0.041034
0.000000
0.000000
0.000000
0.025000
0.000000
0.000000
0.000000
0.015135
0.00000
0.00000
0.00000
Edwards, K.J.
Jenkins, T.C.
Neidle, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
24.370
40.000
66.070
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
C19 H24 N4 O2
340.419
1,5-BIS(4-AMIDINOPHENOXY)PENTANE
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
O
N
145
N
H
N
146
N
H
Y
147
N
C
Y
148
N
C
Y
149
N
C
Y
150
N
C
Y
151
N
C
Y
152
N
C
N
153
N
C
N
154
N
C
N
155
N
C
N
156
N
C
Y
157
N
C
Y
158
N
C
Y
159
N
C
Y
160
N
C
Y
161
N
C
Y
162
N
C
N
163
N
C
N
164
N
C
N
165
N
C
N
166
N
O
N
167
N
O
N
168
N
N
N
169
N
N
N
170
N
N
N
171
N
N
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
H
N
188
N
H
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
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
sing
N
151
N
sing
Y
152
N
doub
Y
153
N
sing
N
154
N
sing
Y
155
N
sing
N
156
N
sing
Y
157
N
doub
N
158
N
sing
Y
159
N
sing
N
160
N
sing
Y
161
N
doub
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
doub
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
Y
176
N
doub
Y
177
N
sing
N
178
N
sing
Y
179
N
sing
N
180
N
sing
Y
181
N
doub
N
182
N
sing
Y
183
N
sing
N
184
N
sing
Y
185
N
doub
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
doub
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
US
Biochemistry
BICHAW
0033
0006-2960
31
7104
7109
10.1021/bi00146a011
1643044
Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties.
1992
10.2210/pdb1d64/pdb
pdb_00001d64
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
292.00
1
AREA DETECTOR
XENTRONICS
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
ENRAF-NONIUS FR571
3663.392
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
2
syn
polymer
340.419
1,5-BIS(4-AMIDINOPHENOXY)PENTANE
1
syn
non-polymer
18.015
water
77
nat
water
no
no
(DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)
CGCGAATTCGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
2.20
44.03
VAPOR DIFFUSION, SITTING DROP
7.00
pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 289.00K
289.00
WATER
1
MPD
1
MGCL2
1
NA CACODYLATE
1
WATER
2
MPD
2
11.361
1
19
A
1
B
24
-3.564
A_DC1:DG24_B
1
-15.897
0.322
-0.192
-0.225
-4.109
1
19
A
2
B
23
-1.474
A_DG2:DC23_B
2
-9.160
-0.159
0.092
-0.181
0.720
1
19
A
3
B
22
-1.090
A_DC3:DG22_B
3
-2.888
0.072
-0.053
-0.092
7.685
1
19
A
4
B
21
0.332
A_DG4:DC21_B
4
-12.913
-0.177
-0.137
-0.147
7.356
1
20
A
5
B
20
2.244
A_DA5:DT20_B
5
-16.360
0.145
-0.168
-0.166
-0.335
1
20
A
6
B
19
-1.274
A_DA6:DT19_B
6
-18.435
0.017
0.019
-0.074
1.713
1
20
A
7
B
18
2.173
A_DT7:DA18_B
7
-18.207
0.514
0.134
-0.203
0.097
1
20
A
8
B
17
-1.789
A_DT8:DA17_B
8
-19.318
