0.041203
0.000000
0.000000
0.000000
0.025240
0.000000
0.000000
0.000000
0.015731
0.00000
0.00000
0.00000
Kopka, M.L.
Yoon, C.
Goodsell, D.
Pjura, P.
Dickerson, R.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
24.270
39.620
63.570
C9 H13 Br N3 O7 P
386.093
n
5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
DNA linking
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
C18 H26 N10 O3
430.464
NETROPSIN
non-polymer
N
1
N
BR
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
N
N
7
N
C
N
8
N
C
N
9
N
O
N
10
N
N
N
11
N
C
N
12
N
N
N
13
N
C
N
14
N
C
N
15
N
C
N
16
R
C
N
17
N
O
N
18
R
C
N
19
S
C
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
O
N
36
N
P
N
37
N
O
N
38
N
O
N
39
N
O
N
40
N
C
N
41
R
C
N
42
N
O
N
43
S
C
N
44
N
O
N
45
N
C
N
46
R
C
Y
47
N
N
Y
48
N
C
Y
49
N
N
Y
50
N
C
Y
51
N
C
N
52
N
N
Y
53
N
N
Y
54
N
C
Y
55
N
N
Y
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
N
83
N
N
N
84
N
C
N
85
N
O
N
86
N
N
N
87
N
C
N
88
N
N
N
89
N
C
N
90
N
C
N
91
N
H
N
92
N
H
N
93
N
H
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
O
N
106
N
P
N
107
N
O
N
108
N
O
N
109
N
O
N
110
N
C
N
111
R
C
N
112
N
O
N
113
S
C
N
114
N
O
N
115
N
C
N
116
R
C
Y
117
N
N
Y
118
N
C
Y
119
N
N
Y
120
N
C
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
N
N
126
N
N
Y
127
N
C
N
128
N
H
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
O
N
143
N
P
N
144
N
O
N
145
N
O
N
146
N
O
N
147
N
C
N
148
R
C
N
149
N
O
N
150
S
C
N
151
N
O
N
152
N
C
N
153
R
C
N
154
N
N
N
155
N
C
N
156
N
O
N
157
N
N
N
158
N
C
N
159
N
O
N
160
N
C
N
161
N
C
N
162
N
C
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
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
O
N
179
N
H
N
180
N
H
N
181
N
C
N
182
N
N
N
183
N
N
N
184
N
N
N
185
N
C
N
186
N
C
N
187
N
O
N
188
N
N
Y
189
N
C
Y
190
N
C
Y
191
N
C
Y
192
N
N
N
193
N
C
Y
194
N
C
N
195
N
C
N
196
N
O
N
197
N
N
Y
198
N
C
Y
199
N
C
Y
200
N
C
Y
201
N
N
N
202
N
C
Y
203
N
C
N
204
N
C
N
205
N
O
N
206
N
N
N
207
N
C
N
208
N
C
N
209
N
C
N
210
N
N
N
211
N
N
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
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
1
N
sing
N
2
N
doub
N
3
N
sing
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
doub
N
12
N
sing
N
13
N
doub
N
14
N
sing
N
15
N
doub
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
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
doub
N
39
N
sing
N
40
N
sing
N
41
N
sing
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
Y
59
N
sing
Y
60
N
sing
Y
61
N
doub
N
62
N
sing
Y
63
N
sing
Y
64
N
sing
Y
65
N
doub
N
66
N
sing
Y
67
N
doub
N
68
N
sing
N
69
N
sing
Y
70
N
sing
Y
71
N
doub
N
72
N
sing
Y
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
N
97
N
sing
N
98
N
sing
N
99
N
doub
N
100
N
sing
N
101
N
doub
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
doub
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
doub
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
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
Y
132
N
sing
Y
133
N
sing
Y
134
N
doub
N
135
N
sing
Y
136
N
sing
N
137
N
sing
Y
138
N
doub
N
139
N
doub
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
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
doub
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
doub
N
178
N
sing
N
179
N
sing
N
180
N
doub
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
doub
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
doub
N
199
N
sing
N
200
N
sing
N
201
N
sing
Y
202
N
sing
Y
203
N
doub
Y
204
N
doub
N
205
N
sing
Y
206
N
sing
N
207
N
sing
N
208
N
sing
Y
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
doub
N
215
N
sing
N
216
N
sing
N
217
N
sing
Y
218
N
sing
Y
219
N
doub
Y
220
N
doub
N
221
N
sing
Y
222
N
sing
N
223
N
sing
N
224
N
sing
Y
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
doub
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
doub
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
183
553
563
10.1016/0022-2836(85)90171-8
2991536
Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G.
