0.039635
0.000000
0.000000
0.000000
0.024643
0.000000
0.000000
0.000000
0.015133
0.00000
0.00000
0.00000
NO DISORDERED DRUG
Teng, M.-K.
Usman, N.
Frederick, C.A.
Wang, A.H.-J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
25.230
40.580
66.080
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
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
O
N
145
N
H
N
146
N
H
N
147
N
O
Y
148
N
C
Y
149
N
C
Y
150
N
C
Y
151
N
C
Y
152
N
C
Y
153
N
C
Y
154
N
C
Y
155
N
N
Y
156
N
C
Y
157
N
C
Y
158
N
N
Y
159
N
C
Y
160
N
C
Y
161
N
C
Y
162
N
C
Y
163
N
C
Y
164
N
N
Y
165
N
C
Y
166
N
C
Y
167
N
N
Y
168
N
C
Y
169
N
C
Y
170
N
C
Y
171
N
C
N
172
N
N
N
173
N
C
N
174
N
C
N
175
N
N
N
176
N
C
N
177
N
C
N
178
N
C
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
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
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
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
Y
154
N
doub
Y
155
N
sing
Y
156
N
sing
N
157
N
sing
Y
158
N
doub
N
159
N
sing
Y
160
N
sing
Y
161
N
sing
Y
162
N
doub
N
163
N
sing
N
164
N
sing
Y
165
N
sing
Y
166
N
doub
Y
167
N
sing
N
168
N
sing
Y
169
N
doub
Y
170
N
sing
Y
171
N
sing
Y
172
N
sing
Y
173
N
doub
N
174
N
sing
Y
175
N
sing
N
176
N
sing
Y
177
N
doub
Y
178
N
sing
N
179
N
sing
Y
180
N
sing
Y
181
N
doub
Y
182
N
sing
N
183
N
sing
Y
184
N
doub
Y
185
N
sing
Y
186
N
sing
Y
187
N
sing
Y
188
N
doub
N
189
N
sing
Y
190
N
sing
N
191
N
sing
Y
192
N
doub
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
16
2671
2690
10.1093/nar/16.6.2671
2452403
The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG).
1988
10.2210/pdb1dnh/pdb
pdb_00001dnh
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
288.00
1
DIFFRACTOMETER
NICOLET P3
x-ray
1
1.0
3663.392
DNA (5'-D(*CP*GP*CP*GP*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
126
nat
water
no
no
(DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)
CGCGAATTCGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
2.31
46.72
VAPOR DIFFUSION
VAPOR DIFFUSION
ROOM TEMPERATURE
WATER
1
MPD
1
NA CACODYLATE
1
SPERMINE
1
WATER
2
MPD
2
15.671
1
19
A
1
B
24
1.788
A_DC1:DG24_B
1
-1.926
-0.451
-0.212
-0.064
1.971
1
19
A
2
B
23
-2.138
A_DG2:DC23_B
2
-9.919
-0.292
0.395
-0.158
-3.202
1
19
A
3
B
22
-8.117
A_DC3:DG22_B
3
-8.110
-0.222
0.241
-0.354
7.637
1
19
A
4
B
21
-5.889
A_DG4:DC21_B
4
-2.984
-0.339
-0.091
-0.416
4.521
1
20
A
5
B
20
0.916
A_DA5:DT20_B
5
-9.383
-0.158
0.006
-0.215
-2.431
