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
O
N
85
N
P
N
86
N
O
N
87
N
O
N
88
N
O
N
89
N
C
N
90
R
C
N
91
N
O
N
92
S
C
N
93
N
O
N
94
N
C
N
95
R
C
N
96
N
N
N
97
N
C
N
98
N
O
N
99
N
N
N
100
N
C
N
101
N
N
N
102
N
C
N
103
N
C
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
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
O
N
119
N
P
N
120
N
O
N
121
N
O
N
122
N
O
N
123
N
C
N
124
R
C
N
125
N
O
N
126
S
C
N
127
N
O
N
128
N
C
N
129
R
C
Y
130
N
N
Y
131
N
C
Y
132
N
N
Y
133
N
C
N
134
N
C
N
135
N
O
N
136
N
N
N
137
N
C
N
138
N
N
N
139
N
N
Y
140
N
C
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
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
O
N
156
N
P
N
157
N
O
N
158
N
O
N
159
N
O
N
160
N
C
N
161
R
C
N
162
N
O
N
163
S
C
N
164
N
O
N
165
N
C
N
166
R
C
N
167
N
N
N
168
N
C
N
169
N
O
N
170
N
N
N
171
N
C
N
172
N
O
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
FE
Y
1
N
doub
Y
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
doub
Y
7
N
doub
Y
8
N
sing
Y
9
N
sing
N
10
N
sing
Y
11
N
doub
N
12
N
sing
Y
13
N
sing
N
14
N
sing
Y
15
N
doub
N
16
N
sing
N
17
N
sing
N
18
N
sing
Y
19
N
doub
Y
20
N
sing
Y
21
N
doub
N
22
N
sing
Y
23
N
sing
N
24
N
sing
Y
25
N
doub
N
26
N
sing
Y
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
Y
31
N
doub
Y
32
N
sing
Y
33
N
doub
N
34
N
sing
Y
35
N
sing
N
36
N
sing
Y
37
N
doub
Y
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
Y
43
N
doub
Y
44
N
sing
N
45
N
sing
Y
46
N
doub
N
47
N
sing
Y
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
doub
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
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
Y
74
N
sing
Y
75
N
sing
Y
76
N
doub
N
77
N
sing
Y
78
N
sing
Y
79
N
sing
Y
80
N
doub
N
81
N
sing
Y
82
N
doub
N
83
N
sing
N
84
N
sing
Y
85
N
sing
Y
86
N
doub
N
87
N
sing
Y
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
doub
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
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
doub
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
doub
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
Y
147
N
sing
Y
148
N
sing
Y
149
N
doub
N
150
N
sing
Y
151
N
sing
N
152
N
sing
Y
153
N
doub
N
154
N
doub
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
doub
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
doub
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
doub
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
doub
N
193
N
sing
N
194
N
sing
N
195
N
doub
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
GE
Angew.Chem.Int.Ed.Engl.
9999
1433-7851
49
2336
2339
10.1002/anie.200906742
20191645
Self-Assembly of Functionalizable Two-Component 3D DNA Arrays through the Induced Formation of DNA Three-Way-Junction Branch Points by Supramolecular Cylinders.
2010
GE
Angew.Chem.Int.Ed.Engl.
9999
1433-7851
45
1227
1231
10.1002/anie.200503822
16463312
Molecular recognition of a three-way DNA junction by a metallosupramolecular helicate.
2006
10.2210/pdb3fx8/pdb
pdb_00003fx8
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2006-02-23
ADSC QUANTUM 315
Si(111)
MAD
M
x-ray
1
1.7366
1.0
1.7410
1.0
1.7311
1.0
ID29
ESRF
1.7366, 1.7410, 1.7311
SYNCHROTRON
ESRF BEAMLINE ID29
