0.039002
0.000000
0.000000
0.000000
0.024207
0.000000
0.000000
0.000000
0.014928
0.00000
0.00000
0.00000
Sriram, M.
Van Der Marel, G.A.
Roelen, H.L.P.F.
Van Boom, J.H.
Wang, A.H.-J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
25.640
41.310
66.990
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
C12 H18 N5 O7 P
375.274
n
O6-ETHYL-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
non-polymer
C25 H24 N6 O
424.498
2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE
HOECHST 33258
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
Y
13
N
N
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
N
18
N
N
Y
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
56
N
C
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
O
N
72
N
P
N
73
N
O
N
74
N
O
N
75
N
O
N
76
N
C
N
77
R
C
N
78
N
O
N
79
S
C
N
80
N
O
N
81
N
C
N
82
R
C
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
N
Y
93
N
C
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
N
C
N
119
R
C
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
C
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
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
P
N
145
N
O
N
146
N
O
N
147
N
O
N
148
N
O
N
149
N
C
N
150
R
C
N
151
N
O
N
152
S
C
N
153
N
O
N
154
N
C
N
155
N
C
N
156
R
C
Y
157
N
N
Y
158
N
C
Y
159
N
N
Y
160
N
C
Y
161
N
C
N
162
N
O
Y
163
N
N
Y
164
N
C
N
165
N
N
N
166
N
C
Y
167
N
N
Y
168
N
C
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
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
O
N
188
N
H
N
189
N
H
N
190
N
O
Y
191
N
C
Y
192
N
C
Y
193
N
C
Y
194
N
C
Y
195
N
C
Y
196
N
C
Y
197
N
C
Y
198
N
N
Y
199
N
C
Y
200
N
C
Y
201
N
N
Y
202
N
C
Y
203
N
C
Y
204
N
C
Y
205
N
C
Y
206
N
C
Y
207
N
N
Y
208
N
C
Y
209
N
C
Y
210
N
N
Y
211
N
C
Y
212
N
C
Y
213
N
C
Y
214
N
C
N
215
N
N
N
216
N
C
N
217
N
C
N
218
N
N
N
219
N
C
N
220
N
C
N
221
N
C
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
Y
24
N
sing
Y
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
sing
Y
30
N
doub
N
31
N
sing
Y
32
N
doub
N
33
N
sing
N
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
doub
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
N
116
N
sing
N
117
N
sing
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
N
138
N
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
doub
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
Y
177
N
sing
Y
178
N
sing
Y
179
N
doub
N
180
N
sing
Y
181
N
sing
Y
182
N
doub
Y
183
N
sing
N
184
N
sing
Y
185
N
sing
N
186
N
sing
Y
187
N
doub
N
188
N
sing
Y
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
Y
194
N
doub
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
Y
199
N
doub
Y
200
N
sing
Y
201
N
sing
N
202
N
sing
Y
203
N
doub
N
204
N
sing
Y
205
N
sing
Y
206
N
sing
Y
207
N
doub
N
208
N
sing
N
209
N
sing
Y
210
N
sing
Y
211
N
doub
Y
212
N
sing
N
213
N
sing
Y
214
N
doub
Y
215
N
sing
Y
216
N
sing
Y
217
N
sing
Y
218
N
doub
N
219
N
sing
Y
220
N
sing
N
221
N
sing
Y
222
N
doub
Y
223
N
sing
N
224
N
sing
Y
225
N
sing
Y
226
N
doub
Y
227
N
sing
N
228
N
sing
Y
229
N
doub
Y
230
N
sing
Y
231
N
sing
Y
232
N
sing
Y
233
N
doub
N
234
N
sing
Y
235
N
sing
N
236
N
sing
Y
237
N
doub
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
UK
EMBO J.
