0.039448
0.000000
0.000000
0.000000
0.024564
0.000000
0.000000
0.000000
0.015031
0.00000
0.00000
0.00000
Larsen, T.
Goodsell, D.S.
Cascio, D.
Grzeskowiak, K.
Dickerson, R.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
25.350
40.710
66.530
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C16 H15 N5
277.324
6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE
non-polymer
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
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
Y
37
N
N
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
N
47
N
N
N
48
N
N
Y
49
N
C
Y
50
N
C
Y
51
N
C
Y
52
N
C
Y
53
N
C
Y
54
N
C
N
55
N
C
N
56
N
N
N
57
N
N
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
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
N
C
N
84
R
C
N
85
N
N
N
86
N
C
N
87
N
O
N
88
N
N
N
89
N
C
N
90
N
N
N
91
N
C
N
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
H
N
107
N
O
N
108
N
P
N
109
N
O
N
110
N
O
N
111
N
O
N
112
N
C
N
113
R
C
N
114
N
O
N
115
S
C
N
116
N
O
N
117
N
C
N
118
R
C
Y
119
N
N
Y
120
N
C
Y
121
N
N
Y
122
N
C
N
123
N
C
N
124
N
O
N
125
N
N
N
126
N
C
N
127
N
N
N
128
N
N
Y
129
N
C
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
P
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
R
C
N
156
N
N
N
157
N
C
N
158
N
O
N
159
N
N
N
160
N
C
N
161
N
O
N
162
N
C
N
163
N
C
N
164
N
C
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
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
O
N
181
N
H
N
182
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
Y
39
N
sing
Y
40
N
sing
N
41
N
sing
Y
42
N
doub
Y
43
N
sing
Y
44
N
sing
N
45
N
sing
Y
46
N
doub
Y
47
N
sing
N
48
N
sing
Y
49
N
sing
N
50
N
sing
Y
51
N
doub
N
52
N
sing
Y
53
N
sing
N
54
N
sing
Y
55
N
doub
N
56
N
doub
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
Y
61
N
doub
Y
62
N
sing
Y
63
N
sing
N
64
N
sing
Y
65
N
doub
N
66
N
sing
Y
67
N
sing
N
68
N
sing
Y
69
N
doub
N
70
N
sing
N
71
N
sing
N
72
N
doub
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
doub
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
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
doub
N
103
N
sing
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
doub
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
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
Y
135
N
sing
Y
136
N
sing
Y
137
N
doub
N
138
N
sing
Y
139
N
sing
N
140
N
sing
Y
141
N
doub
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
doub
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