1985
Adenine Press,Guilderland,New York
Structure and Motion. Membranes, Nucleic Acids and Protein.
The Binding of Netropsin to Double-Helical B-DNA of Sequence C-G-C-G-A-A-T-T-BrC-G-C-G. Single Crystal X-Ray Structure Analysis
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
82
1376
1380
The Molecular Origin of DNA-Drug Specificity in Netropsin and Distamycin
1985
10.2210/pdb6bna/pdb
pdb_00006bna
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
DIFFRACTOMETER
x-ray
1
1.0
3742.288
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*CP*G)-3')
2
syn
polymer
430.464
NETROPSIN
1
syn
non-polymer
18.015
water
75
nat
water
no
yes
(DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(CBR)(DG)(DC)(DG)
CGCGAATTCGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
2.04
39.76
VAPOR DIFFUSION
VAPOR DIFFUSION, temperature 277.00K
277.00
WATER
1
MPD
1
SPERMINE_HCL
1
MG ACETATE
1
WATER
2
MPD
2
-5.504
1
19
A
1
B
24
-3.424
A_DC1:DG24_B
1
-15.807
0.365
-0.015
-0.274
-2.482
1
19
A
2
B
23
-0.561
A_DG2:DC23_B
2
-13.730
-0.452
0.125
-0.305
-3.993
1
19
A
3
B
22
2.481
A_DC3:DG22_B
3
-4.548
0.263
0.113
-0.181
8.690
1
19
A
4
B
21
1.757
A_DG4:CBR21_B
4
-5.783
-0.164
-0.182
-0.150
10.767
1
20
A
5
B
20
2.296
A_DA5:DT20_B
5
-19.744
0.604
0.252
-0.090
7.510
1
20
A
6
B
19
7.923
A_DA6:DT19_B
6
-20.948
-0.135
0.229
-0.120
-2.874
1
20
A
7
B
18
-0.685
A_DT7:DA18_B
7
-25.128
-0.079
0.021
-0.056
-14.620
1
20
A
8
B
17
3.769
A_DT8:DA17_B
8
-22.200
-0.290
0.321
0.086
-18.365
1
19
A
9
B
16
-2.986
A_CBR9:DG16_B
9
-17.342
0.264
0.213
-0.241
10.894
1
19
A
10
B
15
0.865
A_DG10:DC15_B
10
-9.155
-0.432
0.342
-0.101
-3.949
1
19
A
11
B
14
-4.874
A_DC11:DG14_B
11
-19.477
0.576
0.321
-0.345
-2.704
1
19
A
12
B
13
-4.922
A_DG12:DC13_B
12
2.572
0.356
-0.529
-0.207
3.412
30.662
A
A
1
2
8.361
B
B
24
23
3.413
4.388
-0.118
0.403
AA_DC1DG2:DC23DG24_BB
1
-4.897
9.331
29.965
-0.150
-0.796
3.109
46.128
A
A
2
3
-13.635
B
B
23
22
3.308
-10.588
0.955
0.836
AA_DG2DC3:DG22DC23_BB
2
3.618
-4.659
44.822
1.971
-0.911
3.117
27.768
A
A
3
4
13.047
B
B
22
21
3.129
6.177
-0.336
0.792
AA_DC3DG4:CBR21DG22_BB
3
5.000
-10.561
26.627
0.199
1.875
3.291
41.998
A
A
4
5
-2.137
B
B
21
20
3.299
-1.528
-0.090
-0.080
AA_DG4DA5:DT20CBR21_BB
4
-4.738
6.625
41.715
0.049
-0.372
3.063
33.668
A
A
5
6
12.548
B
B
20
19
3.161
7.213
0.178
-0.157
AA_DA5DA6:DT19DT20_BB
5
1.146
-1.993
32.889
-1.403
-0.128
3.417
32.234
A