Synthetic hexanucleotide
1809.217
(5'-D(*CP*GP*TP*AP*CP*G)-3'
1
syn
polymer
55.845
FE (II) ION
4
syn
non-polymer
394.492
4,4'-sulfanediylbis{N-[(1E)-pyridin-2-ylmethylidene]aniline}
2
syn
non-polymer
no
no
(DC)(DG)(DT)(DA)(DC)(DG)
CGTACG
C
polydeoxyribonucleotide
n
n
n
n
n
n
1
5.50
77.64
VAPOR DIFFUSION, SITTING DROP
8.5
1 microliter of 10 mM cylinder, 1 microliter of 3 mM DNA, 2 microliters of crystallization buffer (10 mM Magnesium chloride, 5% v/v Isopropanol, 50 mM Tris-HCl), pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
Magnesium chloride
1
Isopropanol
1
Tris-HCl
1
Magnesium chloride
2
Isopropanol
2
Tris-HCl
2
-6.488
1
19
C
1
C
6
-8.368
C_DC1:DG6_C
1
-0.020
0.155
0.598
-0.201
6.535
1
19
C
2
C
5
2.276
C_DG2:DC5_C
2
-18.819
-0.098
0.724
-0.134
4.765
1
20
C
3
C
4
-4.041
C_DT3:DA4_C
3
-16.856
-0.011
0.080
0.030
3.006
32.277
C
C
1
2
4.504
C
C
6
5
2.982
2.499
-0.063
0.591
CC_DC1DG2:DC5DG6_CC
1
2.352
-4.239
32.098
0.657
0.496
3.374
32.893
C
C
2
3
-2.327
C
C
5
4
3.333
-1.315
0.372
-0.587
CC_DG2DT3:DA4DC5_CC
2
3.459
-6.121
32.690
-0.806
-0.050
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
1
0
2010-03-16
1
1
2011-07-13
1
2
2024-02-21
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Recognition of three-way DNA junctions by a metallo-supramolecular cylinder ('helicate') at two distinct sites
Distinct recognition of three-way DNA junctions by the two enantiomers of a metallo-supramolecular cylinder ('helicate')
RCSB
Y
RCSB
2009-01-20
REL
REL
FE2
FE (II) ION
5PM
4,4'-sulfanediylbis{N-[(1E)-pyridin-2-ylmethylidene]aniline}
Synthetic hexanucleotide. The sequence is palindromic
sample
LIGAND 5PM C 111 WITH TWO IRON ATOMS FE2 C 101 AND C 102
IS THE M HELICAL ENANTIOMER OF [FE2L3], WHERE L IS
4,4'-SULFANEDIYLBIS{N-[(1E)-PYRIDIN-2-YLMETHYLIDENE]ANILINE}
5PM
1
2
FE2
FE2
101
C
5PM
1
2
FE2
FE2
102
C
5PM
1
2
FE2
FE2
201
C
5PM
1
2
FE2
FE2
202
C
5PM
1
3
5PM
5PM
111
C
5PM
1
3
5PM
5PM
211
C
C
1
n
1
DC
1
C
G
2
n
2
DG
2
C
T
3
n
3
DT
3
C
A
4
n
4
DA
4
C
C
5
n
5
DC
5
C
G
6
n
6
DG
6
C
author_and_software_defined_assembly
PISA
3
trimeric
4580
-68.9
2430
C
5PM
111
F
N11
5PM
1_555
C
FE2
101
B
FE
FE2
1_555
C
5PM
111
F
N12
5PM
1_555
81.7
C
5PM
111
F
N13
5PM
1_555
C
FE2
102
C
FE
FE2
1_555
C
5PM
111
F
N14
5PM
1_555
80.9
C
5PM
211
G
N11
5PM
1_555
C
FE2
201
D
FE
FE2
1_555
C
5PM
211
G
N12
5PM
1_555
81.1
C
5PM
211
G
N13
5PM
1_555
C
FE2
202
E
FE
FE2
1_555
C
5PM
211
G
N14
5PM
1_555
81.1
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
0.0000000000
1.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
6_467
z-1/2,-x+3/2,-y+2
crystal symmetry operation
-24.6245000000
73.8735000000
98.4980000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
1.0000000000
0.0000000000
0.0000000000
12_675
-y+3/2,-z+2,x+1/2
crystal symmetry operation
73.8735000000
98.4980000000
24.6245000000
1
C
FE2
101
B
FE2
1
C
FE2
102
C
FE2
1
C
FE2
201
D
FE2
1
C
FE2
202
E
FE2
1
-5.09
0.40
104.50
99.41
C
C
C
O4'
C4'
C3'
DG
DG
DG
2
2
2
N
1
4.31
0.30
108.30
112.61
C
C
C
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
-2.47
0.40
104.50
102.03
C
C
C
O4'
C4'
C3'
DC
DC
DC
5
5
5
N
1
8.88
1.20
119.70
128.58
C
C
C
C3'
O3'
P
DC
DC
DG
5
5
6
Y
1
-5.36
0.80
102.40
97.04
C
C
C
C3'
C2'
C1'