1
20
A
6
B
19
-1.882
A_DA6:DT19_B
6
-27.971
0.908
-0.229
-0.242
9.997
1
20
A
7
B
18
-3.146
A_DT7:DA18_B
7
-16.544
-0.203
-0.866
-0.249
-12.082
1
20
A
8
B
17
5.500
A_DT8:DA17_B
8
-6.287
0.869
-0.377
-0.295
-10.315
1
19
A
9
B
16
-1.656
A_DC9:DG16_B
9
-8.325
-0.111
-0.199
-0.262
5.380
1
19
A
10
B
15
4.702
A_DG10:DC15_B
10
-7.226
0.035
-0.022
-0.195
-0.234
1
19
A
11
B
14
-4.665
A_DC11:DG14_B
11
-20.574
0.486
0.672
-0.400
-7.376
1
19
A
12
B
13
-5.790
A_DG12:DC13_B
12
-6.978
-0.716
-0.294
-0.603
3.666
42.482
A
A
1
2
1.067
B
B
24
23
3.654
0.771
-0.246
0.450
AA_DC1DG2:DC23DG24_BB
1
-4.991
6.902
42.194
0.533
-0.229
3.675
36.969
A
A
2
3
-4.965
B
B
23
22
3.706
-3.137
0.310
0.352
AA_DG2DC3:DG22DC23_BB
2
4.687
-7.418
36.552
1.035
0.228
3.299
32.390
A
A
3
4
6.070
B
B
22
21
3.255
3.379
-0.192
0.747
AA_DC3DG4:DC21DG22_BB
3
1.768
-3.177
32.170
0.741
0.657
3.289
31.812
A
A
4
5
9.229
B
B
21
20
3.389
5.038
-0.048
-0.383
AA_DG4DA5:DT20DC21_BB
4
-0.139
0.254
31.420
-1.645
0.061
3.441
47.214
A
A
5
6
2.359
B
B
20
19
3.449
1.889
-0.317
-0.033
AA_DA5DA6:DT19DT20_BB
5
0.701
-0.875
47.173
-0.204
0.456
2.865
25.165
A
A
6
7
0.166
B
B
19
18
2.822
0.072
0.511
-0.733
AA_DA6DT7:DA18DT19_BB
6
5.265
-12.171
24.617
-1.700
0.185
4.000
42.146
A
A
7
8
6.597
B
B
18
17
4.033
4.735
-0.025
-0.089
AA_DT7DT8:DA17DA18_BB
7
-0.988
1.377
41.880
-0.725
-0.091
2.997
34.388
A
A
8
9
9.814
B
B
17
16
3.031
5.777
0.102
0.041
AA_DT8DC9:DG16DA17_BB
8
0.071
-0.120
33.914
-0.768
-0.162
3.092
33.625
A
A
9
10
-1.434
B
B
16
15
3.196
-0.828
0.401
1.875
AA_DC9DG10:DC15DG16_BB
9
-3.598
6.231
33.428
3.371
-1.260
3.682
41.272
A
A
10
11
-16.488
B
B
15
14
3.772
-11.410
-1.228
0.435
AA_DG10DC11:DG14DC15_BB
10
-8.115
11.726
38.922
2.061
0.715
3.486
33.859
A
A
11
12
9.551
B
B
14
13
3.568
5.426
0.337
0.416
AA_DC11DG12:DC13DG14_BB
11
11.883
-20.917
31.306
-0.269
1.573
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Derived calculations
Data collection
Database references
Derived calculations
1
0
1989-01-09
1
1
2008-05-22
1
2
2011-07-13
1
3
2011-08-24
1
4
2024-02-07
_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
BNL
Y
BNL
1988-02-16
REL
REL
HT
2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE
HOH
water
HT
25
2
HT
HT
25
B
HOH
26
3
HOH
HOH
26
A
HOH
29
3
HOH
HOH
29
A
HOH
31
3
HOH
HOH
31
A
HOH
32
3
HOH
HOH
32
A
HOH
36
3
HOH
HOH
36
A
HOH
37
3
HOH
HOH
37
A
HOH
39
3
HOH
HOH
39
A
HOH
40
3
HOH
HOH
40
A
HOH
41
3
HOH
HOH
41
A
HOH
43