EMJODG
0897
0261-4189
11
225
232
1371249
Conformation of B-DNA containing O6-ethyl-G-C base pairs stabilized by minor groove binding drugs: molecular structure of d(CGC[e6G]AATTCGCG complexed with Hoechst 33258 or Hoechst 33342.
1992
10.2210/pdb128d/pdb
pdb_0000128d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
ROOM TEMPERATURE
1
DIFFRACTOMETER
RIGAKU AFC-5R
x-ray
1
1.0
ROTATING ANODE
3691.445
DNA (5'-D(*CP*GP*CP*(G36)P*AP*AP*TP*TP*CP*GP*CP*G)-3')
2
syn
polymer
424.498
2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE
1
syn
non-polymer
18.015
water
68
nat
water
no
yes
(DC)(DG)(DC)(G36)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)
CGCGAATTCGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
2.40
48.81
VAPOR DIFFUSION
6.00
pH 6.00, VAPOR DIFFUSION
ROOM TEMPERATURE
WATER
1
MPD
1
NA CACODYLATE
1
MGCL2
1
SPERMINE
1
WATER
2
MPD
2
6.673
1
19
A
1
B
24
-5.631
A_DC1:DG24_B
1
-7.587
-0.008
0.229
-0.190
17.743
1
19
A
2
B
23
0.382
A_DG2:DC23_B
2
-6.821
-0.090
0.562
0.126
2.706
1
19
A
3
B
22
-1.158
A_DC3:DG22_B
3
13.780
-0.272
-0.194
-0.041
18.947
1
19
A
4
B
21
5.249
A_G364:DC21_B
4
6.222
0.831
0.355
0.071
14.349
1
20
A
5
B
20
-2.976
A_DA5:DT20_B
5
-11.177
-0.113
0.405
-0.051
20.645
1
20
A
6
B
19
-0.643
A_DA6:DT19_B
6
-17.667
0.311
0.176
-0.043
-1.696
1
20
A
7
B
18
0.199
A_DT7:DA18_B
7
-2.455
-0.285
-0.385
-0.319
2.589
1
20
A
8
B
17
14.833
A_DT8:DA17_B
8
-5.298
0.625
-0.983
-0.320
-9.769
1
19
A
9
B
16
0.604
A_DC9:G3616_B
9
-23.410
-2.152
0.070
-0.145
5.957
1
19
A
10
B
15
-3.879
A_DG10:DC15_B
10
-9.975
0.382
0.044
-0.142
7.759
1
19
A
11
B
14
1.583
A_DC11:DG14_B
11
-13.629
0.198
-0.384
-0.121
-6.111
1
19
A
12
B
13
0.422
A_DG12:DC13_B
12
-3.863
-0.172
-1.218
-0.321
2.977
36.351
A
A
1
2
-0.610
B
B
24
23
2.965
-0.380
-0.571
0.624
AA_DC1DG2:DC23DG24_BB
1
-1.371
2.198
36.324
1.049
0.741
3.957
39.553
A
A
2
3
-6.805
B
B
23
22
3.857
-4.577
1.271
0.228
AA_DG2DC3:DG22DC23_BB
2
6.352
-9.444
38.801
0.986
-0.979
3.302
31.716
A
A
3
4
-2.153
B
B
22
21
3.307
-1.176
0.845
0.830
AA_DC3G364:DC21DG22_BB
3
1.127
-2.063
31.675
1.737
-1.336
3.322
40.318
A
A
4
5
18.245
B
B
21
20
3.475
12.386
-0.957
0.122
AA_G364DA5:DT20DC21_BB
4
1.381
-2.035
38.420
-1.314
1.554
2.763
46.149
A
A
5
6
-21.500
B
B
20
19
2.860
-16.507
0.066
-0.221
AA_DA5DA6:DT19DT20_BB
5
2.870
-3.738
43.156
0.979
0.135
3.418
29.639
A
A
6
7
17.966
B
B
19
18
3.799
9.025
0.874
-0.961