A
6
7
2.165
B
B
19
18
3.427
1.201
-0.502
-0.512
AA_DA6DT7:DA18DT19_BB
6
-0.756
1.363
32.203
-1.146
0.764
3.587
37.309
A
A
7
8
3.083
B
B
18
17
3.587
1.972
0.128
0.088
AA_DT7DT8:DA17DA18_BB
7
0.008
-0.013
37.259
-0.149
-0.198
3.522
40.508
A
A
8
9
-1.423
B
B
17
16
3.535
-0.985
0.122
0.619
AA_DT8CBR9:DG16DA17_BB
8
1.249
-1.805
40.478
1.013
-0.026
2.847
26.034
A
A
9
10
5.221
B
B
16
15
2.786
2.347
0.091
0.941
AA_CBR9DG10:DC15DG16_BB
9
-1.677
3.730
25.876
1.534
-0.598
3.638
48.385
A
A
10
11
-14.689
B
B
15
14
3.918
-11.927
-0.638
0.828
AA_DG10DC11:DG14DC15_BB
10
-1.821
2.243
46.944
2.098
0.612
3.561
38.369
A
A
11
12
-6.897
B
B
14
13
3.566
-4.506
0.840
0.597
AA_DC11DG12:DC13DG14_BB
11
5.946
-9.101
37.664
1.527
-0.461
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
1984-10-29
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-03-13
_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
BNL
1984-08-30
REL
REL
NT
NETROPSIN
HOH
water
NT
25
2
NT
NT
25
B
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
28
3
HOH
HOH
28
A
HOH
30
3
HOH
HOH
30
A
HOH
34
3
HOH
HOH
34
A
HOH
38
3
HOH
HOH
38
A
HOH
39
3
HOH
HOH
39
A
HOH
42
3
HOH
HOH
42
A
HOH
46
3
HOH
HOH
46
A
HOH
49
3
HOH
HOH
49
A
HOH
50
3
HOH
HOH
50
A
HOH
51
3
HOH
HOH
51
A
HOH
52
3
HOH
HOH
52
A
HOH
55
3
HOH
HOH
55
A
HOH
56
3
HOH
HOH
56
A
HOH
57
3
HOH
HOH
57
A
HOH
58
3
HOH
HOH
58
A
HOH
60
3
HOH
HOH
60
A
HOH
61
3
HOH
HOH
61
A
HOH
72
3
HOH
HOH
72
A
HOH
73
3
HOH
HOH
73
A
HOH
78
3
HOH
HOH
78
A
HOH
79
3
HOH
HOH
79
A
HOH
82
3
HOH
HOH
82
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
92
3
HOH
HOH
92
A
HOH
94
3
HOH
HOH
94
A
HOH
97
3
HOH
HOH
97
A
HOH
100
3
HOH
HOH
100
A
HOH
29
3
HOH
HOH
29
B
HOH
31
3
HOH
HOH
31
B
HOH
32
3
HOH
HOH
32
B
HOH
33
3
HOH
HOH
33
B
HOH
35
3
HOH
HOH
35
B
HOH
36
3
HOH
HOH
36
B
HOH
37
3
HOH
HOH
37
B
HOH
40
3
HOH
HOH
40
B
HOH
41
3
HOH
HOH
41
B
HOH
43
3
HOH
HOH
43
B
HOH
44
3
HOH
HOH
44
B
HOH
45
3
HOH
HOH
45
B
HOH
47
3
HOH
HOH
47
B
HOH
48
3
HOH
HOH
48
B
HOH
53
3
HOH
HOH
53
B
HOH
54
3
HOH
HOH
54
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
66
3
HOH
HOH
66
B
HOH
67
3
HOH
HOH
67
B
HOH
68
3
HOH
HOH
68
B
HOH
69
3
HOH
HOH
69
B
HOH
70
3
HOH
HOH
70
B
HOH
71
3
HOH
HOH
71
B
HOH
74
3
HOH
HOH
74
B
HOH
75
3
HOH
HOH
75
B
HOH
76
3
HOH
HOH
76
B
HOH
77
3
HOH
HOH
77
B
HOH
80
3
HOH
HOH
80
B
HOH
81
3
HOH
HOH
81
B
HOH
83
3
HOH
HOH
83
B
HOH
86
3
HOH
HOH
86
B
HOH
87
3
HOH
HOH
87
B
HOH
88
3
HOH