0.372
-0.149
-0.170
-9.048
1
19
A
9
B
16
-0.127
A_DC9:DG16_B
9
-11.477
0.208
-0.277
-0.197
11.417
1
19
A
10
B
15
-0.125
A_DG10:DC15_B
10
-0.556
0.032
0.453
-0.104
2.827
1
19
A
11
B
14
-6.000
A_DC11:DG14_B
11
-31.284
-0.120
0.663
-0.278
10.723
1
19
A
12
B
13
-2.084
A_DG12:DC13_B
12
20.551
-0.177
-0.266
-0.130
3.725
34.240
A
A
1
2
11.333
B
B
24
23
3.728
6.628
-0.062
0.357
AA_DC1DG2:DC23DG24_BB
1
-2.254
3.854
33.538
-0.595
-0.304
3.200
41.778
A
A
2
3
-7.083
B
B
23
22
3.237
-5.033
0.775
0.625
AA_DG2DC3:DG22DC23_BB
2
3.956
-5.568
41.307
1.399
-0.676
3.392
31.511
A
A
3
4
16.541
B
B
22
21
3.321
8.833
-0.137
0.939
AA_DC3DG4:DC21DG22_BB
3
4.808
-9.002
29.902
-0.007
1.198
3.229
35.546
A
A
4
5
11.464
B
B
21
20
3.288
6.956
0.071
0.009
AA_DG4DA5:DT20DC21_BB
4
-0.209
0.345
34.880
-1.006
-0.146
3.446
36.764
A
A
5
6
3.095
B
B
20
19
3.480
1.950
0.020
-0.427
AA_DA5DA6:DT19DT20_BB
5
-2.185
3.468
36.651
-0.959
-0.347
3.233
33.228
A
A
6
7
2.030
B
B
19
18
3.249
1.161
0.309
-0.682
AA_DA6DT7:DA18DT19_BB
6
1.167
-2.042
33.188
-1.385
-0.347
3.128
37.206
A
A
7
8
9.554
B
B
18
17
3.198
6.068
-0.393
-0.043
AA_DT7DT8:DA17DA18_BB
7
1.912
-3.010
36.677
-0.853
0.864
3.502
35.375
A
A
8
9
-4.743
B
B
17
16
3.540
-2.879
-0.168
0.258
AA_DT8DC9:DG16DA17_BB
8
1.121
-1.848
35.244
0.882
0.454
2.953
33.245
A
A
9
10
5.262
B
B
16
15
3.065
2.975
0.400
1.103
AA_DC9DG10:DC15DG16_BB
9
-8.495
15.026
32.036
1.461
-2.032
3.464
41.900
A
A
10
11
-20.296
B
B
15
14
3.866
-14.247
-1.000
0.655
AA_DG10DC11:DG14DC15_BB
10
-1.107
1.577
39.491
2.636
1.265
3.298
38.689
A
A
11
12
-12.089
B
B
14
13
3.357
-7.926
1.096
0.597
AA_DC11DG12:DC13DG14_BB
11
5.994
-9.142
37.439
1.910
-0.892
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1993-01-15
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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
NDB
1992-03-02
REL
REL
PNT
1,5-BIS(4-AMIDINOPHENOXY)PENTANE
HOH
water
PNT
25
2
PNT
PNT
25
B
HOH
27
3
HOH
HOH
27
A
HOH
29
3
HOH
HOH
29
A
HOH
30
3
HOH
HOH
30
A
HOH
31
3
HOH
HOH
31
A
HOH
34
3
HOH
HOH
34
A
HOH
35
3
HOH
HOH
35
A
HOH
36
3
HOH
HOH
36
A
HOH
39
3
HOH
HOH
39
A
HOH
40
3
HOH
HOH
40
A
HOH
44
3
HOH
HOH
44
A
HOH
47
3
HOH
HOH
47
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
55
3
HOH
HOH
55
A
HOH
57
3
HOH
HOH
57
A
HOH
59
3
HOH
HOH
59
A
HOH
61
3
HOH
HOH
61
A
HOH
63
3
HOH
HOH
63
A
HOH
64
3
HOH
HOH
64
A
HOH
66
3
HOH
HOH
66
A
HOH
73
3
HOH
HOH
73
A
HOH
76
3
HOH
HOH
76
A
HOH
79
3
HOH
HOH
79
A
HOH
83
3
HOH
HOH
83
A
HOH
85
3
HOH
HOH
85
A
HOH
86
3
HOH
HOH
86
A
HOH
88
3
HOH
HOH
88
A
HOH
92
3
HOH
HOH
92
A
HOH
93
3
HOH
HOH
93
A
HOH
94
3
HOH
HOH
94
A
HOH
96
3
HOH
HOH
96
A
HOH
97
3
HOH
HOH
97
A
HOH
98
3
HOH
HOH
98
A
HOH
100
3
HOH
