0.041203
0.000000
0.000000
0.000000
0.025240
0.000000
0.000000
0.000000
0.015731
0.00000
0.00000
0.00000
Goodsell, D.S.
Kopka, M.L.
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
Mg 2
24.305
MAGNESIUM ION
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
MG
N
182
N
C
N
183
N
N
N
184
N
N
N
185
N
N
N
186
N
C
N
187
N
C
N
188
N
O
N
189
N
N
Y
190
N
C
Y
191
N
C
Y
192
N
C
Y
193
N
N
N
194
N
C
Y
195
N
C
N
196
N
C
N
197
N
O
N
198
N
N
Y
199
N
C
Y
200
N
C
Y
201
N
C
Y
202
N
N
N
203
N
C
Y
204
N
C
N
205
N
C
N
206
N
O
N
207
N
N
N
208
N
C
N
209
N
C
N
210
N
C
N
211
N
N
N
212
N
N
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
238
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
US
Biochemistry
BICHAW
0033
0006-2960
34
4983
4993
10.1021/bi00015a009
7711020
Refinement of netropsin bound to DNA: bias and feedback in electron density map interpretation.
1995
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
183
553
563
Binding of an Antitumor Drug to DNA. Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G
1985
10.2210/pdb101d/pdb
pdb_0000101d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3742.288
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*CP*G)-3')
2
syn
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
430.464
NETROPSIN
1
syn
non-polymer
18.015
water
36
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
2.00
38.45
2.891
1
19
A
1
B
24
-0.588
A_DC1:DG24_B
1
-17.827
0.147
-0.114
-0.208
-3.485
1
19
A
2
B
23
-3.444
A_DG2:DC23_B
2
-15.195
-0.027
0.219
-0.267
-4.972
1
19
A
3
B
22
-0.364
A_DC3:DG22_B
3
-6.435
0.096
0.286
-0.177
9.060
1
19
A
4
B
21
1.060
A_DG4:CBR21_B
4
-7.744
-0.217
0.018
0.056
6.129
1
20
A
5
B
20
7.183
A_DA5:DT20_B
5
-20.556
0.430
-0.317
-0.075
3.511
1
20
A
6
B
19
1.086
A_DA6:DT19_B
6
-18.034
-0.042
0.219
-0.078
0.306
1
20
A
7
B
18
4.024
A_DT7:DA18_B
7
-20.982
0.297
-0.043
-0.067
-14.255
1
20
A
8
B
17
7.034
A_DT8:DA17_B
8
-21.443
-0.239
0.405
-0.312
-9.615
1
19
A
9
B
16
2.726
A_CBR9:DG16_B
9
-11.260
0.246
-0.171
-0.354
6.362
1
19
A
10
B
15
-0.785
A_DG10:DC15_B
10
-2.898
-0.226
0.029
-0.252
9.834
1
19
A
11
B
14
-2.711
A_DC11:DG14_B
11
-21.915
0.749
-0.044
-0.370
-6.288
1
19
A
12
B
13
-7.468
A_DG12:DC13_B
12
10.370
0.385
-0.668
-0.273
3.577
34.297
A
A
1
2
15.156
B
B
24
23
3.615