HOH
88
B
HOH
93
3
HOH
HOH
93
B
HOH
95
3
HOH
HOH
95
B
HOH
96
3
HOH
HOH
96
B
HOH
98
3
HOH
HOH
98
B
HOH
99
3
HOH
HOH
99
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
DG
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
CBR
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
DG
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
CBR
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
CBR
9
A
CBR
9
DC
B
CBR
21
B
CBR
9
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
1
A
DG
4
0.066
SIDE CHAIN
1
A
DG
10
0.091
SIDE CHAIN
1
A
DC
11
0.060
SIDE CHAIN
1
A
DG
12
0.056
SIDE CHAIN
1
B
DG
14
0.070
SIDE CHAIN
1
B
DC
15
0.102
SIDE CHAIN
1
B
DG
16
0.095
SIDE CHAIN
1
B
DT
19
0.098
SIDE CHAIN
1
B
DG
24
0.086
SIDE CHAIN
1
12.62
1.10
109.80
122.42
A
A
A
C5'
C4'
O4'
DC
DC
DC
1
1
1
N
1
7.17
0.90
103.10
110.27
A
A
A
C4'
C3'
C2'
DC
DC
DC
1
1
1
N
1
4.78
0.30
108.30
113.08
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
-10.05
0.80
109.40
99.35
A
A
A
O5'
C5'
C4'
DG
DG
DG
2
2
2
N
1
3.79
0.50
111.90
115.69
A
A
A
C2
N3
C4
DG
DG
DG
2
2
2
N
1
-4.42
0.50
128.60
124.18
A
A
A
N3
C4
C5
DG
DG
DG
2
2
2
N
1
4.42
0.60
126.00
130.42
A
A
A
N3
C4
N9
DG
DG
DG
2
2
2
N
1
-7.46
1.00
110.10
102.64
A
A
A
C1'
O4'
C4'
DC
DC
DC
3
3
3
N
1
4.19
0.50
106.80
110.99
A
A
A
O4'
C1'
C2'
DC
DC
DC
3
3
3
N
1
3.59
0.50
119.90
123.49
A
A
A
C2
N3
C4
DC
DC
DC
3
3
3
N
1
3.30
0.40
105.40
108.70
A
A
A
N9
C4
C5
DG
DG
DG
4
4
4
N
1
7.51
1.20
119.70
127.21
A
A
A
C3'
O3'
P
DG
DG
DA
4
4
5
Y
1
2.02
0.30
108.30
110.32
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
3.31
0.50
110.60
113.91
A
A
A
C2
N3
C4
DA
DA
DA
5
5
5
N
1
-3.83
0.40
105.80
101.97
A
A
A
C8
N9
C4
DA
DA
DA
5
5
5
N
1
2.89
0.40
105.80
108.69
A
A
A
N9
C4
C5
DA
DA
DA
5
5
5
N
1
10.08
1.10
109.80
119.88
A
A
A
C5'
C4'
O4'
DA
DA
DA
6
6
6
N
1
5.27
0.70
110.30
115.57
A
A
A
C1'
O4'
C4'
DA
DA
DA
6
6
6
N
1
-6.73
0.80
105.90
99.17
A
A
A
O4'
C1'
C2'
DA
DA
DA
6
6
6
N
1
-10.72
0.80
109.40
98.68
A
A
A
O5'
C5'
C4'
DT
DT
DT
7
7
7
N
1
-4.40
0.60
127.20
122.80
A
A
A
C2
N3
C4
DT
DT
DT
7
7
7
N
1
-4.42
0.60
123.70
119.28
A
A
A
C5
C6
N1
DT
DT
DT
7
7
7
N
1
-5.31
0.60
119.90
114.59
A
A
A
N3
C4
O4
DT
DT
DT
7
7
7
N
1
5.37
0.60
119.00
124.37
A
A
A
C4
C5
C7
DT
DT
DT
7
7
7
N
1
-6.73
0.60
122.90
116.17
A
A
A
C6
C5
C7
DT
DT
DT
7
7
7
N
1
9.22
1.20
119.70
128.92
A
A
A
C3'
O3'
P
DT
DT
DT
7
7
8
Y
1
4.04
0.60
115.20
119.24
A
A
A
N3
C4
C5
DT
DT
DT
8
8
8