HOH
100
A
HOH
102
3
HOH
HOH
102
A
HOH
26
3
HOH
HOH
26
B
HOH
28
3
HOH
HOH
28
B
HOH
32
3
HOH
HOH
32
B
HOH
33
3
HOH
HOH
33
B
HOH
37
3
HOH
HOH
37
B
HOH
38
3
HOH
HOH
38
B
HOH
41
3
HOH
HOH
41
B
HOH
42
3
HOH
HOH
42
B
HOH
43
3
HOH
HOH
43
B
HOH
45
3
HOH
HOH
45
B
HOH
46
3
HOH
HOH
46
B
HOH
50
3
HOH
HOH
50
B
HOH
51
3
HOH
HOH
51
B
HOH
54
3
HOH
HOH
54
B
HOH
56
3
HOH
HOH
56
B
HOH
58
3
HOH
HOH
58
B
HOH
60
3
HOH
HOH
60
B
HOH
62
3
HOH
HOH
62
B
HOH
65
3
HOH
HOH
65
B
HOH
67
3
HOH
HOH
67
B
HOH
68
3
HOH
HOH
68
B
HOH
69
3
HOH
HOH
69
B
HOH
70
3
HOH
HOH
70
B
HOH
71
3
HOH
HOH
71
B
HOH
72
3
HOH
HOH
72
B
HOH
74
3
HOH
HOH
74
B
HOH
75
3
HOH
HOH
75
B
HOH
77
3
HOH
HOH
77
B
HOH
78
3
HOH
HOH
78
B
HOH
80
3
HOH
HOH
80
B
HOH
81
3
HOH
HOH
81
B
HOH
82
3
HOH
HOH
82
B
HOH
84
3
HOH
HOH
84
B
HOH
87
3
HOH
HOH
87
B
HOH
89
3
HOH
HOH
89
B
HOH
90
3
HOH
HOH
90
B
HOH
91
3
HOH
HOH
91
B
HOH
95
3
HOH
HOH
95
B
HOH
99
3
HOH
HOH
99
B
HOH
101
3
HOH
HOH
101
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
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
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
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
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
B
B
O
O
HOH
HOH
33
50
1.76
1
B
B
N7
O
DG
HOH
22
99
2.16
1
-9.49
0.80
109.40
99.91
A
A
A
O5'
C5'
C4'
DC
DC
DC
1
1
1
N
1
3.08
0.50
119.90
122.98
A
A
A
C2
N3
C4
DC
DC
DC
1
1
1
N
1
-3.49
0.40
121.90
118.41
A
A
A
N3
C4
C5
DC
DC
DC
1
1
1
N
1
4.58
0.60
118.90
123.48
A
A
A
N1
C2
O2
DC
DC
DC
1
1
1
N
1
6.08
0.70
118.00
124.08
A
A
A
N3
C4
N4
DC
DC
DC
1
1
1
N
1
21.56
1.20
119.70
141.26
A
A
A
C3'
O3'
P
DC
DC
DG
1
1
2
Y
1
-11.65
1.50
119.60
107.95
A
A
A
OP1
P
OP2
DG
DG
DG
2
2
2
N
1
2.45
0.30
108.30
110.75
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
8.72
1.20
110.70
119.42
A
A
A
O5'
P
OP2
DG
DG
DG
4
4
4
N
1
-3.85
0.60
125.10
121.25
A
A
A
C6
N1
C2
DG
DG
DG
4
4
4
N
1
-5.52
0.80
109.40
103.88
A
A
A
O5'
C5'
C4'
DA
DA
DA
5
5
5
N
1
7.95
0.60
118.60
126.55
A
A
A
C6
N1
C2
DA
DA
DA
5
5
5
N
1
-6.87
0.50
129.30
122.43
A
A
A
N1
C2
N3
DA
DA
DA
5
5
5
N
1
-4.88
0.50
117.70
112.82
A
A
A
C5
C6
N1
DA
DA
DA
5
5
5
N
1
9.42
1.20
119.70
129.12
A
A
A
C3'
O3'
P
DA
DA
DA
5
5
6
Y
1
1.94
0.30
108.30
110.24
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
5.50
0.60
118.60
124.10
A
A
A
C6
N1
C2
DA
DA
DA
6
6
6
N
1
-4.96
0.50
129.30
124.34
A
A
A
N1
C2
N3
DA
DA
DA
6
6
6
N
1
-3.59
0.50
117.70
114.11
A
A
A
C5
C6
N1
DA
DA
DA
6
6
6
N
1
-3.68
0.60
127.20
123.52
A
A
A
C2
N3
C4
DT
DT
DT
7
7
7
N
1
-7.88
0.60
119.90
112.02
A
A
A
N3
C4
O4
DT
DT
DT
7
7
7
N
1
4.49
0.70
124.90
129.39
A
A
A
C5
C4
O4
DT
DT
DT
7
7
7
N
1
-3.73
0.60
122.90
119.17
A
A
A
C6
C5
C7
DT
DT
DT
7
7
7
N
1
19.72
1.20
119.70
