0.039635
0.000000
0.000000
0.000000
0.024643
0.000000
0.000000
0.000000
0.015133
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
25.230
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
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/pdb127d/pdb
pdb_0000127d
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
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
121
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
6.00
pH 6.00, VAPOR DIFFUSION
ROOM TEMPERATURE
WATER
1
MPD
1
NA CACODYLATE
1
MGCL2
1
SPERMINE
1
WATER
2
MPD
2
15.599
1
19
A
1
B
24
0.356
A_DC1:DG24_B
1
-3.861
-0.194
-0.156
-0.058
0.037
1
19
A
2
B
23
-3.280
A_DG2:DC23_B
2
-8.341
-0.182
0.308
-0.154
-1.876
1
19
A
3
B
22
-6.024
A_DC3:DG22_B
3
-7.725
-0.133
0.191
-0.283
7.981
1
19
A
4
B
21
-2.684
A_DG4:DC21_B
4
-2.326
-0.171
-0.169
-0.252
4.440
1
20
A
5
B
20
0.815
A_DA5:DT20_B
5
-8.944
-0.086
0.024
-0.193
-1.852
1
20
A
6
B
19
-1.859
A_DA6:DT19_B
6
-27.422
0.880
-0.285
-0.316
9.786
1
20
A
7
B
18
-3.118
A_DT7:DA18_B
7
-17.018
-0.166
-0.917
-0.258
-11.285
1
20
A
8
B
17
6.516
A_DT8:DA17_B
8
-6.262
0.654
-0.427
-0.267
-10.647
1
19
A
9
B
16
-1.808
A_DC9:DG16_B
9
-9.959
-0.082
-0.190
-0.228
6.843
1
19
A
10
B
15
3.091
A_DG10:DC15_B
10
-7.668
0.048
-0.006
-0.192
-0.504
1
19
A
11
B
14
-5.020
A_DC11:DG14_B
11
-18.912
0.211
0.718
-0.339
-8.069
1
19
A
12
B
13
-4.814
A_DG12:DC13_B
12
-5.846
-0.471
-0.448
-0.410
3.706
41.373
A
A
1
2
2.363
B
B
24
23
3.688
1.667
-0.229
0.403
AA_DC1DG2:DC23DG24_BB
1
-4.075
5.777
41.148
0.368
-0.170
3.611
36.509
A
A
2
3
-4.855
B
B
23
22
3.619
-3.029
0.503
0.384
AA_DG2DC3:DG22DC23_BB
2
5.076
-8.136
36.044
1.078
-0.022
3.319
33.828
A
A
3
4
7.701
B
B
22
21
3.244
4.467
-0.183
0.885
AA_DC3DG4:DC21DG22_BB
3
1.634
-2.817
33.502
0.794
0.581
3.343
30.908
A
A
4
5
8.324
B
B
21
20
3.412
4.421
-0.143
-0.279
AA_DG4DA5:DT20DC21_BB
4
-0.830
1.563
30.587
-1.413
0.101
3.411
46.663
A
A
5
6
3.040
B
B
20
19
3.428
2.407
-0.451
-0.050
AA_DA5DA6:DT19DT20_BB
5
1.096
-1.384
46.593
-0.273
0.666
2.922
26.982
A
A
6
7
-1.779
B
B
19
18
2.843
-0.824
0.572
-0.779
AA_DA6DT7:DA18DT19_BB
6
5.578
-12.040
26.397
-1.482
0.041
3.955
39.909
A
A
7
8
8.480
B
B
18
17
3.999
5.769
0.136
-0.021
AA_DT7DT8:DA17DA18_BB
7
-0.580
0.852
39.503
-0.843
-0.282
