0.035112
0.000000
0.000000
0.000000
0.027693
0.000000
0.000000
0.000000
0.014368
0.00000
0.00000
0.00000
Gao, Y.-G.
Sriram, M.
Denny, W.A.
Wang, A.H.-J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
28.480
36.110
69.600
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
C29 H27 N5 O 2
461.558
1-METHYL-4-[4-[4-(4-(1-METHYLQUINOLINIUM)AMINO)BENZAMIDO]ANILINO]PYRIDINIUM
SN6999
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
Y
190
N
C
Y
191
N
C
Y
192
N
C
Y
193
N
C
Y
194
N
C
Y
195
N
C
Y
196
N
N
Y
197
N
C
Y
198
N
C
Y
199
N
C
N
200
N
N
Y
201
N
C
Y
202
N
C
Y
203
N
C
Y
204
N
C
Y
205
N
C
Y
206
N
C
N
207
N
C
N
208
N
O
N
209
N
N
Y
210
N
C
Y
211
N
C
Y
212
N
C
Y
213
N
C
Y
214
N
C
Y
215
N
C
N
216
N
N
Y
217
N
C
Y
218
N
C
Y
219
N
C
Y
220
N
N
Y
221
N
C
Y
222
N
C
N
223
N
C
N
224
N
C
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
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
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
Y
197
N
doub
Y
198
N
sing
N
199
N
sing
Y
200
N
sing
N
201
N
sing
Y
202
N
doub
Y
203
N
sing
Y
204
N
sing
Y
205
N
sing
Y
206
N
doub
N
207
N
sing
N
208
N
sing
Y
209
N
doub
N
210
N
sing
Y
211
N
sing
N
212
N
sing
Y
213
N
doub
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
Y
218
N
doub
Y
219
N
sing
Y
220
N
sing
N
221
N
sing
Y
222
N
doub
N
223
N
sing
Y
224
N
sing
N
225
N
sing
Y
226
N
doub
N
227
N
sing
N
228
N
sing
N
229
N
doub
N
230
N
sing
N
231
N
sing
N
232
N
sing
Y
233
N
doub
Y
234
N
sing
Y
235
N
sing
N
236
N
sing
Y
237
N
doub
N
238
N
sing
Y
239
N
sing
N
240
N
sing
Y
241
N
doub
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
Y
246
N
doub
Y
247
N
sing
Y
248
N
sing
N
249
N
sing
Y
250
N
doub
N
251
N
sing
Y
252
N
sing
N
253
N
sing
Y
254
N
doub
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
32
9639
9648
10.1021/bi00088a016
8373768
Minor groove binding of SN6999 to an alkylated DNA: molecular structure of d(CGC[e6G]AATTCGCG)-SN6999 complex.
1993
10.2210/pdb144d/pdb
pdb_0000144d
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
461.558
1-METHYL-4-[4-[4-(4-(1-METHYLQUINOLINIUM)AMINO)BENZAMIDO]ANILINO]PYRIDINIUM
1
syn
non-polymer
18.015
water
65
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
2.42
49.25
VAPOR DIFFUSION
7.00
pH 7.00, VAPOR DIFFUSION
ROOM TEMPERATURE
WATER
1
MPD
1
NA CACODYLATE
1
MGCL2
1
SPERMINE
1
NH4 ACETATE