3
HOH
HOH
43
A
HOH
45
3
HOH
HOH
45
A
HOH
47
3
HOH
HOH
47
A
HOH
49
3
HOH
HOH
49
A
HOH
50
3
HOH
HOH
50
A
HOH
51
3
HOH
HOH
51
A
HOH
54
3
HOH
HOH
54
A
HOH
56
3
HOH
HOH
56
A
HOH
58
3
HOH
HOH
58
A
HOH
61
3
HOH
HOH
61
A
HOH
65
3
HOH
HOH
65
A
HOH
67
3
HOH
HOH
67
A
HOH
68
3
HOH
HOH
68
A
HOH
72
3
HOH
HOH
72
A
HOH
76
3
HOH
HOH
76
A
HOH
77
3
HOH
HOH
77
A
HOH
80
3
HOH
HOH
80
A
HOH
81
3
HOH
HOH
81
A
HOH
83
3
HOH
HOH
83
A
HOH
84
3
HOH
HOH
84
A
HOH
85
3
HOH
HOH
85
A
HOH
89
3
HOH
HOH
89
A
HOH
90
3
HOH
HOH
90
A
HOH
91
3
HOH
HOH
91
A
HOH
93
3
HOH
HOH
93
A
HOH
94
3
HOH
HOH
94
A
HOH
100
3
HOH
HOH
100
A
HOH
106
3
HOH
HOH
106
A
HOH
111
3
HOH
HOH
111
A
HOH
115
3
HOH
HOH
115
A
HOH
116
3
HOH
HOH
116
A
HOH
119
3
HOH
HOH
119
A
HOH
120
3
HOH
HOH
120
A
HOH
122
3
HOH
HOH
122
A
HOH
123
3
HOH
HOH
123
A
HOH
126
3
HOH
HOH
126
A
HOH
127
3
HOH
HOH
127
A
HOH
128
3
HOH
HOH
128
A
HOH
132
3
HOH
HOH
132
A
HOH
133
3
HOH
HOH
133
A
HOH
134
3
HOH
HOH
134
A
HOH
136
3
HOH
HOH
136
A
HOH
139
3
HOH
HOH
139
A
HOH
140
3
HOH
HOH
140
A
HOH
142
3
HOH
HOH
142
A
HOH
143
3
HOH
HOH
143
A
HOH
144
3
HOH
HOH
144
A
HOH
147
3
HOH
HOH
147
A
HOH
148
3
HOH
HOH
148
A
HOH
150
3
HOH
HOH
150
A
HOH
151
3
HOH
HOH
151
A
HOH
27
3
HOH
HOH
27
B
HOH
28
3
HOH
HOH
28
B
HOH
30
3
HOH
HOH
30
B
HOH
33
3
HOH
HOH
33
B
HOH
34
3
HOH
HOH
34
B
HOH
35
3
HOH
HOH
35
B
HOH
38
3
HOH
HOH
38
B
HOH
42
3
HOH
HOH
42
B
HOH
44
3
HOH
HOH
44
B
HOH
46
3
HOH
HOH
46
B
HOH
48
3
HOH
HOH
48
B
HOH
52
3
HOH
HOH
52
B
HOH
53
3
HOH
HOH
53
B
HOH
55
3
HOH
HOH
55
B
HOH
57
3
HOH
HOH
57
B
HOH
59
3
HOH
HOH
59
B
HOH
60
3
HOH
HOH
60
B
HOH
62
3
HOH
HOH
62
B
HOH
63
3
HOH
HOH
63
B
HOH
64
3
HOH
HOH
64
B
HOH
66
3
HOH
HOH
66
B
HOH
69
3
HOH
HOH
69
B
HOH
70
3
HOH
HOH
70
B
HOH
71
3
HOH
HOH
71
B
HOH
73
3
HOH
HOH
73
B
HOH
74
3
HOH
HOH
74
B
HOH
75
3
HOH
HOH
75
B
HOH
78
3
HOH
HOH
78
B
HOH
79
3
HOH
HOH
79
B
HOH
82
3
HOH
HOH
82
B
HOH
86
3
HOH
HOH
86
B
HOH
87
3
HOH
HOH
87
B
HOH
88
3
HOH
HOH
88
B
HOH
92
3
HOH
HOH
92
B
HOH
95
3
HOH
HOH
95
B
HOH
96
3
HOH
HOH
96
B
HOH
97
3
HOH
HOH
97
B
HOH
98
3
HOH
HOH
98
B
HOH
99
3
HOH
HOH
99
B
HOH
101
3
HOH
HOH
101
B
HOH
102
3
HOH
HOH
102
B
HOH
103
3
HOH
HOH
103
B
HOH
104
3
HOH
HOH
104
B
HOH
105
3
HOH
HOH
105
B
HOH
107
3
HOH
HOH
107
B
HOH
108
3
HOH
HOH
108
B
HOH
109
3
HOH
HOH
109
B
HOH
110
3
HOH
HOH
110
B
HOH
112
3
HOH
HOH
112
B
HOH
113
3
HOH
HOH
113
B
HOH
114
3
HOH
HOH
114
B
HOH
117
3
HOH
HOH
117
B
HOH
118
3
HOH
HOH
118
B
HOH
121
3
HOH
HOH
121
B
HOH
124
3
HOH
HOH
124
B
HOH
