0.035651
0.000000
0.000000
0.000000
0.035651
0.000000
0.000000
0.000000
0.018811
0.00000
0.00000
0.00000
Shi, K.
Pan, B.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
28.05
28.05
53.16
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
C27 H29 N O10
527.520
DAUNOMYCIN
DAUNORUBICIN
non-polymer
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
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
Y
108
N
C
Y
109
N
C
Y
110
N
C
Y
111
N
C
N
112
N
O
Y
113
N
C
N
114
N
C
N
115
N
O
Y
116
N
C
Y
117
N
C
N
118
N
O
Y
119
N
C
N
120
S
C
N
121
N
O
N
122
N
C
N
123
S
C
N
124
N
O
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
C
Y
129
N
C
Y
130
N
C
N
131
N
O
Y
132
N
C
N
133
N
C
N
134
N
O
Y
135
N
C
N
136
N
C
N
137
R
C
N
138
N
C
N
139
S
C
N
140
N
N
N
141
S
C
N
142
N
O
N
143
S
C
N
144
N
O
N
145
N
C
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
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
O
N
176
N
P
N
177
N
O
N
178
N
O
N
179
N
O
N
180
N
C
N
181
R
C
N
182
N
O
N
183
S
C
N
184
N
O
N
185
N
C
N
186
R
C
N
187
N
N
N
188
N
C
N
189
N
O
N
190
N
N
N
191
N
C
N
192
N
O
N
193
N
C
N
194
N
C
N
195
N
C
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
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
O
N
212
N
P
N
213
N
O
N
214
N
O
N
215
N
O
N
216
N
C
N
217
R
C
N
218
N
O
N
219
S
C
N
220
N
O
N
221
R
C
N
222
N
O
N
223
R
C
Y
224
N
N
Y
225
N
C
Y
226
N
N
Y
227
N
C
N
228
N
C
N
229
N
O
N
230
N
N
N
231
N
C
N
232
N
N
N
233
N
N
Y
234
N
C
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
O
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
Y
113
N
doub
Y
114
N
sing
N
115
N
sing
Y
116
N
sing
N
117
N
sing
Y
118
N
doub
N
119
N
sing
N
120
N
sing
Y
121
N
sing
N
122
N
sing
N
123
N
sing
Y
124
N
doub
N
125
N
doub
N
126
N
sing
Y
127
N
doub
Y
128
N
sing
N
129
N
sing
Y
130
N
sing
N
131
N
sing
N
132
N
sing
Y
133
N
doub
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
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
Y
153
N
sing
N
154
N
sing
Y
155
N
doub
N
156
N
sing
N
157
N
sing
N
158
N
doub
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
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
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
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
doub
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
doub
N
214
N
sing
N
215
N
sing
N
216
N
doub
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
doub
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
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
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
Y
245
N
sing
Y
246
N
sing
Y
247
N
doub
N
248
N
sing
Y
249
N
sing
N
250
N
sing
Y
251
N
doub
N
252
N
doub
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
doub
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
59
1377
1383
10.1107/S0907444903011788
12876339
Structure of a B-form DNA/RNA chimera (dC)(rG)d(ATCG) complexed with daunomycin at 1.5 A resolution.
2003
10.2210/pdb1jo2/pdb
pdb_00001jo2
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
293.0
1
MIRRORS
IMAGE PLATE
1996-06-24
RIGAKU RAXIS IIC
GRAPHITE
SINGLE WAVELENGTH
M
x-ray
1
1.54
1.0
1.54
1.54
ROTATING ANODE
RIGAKU
1825.217
5'-D(*C)-R(P*G)-D(P*AP*TP*CP*G)-3'
1
syn
polymer
527.520
DAUNOMYCIN
1
syn
non-polymer
18.015
water
40
nat
water
no
no
(DC)G(DA)(DT)(DC)(DG)
CGATCG
A
polydeoxyribonucleotide/polyribonucleotide hybrid
n
n
n
n
n
n
1
2.77
55.55
EVAPORATION
7.00
magnesium chloride, cacodylate, MPD, pH 7.00, EVAPORATION, temperature 293K
293
MgCl2
1
cacodylate
1
MPD
1
8.887
1
19
A
1
A
6
-0.597
A_DC1:DG6_A
1
1.882
0.211
-0.021
-0.123
-20.355
1
19
A
2
A
5
2.014
A_G2:DC5_A
2
4.981
-0.201
-0.430
0.013
-9.746
1
20
A
3
A
4
1.760
A_DA3:DT4_A
3
-1.771
0.012
0.029
-0.130
9.746
1
20
A
4
A
3
1.760
A_DT4:DA3_A
4
-1.771
-0.012
0.029
-0.130
20.355
1
19
A
5
A
2
2.014
A_DC5:G2_A
5
4.981
0.201
-0.430
0.013
-8.887
1
19
A
6
A
1
-0.597
A_DG6:DC1_A
6
1.882
-0.211
-0.021
-0.123
7.048
33.904
A
A
1
2
-7.608
A
A
6
5
7.200
-4.423
1.366
1.166
AA_DC1G2:DC5DG6_AA
1
1.577
-2.713
33.587
3.555
-1.788
3.333
32.236
A
A
2
3
0.691
A
A
5
4
3.180
0.382