AA_DA6DT7:DA18DT19_BB
6
3.828
-7.621
28.005
-4.041
-0.791
3.176
34.473
A
A
7
8
7.327
B
B
18
17
3.298
4.288
-0.005
0.027
AA_DT7DT8:DA17DA18_BB
7
8.615
-14.721
33.142
-0.627
1.361
3.760
30.555
A
A
8
9
10.731
B
B
17
16
3.732
5.599
-0.288
0.513
AA_DT8DC9:G3616DA17_BB
8
-5.056
9.690
29.631
-0.319
-0.621
3.088
44.900
A
A
9
10
0.242
B
B
16
15
3.164
0.183
-0.041
1.581
AA_DC9DG10:DC15G3616_BB
9
-11.332
14.983
43.518
2.054
-0.943
2.897
38.231
A
A
10
11
-10.187
B
B
15
14
2.939
-6.639
-1.522
0.291
AA_DG10DC11:DG14DC15_BB
10
-1.294
1.986
37.650
1.195
2.178
4.131
32.634
A
A
11
12
7.567
B
B
14
13
4.053
4.229
0.474
0.661
AA_DC11DG12:DC13DG14_BB
11
4.224
-7.557
32.097
0.250
0.082
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1994-01-15
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
NDB
1993-06-30
REL
HT
2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE
HOH
water
HT
25
2
HT
HT
25
A
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
29
3
HOH
HOH
29
A
HOH
31
3
HOH
HOH
31
A
HOH
36
3
HOH
HOH
36
A
HOH
42
3
HOH
HOH
42
A
HOH
44
3
HOH
HOH
44
A
HOH
46
3
HOH
HOH
46
A
HOH
49
3
HOH
HOH
49
A
HOH
53
3
HOH
HOH
53
A
HOH
55
3
HOH
HOH
55
A
HOH
56
3
HOH
HOH
56
A
HOH
57
3
HOH
HOH
57
A
HOH
60
3
HOH
HOH
60
A
HOH
69
3
HOH
HOH
69
A
HOH
70
3
HOH
HOH
70
A
HOH
77
3
HOH
HOH
77
A
HOH
81
3
HOH
HOH
81
A
HOH
91
3
HOH
HOH
91
A
HOH
28
3
HOH
HOH
28
B
HOH
30
3
HOH
HOH
30
B
HOH
32
3
HOH
HOH
32
B
HOH
33
3
HOH
HOH
33
B
HOH
34
3
HOH
HOH
34
B
HOH
35
3
HOH
HOH
35
B
HOH
37
3
HOH
HOH
37
B
HOH
38
3
HOH
HOH
38
B
HOH
39
3
HOH
HOH
39
B
HOH
40
3
HOH
HOH
40
B
HOH
41
3
HOH
HOH
41
B
HOH
43
3
HOH
HOH
43
B
HOH
45
3
HOH
HOH
45
B
HOH
47
3
HOH
HOH
47
B
HOH
48
3
HOH
HOH
48
B
HOH
50
3
HOH
HOH
50
B
HOH
51
3
HOH
HOH
51
B
HOH
52
3
HOH
HOH
52
B
HOH
54
3
HOH
HOH
54
B
HOH
58
3
HOH
HOH
58
B
HOH
59
3
HOH
HOH
59
B
HOH
61
3
HOH
HOH
61
B
HOH
62
3
HOH
HOH
62
B
HOH
63
3
HOH
HOH
63
B
HOH
64
3
HOH
HOH
64
B
HOH
65
3
HOH
HOH
65
B
HOH
66
3
HOH
HOH
66
B
HOH
67
3
HOH
HOH
67
B
HOH
68
3
HOH
HOH
68
B
HOH
71
3
HOH
HOH
71
B
HOH
72
3
HOH
HOH
72
B
HOH
73
3
HOH
HOH
73
B
HOH
74
3
HOH
HOH
74
B
HOH
75
3
HOH
HOH
75
B
HOH
76
3
HOH
HOH
76
B
HOH
78
3
HOH
HOH
78
B
HOH
79
3
HOH
HOH
79
B
HOH
80
3
HOH
HOH
80
B
HOH
82
3
HOH
HOH
82
B
HOH
83
3
HOH
HOH
83
B
HOH
84
3
HOH
HOH
84
B
HOH
85
3
HOH
HOH
85
B
HOH
86
3
HOH
HOH
86
B
HOH
87
3
HOH
HOH
87
B
HOH
88
3
HOH
HOH
88
B
HOH
89
3
HOH
HOH
89
B
HOH
90
3
HOH
HOH
90
B
HOH
92
3
HOH
HOH
92
B
HOH
93