125
3
HOH
HOH
125
B
HOH
129
3
HOH
HOH
129
B
HOH
130
3
HOH
HOH
130
B
HOH
131
3
HOH
HOH
131
B
HOH
135
3
HOH
HOH
135
B
HOH
137
3
HOH
HOH
137
B
HOH
138
3
HOH
HOH
138
B
HOH
141
3
HOH
HOH
141
B
HOH
145
3
HOH
HOH
145
B
HOH
146
3
HOH
HOH
146
B
HOH
149
3
HOH
HOH
149
B
DC
1
n
1
DC
1
A
DG
2
n
2
DG
2
A
DC
3
n
3
DC
3
A
DG
4
n
4
DG
4
A
DA
5
n
5
DA
5
A
DA
6
n
6
DA
6
A
DT
7
n
7
DT
7
A
DT
8
n
8
DT
8
A
DC
9
n
9
DC
9
A
DG
10
n
10
DG
10
A
DC
11
n
11
DC
11
A
DG
12
n
12
DG
12
A
DC
13
n
1
DC
13
B
DG
14
n
2
DG
14
B
DC
15
n
3
DC
15
B
DG
16
n
4
DG
16
B
DA
17
n
5
DA
17
B
DA
18
n
6
DA
18
B
DT
19
n
7
DT
19
B
DT
20
n
8
DT
20
B
DC
21
n
9
DC
21
B
DG
22
n
10
DG
22
B
DC
23
n
11
DC
23
B
DG
24
n
12
DG
24
B
author_defined_assembly
2
dimeric
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
-7.27
0.80
109.40
102.13
A
A
A
O5'
C5'
C4'
DC
DC
DC
1
1
1
N
1
-5.15
0.40
104.50
99.35
A
A
A
O4'
C4'
C3'
DC
DC
DC
1
1
1
N
1
9.05
1.10
109.80
118.85
A
A
A
C5'
C4'
O4'
DG
DG
DG
2
2
2
N
1
7.35
0.30
108.30
115.65
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
-3.22
0.40
104.50
101.28
A
A
A
O4'
C4'
C3'
DC
DC
DC
3
3
3
N
1
-5.58
0.80
102.40
96.82
A
A
A
C3'
C2'
C1'
DC
DC
DC
3
3
3
N
1
8.11
0.30
108.30
116.41
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
3.39
0.50
119.90
123.29
A
A
A
C2
N3
C4
DC
DC
DC
3
3
3
N
1
3.15
0.50
121.00
124.15
A
A
A
C5
C6
N1
DC
DC
DC
3
3
3
N
1
5.25
0.70
118.00
123.25
A
A
A
N3
C4
N4
DC
DC
DC
3
3
3
N
1
10.83
1.20
110.70
121.53
A
A
A
O5'
P
OP2
DG
DG
DG
4
4
4
N
1
-6.37
0.80
109.40
103.03
A
A
A
O5'
C5'
C4'
DG
DG
DG
4
4
4
N
1
-10.96
1.60
120.90
109.94
A
A
A
P
O5'
C5'
DG
DG
DG
4
4
4
N
1
11.01
0.30
108.30
119.31
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
11.03
1.20
110.70
121.73
A
A
A
O5'
P
OP2
DA
DA
DA
5
5
5
N
1
-8.69
0.80
109.40
100.71
A
A
A
O5'
C5'
C4'
DA
DA
DA
5
5
5
N
1
-12.09
1.60
120.90
108.81
A
A
A
P
O5'
C5'
DA
DA
DA
5
5
5
N
1
-5.31
0.80
105.90
100.59
A
A
A
O4'
C1'
C2'
DA
DA
DA
5
5
5
N
1
-3.95
0.50
129.30
125.35
A
A
A
N1
C2
N3
DA
DA
DA
5
5
5
N
1
-9.30
1.50
119.60
110.30
A
A
A
OP1
P
OP2
DA
DA
DA
6
6
6
N
1
8.75
1.20
110.70
119.45
A
A
A
O5'
P
OP2
DA
DA
DA
6
6
6
N
1
-6.71
0.40
104.50
97.79
A
A
A
O4'
C4'
C3'
DA
DA
DA
6
6
6
N
1
9.22
0.30
108.30
117.52
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
3.85
0.60
118.60
122.45
A
A
A
C6
N1
C2
DA
DA
DA
6
6
6
N
1
-3.62
0.50
129.30
125.68
A
A
A
N1
C2
N3
DA
DA
DA
6
6
6
N
1
-5.13
0.80
109.40
104.27
A
A
A
O5'
C5'
C4'
DT
DT
DT
7
7
7
N
1