doub
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
doub
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
doub
N
181
N
sing
N
182
N
sing
N
183
N
doub
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
US
J.Biomol.Struct.Dyn.
JBSDD6
0646
0739-1102
7
477
491
2627296
The structure of DAPI bound to DNA.
1989
10.2210/pdb1d30/pdb
pdb_00001d30
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
AREA DETECTOR
SDMS
x-ray
1
1.0
3663.392
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
2
syn
polymer
277.324
6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE
1
syn
non-polymer
18.015
water
25
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
2.34
47.50
VAPOR DIFFUSION
7.00
pH 7.00, VAPOR DIFFUSION, temperature 277.00K
277.00
WATER
1
MPD
1
SPERMINE
1
MG ACETATE
1
WATER
2
MPD
2
6.150
1
19
A
1
B
24
0.316
A_DC1:DG24_B
1
-12.814
0.046
-0.153
-0.096
2.126
1
19
A
2
B
23
-2.226
A_DG2:DC23_B
2
-20.075
-0.346
0.307
-0.168
-3.141
1
19
A
3
B
22
-5.884
A_DC3:DG22_B
3
-14.431
-0.054
-0.175
-0.213
8.717
1
19
A
4
B
21
-8.995
A_DG4:DC21_B
4
-12.580
-0.055
0.035
-0.391
-0.510
1
20
A
5
B
20
1.733
A_DA5:DT20_B
5
-15.040
-0.102
-0.257
-0.004
8.983
1
20
A
6
B
19
-4.366
A_DA6:DT19_B
6
-22.142
-0.086
0.661
-0.027
-3.842
1
20
A
7
B
18
6.146
A_DT7:DA18_B
7
-23.837
-0.041
0.175
-0.152
-6.864
1
20
A
8
B
17
-2.771
A_DT8:DA17_B
8
-23.138
0.124
0.097
-0.505
-10.111
1
19
A
9
B
16
2.144
A_DC9:DG16_B
9
-12.539
0.148
-0.022
-0.353
8.738
1
19
A
10
B
15
-1.228
A_DG10:DC15_B
10
-6.153
-0.100
0.038
-0.199
1.173
1
19
A
11
B
14
-4.409
A_DC11:DG14_B
11
-16.315
0.098
0.173
-0.460
-3.065
1
19
A
12
B
13
-4.381
A_DG12:DC13_B
12
5.579
-0.059
-0.594
-0.433
3.536
37.897
A
A
1
2
10.790
B
B
24
23
3.546
6.951
-0.192
0.289
AA_DC1DG2:DC23DG24_BB
1
-4.983
7.734
36.954
-0.531
-0.405
3.412
41.062
A
A
2
3
-5.087
B
B
23
22
3.465
-3.553
0.194
0.421
AA_DG2DC3:DG22DC23_BB
2
5.857
-8.386
40.511
1.009
0.397
3.371
30.736
A
A
3
4
7.384
B
B
22
21
3.313
3.902
-0.189
0.629
AA_DC3DG4:DC21DG22_BB
3
-1.635
3.093
30.451
0.401
0.029
3.417
34.341
A
A
4
5
12.773
B
B
21
20
3.510
7.483
0.383
-0.118
AA_DG4DA5:DT20DC21_BB
4
1.331
-2.272
33.514
-1.456
-0.425
2.982
36.135
A
A
5
6
-2.170
B
B
20
19
3.002
-1.336
-0.170
-0.357
AA_DA5DA6:DT19DT20_BB
5
-7.794
12.661
35.288
-0.401
-0.745
3.595
36.758
A
A
6
7
2.372
B
B
19
18
3.604
1.490
0.450
-0.840
AA_DA6DT7:DA18DT19_BB
6
5.797
-9.231
36.284
-1.556
0.161
3.348
35.322
A
A
7
8
5.297
B
B
18
17
3.357
3.209
-0.658
-0.199
AA_DT7DT8:DA17DA18_BB
7
-1.332
