0.035411
0.020444
0.000000
0.000000
0.040889
0.000000
0.000000
0.000000
0.013747
0.00000
0.00000
0.00000
Williams, L.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
28.240
28.240
72.744
C49 H56 N6 O2 2
761.008
1,3-DI[[[10-METHOXY-7H-PYRIDO[4,3-C]CARBAZOL-2-IUMYL]-ETHYL]-PIPERIDIN-4-YL]-PROPANE
BIS INTERCALATOR D232
non-polymer
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
Y
1
N
C
Y
2
N
N
Y
3
N
C
Y
4
N
C
Y
5
N
C
Y
6
N
C
Y
7
N
N
Y
8
N
C
Y
9
N
C
Y
10
N
C
Y
11
N
C
Y
12
N
C
Y
13
N
C
Y
14
N
C
Y
15
N
C
Y
16
N
C
N
17
N
C
Y
18
N
C
N
19
N
O
N
20
N
C
N
21
N
C
N
22
N
N
N
23
N
C
N
24
N
C
N
25
N
C
N
26
N
C
N
27
N
C
N
28
N
C
N
29
N
C
Y
30
N
C
Y
31
N
N
Y
32
N
C
Y
33
N
C
Y
34
N
C
Y
35
N
C
Y
36
N
N
Y
37
N
C
Y
38
N
C
Y
39
N
C
Y
40
N
C
Y
41
N
C
Y
42
N
C
Y
43
N
C
Y
44
N
C
Y
45
N
C
N
46
N
C
Y
47
N
C
N
48
N
O
N
49
N
C
N
50
N
C
N
51
N
N
N
52
N
C
N
53
N
C
N
54
N
C
N
55
N
C
N
56
N
C
N
57
N
C
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
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
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
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
O
N
115
N
P
N
116
N
O
N
117
N
O
N
118
N
O
N
119
N
C
N
120
R
C
N
121
N
O
N
122
S
C
N
123
N
O
N
124
N
C
N
125
R
C
Y
126
N
N
Y
127
N
C
Y
128
N
N
Y
129
N
C
Y
130
N
C
N
131
N
N
Y
132
N
N
Y
133
N
C
Y
134
N
N
Y
135
N
C
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
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
O
N
151
N
P
N
152
N
O
N
153
N
O
N
154
N
O
N
155
N
C
N
156
R
C
N
157
N
O
N
158
S
C
N
159
N
O
N
160
N
C
N
161
R
C
N
162
N
N
N
163
N
C
N
164
N
O
N
165
N
N
N
166
N
C
N
167
N
N
N
168
N
C
N
169
N
C
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
O
N
185
N
P
N
186
N
O
N
187
N
O
N
188
N
O
N
189
N
C
N
190
R
C
N
191
N
O
N
192
S
C
N
193
N
O
N
194
N
C
N
195
R
C
Y
196
N
N
Y
197
N
C
Y
198
N
N
Y
199
N
C
N
200
N
C
N
201
N
O
N
202
N
N
N
203
N
C
N
204
N
N
N
205
N
N
Y
206
N
C
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
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
O
N
222
N
P
N
223
N
O
N
224
N
O
N
225
N
O
N
226
N
C
N
227
R
C
N
228
N
O
N
229
S
C
N
230
N
O
N
231
N
C
N
232
R
C
N
233
N
N
N
234
N
C
N
235
N
O
N
236
N
N
N
237
N
C
N
238
N
O
N
239
N
C
N
240
N
C
N
241
N
C
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
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
Y
1
N
doub
Y
2
N
sing
N
3
N
sing
Y
4
N
sing
N
5
N
sing
Y
6
N
doub
N
7
N
sing
Y
8
N
sing
N
9
N
sing
Y
10
N
doub
Y
11
N
sing
N
12
N
sing
Y
13
N
sing
N
14
N
sing
Y
15
N
sing
Y
16
N
sing
N
17
N
sing
Y
18
N
doub
Y
19
N
sing
N
20
N
sing
Y
21
N
sing
N
22
N
sing
Y
23
N
sing
Y
24
N
doub
N
25
N
sing
Y
26
N
doub
Y
27
N
doub
Y
28
N
doub
Y
29
N
sing
Y
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
sing
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
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
Y
64
N
doub
Y
65
N
sing
N
66
N
sing
Y
67
N
sing
N
68
N
sing
Y
69
N
doub
N
70
N
sing
Y
71
N
sing
N
72
N
sing
Y
73
N
doub
Y
74
N
sing
N
75
N
sing
Y
76
N
sing
N
77
N
sing
Y
78
N
sing
Y
79
N
sing
N
80
N
sing
Y
81
N
doub
Y
82
N
sing
N
83
N
sing
Y
84
N
sing
N
85
N
sing
Y
86
N
sing
Y
87
N
doub
N
88
N
sing
Y
89
N
doub
Y
90
N
doub
Y
91
N
doub
Y
92
N
sing
Y
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
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
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
doub
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
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
Y
146
N
sing
Y
147
N
sing
Y
148
N
doub
N
149
N
sing
Y
150
N
sing
Y
151
N
sing
Y
152
N
doub
N
153
N
sing
Y
154
N
doub
N
155
N
sing
N
156
N
sing
Y
157
N
sing
Y
158
N
doub
N
159
N
sing
Y
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
doub
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
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
doub
N
187
N
sing
N
188
N
doub
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
doub
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
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
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
Y
219
N
sing
Y
220
N
sing
Y
221
N
doub
N
222
N
sing
Y
223
N
sing
N
224
N
sing
Y
225
N
doub
N
226
N
doub
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
doub
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
doub
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
doub
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
doub
N
265
N
sing
N
266
N
sing
N
267
N
doub
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
NE
Curr.Med.Chem.