4.29
0.60
114.60
118.89
A
A
A
N1
C2
N3
DT
DT
DT
7
7
7
N
1
-6.62
0.60
127.20
120.58
A
A
A
C2
N3
C4
DT
DT
DT
7
7
7
N
1
4.97
0.60
115.20
120.17
A
A
A
N3
C4
C5
DT
DT
DT
7
7
7
N
1
-3.77
0.60
119.90
116.13
A
A
A
N3
C4
O4
DT
DT
DT
7
7
7
N
1
9.13
1.50
120.40
129.53
A
A
A
C6
N1
C1'
DT
DT
DT
7
7
7
N
1
10.49
1.20
119.70
130.19
A
A
A
C3'
O3'
P
DT
DT
DT
7
7
8
Y
1
-7.46
0.80
109.40
101.94
A
A
A
O5'
C5'
C4'
DT
DT
DT
8
8
8
N
1
-4.23
0.70
102.20
97.97
A
A
A
C4'
C3'
C2'
DT
DT
DT
8
8
8
N
1
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
9.85
1.20
110.70
120.55
A
A
A
O5'
P
OP2
DC
DC
DC
9
9
9
N
1
-6.01
0.80
109.40
103.39
A
A
A
O5'
C5'
C4'
DC
DC
DC
9
9
9
N
1
-17.44
1.60
120.90
103.46
A
A
A
P
O5'
C5'
DC
DC
DC
9
9
9
N
1
-6.12
0.70
108.00
101.88
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
-10.07
1.60
120.90
110.83
A
A
A
P
O5'
C5'
DG
DG
DG
10
10
10
N
1
-5.24
0.70
119.90
114.66
A
A
A
N3
C2
N2
DG
DG
DG
10
10
10
N
1
15.89
1.20
119.70
135.59
A
A
A
C3'
O3'
P
DG
DG
DC
10
10
11
Y
1
7.87
1.20
110.70
118.57
A
A
A
O5'
P
OP2
DC
DC
DC
11
11
11
N
1
-6.98
0.80
109.40
102.42
A
A
A
O5'
C5'
C4'
DC
DC
DC
11
11
11
N
1
-14.53
1.60
120.90
106.37
A
A
A
P
O5'
C5'
DC
DC
DC
11
11
11
N
1
-5.31
0.80
102.40
97.09
A
A
A
C3'
C2'
C1'
DC
DC
DC
11
11
11
N
1
3.88
0.30
108.30
112.18
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
-3.94
0.60
118.90
114.96
A
A
A
N1
C2
O2
DC
DC
DC
11
11
11
N
1
7.01
0.70
121.90
128.91
A
A
A
N3
C2
O2
DC
DC
DC
11
11
11
N
1
-8.53
0.80
109.40
100.87
A
A
A
O5'
C5'
C4'
DG
DG
DG
12
12
12
N
1
-5.88
0.80
102.40
96.52
A
A
A
C3'
C2'
C1'
DG
DG
DG
12
12
12
N
1
9.22
0.30
108.30
117.52
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
6.41
0.60
119.90
126.31
A
A
A
N1
C6
O6
DG
DG
DG
12
12
12
N
1
-8.62
0.60
128.60
119.98
A
A
A
C5
C6
O6
DG
DG
DG
12
12
12
N
1
3.15
0.50
119.90
123.05
B
B
B
C2
N3
C4
DC
DC
DC
13
13
13
N
1
6.83
0.70
121.90
128.73
B
B
B
N3
C2
O2
DC
DC
DC
13
13
13
N
1
7.17
0.70
118.00
125.17
B
B
B
N3
C4
N4
DC
DC
DC
13
13
13
N
1
-5.49
0.70
120.20
114.71
B
B
B
C5
C4
N4
DC
DC
DC
13
13
13
N
1
11.16
1.20
119.70
130.86
B
B
B
C3'
O3'
P
DC
DC
DG
13
13
14
Y
1
4.51
0.60
123.90
128.41
B
B
B
N1
C2
N3
DG
DG
DG
14
14
14
N
1
-3.11
0.50
111.90
108.79
B
B
B
C2
N3
C4
DG
DG
DG
14
14
14
N
1
-5.69
0.80
109.40
103.71
B
B
B
O5'
C5'
C4'
DC
DC
DC
15
15
15
N
1
-3.73
0.60
128.60
124.87
B
B
B
C5
C6
O6
DG
DG
DG
16
16
16
N
1
16.87
1.20
119.70
136.57
B
B
B
C3'
O3'
P
DG
DG
DA
16
16
17
Y
1
-6.95
0.90
105.70
98.75
B