8.830
-0.183
0.304
AA_DC1DG2:DC23DG24_BB
1
-3.280
5.631
33.016
-1.039
-0.268
3.195
42.837
A
A
2
3
-13.357
B
B
23
22
3.312
-9.673
0.953
0.420
AA_DG2DC3:DG22DC23_BB
2
2.698
-3.726
41.697
1.548
-1.034
3.134
28.476
A
A
3
4
4.267
B
B
22
21
3.187
2.081
-0.097
0.731
AA_DC3DG4:CBR21DG22_BB
3
6.284
-12.889
27.711
1.019
1.606
3.286
42.793
A
A
4
5
7.497
B
B
21
20
3.290
5.455
0.072
0.168
AA_DG4DA5:DT20CBR21_BB
4
1.938
-2.663
42.418
-0.320
0.097
3.177
34.135
A
A
5
6
10.030
B
B
20
19
3.248
5.814
-0.375
-0.181
AA_DA5DA6:DT19DT20_BB
5
-7.525
12.981
32.821
-1.233
-0.556
3.323
33.154
A
A
6
7
-2.856
B
B
19
18
3.304
-1.629
-0.205
-0.604
AA_DA6DT7:DA18DT19_BB
6
0.855
-1.500
33.104
-0.782
0.504
3.584
36.800
A
A
7
8
2.976
B
B
18
17
3.581
1.878
0.275
0.044
AA_DT7DT8:DA17DA18_BB
7
0.973
-1.542
36.741
-0.210
-0.290
3.276
41.760
A
A
8
9
1.237
B
B
17
16
3.269
0.879
0.217
0.648
AA_DT8CBR9:DG16DA17_BB
8
6.578
-9.264
41.253
0.816
0.391
3.204
27.242
A
A
9
10
12.155
B
B
16
15
3.089
5.641
-0.017
1.216
AA_CBR9DG10:DC15DG16_BB
9
-5.850
12.606
26.024
1.192
-1.404
3.011
47.399
A
A
10
11
-13.387
B
B
15
14
3.282
-10.675
-0.565
1.027
AA_DG10DC11:DG14DC15_BB
10
-2.375
2.978
46.191
2.121
0.515
3.948
38.792
A
A
11
12
-13.358
B
B
14
13
4.200
-8.775
0.449
0.791
AA_DC11DG12:DC13DG14_BB
11
5.297
-8.064
37.464
2.551
0.145
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_conn_type
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1995-02-27
1
1
2008-05-22
1
2
2011-07-13
1
3
2023-11-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.value
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn_type.id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
NDB
1994-12-14
REL
MG
MAGNESIUM ION
NT
NETROPSIN
HOH
water
MO3
26
2
MG
MG
26
A
NT
25
3
NT
NT
25
B
HOH
27
4
HOH
HOH
27
A
HOH
28
4
HOH
HOH
28
A
HOH
33
4
HOH
HOH
33
A
HOH
34
4
HOH
HOH
34
A
HOH
35
4
HOH
HOH
35
A
HOH
39
4
HOH
HOH
39
A
HOH
44
4
HOH
HOH
44
A
HOH
46
4
HOH
HOH
46
A
HOH
48
4
HOH
HOH
48
A
HOH
52
4
HOH
HOH
52
A
HOH
53
4
HOH
HOH
53
A
HOH
54
4
HOH
HOH
54
A
HOH
59
4
HOH
HOH
59
A
MO3
26
4
HOH
HOH
61
A
HOH
29
4
HOH
HOH
29
B
HOH
30
4
HOH
HOH
30
B
HOH
31
4
HOH
HOH
31
B
HOH
32
4
HOH
HOH
32
B
HOH
36
4
HOH
HOH
36
B
HOH
37
4
HOH
HOH
37
B
HOH
38
4
HOH
HOH
38
B
HOH
40
4
HOH
HOH
40
B
HOH
41
4
HOH
HOH
41
B
HOH
42
4
HOH
HOH