2.199
35.156
-0.816
0.883
3.397
41.891
A
A
8
9
-7.890
B
B
17
16
3.452
-5.626
-0.027
0.211
AA_DT8DC9:DG16DA17_BB
8
-0.549
0.770
41.525
0.913
-0.023
3.179
24.609
A
A
9
10
4.291
B
B
16
15
3.117
1.827
0.305
0.943
AA_DC9DG10:DC15DG16_BB
9
0.110
-0.259
24.542
1.671
-0.682
3.569
42.531
A
A
10
11
-8.446
B
B
15
14
3.648
-6.105
-0.864
0.618
AA_DG10DC11:DG14DC15_BB
10
-2.283
3.159
42.052
1.538
0.935
3.668
39.312
A
A
11
12
-4.678
B
B
14
13
3.715
-3.128
0.580
1.045
AA_DC11DG12:DC13DG14_BB
11
7.217
-10.794
38.548
1.977
0.115
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
1992-04-15
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
1991-01-04
REL
REL
DAP
6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE
HOH
water
DAP
25
2
DAP
DAP
25
A
HOH
26
3
HOH
HOH
26
A
HOH
28
3
HOH
HOH
28
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
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
42
3
HOH
HOH
42
A
HOH
43
3
HOH
HOH
43
A
HOH
46
3
HOH
HOH
46
A
HOH
47
3
HOH
HOH
47
A
HOH
48
3
HOH
HOH
48
A
HOH
27
3
HOH
HOH
27
B
HOH
29
3
HOH
HOH
29
B
HOH
34
3
HOH
HOH
34
B
HOH
40
3
HOH
HOH
40
B
HOH
41
3
HOH
HOH
41
B
HOH
44
3
HOH
HOH
44
B
HOH
45
3
HOH
HOH
45
B
HOH
49
3
HOH
HOH
49
B
HOH
50
3
HOH
HOH
50
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
-12.32
0.40
104.50
92.18
A
A
A
O4'
C4'
C3'
DC
DC
DC
1
1
1
N
1
10.79
1.20
115.70
126.49
A
A
A
C5'
C4'
C3'
DC
DC
DC
1
1
1
N
1
4.95
0.70
110.30
115.25
A
A
A
C1'
O4'
C4'
DC
DC
DC
1
1
1
N
1
7.93
0.30
108.30
116.23
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
7.87
0.60
118.90
126.77
A
A
A
N1
C2
O2
DC
DC
DC
1
1
1
N
1
-8.84
0.70
121.90
113.06
A
A
A
N3
C2
O2
DC
DC
DC
1
1
1
N
1
-15.41
2.20
105.20
89.79
A
A
A
O3'
P
OP1
DC
DG
DG
1
2
2
Y
1
-6.82
0.80
109.40
102.58
A
A
A
O5'
C5'
C4'
DG
DG
DG
2
2
2
N
1
2.39
0.30
108.30
110.69
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
-10.17
0.90
116.20
106.03
A
A
A
N1
C2
N2
DG
DG
DG
2
2
2
N
1
7.79
0.70
119.90
127.69
A
A
A
N3
C2
N2
DG
DG
DG
2
2
2
N
1
-4.42
0.60
119.90
115.48
A
A
A
N1
C6
O6
DG
DG
DG
2
2
2
N
1
22.66
1.20
110.70
133.36
A
A
A
O5'
P
OP1
DC
DC
DC
3
3
3
N
1
-10.29
0.90
105.70
95.41
A
A
A
O5'
P
OP2
DC
DC
DC
3
3
3
N
1
7.60
1.20
115.70
123.30
A
A
A
C5'
C4'
C3'
DC
DC
DC
3
3
3
N
1
4.67
0.70
110.30
114.97
A
A
A
C1'
O4'
C4'
DC
DC
DC
3
3
3
N
1
-5.18
0.80
105.90
100.72
A
A
A
O4'
C1'
C2'
DC
DC
DC
3
3
3
N
1
5.27
0.30
108.30
113.57
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
3.03
0.50
121.00
124.03
A
A
A
C5
C6
N1
DC
DC
DC
3
3
3
N
1
6.10
0.60
118.90
125.00
A
A
A