B
B
O5'
P
OP1
DA
DA
DA
17
17
17
N
1
11.39
1.20
110.70
122.09
B
B
B
O5'
P
OP2
DA
DA
DA
17
17
17
N
1
-15.52
1.60
120.90
105.38
B
B
B
P
O5'
C5'
DA
DA
DA
17
17
17
N
1
-2.69
0.40
104.50
101.81
B
B
B
O4'
C4'
C3'
DA
DA
DA
17
17
17
N
1
4.82
0.60
118.60
123.42
B
B
B
C6
N1
C2
DA
DA
DA
17
17
17
N
1
-3.30
0.50
110.60
107.30
B
B
B
C2
N3
C4
DA
DA
DA
17
17
17
N
1
-4.05
0.50
117.70
113.65
B
B
B
C5
C6
N1
DA
DA
DA
17
17
17
N
1
4.17
0.60
118.60
122.77
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
1
16.58
1.20
119.70
136.28
B
B
B
C3'
O3'
P
DA
DA
DA
17
17
18
Y
1
-7.50
0.80
102.40
94.90
B
B
B
C3'
C2'
C1'
DA
DA
DA
18
18
18
N
1
3.65
0.30
108.30
111.95
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
3.89
0.60
118.60
122.49
B
B
B
C6
N1
C2
DA
DA
DA
18
18
18
N
1
-4.81
0.50
129.30
124.49
B
B
B
N1
C2
N3
DA
DA
DA
18
18
18
N
1
-5.23
0.70
102.20
96.97
B
B
B
C4'
C3'
C2'
DT
DT
DT
19
19
19
N
1
9.50
0.30
108.30
117.80
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
-3.76
0.60
127.20
123.44
B
B
B
C2
N3
C4
DT
DT
DT
19
19
19
N
1
4.20
0.60
115.20
119.40
B
B
B
N3
C4
C5
DT
DT
DT
19
19
19
N
1
-6.43
0.60
119.90
113.47
B
B
B
N3
C4
O4
DT
DT
DT
19
19
19
N
1
-5.79
0.40
104.50
98.71
B
B
B
O4'
C4'
C3'
DT
DT
DT
20
20
20
N
1
7.62
1.20
115.70
123.32
B
B
B
C5'
C4'
C3'
DT
DT
DT
20
20
20
N
1
3.09
0.30
108.30
111.39
B
B
B
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
-3.65
0.60
127.20
123.55
B
B
B
C2
N3
C4
DT
DT
DT
20
20
20
N
1
-11.03
1.50
119.60
108.57
B
B
B
OP1
P
OP2
DC
DC
DC
21
21
21
N
1
5.92
0.30
108.30
114.22
B
B
B
O4'
C1'
N1
DC
DC
DC
21
21
21
N
1
3.54
0.50
119.90
123.44
B
B
B
C2
N3
C4
DC
DC
DC
21
21
21
N
1
3.15
0.50
121.00
124.15
B
B
B
C5
C6
N1
DC
DC
DC
21
21
21
N
1
5.40
0.70
118.00
123.40
B
B
B
N3
C4
N4
DC
DC
DC
21
21
21
N
1
28.34
1.20
119.70
148.04
B
B
B
C3'
O3'
P
DC
DC
DG
21
21
22
Y
1
14.03
1.10
110.50
124.53
B
B
B
O3'
P
OP1
DC
DG
DG
21
22
22
Y
1
-11.45
1.50
119.60
108.15
B
B
B
OP1
P
OP2
DG
DG
DG
22
22
22
N
1
-8.90
0.80
109.40
100.50
B
B
B
O5'
C5'
C4'
DG
DG
DG
22
22
22
N
1
-5.42
0.70
102.20
96.78
B
B
B
C4'
C3'
C2'
DG
DG
DG
22
22
22
N
1
-8.21
0.80
102.40
94.19
B
B
B
C3'
C2'
C1'
DG
DG
DG
22
22
22
N
1
7.09
0.30
108.30
115.39
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
-3.36
0.50
111.90
108.54
B
B
B
C2
N3
C4
DG
DG
DG
22
22
22
N
1
10.87
1.20
119.70
130.57
B
B
B
C3'
O3'
P
DG
DG
DC
22
22
23
Y
1
-10.36
1.50
119.60
109.24
B
B
B
OP1
P
OP2
DC
DC
DC
23
23
23
N
1
-8.80
0.80
109.40
100.60
B
B