N
1
-3.65
0.60
119.90
116.25
A
A
A
N3
C4
O4
DT
DT
DT
8
8
8
N
1
5.71
0.60
119.00
124.71
A
A
A
C4
C5
C7
DT
DT
DT
8
8
8
N
1
-5.97
0.60
122.90
116.93
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
1
-6.58
0.90
105.70
99.12
A
A
A
O5'
P
OP2
DG
DG
DG
10
10
10
N
1
-5.64
0.80
109.40
103.76
A
A
A
O5'
C5'
C4'
DG
DG
DG
10
10
10
N
1
8.20
1.20
115.70
123.90
A
A
A
C5'
C4'
C3'
DC
DC
DC
11
11
11
N
1
-5.68
0.70
102.20
96.52
A
A
A
C4'
C3'
C2'
DC
DC
DC
11
11
11
N
1
5.77
0.30
108.30
114.07
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
-10.85
0.80
109.40
98.55
A
A
A
O5'
C5'
C4'
DG
DG
DG
12
12
12
N
1
-6.66
0.70
108.00
101.34
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
4.09
0.50
111.90
115.99
A
A
A
C2
N3
C4
DG
DG
DG
12
12
12
N
1
3.06
0.50
111.50
114.56
A
A
A
C5
C6
N1
DG
DG
DG
12
12
12
N
1
4.06
0.60
106.00
110.06
B
B
B
O4'
C4'
C3'
DC
DC
DC
13
13
13
N
1
2.79
0.30
108.30
111.09
B
B
B
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
3.69
0.40
120.30
123.99
B
B
B
C6
N1
C2
DC
DC
DC
13
13
13
N
1
3.77
0.60
106.00
109.77
B
B
B
O4'
C4'
C3'
DG
DG
DG
14
14
14
N
1
-4.11
0.60
123.90
119.79
B
B
B
N1
C2
N3
DG
DG
DG
14
14
14
N
1
5.27
0.50
111.90
117.17
B
B
B
C2
N3
C4
DG
DG
DG
14
14
14
N
1
-3.01
0.50
128.60
125.59
B
B
B
N3
C4
C5
DG
DG
DG
14
14
14
N
1
3.14
0.50
111.50
114.64
B
B
B
C5
C6
N1
DG
DG
DG
14
14
14
N
1
-2.40
0.40
106.40
104.00
B
B
B
C8
N9
C4
DG
DG
DG
14
14
14
N
1
-4.34
0.60
119.90
115.56
B
B
B
N1
C6
O6
DG
DG
DG
14
14
14
N
1
-10.18
0.90
105.70
95.52
B
B
B
O5'
P
OP2
DC
DC
DC
15
15
15
N
1
8.38
0.30
108.30
116.68
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
-5.47
0.80
109.40
103.93
B
B
B
O5'
C5'
C4'
DG
DG
DG
16
16
16
N
1
4.23
0.60
106.00
110.23
B
B
B
O4'
C4'
C3'
DG
DG
DG
16
16
16
N
1
3.55
0.50
106.80
110.35
B
B
B
O4'
C1'
C2'
DG
DG
DG
16
16
16
N
1
3.99
0.30
108.30
112.29
B
B
B
O4'
C1'
N9
DA
DA
DA
17
17
17
N
1
3.89
0.60
118.60
122.49
B
B
B
C6
N1
C2
DA
DA
DA
17
17
17
N
1
3.83
0.60
118.60
122.43
B
B
B
C6
N1
C2
DA
DA
DA
18
18
18
N
1
-4.86
0.50
129.30
124.44
B
B
B
N1
C2
N3
DA
DA
DA
18
18
18
N
1
3.09
0.50
110.60
113.69
B
B
B
C2
N3
C4
DA
DA
DA
18
18
18
N
1
-3.10
0.50
103.90
100.80
B
B
B
C5
N7
C8
DA
DA
DA
18
18
18
N
1
2.19
0.30
108.30
110.49
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
3.82
0.60
114.60
118.42
B
B
B
N1
C2
N3
DT
DT
DT
19
19
19
N
1
-4.12
0.60
122.30
118.18
B
B
B
N3
C2
O2
DT
DT
DT
19
19
19
N
1
3.83
0.60
119.00
122.83
B
B
