0.030066
0.000000
0.020456
0.000000
0.039920
0.000000
0.000000
0.000000
0.042739
0.00000
0.00000
0.00000
Deng, J.
Pan, B.
Sundaralingam, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
124.23
90.00
33.260
25.050
28.300
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 H13 N4 O7 P
332.207
y
2'-DEOXYINOSINE-5'-MONOPHOSPHATE
DNA linking
C22 H27 N9 O4
481.508
DISTAMYCIN A
DISTAMYCIN; STALLIMYCIN
non-polymer
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA 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
Y
92
N
C
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
C
N
107
N
O
N
108
N
N
Y
109
N
C
Y
110
N
C
Y
111
N
C
Y
112
N
N
Y
113
N
C
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
N
Y
118
N
C
Y
119
N
C
Y
120
N
C
Y
121
N
N
Y
122
N
C
N
123
N
C
N
124
N
C
N
125
N
O
N
126
N
N
Y
127
N
C
Y
128
N
C
Y
129
N
C
Y
130
N
N
Y
131
N
C
N
132
N
C
N
133
N
C
N
134
N
O
N
135
N
N
N
136
N
C
N
137
N
C
N
138
N
C
N
139
N
N
N
140
N
N
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
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
O
N
169
N
P
N
170
N
O
N
171
N
O
N
172
N
O
N
173
N
C
N
174
R
C
N
175
N
O
N
176
S
C
N
177
N
O
N
178
N
C
N
179
R
C
N
180
N
N
N
181
N
C
N
182
N
O
N
183
N
N
N
184
N
C
N
185
N
O
N
186
N
C
N
187
N
C
N
188
N
C
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
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
O
N
205
N
H
N
206
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
doub
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
Y
116
N
sing
Y
117
N
doub
Y
118
N
doub
N
119
N
sing
Y
120
N
sing
N
121
N
sing
Y
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
doub
N
129
N
sing
N
130
N
sing
N
131
N
sing
Y
132
N
sing
Y
133
N
doub
Y
134
N
doub
N
135
N
sing
Y
136
N
sing
N
137
N
sing
Y
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
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
Y
148
N
sing
Y
149
N
doub
Y
150
N
doub
N
151
N
sing
Y
152
N
sing
N
153
N
sing
Y
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
doub
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
doub
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
doub
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
sing
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
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
doub
N
205
N
sing
N
206
N
sing
N
207
N
doub
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
59
2342
2344
10.1107/S0907444903020730
14646114
Structure of d(ITITACAC) complexed with distamycin at 1.6 A resolution.
2003
10.2210/pdb1jux/pdb
pdb_00001jux
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298
1
IMAGE PLATE
1997-06-20
RIGAKU RAXIS IIC
graphite
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
Octamer DNA
2396.589
5'-D(*IP*TP*IP*TP*AP*CP*AP*C)-3'
1
syn
polymer
481.508
DISTAMYCIN A
1
syn
non-polymer
18.015
water
36
nat
water
no
no
(DI)(DT)(DI)(DT)(DA)(DC)(DA)(DC)
ITITACAC
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
1
1.96
37.09
2.540
1
20
A
2
A
7
4.810
A_DT2:DA7_A
1
-5.610
0.065
-0.039
-0.144
1.901
1
20
A
4
A
5
-3.163
A_DT4:DA5_A
2
-14.770
0.047
0.048
-0.127
-1.902
1
20
A
5
A
4
-3.163
A_DA5:DT4_A
3
-14.770
-0.047
0.048
-0.127
-2.540
1
20
A
7
A