3.029
35.417
A
A
8
9
9.599
B
B
17
16
3.066
5.814
0.000
0.016
AA_DT8DC9:DG16DA17_BB
8
-0.314
0.518
34.950
-0.775
-0.044
3.008
33.858
A
A
9
10
-2.027
B
B
16
15
3.138
-1.178
0.459
1.968
AA_DC9DG10:DC15DG16_BB
9
-3.499
6.019
33.662
3.559
-1.318
3.764
39.609
A
A
10
11
-15.785
B
B
15
14
3.819
-10.495
-1.177
0.340
AA_DG10DC11:DG14DC15_BB
10
-8.668
13.038
37.286
1.973
0.522
3.512
37.269
A
A
11
12
8.120
B
B
14
13
3.600
5.061
0.310
0.516
AA_DC11DG12:DC13DG14_BB
11
13.584
-21.793
34.427
0.046
1.557
chem_comp_atom
chem_comp_bond
database_2
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_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
B
HOH
28
3
HOH
HOH
28
A
HOH
33
3
HOH
HOH
33
A
HOH
35
3
HOH
HOH
35
A
HOH
37
3
HOH
HOH
37
A
HOH
41
3
HOH
HOH
41
A
HOH
42
3
HOH
HOH
42
A
HOH
45
3
HOH
HOH
45
A
HOH
52
3
HOH
HOH
52
A
HOH
57
3
HOH
HOH
57
A
HOH
60
3
HOH
HOH
60
A
HOH
61
3
HOH
HOH
61
A
HOH
66
3
HOH
HOH
66
A
HOH
68
3
HOH
HOH
68
A
HOH
75
3
HOH
HOH
75
A
HOH
77
3
HOH
HOH
77
A
HOH
78
3
HOH
HOH
78
A
HOH
79
3
HOH
HOH
79
A
HOH
82
3
HOH
HOH
82
A
HOH
83
3
HOH
HOH
83
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
95
3
HOH
HOH
95
A
HOH
96
3
HOH
HOH
96
A
HOH
103
3
HOH
HOH
103
A
HOH
104
3
HOH
HOH
104
A
HOH
105
3
HOH
HOH
105
A
HOH
107
3
HOH
HOH
107
A
HOH
110
3
HOH
HOH
110
A
HOH
111
3
HOH
HOH
111
A
HOH
112
3
HOH
HOH
112
A
HOH
114
3
HOH
HOH
114
A
HOH
115
3
HOH
HOH
115
A
HOH
118
3
HOH
HOH
118
A
HOH
120
3
HOH
HOH
120
A
HOH
122
3
HOH
HOH
122
A
HOH
123
3
HOH
HOH
123
A
HOH
124
3
HOH
HOH
124
A
HOH
125
3
HOH
HOH
125
A
HOH
126
3
HOH
HOH
126
A
HOH
127
3
HOH
HOH
127
A
HOH
129
3
HOH
HOH
129
A
HOH
130
3
HOH
HOH
130
A
HOH
131
3
HOH
HOH
131
A
HOH
134
3
HOH
HOH
134
A
HOH
135
3
HOH
HOH
135
A
HOH
137
3
HOH
HOH
137
A
HOH
138
3
HOH
HOH
138
A
HOH
139
3
HOH
HOH
139
A
HOH
140
3
HOH
HOH
140
A
HOH
141
3
HOH
HOH
141
A
HOH
142
3
HOH
HOH
142
A
HOH
26
3
HOH
HOH
26
B
HOH
27
3
HOH
HOH
27
B
HOH
29
3
HOH
HOH
29
B
HOH
30
3
HOH
HOH
30
B
HOH
31
3
HOH
HOH
31
B
HOH
32
3
HOH
HOH
32
B
HOH
34
3
HOH
HOH
34
B
HOH
36
3
HOH
HOH
36
B
HOH
38
3
HOH
HOH
38
B
HOH
39
3
HOH
HOH
39
B
HOH
40
3
HOH
HOH
40
B
HOH
43
3
HOH
HOH
43
B
HOH
44
3
HOH
HOH
44
B
HOH
46
3
HOH
HOH
46
B
HOH
47
3
HOH
HOH
47
B
HOH
48
3
HOH
HOH
48
B
HOH
49
3
HOH
HOH
49
B
HOH
50
3
HOH
HOH
50
B
HOH
51
3
HOH
HOH