-1.363
0.369
AA_G2DA3:DT4DC5_AA
2
-4.255
7.686
31.959
0.597
1.697
2.880
32.537
A
A
3
4
7.230
A
A
4
3
2.974
4.041
0.000
-0.595
AA_DA3DT4:DA3DT4_AA
3
0.000
0.000
32.292
-1.697
0.000
3.333
32.236
A
A
4
5
0.690
A
A
3
2
3.180
0.382
1.363
0.369
AA_DT4DC5:G2DA3_AA
4
4.256
-7.686
31.959
0.597
-1.697
7.048
33.904
A
A
5
6
-7.608
A
A
2
1
7.200
-4.423
-1.366
1.166
AA_DC5DG6:DC1G2_AA
5
-1.577
2.713
33.587
3.555
1.788
software
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
1
0
2003-07-29
1
1
2008-04-01
1
2
2011-07-13
1
3
2017-10-04
1
4
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
RCSB
Y
RCSB
2001-07-26
REL
REL
DM1
DAUNOMYCIN
HOH
water
DM1
7
2
DM1
DM1
7
A
WAT
101
3
HOH
HOH
101
A
WAT
102
3
HOH
HOH
102
A
WAT
103
3
HOH
HOH
103
A
WAT
104
3
HOH
HOH
104
A
WAT
105
3
HOH
HOH
105
A
WAT
106
3
HOH
HOH
106
A
WAT
107
3
HOH
HOH
107
A
WAT
108
3
HOH
HOH
108
A
WAT
109
3
HOH
HOH
109
A
WAT
110
3
HOH
HOH
110
A
WAT
111
3
HOH
HOH
111
A
WAT
112
3
HOH
HOH
112
A
WAT
113
3
HOH
HOH
113
A
WAT
114
3
HOH
HOH
114
A
WAT
115
3
HOH
HOH
115
A
WAT
116
3
HOH
HOH
116
A
WAT
117
3
HOH
HOH
117
A
WAT
118
3
HOH
HOH
118
A
WAT
119
3
HOH
HOH
119
A
WAT
120
3
HOH
HOH
120
A
WAT
121
3
HOH
HOH
121
A
WAT
122
3
HOH
HOH
122
A
WAT
123
3
HOH
HOH
123
A
WAT
124
3
HOH
HOH
124
A
WAT
125
3
HOH
HOH
125
A
WAT
127
3
HOH
HOH
127
A
WAT
128
3
HOH
HOH
128
A
WAT
129
3
HOH
HOH
129
A
WAT
130
3
HOH
HOH
130
A
WAT
131
3
HOH
HOH
131
A
WAT
132
3
HOH
HOH
132
A
WAT
133
3
HOH
HOH
133
A
WAT
134
3
HOH
HOH
134
A
WAT
135
3
HOH
HOH
135
A
WAT
136
3
HOH
HOH
136
A
WAT
137
3
HOH
HOH
137
A
WAT
138
3
HOH
HOH
138
A
WAT
139
3
HOH
HOH
139
A
WAT
140
3
HOH
HOH
140
A
WAT
141
3
HOH
HOH
141
A
C
1
n
1
DC
1
A
G
2
n
2
G
2
A
A
3
n
3
DA
3
A
T
4
n
4
DT
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
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
8_665
-y+1,-x+1,-z+1/2
crystal symmetry operation
28.0500000000
28.0500000000
26.5800000000
1
A
DC
5
0.090
SIDE CHAIN
22.1
0.12
0.00
0.00
0.12
0.00
-0.24
0.233
0.015
0.198
1.50
10.00
256
2778
2699
10.00
74.3
RANDOM
2.00
2.00
1
THROUGHOUT
2.000
0.21
0.19
5.00
0.14
0.16
1.50
10.00
40
199
38
121
0
0.014
1.5
17.5
1.94
0.40
1.50
0.69
2.00
0.00
2.00
0.00
2.50
0.258
0.072
0.286
1.59
13
112
6
10.4
21.2
14.6
1.500
10.000
1JO2
2.0
1
data scaling
SCALEPACK
refinement
CNS
Crystal Structure of the B-DNA Hexamer (CgATCG).Daunomycin Complex Containing a Ribose at the Intercalation Site
1
N
N
2
N
N
3
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
6
A
N1
DG
6
8_665
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
6
A
O6
DG
6
8_665
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
6
A
N2
DG
6
8_665
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
A
DC
5
A
N3
DC
5
8_665
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
A
DC
5
A
O2
DC
5
8_665
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
A
DC
5
A
N4
DC
5
8_665
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
A
DT
4
A
N3
DT
4
8_665
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
A
DT
4
A
O4
DT
4
8_665
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
A
DA
3
A
N1
DA
3
8_665
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
A
DA
3
A
N6
DA
3
8_665
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
A
G
2
A
N1
G
2
8_665
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
A
G
2
A
O6
G
2
8_665
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
A
G
2
A
N2
G
2
8_665
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
A
DC
1
A
N3
DC
1
8_665
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
A
DC
1
A
O2
DC
1
8_665
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
A
DC
1
A
N4
DC
1
8_665
DNA, RNA
intercalation, DNA/RNA chimer, DNA, RNA
1JO2
PDB
1
1JO2
1
6
1JO2
1
6
1JO2
A
1
1
6
BINDING SITE FOR RESIDUE DM1 A 7
A
DM1
7
Software
12
A
DC
1
A
DC
1
12
1_555
A
G
2
A
G
2
12
1_555
A
DA
3
A
DA
3
12
1_555
A
DT
4
A
DT
4
12
8_665
A
DC
5
A
DC
5
12
8_665
A
DG
6
A
DG
6
12
8_665
A
HOH
102
C
HOH
12
1_555
A
HOH
110
C
HOH
12
1_555
A
HOH
111
C
HOH
12
1_555
A
HOH
113
C
HOH
12
1_555
A
HOH
123
C
HOH
12
1_555
A
HOH
135
C
HOH
12
1_555
92
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