42
B
HOH
43
4
HOH
HOH
43
B
HOH
45
4
HOH
HOH
45
B
HOH
47
4
HOH
HOH
47
B
HOH
49
4
HOH
HOH
49
B
HOH
50
4
HOH
HOH
50
B
HOH
51
4
HOH
HOH
51
B
HOH
55
4
HOH
HOH
55
B
HOH
56
4
HOH
HOH
56
B
HOH
57
4
HOH
HOH
57
B
HOH
58
4
HOH
HOH
58
B
MO3
26
4
HOH
HOH
60
B
MO3
26
4
HOH
HOH
62
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
HOH
61
E
O
HOH
1_555
A
MG
26
C
MG
MG
1_555
B
HOH
60
F
O
HOH
1_555
88.3
A
HOH
61
E
O
HOH
1_555
A
MG
26
C
MG
MG
1_555
B
HOH
62
F
O
HOH
1_555
76.9
B
HOH
60
F
O
HOH
1_555
A
MG
26
C
MG
MG
1_555
B
HOH
62
F
O
HOH
1_555
80.2
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
9.68
1.10
109.80
119.48
A
A
A
C5'
C4'
O4'
DC
DC
DC
1
1
1
N
1
4.12
0.50
119.90
124.02
A
A
A
C2
N3
C4
DC
DC
DC
1
1
1
N
1
-5.18
0.40
121.90
116.72
A
A
A
N3
C4
C5
DC
DC
DC
1
1
1
N
1
7.40
0.70
120.20
127.60
A
A
A
C5
C4
N4
DC
DC
DC
1
1
1
N
1
-10.62
1.50
119.60
108.98
A
A
A
OP1
P
OP2
DG
DG
DG
2
2
2
N
1
-5.50
0.80
109.40
103.90
A
A
A
O5'
C5'
C4'
DG
DG
DG
2
2
2
N
1
19.16
1.20
119.70
138.86
A
A
A
C3'
O3'
P
DG
DG
DC
2
2
3
Y
1
-2.55
0.40
121.90
119.35
A
A
A
N3
C4
C5
DC
DC
DC
3
3
3
N
1
12.25
1.10
109.80
122.05
A
A
A
C5'
C4'
O4'
DG
DG
DG
4
4
4
N
1
6.79
0.30
108.30
115.09
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
-4.73
0.60
125.10
120.37
A
A
A
C6
N1
C2
DG
DG
DG
4
4
4
N
1
4.66
0.60
123.90
128.56
A
A
A
N1
C2
N3
DG
DG
DG
4
4
4
N
1
3.87
0.50
111.50
115.37
A
A
A
C5
C6
N1
DG
DG
DG
4
4
4
N
1
-5.28
0.70
119.90
114.62
A
A
A
N3
C2
N2
DG
DG
DG
4
4
4
N
1
-3.69
0.60
128.60
124.91
A
A
A
C5
C6
O6
DG
DG
DG
4
4
4
N
1
4.00
0.60
118.60
122.60
A
A
A
C6
N1
C2
DA
DA
DA
5
5
5
N
1
-3.15
0.50
129.30
126.15
A
A
A
N1
C2
N3
DA
DA
DA
5
5
5
N
1
8.68
1.20
119.70
128.38
A
A
A
C3'
O3'
P
DA
DA
DA
5
5
6
Y
1
-5.52
0.70
108.00
102.48
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
3.96
0.60
118.60
122.56
A
A
A
C6
N1
C2
DA
DA
DA
6
6
6
N
1
-3.05
0.50
117.70
114.65
A
A
A
C5
C6
N1
DA
DA
DA
6
6
6
N
1
10.09
1.20
119.70
129.79
A
A
A
C3'
O3'
P
DA
DA
DT
6
6
7
Y
1
-13.42
1.50
119.60
106.18
A
A
A
OP1
P
OP2
DT
DT
DT
7
7
7
N
1
8.52
1.20
110.70
119.22
A
A
A
O5'
P
OP2
DT
DT
DT
7
7
7
N
1
-7.65
0.80
109.40
101.75
A
A
A
O5'
C5'
C4'
DT
DT
DT
7
7
7
N
1
-5.93
0.80
105.90
99.97
A
A
A
O4'
C1'
C2'
DT
DT
DT
7
7
7
N
1
-6.60
0.60
127.20
120.60
A
A
A
C2
N3
C4
DT
DT
DT
7
7
7
N
1
5.63
0.60
115.20
120.83