1
WATER
2
MPD
2
-8.605
1
19
A
1
B
24
-2.868
A_DC1:DG24_B
1
-3.201
0.078
0.231
-0.056
4.582
1
19
A
2
B
23
-7.193
A_DG2:DC23_B
2
-17.716
0.290
0.167
-0.211
-7.193
1
19
A
3
B
22
-4.923
A_DC3:DG22_B
3
-6.780
0.001
0.469
-0.327
9.802
1
19
A
4
B
21
-7.061
A_G364:DC21_B
4
-6.525
-0.973
-0.019
-0.717
-1.022
1
20
A
5
B
20
3.633
A_DA5:DT20_B
5
-11.806
-0.528
0.015
-0.248
0.209
1
20
A
6
B
19
-4.025
A_DA6:DT19_B
6
-10.025
-0.189
-0.073
-0.098
8.900
1
20
A
7
B
18
1.174
A_DT7:DA18_B
7
-17.758
0.308
-0.219
-0.328
-11.682
1
20
A
8
B
17
2.909
A_DT8:DA17_B
8
-3.878
0.107
0.277
-0.167
-1.559
1
19
A
9
B
16
-4.312
A_DC9:G3616_B
9
-13.443
-1.093
0.106
-0.429
-4.128
1
19
A
10
B
15
1.808
A_DG10:DC15_B
10
-3.989
-0.629
0.099
-0.289
-5.013
1
19
A
11
B
14
-3.042
A_DC11:DG14_B
11
-13.543
0.108
0.498
-0.251
16.267
1
19
A
12
B
13
-4.538
A_DG12:DC13_B
12
-11.589
0.263
1.105
-0.220
3.334
31.987
A
A
1
2
-2.248
B
B
24
23
3.139
-1.226
-1.174
-0.193
AA_DC1DG2:DC23DG24_BB
1
-7.822
14.336
31.017
-0.128
0.708
3.697
41.252
A
A
2
3
-5.249
B
B
23
22
3.749
-3.694
1.023
0.650
AA_DG2DC3:DG22DC23_BB
2
0.744
-1.057
41.087
1.376
-1.361
3.028
23.661
A
A
3
4
8.983
B
B
22
21
3.238
3.646
-0.587
0.021
AA_DC3G364:DC21DG22_BB
3
4.640
-11.433
22.924
-1.129
2.933
3.505
40.565
A
A
4
5
-1.924
B
B
21
20
3.479
-1.334
1.063
0.269
AA_G364DA5:DT20DC21_BB
4
1.526
-2.203
40.516
0.547
-1.352
3.372
37.164
A
A
5
6
1.848
B
B
20
19
3.371
1.178
-0.217
0.142
AA_DA5DA6:DT19DT20_BB
5
0.313
-0.491
37.144
0.060
0.383
3.062
36.328
A
A
6
7
-0.203
B
B
19
18
3.023
-0.127
0.503
-0.694
AA_DA6DT7:DA18DT19_BB
6
4.193
-6.740
36.093
-1.097
-0.260
3.889
33.389
A
A
7
8
2.979
B
B
18
17
3.907
1.707
0.095
0.505
AA_DT7DT8:DA17DA18_BB
7
-4.038
7.048
33.108
0.541
-0.967
3.093
34.191
A
A
8
9
-3.979
B
B
17
16
3.032
-2.335
-1.201
0.396
AA_DT8DC9:G3616DA17_BB
8
-3.090
5.267
33.978
1.020
1.584
3.659
31.874
A
A
9
10
-1.064
B
B
16
15
3.736
-0.584
0.404
2.058
AA_DC9DG10:DC15G3616_BB
9
-2.411
4.395
31.780
3.867
-1.232
3.653
40.316
A
A
10
11
-5.692
B
B
15
14
3.671
-3.909
-0.804
0.734
AA_DG10DC11:DG14DC15_BB
10
-4.656
6.779
39.873
1.562
0.574
2.769
34.338
A
A
11
12
-9.333
B
B
14
13
2.810
-5.488
1.248
0.107
AA_DC11DG12:DC13DG14_BB
11
0.267
-0.454
33.908
0.919
-2.078
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
1995-05-30
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