0929-8673
7
59
71
10637357
Effects of cationic charge on three-dimensional structures of intercalative complexes: structure of a bis-intercalated DNA complex solved by MAD phasing.
2000
10.2210/pdb1c9z/pdb
pdb_00001c9z
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
300
1
AREA DETECTOR
1995-09-09
UCSD MARK II
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
COMPLEXED WITH BIS-INTERCALATOR D232
1809.217
5'-D(*CP*GP*TP*AP*CP*G)-3'
1
syn
polymer
761.008
1,3-DI[[[10-METHOXY-7H-PYRIDO[4,3-C]CARBAZOL-2-IUMYL]-ETHYL]-PIPERIDIN-4-YL]-PROPANE
1
syn
non-polymer
no
no
(DC)(DG)(DT)(DA)(DC)(DG)
CGTACG
A
polydeoxyribonucleotide
n
n
n
n
n
n
1
2.22
44.50
VAPOR DIFFUSION, SITTING DROP
6.0
MPD, SPERMINE, MAGNESIUM CHLORIDE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K
300
SPERMINE
1
MGCL2
1
SODIUM CACODYLATE
1
MPD
1
MPD
2
-6.552
1
19
A
1
A
6
0.943
A_DC1:DG6_A
1
-6.046
0.589
0.685
-0.378
-6.426
1
19
A
2
A
5
-4.641
A_DG2:DC5_A
2
-2.145
-0.252
0.131
-0.473
4.780
1
20
A
3
A
4
-9.422
A_DT3:DA4_A
3
-10.356
0.246
-0.145
-0.121
-4.780
1
20
A
4
A
3
-9.422
A_DA4:DT3_A
4
-10.356
-0.246
-0.145
-0.121
6.426
1
19
A
5
A
2
-4.641
A_DC5:DG2_A
5
-2.145
0.252
0.131
-0.473
6.553
1
19
A
6
A
1
0.943
A_DG6:DC1_A
6
-6.046
-0.589
0.685
-0.378
6.390
14.413
A
A
1
2
2.991
A
A
6
5
6.815
0.734
0.078
-0.098
AA_DC1DG2:DC5DG6_AA
1
5.112
-20.833
13.460
-1.768
9.295
3.129
34.907
A
A
2
3
-0.555
A
A
5
4
3.156
-0.333
-0.633
-0.218
AA_DG2DT3:DA4DC5_AA
2
1.495
-2.493
34.875
-0.315
1.273
3.671
38.509
A
A
3
4
14.770
A
A
4
3
3.597
9.645
0.000
0.747
AA_DT3DA4:DT3DA4_AA
3
0.000
0.000
37.326
-0.218
0.000
3.129
34.907
A
A
4
5
-0.555
A
A
3
2
3.156
-0.333
0.633
-0.218
AA_DA4DC5:DG2DT3_AA
4
-1.495
2.493
34.875
-0.315
-1.273
6.390
14.413
A
A
5
6
2.991
A
A
2
1
6.815
0.734
-0.078
-0.098
AA_DC5DG6:DC1DG2_AA
5
-5.112
20.833
13.460
-1.768
-9.294
chem_comp_atom
chem_comp_bond
database_2
pdbx_unobs_or_zero_occ_atoms
struct_conn
struct_site
pdbx_database_status
repository
Initial release
Version format compliance
Version format compliance
Database references
Advisory
Data collection
Database references
Derived calculations
Other
1
0
2000-04-02
1
1
2008-04-27
1
2
2011-07-13
1
3
2011-12-07
1
4
2024-02-07
1
5
2024-04-17
_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
_pdbx_database_status.status_code_sf
DITERCALINIUM-CGCG
RCSB
Y
RCSB
1999-08-03
REL
REL
232
1,3-DI[[[10-METHOXY-7H-PYRIDO[4,3-C]CARBAZOL-2-IUMYL]-ETHYL]-PIPERIDIN-4-YL]-PROPANE
SYNTHETIC
sample
232
7
2
232
232
7
A
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
T
3
n
3
DT
3
A
A
4
n
4
DA
4
A
C
5
n
5
DC
5
A
G
6
n
6
DG
6
A
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
11_556
-x+y,y,-z+3/2