B
O5'
C5'
C4'
DC
DC
DC
23
23
23
N
1
-10.14
1.60
120.90
110.76
B
B
B
P
O5'
C5'
DC
DC
DC
23
23
23
N
1
12.85
0.30
108.30
121.15
B
B
B
O4'
C1'
N1
DC
DC
DC
23
23
23
N
1
-4.21
0.60
125.10
120.89
B
B
B
C6
N1
C2
DG
DG
DG
24
24
24
N
1
-4.64
0.60
119.90
115.26
B
B
B
N1
C6
O6
DG
DG
DG
24
24
24
N
1
A
A
O3'
P
DC
DG
1
2
-0.076
0.012
1.607
1.531
Y
1
A
A
C3'
C2'
DG
DG
2
2
-0.052
0.008
1.516
1.464
N
1
A
A
O5'
C5'
DG
DG
4
4
0.111
0.016
1.440
1.551
N
1
A
A
P
O5'
DC
DC
9
9
0.064
0.010
1.593
1.657
N
1
A
A
O4'
C4'
DG
DG
10
10
-0.067
0.010
1.446
1.379
N
1
A
A
N7
C8
DG
DG
10
10
0.044
0.006
1.305
1.349
N
1
A
A
N3
C4
DC
DC
11
11
0.051
0.007
1.335
1.386
N
1
A
A
C2'
C1'
DG
DG
12
12
0.063
0.010
1.519
1.582
N
1
B
B
O4'
C4'
DG
DG
14
14
-0.061
0.010
1.446
1.385
N
1
B
B
C5'
C4'
DC
DC
15
15
0.043
0.007
1.512
1.555
N
1
B
B
C5'
C4'
DA
DA
17
17
-0.073
0.011
1.509
1.436
N
1
B
B
P
O5'
DT
DT
19
19
0.095
0.010
1.593
1.688
N
1
B
B
N3
C4
DT
DT
19
19
-0.053
0.008
1.382
1.329
N
1
B
B
C4
O4
DT
DT
19
19
0.054
0.009
1.228
1.282
N
1
B
B
O3'
C3'
DC
DC
21
21
-0.073
0.006
1.419
1.346
N
1
B
B
O3'
P
DC
DG
21
22
-0.095
0.012
1.607
1.512
Y
1
B
B
P
O5'
DG
DG
22
22
0.068
0.010
1.593
1.661
N
1
B
B
C6
N1
DG
DG
22
22
-0.048
0.007
1.391
1.343
N
1
B
B
P
O5'
DG
DG
24
24
0.078
0.010
1.593
1.671
N
0.1570000
2.250
20.000
2000
1
2.000
TR
isotropic
TR
isotropic
2.250
20.000
126
644
32
486
0
fix
fix
2.250
20.000
1DNH
3634
0.000
1
refinement
NUCLSQ
THE MOLECULAR STRUCTURE OF THE COMPLEX OF HOECHST 33258 AND THE DNA DODECAMER D(CGCGAATTCGCG)
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
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
DG
4
A
N1
DG
4
1_555
B
DC
21
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
21
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
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
DG
16
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
16
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
16
B
N2
DG
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, DNA
1DNH
PDB
1
1DNH
1
12
1DNH
1
12
1DNH
A
1
1
12
13
24
1DNH
13
24
1DNH
B
1
1
12
BINDING SITE FOR RESIDUE HT B 25
B
HT
25
Software
12
A
DA
5
A
DA
5
12
1_555
A
DA
6
A
DA
6
12
1_555
A
DT
7
A
DT
7
12
1_555
A
DT
8
A
DT
8
12
1_555
A
DC
9
A
DC
9
12
1_555
B
DA
17
B
DA
5
12
1_555
B
DA
18
B
DA
6
12
1_555
B
DT
19
B
DT
7
12
1_555
B
DT
20
B
DT
8
12
1_555
B
DC
21
B
DC
9
12
1_555
B
HOH
73
E
HOH
12
1_555
B
HOH
88
E
HOH
12
1_555
19
P 21 21 21