3
HOH
HOH
93
B
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
+G
4
n
4
G36
4
A
A
5
n
5
DA
5
A
A
6
n
6
DA
6
A
T
7
n
7
DT
7
A
T
8
n
8
DT
8
A
C
9
n
9
DC
9
A
G
10
n
10
DG
10
A
C
11
n
11
DC
11
A
G
12
n
12
DG
12
A
C
13
n
1
DC
13
B
G
14
n
2
DG
14
B
C
15
n
3
DC
15
B
+G
16
n
4
G36
16
B
A
17
n
5
DA
17
B
A
18
n
6
DA
18
B
T
19
n
7
DT
19
B
T
20
n
8
DT
20
B
C
21
n
9
DC
21
B
G
22
n
10
DG
22
B
C
23
n
11
DC
23
B
G
24
n
12
DG
24
B
author_defined_assembly
2
dimeric
A
G36
4
A
G36
4
DG
B
G36
16
B
G36
4
DG
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
4.63
0.60
118.90
123.53
A
A
A
N1
C2
O2
DC
DC
DC
1
1
1
N
1
8.01
1.20
119.70
127.71
A
A
A
C3'
O3'
P
DC
DC
DG
1
1
2
Y
1
-11.77
1.50
119.60
107.83
A
A
A
OP1
P
OP2
DG
DG
DG
2
2
2
N
1
-8.22
0.80
109.40
101.18
A
A
A
O5'
C5'
C4'
DG
DG
DG
2
2
2
N
1
-3.06
0.40
104.50
101.44
A
A
A
O4'
C4'
C3'
DG
DG
DG
2
2
2
N
1
5.13
0.30
108.30
113.43
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
-5.32
0.60
125.10
119.78
A
A
A
C6
N1
C2
DG
DG
DG
2
2
2
N
1
4.46
0.50
111.50
115.96
A
A
A
C5
C6
N1
DG
DG
DG
2
2
2
N
1
-4.21
0.60
119.90
115.69
A
A
A
N1
C6
O6
DG
DG
DG
2
2
2
N
1
6.97
1.10
110.50
117.47
A
A
A
O3'
P
OP1
DG
DC
DC
2
3
3
Y
1
-4.28
0.40
104.50
100.22
A
A
A
O4'
C4'
C3'
DC
DC
DC
3
3
3
N
1
10.07
0.30
108.30
118.37
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
-2.82
0.40
121.90
119.08
A
A
A
N3
C4
C5
DC
DC
DC
3
3
3
N
1
6.41
0.60
118.90
125.31
A
A
A
N1
C2
O2
DC
DC
DC
3
3
3
N
1
-5.46
0.70
121.90
116.44
A
A
A
N3
C2
O2
DC
DC
DC
3
3
3
N
1
-9.55
1.50
119.60
110.05
A
A
A
OP1
P
OP2
DA
DA
DA
5
5
5
N
1
7.75
1.20
110.70
118.45
A
A
A
O5'
P
OP2
DA
DA
DA
6
6
6
N
1
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
-3.77
0.50
129.30
125.53
A
A
A
N1
C2
N3
DA
DA
DA
6
6
6
N
1
-10.61
1.20
119.70
109.09
A
A
A
C3'
O3'
P
DA
DA
DT
6
6
7
Y
1
-3.84
0.60
127.20
123.36
A
A
A
C2
N3
C4
DT
DT
DT
7
7
7
N
1
9.31
1.20
119.70
129.01
A
A
A
C3'
O3'
P
DT
DT
DT
7
7
8
Y
1
-10.53
1.50
119.60
109.07
A
A
A
OP1
P
OP2
DT
DT
DT
8
8
8
N
1
-4.00
0.40
104.50
100.50
A
A
A
O4'
C4'
C3'
DT
DT
DT
8
8
8
N
1
2.74
0.30
108.30
111.04
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
-4.01
0.60
119.90
115.89
A
A
A
N3
C4
O4
DT
DT
DT
8
8
8
N
1
8.42
1.20
110.70
119.12
A
A
A
O5'
P
OP2
DC
DC
DC
9
9
9
N
1
-10.74
1.60
120.90
110.16
A
A
A
P
O5'
C5'
DC
DC
DC
9
9
9
N
1
-5.55
0.70
102.20
96.65
A
A
A
C4'
C3'
C2'
DC
DC
DC
9
9
9
N
1
6.53
0.30
108.30
114.83