A
A
A
N3
C4
C5
DT
DT
DT
7
7
7
N
1
14.71
1.20
119.70
134.41
A
A
A
C3'
O3'
P
DT
DT
DT
7
7
8
Y
1
3.94
0.60
114.60
118.54
A
A
A
N1
C2
N3
DT
DT
DT
8
8
8
N
1
-4.60
0.60
127.20
122.60
A
A
A
C2
N3
C4
DT
DT
DT
8
8
8
N
1
3.62
0.60
115.20
118.82
A
A
A
N3
C4
C5
DT
DT
DT
8
8
8
N
1
-3.82
0.60
119.90
116.08
A
A
A
N3
C4
O4
DT
DT
DT
8
8
8
N
1
24.02
1.20
119.70
143.72
A
A
A
C3'
O3'
P
DT
DT
CBR
8
8
9
Y
1
15.63
1.20
119.70
135.33
A
A
A
C3'
O3'
P
CBR
CBR
DG
9
9
10
Y
1
-10.73
1.50
119.60
108.87
A
A
A
OP1
P
OP2
DG
DG
DG
10
10
10
N
1
18.33
1.60
120.90
139.23
A
A
A
P
O5'
C5'
DG
DG
DG
10
10
10
N
1
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
-4.76
0.60
125.10
120.34
A
A
A
C6
N1
C2
DG
DG
DG
10
10
10
N
1
4.01
0.60
123.90
127.91
A
A
A
N1
C2
N3
DG
DG
DG
10
10
10
N
1
3.89
0.50
111.50
115.39
A
A
A
C5
C6
N1
DG
DG
DG
10
10
10
N
1
12.06
1.20
119.70
131.76
A
A
A
C3'
O3'
P
DG
DG
DC
10
10
11
Y
1
-9.99
1.50
119.60
109.61
A
A
A
OP1
P
OP2
DC
DC
DC
11
11
11
N
1
-4.85
0.70
108.00
103.15
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
-13.02
1.50
119.60
106.58
A
A
A
OP1
P
OP2
DG
DG
DG
12
12
12
N
1
-8.18
0.80
109.40
101.22
A
A
A
O5'
C5'
C4'
DG
DG
DG
12
12
12
N
1
3.71
0.50
106.80
110.51
A
A
A
O4'
C1'
C2'
DG
DG
DG
12
12
12
N
1
3.33
0.50
111.90
115.23
A
A
A
C2
N3
C4
DG
DG
DG
12
12
12
N
1
-4.92
0.80
109.40
104.48
B
B
B
O5'
C5'
C4'
DC
DC
DC
13
13
13
N
1
-2.46
0.40
121.90
119.44
B
B
B
N3
C4
C5
DC
DC
DC
13
13
13
N
1
3.81
0.60
118.90
122.71
B
B
B
N1
C2
O2
DC
DC
DC
13
13
13
N
1
-6.26
0.80
109.40
103.14
B
B
B
O5'
C5'
C4'
DG
DG
DG
14
14
14
N
1
4.28
0.60
106.00
110.28
B
B
B
O4'
C4'
C3'
DG
DG
DG
14
14
14
N
1
-6.08
1.00
110.10
104.02
B
B
B
C1'
O4'
C4'
DG
DG
DG
14
14
14
N
1
13.89
1.20
119.70
133.59
B
B
B
C3'
O3'
P
DG
DG
DC
14
14
15
Y
1
1.92
0.30
108.30
110.22
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
21.88
1.20
119.70
141.58
B
B
B
C3'
O3'
P
DC
DC
DG
15
15
16
Y
1
-5.55
0.80
102.40
96.85
B
B
B
C3'
C2'
C1'
DG
DG
DG
16
16
16
N
1
2.70
0.30
108.30
111.00
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
1
-4.94
0.60
125.10
120.16
B
B
B
C6
N1
C2
DG
DG
DG
16
16
16
N
1
3.99
0.50
111.50
115.49
B
B
B
C5
C6
N1
DG
DG
DG
16
16
16
N
1
-11.36
1.50
119.60
108.24
B
B
B
OP1
P
OP2
DA
DA
DA
17
17
17
N
1
11.98
1.20
110.70
122.68
B
B
B
O5'
P
OP2
DA
DA
DA
17
17
17
N
1