DG
DG
DG
6
6
6
N
1
1.95
0.30
108.30
110.25
C
C
C
O4'
C1'
N9
DG
DG
DG
6
6
6
N
79.4
0.212
0.187
0.187
0.187
2.44
24.63
74
1573
1540
98
Random
1
isotropic
MAD
BABINET (SHELXL SWAT)
2.44
24.63
0
182
62
120
0
0.021
0.005
0.006
0.006
0.031
0.358
2.55
165
94
2.44
24.63
3FX8
1573
1573
0
-3
0.041
1
36.1
8.4
99.4
0.447
2.44
2.58
2.2
228
5.1
100
data collection
ProDC
phasing
SHELXDE
refinement
SHELXL-97
data reduction
MOSFLM
data scaling
SCALA
Distinct recognition of three-way DNA junctions by a thioester variant of a metallo-supramolecular cylinder ('helicate')
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
A THREE-WAY JUNCTION (CHAINS A AND C) WITH DISCONTINUOUS DNA STRANDS CAN BE GENERATED THROUGH THE FOLLOWING TRANSFORMATIONS ON CHAIN C: [Z+1/2,-X+1/2,-Y+(0 1 1)], [Y+1/2,-Z+1/2,-X+(-1 1 1)], [-X, Y+1/2,-Z+1/2+(0 1 0)], [-Z,X+1/2,-Y+1/2+(0 1 1)], [Y,Z,X+(0 2 1)] AND THE FOLLOWING TRANSFORMATIONS ON CHAIN A: [-Z,X+1/2,-Y+1/2 +(0 1 1)], [Y+1/2,-Z+1/2,-X +(-1 1 1)]
metalc
1.982
C
FE2
101
B
FE
FE2
1_555
C
5PM
111
F
N11
5PM
1_555
metalc
1.936
C
FE2
101
B
FE
FE2
1_555
C
5PM
111
F
N12
5PM
1_555
metalc
1.982
C
FE2
102
C
FE
FE2
1_555
C
5PM
111
F
N13
5PM
1_555
metalc
1.977
C
FE2
102
C
FE
FE2
1_555
C
5PM
111
F
N14
5PM
1_555
metalc
1.989
C
FE2
201
D
FE
FE2
1_555
C
5PM
211
G
N11
5PM
1_555
metalc
1.957
C
FE2
201
D
FE
FE2
1_555
C
5PM
211
G
N12
5PM
1_555
metalc
1.990
C
FE2
202
E
FE
FE2
1_555
C
5PM
211
G
N13
5PM
1_555
metalc
1.969
C
FE2
202
E
FE
FE2
1_555
C
5PM
211
G
N14
5PM
1_555
hydrog
WATSON-CRICK
C
DC
1
A
N3
DC
1
1_555
C
DG
6
A
N1
DG
6
6_467
hydrog
WATSON-CRICK
C
DC
1
A
N4
DC
1
1_555
C
DG
6
A
O6
DG
6
6_467
hydrog
WATSON-CRICK
C
DC
1
A
O2
DC
1
1_555
C
DG
6
A
N2
DG
6
6_467
hydrog
WATSON-CRICK
C
DG
2
A
N1
DG
2
1_555
C
DC
5
A
N3
DC
5
6_467
hydrog
WATSON-CRICK
C
DG
2
A
N2
DG
2
1_555
C
DC
5
A
O2
DC
5
6_467
hydrog
WATSON-CRICK
C
DG
2
A
O6
DG
2
1_555
C
DC
5
A
N4
DC
5
6_467
hydrog
WATSON-CRICK
C
DT
3
A
N3
DT
3
1_555
C
DA
4
A
N1
DA
4
6_467
hydrog
WATSON-CRICK
C
DT
3
A
O4
DT
3
1_555
C
DA
4
A
N6
DA
4
6_467
DNA
Self-assembly, DNA-based nanomaterial, DNA
3FX8
PDB
1
1
3FX8
CGTACG
1
6
3FX8
1
6
3FX8
C
1
1
6
BINDING SITE FOR RESIDUE FE2 C 101
C
FE2
101
Software
3
BINDING SITE FOR RESIDUE FE2 C 102
C
FE2
102
Software
3
BINDING SITE FOR RESIDUE FE2 C 201
C
FE2
201
Software
3
BINDING SITE FOR RESIDUE FE2 C 202
C
FE2
202
Software
3
BINDING SITE FOR RESIDUE 5PM C 111
C
5PM
111
Software
8
BINDING SITE FOR RESIDUE 5PM C 211
C
5PM
211
Software
10
C
5PM
111
F
5PM
3
8_667
C
5PM
111
F
5PM
3
11_376
C
5PM
111
F
5PM
3
1_555
C
5PM
111
F
5PM
3
1_555
C
5PM
111
F
5PM
3
8_667
C
5PM
111
F
5PM
3
11_376
C
5PM
211
G
5PM
3
1_555
C
5PM
211
G
5PM
3
6_467
C
5PM
211
G
5PM
3
12_675
C
5PM
211
G
5PM
3
12_675
C
5PM
211
G
5PM
3
1_555
C
5PM
211
G
5PM
3
6_467
C
DC
1
A
DC
1
8
11_376
C
DG
6
A
DG
6
8
6_467
C
FE2
101
B
FE2
8
11_376
C
FE2
101
B
FE2
8
8_667
C
FE2
101
B
FE2
8
1_555
C
FE2
102
C
FE2
8
11_376
C
FE2
102
C
FE2
8
8_667
C
FE2
102
C
FE2
8
1_555
C
DT
3
A
DT
3
10
1_555
C
DA
4
A
DA
4
10
1_555
C
DA
4
A
DA
4
10
12_675
C
DC
5
A
DC
5
10
1_555
C
FE2
201
D
FE2
10
1_555
C
FE2
201
D
FE2
10
12_675
C
FE2
201
D
FE2
10
6_467
C
FE2
202
E
FE2
10
12_675
C
FE2
202
E
FE2
10
6_467
C
FE2
202
E
FE2
10
1_555
198
P 21 3