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
3.18
0.50
119.90
123.08
A
A
A
C2
N3
C4
DC
DC
DC
9
9
9
N
1
-3.59
0.40
121.90
118.31
A
A
A
N3
C4
C5
DC
DC
DC
9
9
9
N
1
4.65
0.30
108.30
112.95
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
3.32
0.50
111.50
114.82
A
A
A
C5
C6
N1
DG
DG
DG
10
10
10
N
1
9.30
1.10
110.50
119.80
A
A
A
O3'
P
OP1
DG
DC
DC
10
11
11
Y
1
-10.72
1.50
119.60
108.88
A
A
A
OP1
P
OP2
DC
DC
DC
11
11
11
N
1
-10.32
0.80
109.40
99.08
A
A
A
O5'
C5'
C4'
DC
DC
DC
11
11
11
N
1
10.51
1.20
110.70
121.21
A
A
A
O5'
P
OP2
DG
DG
DG
12
12
12
N
1
11.97
1.60
120.90
132.87
A
A
A
P
O5'
C5'
DG
DG
DG
12
12
12
N
1
-2.69
0.40
104.50
101.81
A
A
A
O4'
C4'
C3'
DG
DG
DG
12
12
12
N
1
-4.09
0.60
125.10
121.01
A
A
A
C6
N1
C2
DG
DG
DG
12
12
12
N
1
3.60
0.50
111.50
115.10
A
A
A
C5
C6
N1
DG
DG
DG
12
12
12
N
1
-4.67
0.60
128.60
123.93
A
A
A
C5
C6
O6
DG
DG
DG
12
12
12
N
1
3.67
0.30
108.30
111.97
B
B
B
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
3.09
0.50
119.90
122.99
B
B
B
C2
N3
C4
DC
DC
DC
13
13
13
N
1
-3.08
0.40
121.90
118.82
B
B
B
N3
C4
C5
DC
DC
DC
13
13
13
N
1
4.81
0.70
120.20
125.01
B
B
B
C5
C4
N4
DC
DC
DC
13
13
13
N
1
21.48
1.20
119.70
141.18
B
B
B
C3'
O3'
P
DC
DC
DG
13
13
14
Y
1
-14.09
1.50
119.60
105.51
B
B
B
OP1
P
OP2
DG
DG
DG
14
14
14
N
1
-2.52
0.40
104.50
101.98
B
B
B
O4'
C4'
C3'
DG
DG
DG
14
14
14
N
1
9.78
0.30
108.30
118.08
B
B
B
O4'
C1'
N9
DG
DG
DG
14
14
14
N
1
7.39
1.20
110.70
118.09
B
B
B
O5'
P
OP2
DC
DC
DC
15
15
15
N
1
4.75
0.30
108.30
113.05
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
-9.63
1.50
119.60
109.97
B
B
B
OP1
P
OP2
DA
DA
DA
17
17
17
N
1
11.41
1.20
110.70
122.11
B
B
B
O5'
P
OP1
DA
DA
DA
17
17
17
N
1
-5.16
0.80
109.40
104.24
B
B
B
O5'
C5'
C4'
DA
DA
DA
17
17
17
N
1
-3.35
0.50
117.70
114.35
B
B
B
C5
C6
N1
DA
DA
DA
17
17
17
N
1
-5.72
0.40
104.50
98.78
B
B
B
O4'
C4'
C3'
DT
DT
DT
19
19
19
N
1
7.70
1.20
115.70
123.40
B
B
B
C5'
C4'
C3'
DT
DT
DT
19
19
19
N
1
-6.62
1.00
110.10
103.48
B
B
B
C1'
O4'
C4'
DT
DT
DT
19
19
19
N
1
-5.91
0.70
102.20
96.29
B
B
B
C4'
C3'
C2'
DT
DT
DT
19
19
19
N
1
7.56
0.30
108.30
115.86
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
4.03
0.60
114.60
118.63
B
B
B
N1
C2
N3
DT
DT
DT
19
19
19
N
1
-5.42
0.60
127.20
121.78
B
B
B
C2
N3
C4
DT
DT
DT
19
19
19
N
1
-6.17
0.60
119.90
113.73
B
B
B
N3
C4
O4
DT
DT
DT
19
19
19
N
1
10.30
1.50
120.40
130.70
B
B
B
C6
N1
C1'
DT
DT
DT
19
19
19
N
1
9.00
1.20
119.70