2
4.810
A_DA7:DT2_A
4
-5.610
-0.065
-0.039
-0.144
6.963
69.697
A
A
2
4
11.133
A
A
7
5
6.730
12.663
-1.846
1.458
AA_DT2DT4:DA5DA7_AA
1
-4.109
3.612
68.572
0.314
1.303
2.685
49.735
A
A
4
5
-12.310
A
A
5
4
3.362
-10.287
0.000
3.154
AA_DT4DA5:DT4DA5_AA
2
0.000
0.000
48.726
4.455
0.000
6.963
69.697
A
A
5
7
11.133
A
A
4
2
6.730
12.663
1.846
1.458
AA_DA5DA7:DT2DT4_AA
3
4.109
-3.612
68.572
0.314
-1.303
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
2004-01-27
1
1
2008-04-27
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
DNA octamer d(IUATATAC) and Distamycin
RCSB
Y
RCSB
2001-08-28
REL
REL
DMY
DISTAMYCIN A
HOH
water
DMA
45
2
DMY
DMY
45
A
HOH
9
3
HOH
HOH
9
A
HOH
10
3
HOH
HOH
10
A
HOH
11
3
HOH
HOH
11
A
HOH
12
3
HOH
HOH
12
A
HOH
13
3
HOH
HOH
13
A
HOH
14
3
HOH
HOH
14
A
HOH
15
3
HOH
HOH
15
A
HOH
16
3
HOH
HOH
16
A
HOH
17
3
HOH
HOH
17
A
HOH
18
3
HOH
HOH
18
A
HOH
19
3
HOH
HOH
19
A
HOH
20
3
HOH
HOH
20
A
HOH
21
3
HOH
HOH
21
A
HOH
22
3
HOH
HOH
22
A
HOH
23
3
HOH
HOH
23
A
HOH
24
3
HOH
HOH
24
A
HOH
25
3
HOH
HOH
25
A
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
28
3
HOH
HOH
28
A
HOH
29
3
HOH
HOH
29
A
HOH
30
3
HOH
HOH
30
A
HOH
31
3
HOH
HOH
31
A
HOH
32
3
HOH
HOH
32
A
HOH
33
3
HOH
HOH
33
A
HOH
34
3
HOH
HOH
34
A
HOH
35
3
HOH
HOH
35
A
HOH
36
3
HOH
HOH
36
A
HOH
37
3
HOH
HOH
37
A
HOH
38
3
HOH
HOH
38
A
HOH
39
3
HOH
HOH
39
A
HOH
40
3
HOH
HOH
40
A
HOH
41
3
HOH
HOH
41
A
HOH
42
3
HOH
HOH
42
A
HOH
43
3
HOH
HOH
43
A
HOH
44
3
HOH
HOH
44
A
INO
1
n
1
DI
1
A
THY
2
n
2
DT
2
A
INO
3
n
3
DI
3
A
THY
4
n
4
DT
4
A
ADE
5
n
5
DA
5
A
CYT
6
n
6
DC
6
A
ADE
7
n
7
DA
7
A
CYT
8
n
8
DC
8
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
2_555
-x,y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1
A
DI
3
0.064
SIDE CHAIN
1
A
DA
5
0.068
SIDE CHAIN
0.179
0.149
1.6
10
234
2609
2468
94.6
random
1
2
MOLECULAR REPLACEMENT
1.6
10
36
230
35
159
0
1.60
10.00
1JUX
2609
2468
2.000
1
phasing
AMoRE
refinement
CNS
1.6A Resolution Crystal Structures of the DNA Octamers d(IUATATAC) and d(ITITACAC):Binding of Two Distamycin Drugs Side-by-Side
1
N
N
2
N
N
3
N
N
One strand in the assymetric unit.
The duplex is generated by the
2 fold axis.
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
A
DA
7
A
N1
DA
7
2_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
A
DA
7
A
N6
DA
7
2_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
A
DA
5
A
N1
DA
5
2_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
A
DA
5
A
N6
DA
5
2_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
A
DT
4
A
N3
DT
4
2_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
A
DT
4
A
O4
DT
4
2_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
A
DT
2
A
N3
DT
2
2_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
A
DT
2
A
O4
DT
2
2_555
DNA
DNA, Octamer, Distamycin, Side-by-Side
1JUX
PDB
1
1JUX
1
8
1JUX
1
8
1JUX
A
1
1
8
BINDING SITE FOR RESIDUE DMY A 45
A
DMY
45
Software
13
A
DT
2
A
DT
2
13
1_555
A
DI
3
A
DI
3
13
1_555
A
DT
4
A
DT
4
13
2_555
A
DA
5
A
DA
5
13
2_555
A
DC
6
A
DC
6
13
2_555
A
DA
7
A
DA
7
13
2_555
A
DC
8
A
DC
8
13
3_454
A
DC
8
A
DC
8
13
2_555
A
HOH
10
C
HOH
13
1_555
A
HOH
18
C
HOH
13
1_555
A
HOH
36
C
HOH
13
3_454
A
HOH
37
C
HOH
13
2_555
A
HOH
42
C
HOH
13
1_555
5
C 1 2 1