1993-10-26
REL
SN6
1-METHYL-4-[4-[4-(4-(1-METHYLQUINOLINIUM)AMINO)BENZAMIDO]ANILINO]PYRIDINIUM
HOH
water
SN6
25
2
SN6
SN6
25
B
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
30
3
HOH
HOH
30
A
HOH
31
3
HOH
HOH
31
A
HOH
33
3
HOH
HOH
33
A
HOH
37
3
HOH
HOH
37
A
HOH
38
3
HOH
HOH
38
A
HOH
39
3
HOH
HOH
39
A
HOH
43
3
HOH
HOH
43
A
HOH
46
3
HOH
HOH
46
A
HOH
48
3
HOH
HOH
48
A
HOH
49
3
HOH
HOH
49
A
HOH
52
3
HOH
HOH
52
A
HOH
53
3
HOH
HOH
53
A
HOH
54
3
HOH
HOH
54
A
HOH
61
3
HOH
HOH
61
A
HOH
64
3
HOH
HOH
64
A
HOH
66
3
HOH
HOH
66
A
HOH
67
3
HOH
HOH
67
A
HOH
70
3
HOH
HOH
70
A
HOH
72
3
HOH
HOH
72
A
HOH
73
3
HOH
HOH
73
A
HOH
74
3
HOH
HOH
74
A
HOH
75
3
HOH
HOH
75
A
HOH
77
3
HOH
HOH
77
A
HOH
80
3
HOH
HOH
80
A
HOH
81
3
HOH
HOH
81
A
HOH
82
3
HOH
HOH
82
A
HOH
83
3
HOH
HOH
83
A
HOH
84
3
HOH
HOH
84
A
HOH
85
3
HOH
HOH
85
A
HOH
86
3
HOH
HOH
86
A
HOH
87
3
HOH
HOH
87
A
HOH
89
3
HOH
HOH
89
A
HOH
90
3
HOH
HOH
90
A
HOH
28
3
HOH
HOH
28
B
HOH
29
3
HOH
HOH
29
B
HOH
32
3
HOH
HOH
32
B
HOH
34
3
HOH
HOH
34
B
HOH
35
3
HOH
HOH
35
B
HOH
36
3
HOH
HOH
36
B
HOH
40
3
HOH
HOH
40
B
HOH
41
3
HOH
HOH
41
B
HOH
42
3
HOH
HOH
42
B
HOH
44
3
HOH
HOH
44
B
HOH
45
3
HOH
HOH
45
B
HOH
47
3
HOH
HOH
47
B
HOH
50
3
HOH
HOH
50
B
HOH
51
3
HOH
HOH
51
B
HOH
55
3
HOH
HOH
55
B
HOH
56
3
HOH
HOH
56
B
HOH
57
3
HOH
HOH
57
B
HOH
58
3
HOH
HOH
58
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
65
3
HOH
HOH
65
B
HOH
68
3
HOH
HOH
68
B
HOH
69
3
HOH
HOH
69
B
HOH
71
3
HOH
HOH
71
B
HOH
76
3
HOH
HOH
76
B
HOH
78
3
HOH
HOH
78
B
HOH
79
3
HOH
HOH
79
B
HOH
88
3
HOH
HOH
88
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
-6.56
0.40
104.50
97.94
A
A
A
O4'
C4'
C3'
DC
DC
DC
1
1
1
N
1
-6.72
0.80
102.40
95.68
A
A
A
C3'
C2'
C1'
DC
DC
DC
1
1
1
N
1
8.46
1.20
110.70
119.16
A
A
A
O5'
P
OP2
DG
DG
DG
2
2
2
N
1
3.61
0.30
108.30
111.91
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
-8.98
0.80
109.40
100.42
A
A
A
O5'
C5'
C4'
DC
DC
DC
3
3
3
N
1
-6.84
0.80
102.40
95.56
A
A
A
C3'
C2'
C1'
DC
DC
DC
3
3
3
N
1
10.78
0.30
108.30
119.08
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
3.48
0.50
121.00
124.48
A
A
A
C5
C6
N1
DC
DC
DC
3
3
3
N
1
5.09
0.70
121.90
126.99
A
A
A
N3
C2
O2
DC
DC
DC
3
3
3
N
1
6.00
0.70
118.00
124.00
A
A
A
N3
C4
N4
DC
DC
DC
3
3
3
N
1
-5.28
0.70
120.20
114.92
A
A
A
C5
C4
N4
DC
DC
DC
3
3
3
N
1
20.79
1.20
119.70
140.49
A
A
A
C3'