128.70
B
B
B
C3'
O3'
P
DT
DT
DT
19
19
20
Y
1
9.82
1.10
110.50
120.32
B
B
B
O3'
P
OP1
DT
DT
DT
19
20
20
Y
1
-13.87
1.50
119.60
105.73
B
B
B
OP1
P
OP2
DT
DT
DT
20
20
20
N
1
-7.96
0.80
109.40
101.44
B
B
B
O5'
C5'
C4'
DT
DT
DT
20
20
20
N
1
6.83
0.30
108.30
115.13
B
B
B
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
-4.12
0.60
127.20
123.08
B
B
B
C2
N3
C4
DT
DT
DT
20
20
20
N
1
-11.01
1.50
119.60
108.59
B
B
B
OP1
P
OP2
DC
DC
DC
21
21
21
N
1
-3.47
0.40
121.90
118.43
B
B
B
N3
C4
C5
DC
DC
DC
21
21
21
N
1
-3.16
0.40
104.50
101.34
B
B
B
O4'
C4'
C3'
DG
DG
DG
22
22
22
N
1
-5.94
0.70
102.20
96.26
B
B
B
C4'
C3'
C2'
DG
DG
DG
22
22
22
N
1
-4.83
0.60
125.10
120.27
B
B
B
C6
N1
C2
DG
DG
DG
22
22
22
N
1
4.46
0.50
111.50
115.96
B
B
B
C5
C6
N1
DG
DG
DG
22
22
22
N
1
-5.78
0.60
119.90
114.12
B
B
B
N1
C6
O6
DG
DG
DG
22
22
22
N
1
10.29
1.20
119.70
129.99
B
B
B
C3'
O3'
P
DG
DG
DC
22
22
23
Y
1
6.63
0.30
108.30
114.93
B
B
B
O4'
C1'
N1
DC
DC
DC
23
23
23
N
1
-4.96
0.70
118.00
113.04
B
B
B
N3
C4
N4
DC
DC
DC
23
23
23
N
1
5.20
0.70
120.20
125.40
B
B
B
C5
C4
N4
DC
DC
DC
23
23
23
N
1
-9.41
1.50
119.60
110.19
B
B
B
OP1
P
OP2
DG
DG
DG
24
24
24
N
1
-2.90
0.40
104.50
101.60
B
B
B
O4'
C4'
C3'
DG
DG
DG
24
24
24
N
1
-5.42
0.80
102.40
96.98
B
B
B
C3'
C2'
C1'
DG
DG
DG
24
24
24
N
1
3.96
0.60
119.90
123.86
B
B
B
N1
C6
O6
DG
DG
DG
24
24
24
N
1
-5.79
0.60
128.60
122.81
B
B
B
C5
C6
O6
DG
DG
DG
24
24
24
N
1
A
A
O3'
P
DA
DT
6
7
0.088
0.012
1.607
1.695
Y
1
A
A
P
O5'
DT
DT
7
7
0.060
0.010
1.593
1.653
N
1
A
A
P
O5'
DC
DC
9
9
0.086
0.010
1.593
1.679
N
1
A
A
P
OP2
DC
DC
11
11
0.109
0.017
1.485
1.594
N
1
A
A
P
O5'
DG
DG
12
12
-0.075
0.010
1.593
1.518
N
1
B
B
O3'
P
DC
DG
13
14
-0.088
0.012
1.607
1.519
Y
1
B
B
N3
C4
DC
DC
23
23
0.043
0.007
1.335
1.378
N
1
A
A
O5'
OP2
DC
DT
1
7
2.05
1_555
3_655
1
A
A
C5'
OP2
DC
DT
1
7
2.08
1_555
3_655
0.145
2.500
1225
1
2.000
TR
isotropic
TR
isotropic
2.500
68
590
36
486
0
0.020
fix
fix
2.500
128D
1225
2.000
1
refinement
NUCLSQ
MOLECULAR STRUCTURE OF D(CGC[E6G]AATTCGCG) COMPLEXED WITH HOECHST 33258
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
covale
1.622
both
A
DC
3
A
O3'
DC
3
1_555
A
G36
4
A
P
G36
4
1_555
covale
1.629
one
A
G36
4
A
O3'
G36
4
1_555
A
DA
5
A
P
DA
5
1_555
covale
1.597
both
B
DC
15
B
O3'
DC
3
1_555
B
G36
16
B
P
G36
4
1_555
covale
1.642
one
B
G36
16
B
O3'
G36
4
1_555
B
DA
17
B
P
DA
5
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
