0.038986
0.000000
0.000000
0.000000
0.023793
0.000000
0.000000
0.000000
0.015307
0.00000
0.00000
0.00000
Tabernero, L.
Verdaguer, N.
Coll, M.
Fita, I.
Van Der Marel, G.A.
Van Boom, J.H.
Rich, A.
Aymami, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
25.650
42.030
65.330
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
C18 H26 N10 O3
430.464
NETROPSIN
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
N
147
N
C
N
148
N
N
N
149
N
N
N
150
N
N
N
151
N
C
N
152
N
C
N
153
N
O
N
154
N
N
Y
155
N
C
Y
156
N
C
Y
157
N
C
Y
158
N
N
N
159
N
C
Y
160
N
C
N
161
N
C
N
162
N
O
N
163
N
N
Y
164
N
C
Y
165
N
C
Y
166
N
C
Y
167
N
N
N
168
N
C
Y
169
N
C
N
170
N
C
N
171
N
O
N
172
N
N
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
N
N
177
N
N
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
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
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
N
152
N
doub
N
153
N
sing
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
doub
N
164
N
sing
N
165
N
sing
N
166
N
sing
Y
167
N
sing
Y
168
N
doub
Y
169
N
doub
N
170
N
sing
Y
171
N
sing
N
172
N
sing
N
173
N
sing
Y
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
Y
183
N
sing
Y
184
N
doub
Y
185
N
doub
N
186
N
sing
Y
187
N
sing
N
188
N
sing
N
189
N
sing
Y
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
doub
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
doub
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
32
8403
8410
10.1021/bi00084a004
8395202
Molecular structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor groove binding drug netropsin.
1993
10.2210/pdb121d/pdb
pdb_0000121d
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
DIFFRACTOMETER
ENRAF-NONIUS CAD4
x-ray
1
1.0
ROTATING ANODE
ELLIOTT GX-21
3662.404
DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')
2
syn
polymer
430.464
NETROPSIN
1
syn
non-polymer
18.015
water
47
nat
water
no
no
(DC)(DG)(DC)(DA)(DA)(DA)(DT)(DT)(DT)(DG)(DC)(DG)
CGCAAATTTGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
2.40
48.83
VAPOR DIFFUSION
6.50
pH 6.50, VAPOR DIFFUSION
ROOM TEMPERATURE
WATER
1
MPD
1
NA CACODYLATE
1
MGCL2
1
SPERMINE
1
WATER
2
MPD
2
-6.543
1
19
A
1
B
24
-0.237
A_DC1:DG24_B
1
8.236
0.407
0.576
-0.467
-5.263
1
19
A
2
B
23
3.676
A_DG2:DC23_B
2
-21.980
-0.075
-0.051
0.032
-2.440
1
19
A
3
B
22
-2.446
A_DC3:DG22_B
3
-5.545
-0.166
-0.560
-0.207
-1.883
1
20
A
4
B
21
1.000
A_DA4:DT21_B
4
-1.149
0.282
1.151
-0.412
-9.974
1
20
A
5
B
20
-0.666
A_DA5:DT20_B
5
-12.168
0.434
0.306
-0.287
12.296
1
20
A
6
B
19
-11.071
A_DA6:DT19_B
6
-25.798
0.444
0.171
-0.162
-0.984
1
A
7
B
18
12.978
A_DT7:DA18_B
7
-12.041
-0.166
-0.030
0.174