O3'
P
G36
G36
DA
4
4
5
Y
1
5.04
0.30
108.30
113.34
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
-3.99
0.50
129.30
125.31
A
A
A
N1
C2
N3
DA
DA
DA
5
5
5
N
1
10.65
1.20
119.70
130.35
A
A
A
C3'
O3'
P
DA
DA
DA
5
5
6
Y
1
-4.95
0.80
105.90
100.95
A
A
A
O4'
C1'
C2'
DA
DA
DA
6
6
6
N
1
4.51
0.60
118.60
123.11
A
A
A
N1
C6
N6
DA
DA
DA
6
6
6
N
1
8.02
1.20
110.70
118.72
A
A
A
O5'
P
OP2
DT
DT
DT
7
7
7
N
1
-3.38
0.50
121.30
117.92
A
A
A
C6
N1
C2
DT
DT
DT
7
7
7
N
1
9.11
1.50
120.40
129.51
A
A
A
C6
N1
C1'
DT
DT
DT
7
7
7
N
1
-10.22
1.60
120.90
110.68
A
A
A
P
O5'
C5'
DT
DT
DT
8
8
8
N
1
-5.10
0.70
102.20
97.10
A
A
A
C4'
C3'
C2'
DT
DT
DT
8
8
8
N
1
-5.02
0.80
102.40
97.38
A
A
A
C3'
C2'
C1'
DT
DT
DT
8
8
8
N
1
12.16
0.30
108.30
120.46
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
3.76
0.60
119.00
122.76
A
A
A
C4
C5
C7
DT
DT
DT
8
8
8
N
1
-9.50
1.50
119.60
110.10
A
A
A
OP1
P
OP2
DC
DC
DC
9
9
9
N
1
7.67
1.20
110.70
118.37
A
A
A
O5'
P
OP2
DC
DC
DC
9
9
9
N
1
-4.98
0.70
102.20
97.22
A
A
A
C4'
C3'
C2'
DC
DC
DC
9
9
9
N
1
6.21
0.30
108.30
114.51
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
3.67
0.50
121.00
124.67
A
A
A
C5
C6
N1
DC
DC
DC
9
9
9
N
1
10.02
1.20
119.70
129.72
A
A
A
C3'
O3'
P
DC
DC
DG
9
9
10
Y
1
7.61
1.20
110.70
118.31
A
A
A
O5'
P
OP2
DG
DG
DG
10
10
10
N
1
-14.51
1.60
120.90
106.39
A
A
A
P
O5'
C5'
DG
DG
DG
10
10
10
N
1
5.07
0.30
108.30
113.37
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
3.24
0.50
111.50
114.74
A
A
A
C5
C6
N1
DG
DG
DG
10
10
10
N
1
-4.24
0.60
128.60
124.36
A
A
A
C5
C6
O6
DG
DG
DG
10
10
10
N
1
13.56
0.30
108.30
121.86
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
-2.43
0.40
121.90
119.47
A
A
A
N3
C4
C5
DC
DC
DC
11
11
11
N
1
4.41
0.60
106.00
110.41
A
A
A
O4'
C4'
C3'
DG
DG
DG
12
12
12
N
1
-6.51
0.80
109.40
102.89
B
B
B
O5'
C5'
C4'
DC
DC
DC
13
13
13
N
1
-8.99
1.20
119.70
110.71
B
B
B
C3'
O3'
P
DC
DC
DG
13
13
14
Y
1
-9.33
1.50
119.60
110.27
B
B
B
OP1
P
OP2
DG
DG
DG
14
14
14
N
1
-9.51
0.80
109.40
99.89
B
B
B
O5'
C5'
C4'
DG
DG
DG
14
14
14
N
1
-8.33
0.70
108.00
99.67
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
36.69
1.20
119.70
156.39
B
B
B
C3'
O3'
P
G36
G36
DA
16
16
17
Y
1
13.53
1.90
104.00
117.53
B
B
B
O3'
P
O5'
G36
DA
DA
16
17
17
Y
1
-18.18
1.50
119.60
101.42
B
B
B
OP1
P
OP2
DA
DA
DA
17
17
17
N
1
6.16
0.30
108.30
114.46
B
B
B
O4'