crystal symmetry operation
0.0000000000
0.0000000000
109.1160000000
1
A
232
7
B
232
1
-7.98
0.80
109.40
101.42
A
A
A
O5'
C5'
C4'
DG
DG
DG
2
2
2
N
1
4.38
0.60
106.00
110.38
A
A
A
O4'
C4'
C3'
DG
DG
DG
2
2
2
N
1
-5.31
0.80
105.90
100.59
A
A
A
O4'
C1'
C2'
DT
DT
DT
3
3
3
N
1
-4.73
0.60
122.30
117.57
A
A
A
N3
C2
O2
DT
DT
DT
3
3
3
N
1
-5.93
0.70
108.00
102.07
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
3.59
0.50
129.30
132.89
A
A
A
N1
C2
N3
DA
DA
DA
4
4
4
N
1
-4.69
0.50
110.60
105.91
A
A
A
C2
N3
C4
DA
DA
DA
4
4
4
N
1
A
A
C5'
C4'
DC
DC
1
1
0.043
0.007
1.512
1.555
N
1
A
A
C4'
C3'
DG
DG
2
2
-0.064
0.010
1.521
1.457
N
1
A
A
C6
N1
DA
DA
4
4
-0.045
0.007
1.351
1.306
N
1
A
A
N9
C4
DA
DA
4
4
-0.044
0.006
1.374
1.330
N
0.1961000
0.1961000
0.1961000
2.4
10
99
5220
4682
90
RANDOM
1
4.
2.
PARKINSON ET AL.
2.4
10
0
149
29
120
0
21
2.4
10.0
1C9Z
5220
4698
2.0
4.0
0.0510000
1
9.2
3.2
91
0.0600000
2.4
2.51
1
4.2
84
phasing
MADSYS
refinement
X-PLOR
3.851
data reduction
SDMS
data scaling
SDMS
D232-CGTACG
1
N
N
2
N
N
covale
1.533
none
A
232
7
B
C27
232
1_555
A
232
7
B
C28
232
11_556
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
6
A
N1
DG
6
11_556
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
6
A
O6
DG
6
11_556
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
6
A
N2
DG
6
11_556
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
A
DC
5
A
N3
DC
5
11_556
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
A
DC
5
A
O2
DC
5
11_556
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
A
DC
5
A
N4
DC
5
11_556
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
A
DA
4
A
N1
DA
4
11_556
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
A
DA
4
A
N6
DA
4
11_556
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
A
DT
3
A
N3
DT
3
11_556
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
A
DT
3
A
O4
DT
3
11_556
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
A
DG
2
A
N1
DG
2
11_556
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
A
DG
2
A
O6
DG
2
11_556
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
A
DG
2
A
N2
DG
2
11_556
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
A
DC
1
A
N3
DC
1
11_556
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
A
DC
1
A
O2
DC
1
11_556
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
A
DC
1
A
N4
DC
1
11_556
DNA
DNA, INTERCALATOR, INTERCALATION, DRUG, MAJOR GROOVE
1C9Z
PDB
1
1C9Z
1
6
1C9Z
1
6
1C9Z
A
1
1
6
BINDING SITE FOR RESIDUE 232 A 7
A
232
7
Software
7
A
DC
1
A
DC
1
7
1_555
A
DG
2
A
DG
2
7
1_555
A
DT
3
A
DT
3
7
1_555
A
DA
4
A
DA
4
7
5_565
A
DC
5
A
DC
5
7
11_556
A
DG
6
A
DG
6
7
11_556
A
DG
6
A
DG
6
7
5_555
179
hexagonal
P 65 2 2