-12.685
1
20
A
8
B
17
5.190
A_DT8:DA17_B
8
-16.903
-0.659
0.166
0.098
-23.609
1
20
A
9
B
16
-12.131
A_DT9:DA16_B
9
-14.498
-0.008
0.453
-0.273
-6.308
1
19
A
10
B
15
4.204
A_DG10:DC15_B
10
-16.514
-0.072
-0.367
-0.194
2.423
1
19
A
11
B
14
4.966
A_DC11:DG14_B
11
-23.798
1.358
-0.559
-0.658
16.235
1
19
A
12
B
13
-6.590
A_DG12:DC13_B
12
0.473
-0.652
0.330
-0.313
3.188
38.572
A
A
1
2
-0.891
B
B
24
23
3.278
-0.587
-0.422
0.525
AA_DC1DG2:DC23DG24_BB
1
5.167
-7.845
38.233
0.867
1.273
3.419
37.416
A
A
2
3
1.777
B
B
23
22
3.413
1.139
0.133
0.167
AA_DG2DC3:DG22DC23_BB
2
2.119
-3.306
37.341
0.105
0.085
3.641
34.506
A
A
3
4
15.658
B
B
22
21
3.715
8.975
-0.543
0.422
AA_DC3DA4:DT21DG22_BB
3
-12.634
22.042
30.925
-0.946
-1.417
3.424
32.980
A
A
4
5
-1.462
B
B
21
20
3.461
-0.830
-0.575
-0.257
AA_DA4DA5:DT20DT21_BB
4
2.137
-3.768
32.903
-0.304
1.395
2.719
40.711
A
A
5
6
-9.766
B
B
20
19
2.596
-6.752
-0.847
-0.507
AA_DA5DA6:DT19DT20_BB
5
-4.512
6.526
39.926
-0.116
0.807
3.466
29.634
A
A
6
7
5.657
B
B
19
18
3.425
2.881
1.187
-0.731
AA_DA6DT7:DA18DT19_BB
6
4.005
-7.866
29.229
-2.073
-1.425
3.774
35.068
A
A
7
8
5.431
B
B
18
17
3.744
3.267
-0.410
0.356
AA_DT7DT8:DA17DA18_BB
7
-1.522
2.530
34.888
0.026
0.417
3.766
43.449
A
A
8
9
-0.811
B
B
17
16
3.747
-0.600
-0.798
0.072
AA_DT8DT9:DA16DA17_BB
8
-1.256
1.696
43.427
0.164
0.938
2.920
33.290
A
A
9
10
-6.848
B
B
16
15
3.070
-3.914
0.718
1.350
AA_DT9DG10:DC15DA16_BB
9
1.266
-2.215
33.042
2.956
-1.060
2.652
45.383
A
A
10
11
-10.919
B
B
15
14
2.885
-8.367
-0.246
0.850
AA_DG10DC11:DG14DC15_BB
10
4.778
-6.235
44.401
1.737
0.681
3.040
29.196
A
A
11
12
11.147
B
B
14
13
3.022
5.568
0.217
0.687
AA_DC11DG12:DC13DG14_BB
11
-4.008
8.024
28.395
0.225
-1.249
diffrn_detector
pdbx_unobs_or_zero_occ_atoms
chem_comp_atom
chem_comp_bond
database_2
pdbx_unobs_or_zero_occ_atoms
struct_site
repository
Initial release
Version format compliance
Version format compliance
Advisory
Data collection
Advisory
Data collection
Database references
Derived calculations
1
0
1994-01-15
1
1
2008-05-22
1
2
2011-07-13
1
3
2018-04-18
1
4
2024-02-07
_diffrn_detector.detector
_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
1993-04-14
REL
NT
NETROPSIN
HOH
water
NT
25
2
NT
NT
25
A
HOH
27
3
HOH
HOH
27
A
HOH
28
3
HOH
HOH
28
A
HOH
29
3
HOH
HOH
29
A
HOH
32
3
HOH
HOH
32
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
42
3
HOH
HOH
42
A
HOH
43
3
HOH
HOH
43
A
HOH
45
3
HOH
HOH
45
A
HOH
46
3
HOH
HOH
46
A
HOH
47
3
HOH
HOH
47
A
HOH
51
3
HOH
HOH
51
A
HOH
54
3
HOH
HOH
54
A
HOH
57
3
HOH
HOH
57
A
HOH
58
3
HOH
HOH
58
A
HOH
60
3
HOH
HOH
60
A
HOH
61
3
HOH
HOH
61
A
HOH
65
3
HOH
HOH
65
A
HOH
67
3
HOH
HOH
67
A
HOH
68