C1'
N9
DA
DA
DA
17
17
17
N
1
3.70
0.60
118.60
122.30
B
B
B
C6
N1
C2
DA
DA
DA
17
17
17
N
1
-3.87
0.50
129.30
125.43
B
B
B
N1
C2
N3
DA
DA
DA
17
17
17
N
1
-3.61
0.50
117.70
114.09
B
B
B
C5
C6
N1
DA
DA
DA
17
17
17
N
1
24.94
1.20
119.70
144.64
B
B
B
C3'
O3'
P
DA
DA
DA
17
17
18
Y
1
-14.15
1.50
119.60
105.45
B
B
B
OP1
P
OP2
DA
DA
DA
18
18
18
N
1
-16.49
1.60
120.90
104.41
B
B
B
P
O5'
C5'
DA
DA
DA
18
18
18
N
1
-2.84
0.40
104.50
101.66
B
B
B
O4'
C4'
C3'
DA
DA
DA
18
18
18
N
1
-8.05
0.80
102.40
94.35
B
B
B
C3'
C2'
C1'
DA
DA
DA
18
18
18
N
1
-7.08
0.80
105.90
98.82
B
B
B
O4'
C1'
C2'
DA
DA
DA
18
18
18
N
1
5.64
0.30
108.30
113.94
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
5.26
0.60
118.60
123.86
B
B
B
C6
N1
C2
DA
DA
DA
18
18
18
N
1
-5.17
0.50
129.30
124.13
B
B
B
N1
C2
N3
DA
DA
DA
18
18
18
N
1
7.25
0.60
118.60
125.85
B
B
B
N1
C6
N6
DA
DA
DA
18
18
18
N
1
-9.72
0.80
109.40
99.68
B
B
B
O5'
C5'
C4'
DT
DT
DT
19
19
19
N
1
-10.08
1.60
120.90
110.82
B
B
B
P
O5'
C5'
DT
DT
DT
19
19
19
N
1
6.65
0.70
110.30
116.95
B
B
B
C1'
O4'
C4'
DT
DT
DT
19
19
19
N
1
-7.60
0.80
105.90
98.30
B
B
B
O4'
C1'
C2'
DT
DT
DT
19
19
19
N
1
4.88
0.60
114.60
119.48
B
B
B
N1
C2
N3
DT
DT
DT
19
19
19
N
1
-6.28
0.60
127.20
120.92
B
B
B
C2
N3
C4
DT
DT
DT
19
19
19
N
1
-5.70
0.60
122.30
116.60
B
B
B
N3
C2
O2
DT
DT
DT
19
19
19
N
1
-3.90
0.60
119.90
116.00
B
B
B
N3
C4
O4
DT
DT
DT
19
19
19
N
1
-7.21
1.20
119.70
112.49
B
B
B
C3'
O3'
P
DT
DT
DT
19
19
20
Y
1
12.71
1.10
110.50
123.21
B
B
B
O3'
P
OP1
DT
DT
DT
19
20
20
Y
1
-15.33
1.60
120.90
105.57
B
B
B
P
O5'
C5'
DT
DT
DT
20
20
20
N
1
7.60
1.20
115.70
123.30
B
B
B
C5'
C4'
C3'
DT
DT
DT
20
20
20
N
1
-2.84
0.40
104.50
101.66
B
B
B
O4'
C4'
C3'
DC
DC
DC
21
21
21
N
1
-6.04
0.80
102.40
96.36
B
B
B
C3'
C2'
C1'
DC
DC
DC
21
21
21
N
1
7.36
0.70
118.00
125.36
B
B
B
N3
C4
N4
DC
DC
DC
21
21
21
N
1
-5.64
0.70
120.20
114.56
B
B
B
C5
C4
N4
DC
DC
DC
21
21
21
N
1
-11.30
1.50
119.60
108.30
B
B
B
OP1
P
OP2
DG
DG
DG
22
22
22
N
1
10.39
1.60
120.90
131.29
B
B
B
P
O5'
C5'
DG
DG
DG
22
22
22
N
1
-6.19
0.80
105.90
99.71
B
B
B
O4'
C1'
C2'
DG
DG
DG
22
22
22
N
1
12.41
0.30
108.30
120.71
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
4.52
0.50
111.50
116.02
B
B
B
C5
C6
N1
DG
DG
DG
22
22
22
N
1
-3.91
0.60
119.90
115.99
B
B
B
N1
C6
O6
DG
DG
DG
22
22
22
N
1
-4.50
0.70
102.20
97.70
B
B
B
C4'
C3'
C2'
DC
DC
DC