6.85
0.60
118.60
125.45
B
B
B
C6
N1
C2
DA
DA
DA
17
17
17
N
1
-5.55
0.50
129.30
123.75
B
B
B
N1
C2
N3
DA
DA
DA
17
17
17
N
1
-4.08
0.50
117.70
113.62
B
B
B
C5
C6
N1
DA
DA
DA
17
17
17
N
1
3.93
0.60
118.60
122.53
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
1
10.06
1.20
110.70
120.76
B
B
B
O5'
P
OP1
DA
DA
DA
18
18
18
N
1
12.06
1.20
115.70
127.76
B
B
B
C5'
C4'
C3'
DA
DA
DA
18
18
18
N
1
5.20
0.60
118.60
123.80
B
B
B
C6
N1
C2
DA
DA
DA
18
18
18
N
1
-5.83
0.50
129.30
123.47
B
B
B
N1
C2
N3
DA
DA
DA
18
18
18
N
1
-3.61
0.50
117.70
114.09
B
B
B
C5
C6
N1
DA
DA
DA
18
18
18
N
1
7.44
0.60
118.60
126.04
B
B
B
N1
C6
N6
DA
DA
DA
18
18
18
N
1
-5.70
0.80
109.40
103.70
B
B
B
O5'
C5'
C4'
DT
DT
DT
19
19
19
N
1
-7.79
1.00
110.10
102.31
B
B
B
C1'
O4'
C4'
DT
DT
DT
19
19
19
N
1
-4.53
0.60
127.20
122.67
B
B
B
C2
N3
C4
DT
DT
DT
19
19
19
N
1
-6.18
0.60
119.90
113.72
B
B
B
N3
C4
O4
DT
DT
DT
19
19
19
N
1
22.28
1.20
119.70
141.98
B
B
B
C3'
O3'
P
DT
DT
DT
19
19
20
Y
1
11.71
1.90
104.00
115.71
B
B
B
O3'
P
O5'
DT
DT
DT
19
20
20
Y
1
-6.32
1.00
110.10
103.78
B
B
B
C1'
O4'
C4'
DT
DT
DT
20
20
20
N
1
-4.92
0.60
127.20
122.28
B
B
B
C2
N3
C4
DT
DT
DT
20
20
20
N
1
5.17
0.60
115.20
120.37
B
B
B
N3
C4
C5
DT
DT
DT
20
20
20
N
1
-6.56
0.60
119.90
113.34
B
B
B
N3
C4
O4
DT
DT
DT
20
20
20
N
1
10.47
1.20
119.70
130.17
B
B
B
C3'
O3'
P
DT
DT
CBR
20
20
21
Y
1
7.41
1.20
119.70
127.11
B
B
B
C3'
O3'
P
CBR
CBR
DG
21
21
22
Y
1
-8.07
0.80
102.40
94.33
B
B
B
C3'
C2'
C1'
DG
DG
DG
22
22
22
N
1
4.53
0.30
108.30
112.83
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
-4.89
0.70
119.90
115.01
B
B
B
N3
C2
N2
DG
DG
DG
22
22
22
N
1
-4.41
0.60
128.60
124.19
B
B
B
C5
C6
O6
DG
DG
DG
22
22
22
N
1
-6.20
0.70
108.00
101.80
B
B
B
O4'
C1'
N1
DC
DC
DC
23
23
23
N
1
4.41
0.50
119.90
124.31
B
B
B
C2
N3
C4
DC
DC
DC
23
23
23
N
1
-4.25
0.40
121.90
117.65
B
B
B
N3
C4
C5
DC
DC
DC
23
23
23
N
1
16.38
1.60
120.90
137.28
B
B
B
P
O5'
C5'
DG
DG
DG
24
24
24
N
1
-4.68
0.70
108.00
103.32
B
B
B
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
-5.94
0.90
116.20
110.26
B
B
B
N1
C2
N2
DG
DG
DG
24
24
24
N
1
4.26
0.70
119.90
124.16
B
B
B
N3
C2
N2
DG
DG
DG
24
24
24
N
1
A
A
C2'
C1'
DC
DC
1
1
-0.069
0.010
1.518
1.449
N
1
A
A
O4'
C1'
DC
DC
1
1
0.068
0.011
1.420
1.488
N
1
A
A
O4'
C4'
DC
DC
1
1
-0.071
0.010