139.42
A
A
A
C3'
O3'
P
DT
DT
DT
7
7
8
Y
1
-7.25
0.80
109.40
102.15
A
A
A
O5'
C5'
C4'
DT
DT
DT
8
8
8
N
1
-5.49
0.80
105.90
100.41
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
1
3.95
0.60
114.60
118.55
A
A
A
N1
C2
N3
DT
DT
DT
8
8
8
N
1
-5.30
0.60
127.20
121.90
A
A
A
C2
N3
C4
DT
DT
DT
8
8
8
N
1
4.15
0.60
115.20
119.35
A
A
A
N3
C4
C5
DT
DT
DT
8
8
8
N
1
-4.71
0.60
119.90
115.19
A
A
A
N3
C4
O4
DT
DT
DT
8
8
8
N
1
15.12
1.20
110.70
125.82
A
A
A
O5'
P
OP1
DC
DC
DC
9
9
9
N
1
3.05
0.30
108.30
111.35
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
4.24
0.60
118.90
123.14
A
A
A
N1
C2
O2
DC
DC
DC
9
9
9
N
1
11.28
1.20
119.70
130.98
A
A
A
C3'
O3'
P
DC
DC
DG
9
9
10
Y
1
-8.40
0.80
102.40
94.00
A
A
A
C3'
C2'
C1'
DG
DG
DG
10
10
10
N
1
-4.96
0.70
119.90
114.94
A
A
A
N3
C2
N2
DG
DG
DG
10
10
10
N
1
3.90
0.30
108.30
112.20
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
7.23
1.20
119.70
126.93
A
A
A
C3'
O3'
P
DC
DC
DG
11
11
12
Y
1
9.89
1.60
120.90
130.79
A
A
A
P
O5'
C5'
DG
DG
DG
12
12
12
N
1
-5.66
0.80
109.40
103.74
B
B
B
O5'
C5'
C4'
DC
DC
DC
13
13
13
N
1
7.65
1.20
110.70
118.35
B
B
B
O5'
P
OP1
DG
DG
DG
14
14
14
N
1
-5.22
0.80
109.40
104.18
B
B
B
O5'
C5'
C4'
DG
DG
DG
14
14
14
N
1
4.14
0.50
106.80
110.94
B
B
B
O4'
C1'
C2'
DG
DG
DG
14
14
14
N
1
9.58
1.20
119.70
129.28
B
B
B
C3'
O3'
P
DG
DG
DC
14
14
15
Y
1
-9.33
0.80
109.40
100.07
B
B
B
O5'
C5'
C4'
DC
DC
DC
15
15
15
N
1
11.00
1.20
119.70
130.70
B
B
B
C3'
O3'
P
DC
DC
DG
15
15
16
Y
1
3.19
0.50
111.50
114.69
B
B
B
C5
C6
N1
DG
DG
DG
16
16
16
N
1
-2.73
0.40
104.50
101.77
B
B
B
O4'
C4'
C3'
DA
DA
DA
17
17
17
N
1
-6.77
0.70
102.20
95.43
B
B
B
C4'
C3'
C2'
DA
DA
DA
17
17
17
N
1
-10.22
0.80
102.40
92.18
B
B
B
C3'
C2'
C1'
DA
DA
DA
17
17
17
N
1
11.68
0.30
108.30
119.98
B
B
B
O4'
C1'
N9
DA
DA
DA
17
17
17
N
1
3.76
0.60
118.60
122.36
B
B
B
C6
N1
C2
DA
DA
DA
17
17
17
N
1
-3.34
0.50
129.30
125.96
B
B
B
N1
C2
N3
DA
DA
DA
17
17
17
N
1
3.67
0.60
118.60
122.27
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
1
4.51
0.60
118.60
123.11
B
B
B
C6
N1
C2
DA
DA
DA
18
18
18
N
1
-3.87
0.50
117.70
113.83
B
B
B
C5
C6
N1
DA
DA
DA
18
18
18
N
1
-14.95
1.60
120.90
105.95
B
B
B
P
O5'
C5'
DT
DT
DT
19
19
19
N
1
-5.40
0.80
105.90
100.50
B
B
B
O4'
C1'
C2'
DT
DT
DT
19
19
19
N
1
4.18
0.30
108.30
112.48
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
-5.08
0.60
127.20
122.12
B
B
B
C2
N3
C4
DT
DT
DT
19
19
19
N
1
3.68
0.60
115.20
118.88
B
B
B
N3
C4
C5
DT
DT
DT
19
19
19
N
1
18.01
1.20
119.70
137.71
B
B
B
C3'
O3'
P
DT
DT
DT
19
19
20
Y
1
-9.67
0.80
109.40
99.73
B
B
B
O5'
C5'
C4'
DT
DT
DT
20
20
20
N
1
-4.08
0.60
127.20
123.12
B
B
B
C2
N3
C4
DT
DT
DT
20
20
20
N
1
4.23
0.60
119.00
123.23
B
B
B
C4
C5
C7
DT