N1
C2
O2
DC
DC
DC
3
3
3
N
1
-14.23
1.90
104.00
89.77
A
A
A
O3'
P
O5'
DC
DG
DG
3
4
4
Y
1
-13.90
2.20
105.20
91.30
A
A
A
O3'
P
OP1
DC
DG
DG
3
4
4
Y
1
14.47
1.50
119.60
134.07
A
A
A
OP1
P
OP2
DG
DG
DG
4
4
4
N
1
8.26
1.20
110.70
118.96
A
A
A
O5'
P
OP2
DG
DG
DG
4
4
4
N
1
6.69
1.10
109.80
116.49
A
A
A
C5'
C4'
O4'
DG
DG
DG
4
4
4
N
1
-5.51
0.80
105.90
100.39
A
A
A
O4'
C1'
C2'
DG
DG
DG
4
4
4
N
1
4.41
0.30
108.30
112.71
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
-3.47
0.50
111.90
108.43
A
A
A
C2
N3
C4
DG
DG
DG
4
4
4
N
1
3.09
0.50
128.60
131.69
A
A
A
N3
C4
C5
DG
DG
DG
4
4
4
N
1
3.46
0.40
110.80
114.26
A
A
A
C4
C5
N7
DG
DG
DG
4
4
4
N
1
-4.97
0.50
104.30
99.33
A
A
A
C5
N7
C8
DG
DG
DG
4
4
4
N
1
3.50
0.50
113.10
116.60
A
A
A
N7
C8
N9
DG
DG
DG
4
4
4
N
1
6.88
0.60
119.90
126.78
A
A
A
N1
C6
O6
DG
DG
DG
4
4
4
N
1
-5.43
0.60
128.60
123.17
A
A
A
C5
C6
O6
DG
DG
DG
4
4
4
N
1
-20.10
2.20
105.20
85.10
A
A
A
O3'
P
OP1
DG
DA
DA
4
5
5
Y
1
-5.25
0.80
109.40
104.15
A
A
A
O5'
C5'
C4'
DA
DA
DA
5
5
5
N
1
-5.15
0.80
105.90
100.75
A
A
A
O4'
C1'
C2'
DA
DA
DA
5
5
5
N
1
9.40
0.30
108.30
117.70
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
-4.42
0.50
129.30
124.88
A
A
A
N1
C2
N3
DA
DA
DA
5
5
5
N
1
4.35
0.50
110.60
114.95
A
A
A
C2
N3
C4
DA
DA
DA
5
5
5
N
1
-6.10
0.60
118.60
112.50
A
A
A
N1
C6
N6
DA
DA
DA
5
5
5
N
1
5.31
0.80
123.70
129.01
A
A
A
C5
C6
N6
DA
DA
DA
5
5
5
N
1
32.67
1.20
119.70
152.37
A
A
A
C3'
O3'
P
DA
DA
DA
5
5
6
Y
1
15.41
1.50
119.60
135.01
A
A
A
OP1
P
OP2
DA
DA
DA
6
6
6
N
1
-15.93
0.90
105.70
89.77
A
A
A
O5'
P
OP1
DA
DA
DA
6
6
6
N
1
7.66
0.30
108.30
115.96
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
2.60
0.40
105.80
108.40
A
A
A
N9
C4
C5
DA
DA
DA
6
6
6
N
1
-14.02
1.90
104.00
89.98
A
A
A
O3'
P
O5'
DA
DT
DT
6
7
7
Y
1
-18.18
2.20
105.20
87.02
A
A
A
O3'
P
OP1
DA
DT
DT
6
7
7
Y
1
32.67
1.50
119.60
152.27
A
A
A
OP1
P
OP2
DT
DT
DT
7
7
7
N
1
-5.68
0.90
105.70
100.02
A
A
A
O5'
P
OP1
DT
DT
DT
7
7
7
N
1
-8.91
0.80
105.90
96.99
A
A
A
O4'
C1'
C2'
DT
DT
DT
7
7
7
N
1
3.52
0.30
108.30
111.82
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
3.65
0.60
114.60
118.25
A
A
A
N1
C2
N3
DT
DT
DT
7
7
7
N
1
-6.14
0.60
127.20
121.06
A
A
A
C2
N3
C4
DT
DT
DT
7
7
7
N
1
3.94
0.60
115.20
119.14
A
A
A
N3
C4
C5
DT
DT
DT
7
7
7
N
1
-6.74
0.60
122.30
115.56
A
A
A
N3
C2
O2
DT
DT
DT
7
7
7
N
1
-4.29
0.70
124.90
120.61
A
A
A
C5
C4
O4
DT
DT
DT
7
7
7
N
1
12.18
1.20
119.70
131.88
A
A
A
C3'
O3'
P
DT
DT
DT
7
7
8
Y
1
19.76
1.50
119.60
139.36
A
A
A
OP1
P
OP2
DT
DT
DT
8
8
8
N