B
C4
C5
C7
DT
DT
DT
19
19
19
N
1
-4.11
0.60
122.90
118.79
B
B
B
C6
C5
C7
DT
DT
DT
19
19
19
N
1
-4.01
0.40
104.50
100.49
B
B
B
O4'
C4'
C3'
DT
DT
DT
20
20
20
N
1
-6.64
0.80
105.90
99.26
B
B
B
O4'
C1'
C2'
DT
DT
DT
20
20
20
N
1
-3.88
0.60
127.20
123.32
B
B
B
C2
N3
C4
DT
DT
DT
20
20
20
N
1
6.67
1.10
110.50
117.17
B
B
B
O3'
P
OP2
DT
CBR
CBR
20
21
21
Y
1
-2.59
0.40
104.50
101.91
B
B
B
O4'
C4'
C3'
DG
DG
DG
22
22
22
N
1
2.68
0.30
108.30
110.98
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
-7.41
0.80
109.40
101.99
B
B
B
O5'
C5'
C4'
DC
DC
DC
23
23
23
N
1
7.48
1.20
115.70
123.18
B
B
B
C5'
C4'
C3'
DC
DC
DC
23
23
23
N
1
3.18
0.50
119.90
123.08
B
B
B
C2
N3
C4
DC
DC
DC
23
23
23
N
1
-4.56
0.60
123.90
119.34
B
B
B
N1
C2
N3
DG
DG
DG
24
24
24
N
1
5.06
0.50
111.90
116.96
B
B
B
C2
N3
C4
DG
DG
DG
24
24
24
N
1
-3.06
0.50
128.60
125.54
B
B
B
N3
C4
C5
DG
DG
DG
24
24
24
N
1
2.57
0.40
105.40
107.97
B
B
B
N9
C4
C5
DG
DG
DG
24
24
24
N
1
A
A
C4'
C3'
DC
DC
1
1
-0.103
0.010
1.521
1.418
N
1
A
A
O3'
C3'
DC
DC
1
1
-0.067
0.006
1.419
1.352
N
1
A
A
C5
C6
DC
DC
1
1
0.059
0.008
1.339
1.398
N
1
A
A
O3'
P
DC
DG
1
2
-0.075
0.012
1.607
1.532
Y
1
A
A
N3
C4
DG
DG
2
2
0.051
0.007
1.350
1.401
N
1
A
A
C5
N7
DG
DG
2
2
-0.072
0.006
1.388
1.316
N
1
A
A
P
O5'
DC
DC
3
3
0.067
0.010
1.593
1.660
N
1
A
A
N1
C2
DC
DC
3
3
-0.061
0.010
1.397
1.336
N
1
A
A
O4'
C4'
DG
DG
4
4
-0.087
0.010
1.446
1.359
N
1
A
A
N9
C4
DG
DG
4
4
-0.051
0.008
1.375
1.324
N
1
A
A
O3'
C3'
DA
DA
5
5
-0.057
0.006
1.419
1.362
N
1
A
A
C5
N7
DA
DA
5
5
-0.071
0.006
1.388
1.317
N
1
A
A
C4'
C3'
DA
DA
6
6
-0.117
0.010
1.521
1.404
N
1
A
A
C2'
C1'
DA
DA
6
6
-0.087
0.010
1.518
1.431
N
1
A
A
C5
C6
DA
DA
6
6
0.071
0.009
1.406
1.477
N
1
A
A
C5
N7
DA
DA
6
6
-0.037
0.006
1.388
1.351
N
1
A
A
C6
N6
DA
DA
6
6
0.059
0.008
1.335
1.394
N
1
A
A
O3'
P
DA
DT
6
7
-0.121
0.012
1.607
1.486
Y
1
A
A
P
O5'
DT
DT
7
7
-0.093
0.010
1.593
1.500
N
1
A
A
O4'
C4'
DT
DT
7
7
-0.106
0.010
1.446
1.340
N
1
A
A
O3'
C3'
DT
DT
7
7
-0.045
0.006
1.419
1.374
N
1
A
A
C5
C6
DT
DT
7
7
0.066
0.007
1.339
1.405
N
1
A
A
P
OP2
DT
DT
8
8
-0.193
0.017
1.485
1.292
N
1
A
A
O4'
C4'
DT
DT
8
8
-0.066
0.010
1.446
1.380
N
1
A
A
C5
C6
DT
DT
8
8
0.068
0.007
1.339
1.407
N
1
A
A
N3
C4
DG
DG
10
10
0.062
0.007
1.350
1.412
N
1
A
A
C5
N7
DG
DG
10
10
-0.053
0.006
1.388
1.335
N
1
A
A
C5
C6
DC
DC
11
11
0.066
0.008
1.339
1.405
N
1
A
A
C5
N7
DG
DG
12
12
-0.039
0.006
1.388
1.349
N
1
A
A
N9
C4