1.446
1.375
N
1
A
A
N7
C8
DG
DG
2
2
-0.038
0.006
1.305
1.267
N
1
A
A
C2'
C1'
DC
DC
3
3
-0.067
0.010
1.518
1.451
N
1
A
A
C4'
C3'
DG
DG
4
4
0.061
0.010
1.529
1.590
N
1
A
A
C2'
C1'
DA
DA
6
6
-0.090
0.010
1.518
1.428
N
1
A
A
O4'
C1'
DT
DT
7
7
0.067
0.011
1.420
1.487
N
1
A
A
O4'
C4'
DT
DT
7
7
-0.064
0.010
1.446
1.382
N
1
A
A
O4'
C1'
DT
DT
8
8
0.072
0.011
1.420
1.492
N
1
A
A
O3'
C3'
DT
DT
8
8
-0.038
0.006
1.419
1.381
N
1
A
A
C2'
C1'
DC
DC
11
11
-0.069
0.010
1.518
1.449
N
1
A
A
O4'
C1'
DC
DC
11
11
0.083
0.011
1.420
1.503
N
1
B
B
C5'
C4'
DG
DG
14
14
0.050
0.007
1.512
1.562
N
1
B
B
O4'
C1'
DG
DG
14
14
0.068
0.011
1.420
1.488
N
1
B
B
O3'
C3'
DC
DC
15
15
-0.039
0.006
1.419
1.380
N
1
B
B
N7
C8
DA
DA
17
17
-0.056
0.007
1.311
1.255
N
1
B
B
O3'
C3'
DT
DT
19
19
-0.063
0.006
1.419
1.356
N
1
B
B
C2'
C1'
DT
DT
20
20
-0.069
0.010
1.518
1.449
N
1
B
B
O4'
C4'
DG
DG
24
24
-0.071
0.010
1.446
1.375
N
0.252
0.163
2.250
8.000
2430
1
2.000
TR
isotropic
TR
isotropic
2.250
8.000
33
556
37
486
0
4.282
6.000
4.990
6.000
5.693
6.000
5.227
6.000
0.024
0.030
0.040
0.040
0.026
0.040
0.057
0.050
0.014
0.020
0.161
0.150
0.093
0.100
0.097
0.100
fix
fix
refinement
NUCLSQ
REFINEMENT OF NETROPSIN BOUND TO DNA: BIAS AND FEEDBACK IN ELECTRON DENSITY MAP INTERPRETATION
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
covale
1.624
both
A
DT
8
A
O3'
DT
8
1_555
A
CBR
9
A
P
CBR
9
1_555
covale
1.551
both
A
CBR
9
A
O3'
CBR
9
1_555
A
DG
10
A
P
DG
10
1_555
covale
1.578
both
B
DT
20
B
O3'
DT
8
1_555
B
CBR
21
B
P
CBR
9
1_555
covale
1.595
both
B
CBR
21
B
O3'
CBR
9
1_555
B
DG
22
B
P
DG
10
1_555
metalc
2.164
A
MG
26
C
MG
MG
1_555
A
HOH
61
E
O
HOH
1_555
metalc
2.101
A
MG
26
C
MG
MG
1_555
B
HOH
60
F
O
HOH
1_555
metalc
2.110
A
MG
26
C
MG
MG
1_555
B
HOH
62
F
O
HOH
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
101D
PDB
1
101D
1
12
101D
1
12
101D
A
1
1
12
13
24
101D
13
24
101D
B
1
1
12
BINDING SITE FOR RESIDUE NT B 25
B
NT
25
Software
9
BINDING SITE FOR RESIDUE MG A 26
A
MG
26
Software
3
A
DA
6
A
DA
6
9
1_555
A
DT
7
A
DT
7
9
1_555
A
DT
8
A
DT
8
9
1_555
B
DA
17
B
DA
5
9
1_555
B
DA
18
B
DA
6
9
1_555
B
DT
19
B
DT
7
9
1_555
B
DT
20
B
DT
8
9
1_555
B
CBR
21
B
CBR
9
9
1_555
B
DG
22
B
DG
10
9
1_555
A
HOH
61
E
HOH
3
1_555
B
HOH
60
F
HOH
3
1_555
B
HOH
62
F
HOH
3
1_555
19
P 21 21 21