51
B
HOH
53
3
HOH
HOH
53
B
HOH
54
3
HOH
HOH
54
B
HOH
55
3
HOH
HOH
55
B
HOH
56
3
HOH
HOH
56
B
HOH
58
3
HOH
HOH
58
B
HOH
59
3
HOH
HOH
59
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
67
3
HOH
HOH
67
B
HOH
69
3
HOH
HOH
69
B
HOH
70
3
HOH
HOH
70
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
76
3
HOH
HOH
76
B
HOH
80
3
HOH
HOH
80
B
HOH
81
3
HOH
HOH
81
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
92
3
HOH
HOH
92
B
HOH
97
3
HOH
HOH
97
B
HOH
98
3
HOH
HOH
98
B
HOH
99
3
HOH
HOH
99
B
HOH
100
3
HOH
HOH
100
B
HOH
101
3
HOH
HOH
101
B
HOH
102
3
HOH
HOH
102
B
HOH
106
3
HOH
HOH
106
B
HOH
108
3
HOH
HOH
108
B
HOH
109
3
HOH
HOH
109
B
HOH
113
3
HOH
HOH
113
B
HOH
116
3
HOH
HOH
116
B
HOH
117
3
HOH
HOH
117
B
HOH
119
3
HOH
HOH
119
B
HOH
121
3
HOH
HOH
121
B
HOH
128
3
HOH
HOH
128
B
HOH
132
3
HOH
HOH
132
B
HOH
133
3
HOH
HOH
133
B
HOH
136
3
HOH
HOH
136
B
HOH
143
3
HOH
HOH
143
B
HOH
144
3
HOH
HOH
144
B
HOH
145
3
HOH
HOH
145
B
HOH
146
3
HOH
HOH
146
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
B
B
OP1
O
DC
HOH
23
62
1.68
1
B
B
OP2
O
DC
HOH
15
98
1.95
1
B
B
O
O
HOH
HOH
27
71
2.06
1
B
B
O3'
O
DG
HOH
14
98
2.12
1
-4.36
0.40
104.50
100.14
A
A
A
O4'
C4'
C3'
DC
DC
DC
1
1
1
N
1
7.76
1.20
119.70
127.46
A
A
A
C3'
O3'
P
DC
DC
DG
1
1
2
Y
1
4.14
0.30
108.30
112.44
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
-2.69
0.40
104.50
101.81
A
A
A
O4'
C4'
C3'
DC
DC
DC
3
3
3
N
1
9.11
0.30
108.30
117.41
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
-2.43
0.40
121.90
119.47
A
A
A
N3
C4
C5
DC
DC
DC
3
3
3
N
1
-7.73
0.80
109.40
101.67
A
A
A
O5'
C5'
C4'
DG
DG
DG
4
4
4
N
1
7.86
0.30
108.30
116.16
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
-6.06
0.80
109.40
103.34
A
A
A
O5'
C5'
C4'
DA
DA
DA
5
5
5
N
1
3.75
0.60
118.60
122.35
A
A
A
C6
N1
C2
DA
DA
DA
5
5
5
N
1
-3.87
0.50
129.30
125.43
A
A
A
N1
C2
N3
DA
DA
DA
5
5
5
N
1
-5.12
0.40
104.50
99.38
A
A
A
O4'
C4'
C3'
DA
DA
DA
6
6
6
N
1
7.83
0.30
108.30
116.13
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
4.47
0.60
118.60
123.07
A
A
A
C6
N1
C2
DA
DA
DA
6
6
6
N
1
-4.33
0.50
129.30
124.97
A
A
A
N1
C2
N3
DA
DA
DA
6
6
6
N
1
3.71
0.60
114.60
118.31
A
A
A
N1
C2
N3
DT
DT
DT
7
7
7
N
1
-5.88
0.60
127.20
121.32
A
A
A
C2
N3
C4
DT
DT
DT
7
7
7
N
1
4.64
0.60
115.20
119.84