1
-7.05
0.80
109.40
102.35
A
A
A
O5'
C5'
C4'
DT
DT
DT
8
8
8
N
1
-8.55
0.80
105.90
97.35
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
1
4.82
0.30
108.30
113.12
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
-5.01
0.50
121.30
116.29
A
A
A
C6
N1
C2
DT
DT
DT
8
8
8
N
1
4.53
0.60
114.60
119.13
A
A
A
N1
C2
N3
DT
DT
DT
8
8
8
N
1
-3.85
0.60
127.20
123.35
A
A
A
C2
N3
C4
DT
DT
DT
8
8
8
N
1
-5.38
0.80
123.10
117.72
A
A
A
N1
C2
O2
DT
DT
DT
8
8
8
N
1
8.60
0.60
119.00
127.60
A
A
A
C4
C5
C7
DT
DT
DT
8
8
8
N
1
-8.12
0.60
122.90
114.78
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
1
27.48
1.20
119.70
147.18
A
A
A
C3'
O3'
P
DT
DT
DC
8
8
9
Y
1
18.67
1.50
119.60
138.27
A
A
A
OP1
P
OP2
DC
DC
DC
9
9
9
N
1
-7.57
0.80
109.40
101.83
A
A
A
O5'
C5'
C4'
DC
DC
DC
9
9
9
N
1
4.82
0.70
110.30
115.12
A
A
A
C1'
O4'
C4'
DC
DC
DC
9
9
9
N
1
7.91
1.20
102.50
110.41
A
A
A
C3'
C2'
C1'
DC
DC
DC
9
9
9
N
1
-13.02
0.80
105.90
92.88
A
A
A
O4'
C1'
C2'
DC
DC
DC
9
9
9
N
1
-10.93
0.70
108.00
97.07
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
-3.29
0.40
121.90
118.61
A
A
A
N3
C4
C5
DC
DC
DC
9
9
9
N
1
-3.84
0.40
104.50
100.66
A
A
A
O4'
C4'
C3'
DG
DG
DG
10
10
10
N
1
-5.28
0.70
102.20
96.92
A
A
A
C4'
C3'
C2'
DG
DG
DG
10
10
10
N
1
-5.12
0.80
102.40
97.28
A
A
A
C3'
C2'
C1'
DG
DG
DG
10
10
10
N
1
11.68
0.30
108.30
119.98
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
3.74
0.50
111.50
115.24
A
A
A
C5
C6
N1
DG
DG
DG
10
10
10
N
1
-11.93
0.90
105.70
93.77
A
A
A
O5'
P
OP1
DC
DC
DC
11
11
11
N
1
-10.55
1.60
120.90
110.35
A
A
A
P
O5'
C5'
DC
DC
DC
11
11
11
N
1
-6.41
0.80
105.90
99.49
A
A
A
O4'
C1'
C2'
DC
DC
DC
11
11
11
N
1
-7.48
0.70
108.00
100.52
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
-3.92
0.40
121.90
117.98
A
A
A
N3
C4
C5
DC
DC
DC
11
11
11
N
1
8.34
0.70
118.00
126.34
A
A
A
N3
C4
N4
DC
DC
DC
11
11
11
N
1
-4.54
0.70
120.20
115.66
A
A
A
C5
C4
N4
DC
DC
DC
11
11
11
N
1
13.91
1.50
119.60
133.51
A
A
A
OP1
P
OP2
DG
DG
DG
12
12
12
N
1
-8.74
0.80
109.40
100.66
A
A
A
O5'
C5'
C4'
DG
DG
DG
12
12
12
N
1
11.02
1.60
120.90
131.92
A
A
A
P
O5'
C5'
DG
DG
DG
12
12
12
N
1
3.60
0.50
106.80
110.40
A
A
A
O4'
C1'
C2'
DG
DG
DG
12
12
12
N
1
-4.99
0.60
125.10
120.11
A
A
A
C6
N1
C2
DG
DG
DG
12
12
12
N
1
4.48
0.50
111.50
115.98
A
A
A
C5
C6
N1
DG
DG
DG
12
12
12
N
1
-4.70
0.60
119.90
115.20
A
A
A
N1
C6
O6
DG
DG
DG
12
12
12
N
1
-7.80
0.80
109.40
101.60
B
B
B
O5'
C5'
C4'
DC
DC
DC
13
13
13
N
1
-6.81
0.80
105.90
99.09
B
B
B
O4'
C1'
C2'
DC
DC
DC
13
13
13
N
1
-8.52
0.70
108.00
99.48