23
23
23
N
1
3.55
0.50
119.90
123.45
B
B
B
C2
N3
C4
DC
DC
DC
23
23
23
N
1
-2.73
0.40
121.90
119.17
B
B
B
N3
C4
C5
DC
DC
DC
23
23
23
N
1
3.47
0.50
121.00
124.47
B
B
B
C5
C6
N1
DC
DC
DC
23
23
23
N
1
4.31
0.60
118.90
123.21
B
B
B
N1
C2
O2
DC
DC
DC
23
23
23
N
1
4.32
0.70
118.00
122.32
B
B
B
N3
C4
N4
DC
DC
DC
23
23
23
N
1
-8.70
0.80
109.40
100.70
B
B
B
O5'
C5'
C4'
DG
DG
DG
24
24
24
N
1
3.50
0.30
108.30
111.80
B
B
B
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
-4.06
0.60
125.10
121.04
B
B
B
C6
N1
C2
DG
DG
DG
24
24
24
N
1
3.22
0.50
111.50
114.72
B
B
B
C5
C6
N1
DG
DG
DG
24
24
24
N
1
A
A
C2'
C1'
DC
DC
3
3
0.065
0.010
1.519
1.584
N
1
A
A
O4'
C1'
DT
DT
7
7
0.077
0.011
1.420
1.497
N
1
A
A
P
O5'
DT
DT
8
8
0.074
0.010
1.593
1.667
N
1
A
A
C4'
C3'
DT
DT
8
8
0.073
0.010
1.529
1.602
N
1
A
A
P
O5'
DC
DC
11
11
0.076
0.010
1.593
1.669
N
1
A
A
C2'
C1'
DC
DC
11
11
0.065
0.010
1.519
1.584
N
1
B
B
O4'
C4'
DC
DC
13
13
-0.072
0.010
1.446
1.374
N
1
B
B
O5'
C5'
DG
DG
14
14
0.110
0.016
1.440
1.550
N
1
B
B
N3
C4
DC
DC
15
15
0.042
0.007
1.335
1.377
N
1
B
B
O3'
P
G36
DA
16
17
-0.157
0.012
1.607
1.450
Y
1
B
B
O3'
P
DA
DA
17
18
-0.095
0.012
1.607
1.512
Y
1
B
B
P
O5'
DA
DA
18
18
0.064
0.010
1.593
1.657
N
1
B
B
O4'
C4'
DT
DT
19
19
-0.072
0.010
1.446
1.374
N
1
B
B
P
O5'
DT
DT
20
20
0.099
0.010
1.593
1.692
N
1
B
B
OP1
O
DT
HOH
20
88
2.18
1_555
1_455
0.17
2.250
10.000
1618
1
2.000
TR
isotropic
TR
isotropic
2.250
10.000
65
590
39
486
0
fix
fix
2.250
144D
1618
2.000
1
refinement
NUCLSQ
MINOR GROOVE BINDING OF SN6999 TO AN ALKYLATED DNA: MOLECULAR STRUCTURE OF D(CGC[E6G]AATTCGCG)-SN6999 COMPLEX
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
1.567
one
A
G36
4
A
O3'
G36
4
1_555
A
DA
5
A
P
DA
5
1_555
covale
1.607
both
B
DC
15
B
O3'
DC
3
1_555
B
G36
16
B
P
G36
4
1_555
covale
1.450
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
144D
PDB
1
144D
1
12
144D
1
12
144D
A
1
1
12
13
24
144D
13
24
144D
B
1
1
12
BINDING SITE FOR RESIDUE SN6 B 25
B
SN6
25
Software
14
A
G36
4
A
G36
4
14
1_555
A
DA
5
A
DA
5
14
1_555
A
DA
6
A
DA
6
14
1_555
A
DT
7
A
DT
7
14
1_555
A
DT
8
A
DT
8
14
1_555
A
DC
9
A
DC
9
14
1_555
A
DG
12
A
DG
12
14
2_565
A
HOH
90
D
HOH
14
1_555
B
DA
18
B
DA
6
14
1_555
B
DT
19
B
DT
7
14
1_555
B
DT
20
B
DT
8
14
1_555
B
DC
21
B
DC
9
14
1_555
B
DG
22
B
DG
10
14
1_555
B
DC
23
B
DC
11
14
1_555
19
P 21 21 21