A
A
A
N3
C4
C5
DT
DT
DT
7
7
7
N
1
9.44
1.20
119.70
129.14
A
A
A
C3'
O3'
P
DT
DT
DT
7
7
8
Y
1
-6.10
0.80
109.40
103.30
A
A
A
O5'
C5'
C4'
DT
DT
DT
8
8
8
N
1
7.42
1.20
110.70
118.12
A
A
A
O5'
P
OP2
DC
DC
DC
9
9
9
N
1
-5.72
0.80
109.40
103.68
A
A
A
O5'
C5'
C4'
DC
DC
DC
9
9
9
N
1
-9.78
1.60
120.90
111.12
A
A
A
P
O5'
C5'
DC
DC
DC
9
9
9
N
1
-4.51
0.70
108.00
103.49
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
16.43
1.20
119.70
136.13
A
A
A
C3'
O3'
P
DG
DG
DC
10
10
11
Y
1
-4.86
0.80
109.40
104.54
A
A
A
O5'
C5'
C4'
DC
DC
DC
11
11
11
N
1
6.06
0.30
108.30
114.36
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
-5.27
0.80
109.40
104.13
A
A
A
O5'
C5'
C4'
DG
DG
DG
12
12
12
N
1
8.35
0.30
108.30
116.65
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
3.63
0.60
119.90
123.53
A
A
A
N1
C6
O6
DG
DG
DG
12
12
12
N
1
-6.16
0.60
128.60
122.44
A
A
A
C5
C6
O6
DG
DG
DG
12
12
12
N
1
-4.19
0.40
104.50
100.31
B
B
B
O4'
C4'
C3'
DC
DC
DC
13
13
13
N
1
4.76
0.70
118.00
122.76
B
B
B
N3
C4
N4
DC
DC
DC
13
13
13
N
1
7.35
1.20
119.70
127.05
B
B
B
C3'
O3'
P
DC
DC
DG
13
13
14
Y
1
3.42
0.30
108.30
111.72
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
1
3.14
0.50
111.50
114.64
B
B
B
C5
C6
N1
DG
DG
DG
16
16
16
N
1
19.45
1.20
119.70
139.15
B
B
B
C3'
O3'
P
DG
DG
DA
16
16
17
Y
1
-11.86
1.60
120.90
109.04
B
B
B
P
O5'
C5'
DA
DA
DA
17
17
17
N
1
-3.74
0.40
104.50
100.76
B
B
B
O4'
C4'
C3'
DA
DA
DA
17
17
17
N
1
4.15
0.60
118.60
122.75
B
B
B
C6
N1
C2
DA
DA
DA
17
17
17
N
1
-3.44
0.50
117.70
114.26
B
B
B
C5
C6
N1
DA
DA
DA
17
17
17
N
1
13.65
1.20
119.70
133.35
B
B
B
C3'
O3'
P
DA
DA
DA
17
17
18
Y
1
-6.67
0.80
102.40
95.73
B
B
B
C3'
C2'
C1'
DA
DA
DA
18
18
18
N
1
3.17
0.30
108.30
111.47
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
3.78
0.60
118.60
122.38
B
B
B
C6
N1
C2
DA
DA
DA
18
18
18
N
1
-4.35
0.50
129.30
124.95
B
B
B
N1
C2
N3
DA
DA
DA
18
18
18
N
1
3.61
0.60
118.60
122.21
B
B
B
N1
C6
N6
DA
DA
DA
18
18
18
N
1
7.67
0.30
108.30
115.97
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
-4.57
0.60
127.20
122.63
B
B
B
C2
N3
C4
DT
DT
DT
19
19
19
N
1
4.55
0.60
115.20
119.75
B
B
B
N3
C4
C5
DT
DT
DT
19
19
19
N
1
-3.82
0.60
119.90
116.08
B
B
B
N3
C4
O4
DT
DT
DT
19
19
19
N
1
-5.55
0.40
104.50
98.95
B
B
B
O4'
C4'
C3'
DT
DT
DT
20