B
B
B
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
3.10
0.50
119.90
123.00
B
B
B
C2
N3
C4
DC
DC
DC
13
13
13
N
1
5.55
0.70
121.90
127.45
B
B
B
N3
C2
O2
DC
DC
DC
13
13
13
N
1
6.93
0.70
118.00
124.93
B
B
B
N3
C4
N4
DC
DC
DC
13
13
13
N
1
-6.20
0.70
120.20
114.00
B
B
B
C5
C4
N4
DC
DC
DC
13
13
13
N
1
20.12
1.20
119.70
139.82
B
B
B
C3'
O3'
P
DC
DC
DG
13
13
14
Y
1
24.74
1.50
119.60
144.34
B
B
B
OP1
P
OP2
DG
DG
DG
14
14
14
N
1
-15.00
0.90
105.70
90.70
B
B
B
O5'
P
OP1
DG
DG
DG
14
14
14
N
1
-11.39
1.60
120.90
109.51
B
B
B
P
O5'
C5'
DG
DG
DG
14
14
14
N
1
5.23
0.60
106.00
111.23
B
B
B
O4'
C4'
C3'
DG
DG
DG
14
14
14
N
1
5.12
0.50
106.80
111.92
B
B
B
O4'
C1'
C2'
DG
DG
DG
14
14
14
N
1
8.47
1.10
110.50
118.97
B
B
B
O3'
P
OP2
DG
DC
DC
14
15
15
Y
1
17.98
1.50
119.60
137.58
B
B
B
OP1
P
OP2
DC
DC
DC
15
15
15
N
1
-7.87
0.90
105.70
97.83
B
B
B
O5'
P
OP1
DC
DC
DC
15
15
15
N
1
-8.81
0.80
105.90
97.09
B
B
B
O4'
C1'
C2'
DC
DC
DC
15
15
15
N
1
-5.79
0.70
108.00
102.21
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
3.25
0.50
121.00
124.25
B
B
B
C5
C6
N1
DC
DC
DC
15
15
15
N
1
7.94
1.10
110.50
118.44
B
B
B
O3'
P
OP2
DC
DG
DG
15
16
16
Y
1
4.91
0.30
108.30
113.21
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
1
3.94
0.50
111.50
115.44
B
B
B
C5
C6
N1
DG
DG
DG
16
16
16
N
1
-4.43
0.60
119.90
115.47
B
B
B
N1
C6
O6
DG
DG
DG
16
16
16
N
1
31.53
1.20
119.70
151.23
B
B
B
C3'
O3'
P
DG
DG
DA
16
16
17
Y
1
-9.48
1.50
119.60
110.12
B
B
B
OP1
P
OP2
DA
DA
DA
17
17
17
N
1
10.28
1.20
110.70
120.98
B
B
B
O5'
P
OP2
DA
DA
DA
17
17
17
N
1
6.71
1.10
109.80
116.51
B
B
B
C5'
C4'
O4'
DA
DA
DA
17
17
17
N
1
-5.37
0.80
105.90
100.53
B
B
B
O4'
C1'
C2'
DA
DA
DA
17
17
17
N
1
15.44
0.30
108.30
123.74
B
B
B
O4'
C1'
N9
DA
DA
DA
17
17
17
N
1
8.13
0.60
118.60
126.73
B
B
B
C6
N1
C2
DA
DA
DA
17
17
17
N
1
-9.30
0.50
129.30
120.00
B
B
B
N1
C2
N3
DA
DA
DA
17
17
17
N
1
4.40
0.50
110.60
115.00
B
B
B
C2
N3
C4
DA
DA
DA
17
17
17
N
1
-3.40
0.50
117.70
114.30
B
B
B
C5
C6
N1
DA
DA
DA
17
17
17
N
1
-4.51
0.50
103.90
99.39
B
B
B
C5
N7
C8
DA
DA
DA
17
17
17
N
1
4.13
0.50
113.80
117.93
B
B
B
N7
C8
N9
DA
DA
DA
17
17
17
N
1
7.52
0.60
118.60
126.12
B
B
B
N1
C6
N6
DA
DA
DA
17
17
17
N
1
10.05
1.20
119.70
129.75
B
B
B
C3'
O3'
P
DA
DA
DA
17
17
18
Y
1
13.98
1.20
110.70
124.68
B
B
B
O5'
P
OP2
DA
DA
DA
18
18
18
N
1
-5.34
0.40
104.50
99.16
B
B
B
O4'
C4'
C3'
DA
DA
DA
18
18
18
N
1
6.54
0.70
110.30
116.84
B
B
B
C1'
O4'
C4'
DA
DA
DA
18
18
18
N
1
-6.43
0.80
105.90
99.47
B
B
B
O4'
C1'
C2'
DA
DA
DA
18
18
18
N
1
15.20