DT
DT
20
20
20
N
1
-4.37
0.60
122.90
118.53
B
B
B
C6
C5
C7
DT
DT
DT
20
20
20
N
1
23.67
1.20
119.70
143.37
B
B
B
C3'
O3'
P
DT
DT
DC
20
20
21
Y
1
-12.30
1.50
119.60
107.30
B
B
B
OP1
P
OP2
DC
DC
DC
21
21
21
N
1
8.47
1.20
110.70
119.17
B
B
B
O5'
P
OP2
DC
DC
DC
21
21
21
N
1
-8.94
0.80
109.40
100.46
B
B
B
O5'
C5'
C4'
DC
DC
DC
21
21
21
N
1
-5.21
0.70
108.00
102.79
B
B
B
O4'
C1'
N1
DC
DC
DC
21
21
21
N
1
-4.93
0.80
109.40
104.47
B
B
B
O5'
C5'
C4'
DG
DG
DG
22
22
22
N
1
-6.37
0.80
102.40
96.03
B
B
B
C3'
C2'
C1'
DG
DG
DG
22
22
22
N
1
3.81
0.30
108.30
112.11
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
-4.62
0.60
125.10
120.48
B
B
B
C6
N1
C2
DG
DG
DG
22
22
22
N
1
3.62
0.60
123.90
127.52
B
B
B
N1
C2
N3
DG
DG
DG
22
22
22
N
1
3.28
0.50
111.50
114.78
B
B
B
C5
C6
N1
DG
DG
DG
22
22
22
N
1
8.22
1.20
119.70
127.92
B
B
B
C3'
O3'
P
DG
DG
DC
22
22
23
Y
1
-14.94
1.60
120.90
105.96
B
B
B
P
O5'
C5'
DC
DC
DC
23
23
23
N
1
4.30
0.60
106.00
110.30
B
B
B
O4'
C4'
C3'
DC
DC
DC
23
23
23
N
1
A
A
O3'
P
DC
DG
1
2
-0.076
0.012
1.607
1.531
Y
1
A
A
P
OP1
DG
DG
2
2
0.104
0.017
1.485
1.589
N
1
A
A
O4'
C4'
DA
DA
5
5
-0.068
0.010
1.446
1.378
N
1
A
A
C5
C7
DT
DT
7
7
0.044
0.006
1.496
1.540
N
1
A
A
O4'
C4'
DT
DT
8
8
-0.061
0.010
1.446
1.385
N
1
A
A
P
O5'
DG
DG
10
10
0.074
0.010
1.593
1.667
N
1
B
B
C6
N1
DG
DG
14
14
-0.050
0.007
1.391
1.341
N
1
A
B
O
O
HOH
HOH
85
84
1.28
1_555
1_655
1
A
B
O
O
HOH
HOH
27
32
1.28
1_555
4_465
1
B
A
OP2
O
DT
HOH
19
83
2.04
1_555
4_565
1
B
A
O4'
O
DC
HOH
13
85
2.05
1_555
2_664
1
A
B
O
O
HOH
HOH
93
32
2.19
1_555
4_465
0.1940000
2.100
7.000
3113
1
2.000
TR
isotropic
TR
isotropic
TR
isotropic
2.100
7.000
77
588
25
486
0
0.017
0.030
0.032
0.041
fix
fix
fix
2.100
1D64
10630
3824
0.0699000
1
refinement
NUCLSQ
CRYSTAL STRUCTURE OF A PENTAMIDINE-OLIGONUCLEOTIDE COMPLEX: IMPLICATIONS FOR DNA-BINDING PROPERTIES
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
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
DC
21
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
21
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
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
DG
16
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
16
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
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, DNA
1D64
PDB
1
1D64
1
12
1D64
1
12
1D64
A
1
1
12
13
24
1D64
13
24
1D64
B
1
1
12
BINDING SITE FOR RESIDUE PNT B 25
B
PNT
25
Software
10
A
DA
5
A
DA
5
10
1_555
A
DA
6
A
DA
6
10
1_555
A
DT
7
A
DT
7
10
1_555
A
DT
8
A
DT
8
10
1_555
A
DC
9
A
DC
9
10
1_555
B
DA
17
B
DA
5
10
1_555
B
DA
18
B
DA
6
10
1_555
B
DT
19
B
DT
7
10
1_555
B
DT
20
B
DT
8
10
1_555
B
DC
21
B
DC
9
10
1_555
19
P 21 21 21