24
B
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
24
B
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
24
B
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
23
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
23
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
23
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
22
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
22
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
22
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
G36
4
A
N1
G36
4
1_555
B
DC
21
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
G36
4
A
N2
G36
4
1_555
B
DC
21
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
G36
4
A
O6
G36
4
1_555
B
DC
21
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
20
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
20
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
19
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
19
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
18
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
18
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
17
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
17
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
G36
16
B
N1
G36
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
G36
16
B
O6
G36
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
G36
16
B
N2
G36
4
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
15
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
15
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
15
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
14
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
14
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
14
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
B
DC
13
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
B
DC
13
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
B
DC
13
B
N4
DC
1
1_555
DNA
B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, DNA
128D
PDB
1
128D
1
12
128D
1
12
128D
A
1
1
12
13
24
128D
13
24
128D
B
1
1
12
BINDING SITE FOR RESIDUE HT A 25
A
HT
25
Software
10
A
DA
5
A
DA
5
10
1_555
A
DA
6
A
DA
6
10
1_555
A
DT
7
A
DT
7
10
1_555
A
DT
8
A
DT
8
10
1_555
A
DC
9
A
DC
9
10
1_555
B
DA
17
B
DA
5
10
1_555
B
DA
18
B
DA
6
10
1_555
B
DT
19
B
DT
7
10
1_555
B
DT
20
B
DT
8
10
1_555
B
DC
21
B
DC
9
10
1_555
19
P 21 21 21