0.30
108.30
123.50
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
5.48
0.60
118.60
124.08
B
B
B
C6
N1
C2
DA
DA
DA
18
18
18
N
1
-8.11
0.50
129.30
121.19
B
B
B
N1
C2
N3
DA
DA
DA
18
18
18
N
1
4.78
0.50
110.60
115.38
B
B
B
C2
N3
C4
DA
DA
DA
18
18
18
N
1
11.21
1.50
119.60
130.81
B
B
B
OP1
P
OP2
DT
DT
DT
19
19
19
N
1
-3.32
0.40
104.50
101.18
B
B
B
O4'
C4'
C3'
DT
DT
DT
19
19
19
N
1
-6.50
1.00
110.10
103.60
B
B
B
C1'
O4'
C4'
DT
DT
DT
19
19
19
N
1
3.67
0.60
114.60
118.27
B
B
B
N1
C2
N3
DT
DT
DT
19
19
19
N
1
-7.04
0.60
127.20
120.16
B
B
B
C2
N3
C4
DT
DT
DT
19
19
19
N
1
6.02
0.60
115.20
121.22
B
B
B
N3
C4
C5
DT
DT
DT
19
19
19
N
1
-4.44
0.60
119.90
115.46
B
B
B
N3
C4
O4
DT
DT
DT
19
19
19
N
1
5.96
0.60
119.00
124.96
B
B
B
C4
C5
C7
DT
DT
DT
19
19
19
N
1
-4.88
0.60
122.90
118.02
B
B
B
C6
C5
C7
DT
DT
DT
19
19
19
N
1
-5.54
0.90
105.70
100.16
B
B
B
O5'
P
OP2
DT
DT
DT
20
20
20
N
1
3.87
0.60
106.00
109.87
B
B
B
O4'
C4'
C3'
DT
DT
DT
20
20
20
N
1
-12.46
1.90
109.30
96.84
B
B
B
C5'
C4'
O4'
DT
DT
DT
20
20
20
N
1
-7.37
0.70
108.00
100.63
B
B
B
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
4.31
0.60
115.20
119.51
B
B
B
N3
C4
C5
DT
DT
DT
20
20
20
N
1
-6.19
0.70
124.90
118.71
B
B
B
C5
C4
O4
DT
DT
DT
20
20
20
N
1
21.87
1.20
119.70
141.57
B
B
B
C3'
O3'
P
DT
DT
DC
20
20
21
Y
1
7.93
1.10
110.50
118.43
B
B
B
O3'
P
OP2
DT
DC
DC
20
21
21
Y
1
-11.22
0.90
105.70
94.48
B
B
B
O5'
P
OP2
DC
DC
DC
21
21
21
N
1
-6.24
0.70
102.20
95.96
B
B
B
C4'
C3'
C2'
DC
DC
DC
21
21
21
N
1
-11.27
0.80
105.90
94.63
B
B
B
O4'
C1'
C2'
DC
DC
DC
21
21
21
N
1
3.06
0.50
119.90
122.96
B
B
B
C2
N3
C4
DC
DC
DC
21
21
21
N
1
-3.71
0.40
121.90
118.19
B
B
B
N3
C4
C5
DC
DC
DC
21
21
21
N
1
5.92
0.60
118.90
124.82
B
B
B
N1
C2
O2
DC
DC
DC
21
21
21
N
1
-4.34
0.70
121.90
117.56
B
B
B
N3
C2
O2
DC
DC
DC
21
21
21
N
1
11.38
1.10
109.80
121.18
B
B
B
C5'
C4'
O4'
DG
DG
DG
22
22
22
N
1
-5.32
0.80
102.40
97.08
B
B
B
C3'
C2'
C1'
DG
DG
DG
22
22
22
N
1
8.91
0.30
108.30
117.21
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
-10.16
0.90
116.20
106.04
B
B
B
N1
C2
N2
DG
DG
DG
22
22
22
N
1
9.07
0.70
119.90
128.97
B
B
B
N3
C2
N2
DG
DG
DG
22
22
22
N
1
12.54
1.50
119.60
132.14
B
B
B
OP1
P
OP2
DC
DC
DC
23
23
23
N
1
-5.72
0.90
105.70
99.98
B
B
B
O5'
P
OP1
DC
DC
DC
23
23
23
N
1
11.59
1.40
114.30
125.89
B
B
B
N1
C1'
C2'
DC
DC
DC
23
23
23
N
1
2.54
0.30
108.30
110.84
B
B
B
O4'
C1'
N1
DC
DC
DC
23
23
23
N
1
-2.53
0.40
120.30
117.77
B
B
B
C6
N1
C2
DC
DC
DC
23
23
23
N
1
5.14
0.50
121.00
126.14
B
B
B
C5
C6
N1
DC
DC
DC
23