20
20
N
1
8.08
1.20
115.70
123.78
B
B
B
C5'
C4'
C3'
DT
DT
DT
20
20
20
N
1
3.52
0.30
108.30
111.82
B
B
B
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
-9.11
1.50
119.60
110.49
B
B
B
OP1
P
OP2
DC
DC
DC
21
21
21
N
1
5.56
0.30
108.30
113.86
B
B
B
O4'
C1'
N1
DC
DC
DC
21
21
21
N
1
23.15
1.20
119.70
142.85
B
B
B
C3'
O3'
P
DC
DC
DG
21
21
22
Y
1
6.69
1.10
110.50
117.19
B
B
B
O3'
P
OP1
DC
DG
DG
21
22
22
Y
1
-9.71
1.50
119.60
109.89
B
B
B
OP1
P
OP2
DG
DG
DG
22
22
22
N
1
-6.37
0.80
109.40
103.03
B
B
B
O5'
C5'
C4'
DG
DG
DG
22
22
22
N
1
-9.01
0.80
102.40
93.39
B
B
B
C3'
C2'
C1'
DG
DG
DG
22
22
22
N
1
8.39
0.30
108.30
116.69
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
-3.82
0.60
128.60
124.78
B
B
B
C5
C6
O6
DG
DG
DG
22
22
22
N
1
-9.26
1.50
119.60
110.34
B
B
B
OP1
P
OP2
DC
DC
DC
23
23
23
N
1
-8.71
0.80
109.40
100.69
B
B
B
O5'
C5'
C4'
DC
DC
DC
23
23
23
N
1
9.67
0.30
108.30
117.97
B
B
B
O4'
C1'
N1
DC
DC
DC
23
23
23
N
1
3.06
0.30
108.30
111.36
B
B
B
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
-3.61
0.60
119.90
116.29
B
B
B
N1
C6
O6
DG
DG
DG
24
24
24
N
1
A
A
O4'
C4'
DG
DG
10
10
-0.072
0.010
1.446
1.374
N
1
B
B
O3'
C3'
DG
DG
16
16
-0.036
0.006
1.419
1.383
N
1
B
B
P
O5'
DA
DA
17
17
0.068
0.010
1.593
1.661
N
1
B
B
C5'
C4'
DA
DA
17
17
-0.066
0.011
1.509
1.443
N
1
B
B
O3'
C3'
DC
DC
21
21
-0.060
0.006
1.419
1.359
N
1
B
B
O3'
P
DC
DG
21
22
-0.074
0.012
1.607
1.533
Y
1
B
A
OP1
O
DG
HOH
14
138
1.96
1_555
2_664
1
B
A
OP2
O
DG
HOH
24
130
2.03
1_555
3_655
1
A
B
OP1
O
DG
HOH
10
80
2.19
1_555
4_465
0.1720000
2.000
2000
1
2.000
TR
isotropic
TR
isotropic
2.000
121
639
32
486
0
0.020
fix
fix
2.000
127D
2000
2.000
1
refinement
NUCLSQ
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') COMPLEXED WITH HOECHST 33258
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
127D
PDB
1
127D
1
12
127D
1
12
127D
A
1
1
12
13
24
127D
13
24
127D
B
1
1
12
BINDING SITE FOR RESIDUE HT B 25
B
HT
25
Software
13
A
DA
5
A
DA
5
13
1_555
A
DA
6
A
DA
6
13
1_555
A
DT
7
A
DT
7
13
1_555
A
DT
8
A
DT
8
13
1_555
A
DC
9
A
DC
9
13
1_555
A
HOH
66
D
HOH
13
3_645
B
DA
17
B
DA
5
13
1_555
B
DA
18
B
DA
6
13
1_555
B
DT
19
B
DT
7
13
1_555
B
DT
20
B
DT
8
13
1_555
B
DC
21
B
DC
9
13
1_555
B
HOH
48
E
HOH
13
2_664
B
HOH
92
E
HOH
13
1_555
19
P 21 21 21