DG
DG
12
12
-0.055
0.008
1.375
1.320
N
1
B
B
C5
C6
DC
DC
13
13
0.060
0.008
1.339
1.399
N
1
B
B
P
OP1
DC
DC
15
15
-0.143
0.017
1.485
1.342
N
1
B
B
N3
C4
DG
DG
16
16
0.044
0.007
1.350
1.394
N
1
B
B
C5
N7
DG
DG
16
16
-0.041
0.006
1.388
1.347
N
1
B
B
N3
C4
DA
DA
17
17
0.051
0.006
1.344
1.395
N
1
B
B
C5
N7
DA
DA
17
17
-0.063
0.006
1.388
1.325
N
1
B
B
N3
C4
DA
DA
18
18
0.039
0.006
1.344
1.383
N
1
B
B
C5
C6
DT
DT
19
19
0.062
0.007
1.339
1.401
N
1
B
B
C5
C6
DT
DT
20
20
0.059
0.007
1.339
1.398
N
1
B
B
O3'
C3'
DG
DG
22
22
-0.068
0.006
1.419
1.351
N
1
B
B
C5
N7
DG
DG
22
22
-0.049
0.006
1.388
1.339
N
1
B
B
N7
C8
DG
DG
22
22
0.045
0.006
1.305
1.350
N
1
B
B
O3'
P
DG
DC
22
23
-0.072
0.012
1.607
1.535
Y
1
B
B
O4'
C4'
DC
DC
23
23
-0.084
0.010
1.446
1.362
N
1
B
B
C5
C6
DC
DC
23
23
0.051
0.008
1.339
1.390
N
1
B
B
C5
N7
DG
DG
24
24
-0.041
0.006
1.388
1.347
N
1
B
B
N7
C8
DG
DG
24
24
0.058
0.006
1.305
1.363
N
0.211
2.210
8.000
2528
1
2.000
TR
isotropic
TR
isotropic
2.210
8.000
75
594
33
486
0
fix
fix
2.200
6BNA
3240
1
refinement
JACK-LEVITT
BINDING OF AN ANTITUMOR DRUG TO DNA. NETROPSIN AND C-G-C-G-A-A-T-T-BRC-G-C-G
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
covale
1.589
both
A
DT
8
A
O3'
DT
8
1_555
A
CBR
9
A
P
CBR
9
1_555
covale
1.609
both
A
CBR
9
A
O3'
CBR
9
1_555
A
DG
10
A
P
DG
10
1_555
covale
1.587
both
B
DT
20
B
O3'
DT
8
1_555
B
CBR
21
B
P
CBR
9
1_555
covale
1.646
both
B
CBR
21
B
O3'
CBR
9
1_555
B
DG
22
B
P
DG
10
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
DG
4
A
N1
DG
4
1_555
B
CBR
21
B
N3
CBR
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
CBR
21
B
O2
CBR
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
CBR
21
B
N4
CBR
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
CBR
9
A
N3
CBR
9
1_555
B
DG
16
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
CBR
9
A
N4
CBR
9
1_555
B
DG
16
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
CBR
9
A
O2
CBR
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, MODIFIED, DNA
6BNA
PDB
1
6BNA
1
12
6BNA
1
12
6BNA
A
1
1
12
13
24
6BNA
13
24
6BNA
B
1
1
12
BINDING SITE FOR RESIDUE NT B 25
B
NT
25
Software
11
A
DA
5
A
DA
5
11
1_555
A
DA
6
A
DA
6
11
1_555
A
DT
7
A
DT
7
11
1_555
A
DT
8
A
DT
8
11
1_555
A
CBR
9
A
CBR
9
11
1_555
B
DA
17
B
DA
5
11
1_555
B
DA
18
B
DA
6
11
1_555
B
DT
20
B
DT
8
11
1_555
B
CBR
21
B
CBR
9
11
1_555
B
DG
22
B
DG
10
11
1_555
B
HOH
66
E
HOH
11
1_555
19
P 21 21 21