23
23
N
1
-5.43
0.70
118.00
112.57
B
B
B
N3
C4
N4
DC
DC
DC
23
23
23
N
1
5.22
0.70
120.20
125.42
B
B
B
C5
C4
N4
DC
DC
DC
23
23
23
N
1
8.93
1.20
120.80
129.73
B
B
B
C6
N1
C1'
DC
DC
DC
23
23
23
N
1
-6.94
1.10
118.80
111.86
B
B
B
C2
N1
C1'
DC
DC
DC
23
23
23
N
1
-14.34
1.50
119.60
105.26
B
B
B
OP1
P
OP2
DG
DG
DG
24
24
24
N
1
12.35
1.20
110.70
123.05
B
B
B
O5'
P
OP2
DG
DG
DG
24
24
24
N
1
-4.28
0.40
104.50
100.22
B
B
B
O4'
C4'
C3'
DG
DG
DG
24
24
24
N
1
-5.53
0.70
102.20
96.67
B
B
B
C4'
C3'
C2'
DG
DG
DG
24
24
24
N
1
-5.02
0.80
102.40
97.38
B
B
B
C3'
C2'
C1'
DG
DG
DG
24
24
24
N
1
9.10
1.40
114.30
123.40
B
B
B
N9
C1'
C2'
DG
DG
DG
24
24
24
N
1
-7.70
0.70
108.00
100.30
B
B
B
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
-4.18
0.60
125.10
120.92
B
B
B
C6
N1
C2
DG
DG
DG
24
24
24
N
1
2.54
0.40
105.40
107.94
B
B
B
N9
C4
C5
DG
DG
DG
24
24
24
N
1
A
A
P
O5'
DG
DG
4
4
0.081
0.010
1.593
1.674
N
1
A
A
O3'
P
DG
DA
4
5
0.109
0.012
1.607
1.716
Y
1
A
A
C4
C5
DA
DA
6
6
-0.048
0.007
1.383
1.335
N
1
A
A
C5
N7
DA
DA
6
6
0.037
0.006
1.388
1.425
N
1
A
A
O3'
P
DA
DT
6
7
0.075
0.012
1.607
1.682
Y
1
A
A
O3'
C3'
DT
DT
7
7
-0.036
0.006
1.419
1.383
N
1
A
A
C4
O4
DT
DT
7
7
0.061
0.009
1.228
1.289
N
1
A
A
P
OP1
DT
DT
8
8
-0.149
0.017
1.485
1.336
N
1
A
A
P
O5'
DT
DT
8
8
0.091
0.010
1.593
1.684
N
1
A
A
O4'
C4'
DT
DT
8
8
-0.068
0.010
1.446
1.378
N
1
A
A
O3'
C3'
DT
DT
8
8
-0.049
0.006
1.419
1.370
N
1
A
A
N3
C4
DT
DT
8
8
-0.058
0.008
1.382
1.324
N
1
B
B
P
O5'
DG
DG
14
14
0.084
0.010
1.593
1.677
N
1
B
B
C6
N1
DG
DG
14
14
-0.052
0.007
1.391
1.339
N
1
B
B
C8
N9
DG
DG
14
14
-0.046
0.007
1.374
1.328
N
1
B
B
N1
C2
DC
DC
15
15
-0.067
0.010
1.397
1.330
N
1
B
B
O4'
C4'
DG
DG
16
16
-0.062
0.010
1.446
1.384
N
1
B
B
C2'
C1'
DT
DT
19
19
-0.063
0.010
1.518
1.455
N
1
B
B
C4
O4
DT
DT
19
19
0.055
0.009
1.228
1.283
N
1
B
B
C6
N1
DT
DT
20
20
-0.055
0.007
1.378
1.323
N
1
B
B
C4
O4
DT
DT
20
20
0.058
0.009
1.228
1.286
N
1
B
B
P
O5'
DG
DG
22
22
0.074
0.010
1.593
1.667
N
1
B
B
C5
N7
DG
DG
22
22
0.046
0.006
1.388
1.434
N
0.2220000
2.400
10.000
2541
1
2.000
TR
isotropic
TR
isotropic
2.400
10.000
25
532
21
486
0
fix
fix
2.400
1D30
9292
2541
1
refinement
NUCLSQ
THE STRUCTURE OF DAPI BOUND TO DNA
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
1D30
PDB
1
1D30
1
12
1D30
1
12
1D30
A
1
1
12
13
24
1D30
13
24
1D30
B
1
1
12
BINDING SITE FOR RESIDUE DAP A 25
A
DAP
25
Software
10
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
A
HOH
26
D
HOH
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