3
HOH
HOH
68
A
HOH
69
3
HOH
HOH
69
A
HOH
70
3
HOH
HOH
70
A
HOH
71
3
HOH
HOH
71
A
HOH
72
3
HOH
HOH
72
A
HOH
26
3
HOH
HOH
26
B
HOH
30
3
HOH
HOH
30
B
HOH
31
3
HOH
HOH
31
B
HOH
33
3
HOH
HOH
33
B
HOH
40
3
HOH
HOH
40
B
HOH
41
3
HOH
HOH
41
B
HOH
44
3
HOH
HOH
44
B
HOH
48
3
HOH
HOH
48
B
HOH
49
3
HOH
HOH
49
B
HOH
50
3
HOH
HOH
50
B
HOH
52
3
HOH
HOH
52
B
HOH
53
3
HOH
HOH
53
B
HOH
55
3
HOH
HOH
55
B
HOH
56
3
HOH
HOH
56
B
HOH
59
3
HOH
HOH
59
B
HOH
62
3
HOH
HOH
62
B
HOH
63
3
HOH
HOH
63
B
HOH
64
3
HOH
HOH
64
B
HOH
66
3
HOH
HOH
66
B
DC
1
n
1
DC
1
A
DG
2
n
2
DG
2
A
DC
3
n
3
DC
3
A
DA
4
n
4
DA
4
A
DA
5
n
5
DA
5
A
DA
6
n
6
DA
6
A
DT
7
n
7
DT
7
A
DT
8
n
8
DT
8
A
DT
9
n
9
DT
9
A
DG
10
n
10
DG
10
A
DC
11
n
11
DC
11
A
DG
12
n
12
DG
12
A
DC
13
n
1
DC
13
B
DG
14
n
2
DG
14
B
DC
15
n
3
DC
15
B
DA
16
n
4
DA
16
B
DA
17
n
5
DA
17
B
DA
18
n
6
DA
18
B
DT
19
n
7
DT
19
B
DT
20
n
8
DT
20
B
DT
21
n
9
DT
21
B
DG
22
n
10
DG
22
B
DC
23
n
11
DC
23
B
DG
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
A
O2
DT
9
A
O2
DT
9
0
Y
1
A
DT
8
0.097
SIDE CHAIN
1
B
DG
14
0.060
SIDE CHAIN
1
-5.89
0.70
102.20
96.31
A
A
A
C4'
C3'
C2'
DC
DC
DC
1
1
1
N
1
-5.07
0.80
105.90
100.83
A
A
A
O4'
C1'
C2'
DC
DC
DC
1
1
1
N
1
4.54
0.60
118.90
123.44
A
A
A
N1
C2
O2
DC
DC
DC
1
1
1
N
1
-4.98
0.70
121.90
116.92
A
A
A
N3
C2
O2
DC
DC
DC
1
1
1
N
1
-11.62
1.90
112.60
100.98
A
A
A
N9
C1'
C2'
DG
DG
DG
2
2
2
N
1
14.11
0.30
108.30
122.41
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
3.95
0.50
113.10
117.05
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
-3.47
0.40
106.40
102.93
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
-4.10
0.40
104.50
100.40
A
A
A
O4'
C4'
C3'
DC
DC
DC
3
3
3
N
1
-5.04
0.80
105.90
100.86
A
A
A
O4'
C1'
C2'
DC
DC
DC
3
3
3
N
1
-5.91
0.80
105.90
99.99
A
A
A
O4'
C1'
C2'
DA
DA
DA
4
4
4
N
1
-3.05
0.40
105.80
102.75
A
A
A
C8
N9
C4
DA
DA
DA
4
4
4
N
1
3.44
0.30
108.30
111.74
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
12.00
1.20
119.70
131.70
A
A
A
C3'
O3'
P
DA
DA
DA
5
5
6
Y
1
-8.02
0.80
105.90
97.88
A
A
A
O4'
C1'
C2'
DT
DT
DT
7
7
7
N
1
3.29
0.30
108.30
111.59
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
3.99
0.60
118.00
121.99
A
A
A
C4
C5
C6
DT
DT
DT
7
7
7
N
1
-4.99
0.60
122.90
117.91
A
A
A
C6
C5
C7
DT
DT
DT
7
7
7
N
1
-4.13
0.40
104.50
100.37
A
A
A
O4'
C4'
C3'
DT
DT
DT
8
8
8
N
1
-4.48
0.70
108.00
103.52
A
A
A
O4'
C1'
N1
DT
DT
DT
9
9
9
N
1
7.25
1.10
109.80
117.05
A
A
A
C5'
C4'
O4'
DG
DG
DG
10
10
10
N
1
-2.58
0.40
106.40
103.82
A
A
A
C8
N9
C4
DG
DG
DG
10
10
10
N
1
-4.02
0.60
119.90
115.88
A
A
A
N1
C6
O6
DG
DG
DG
10
10
10
N
1
4.60
0.60
106.00
110.60
A
A
A
O4'
C4'
C3'
DC
DC
DC
11
11
11
N
1
5.79
0.60
118.90
124.69
A
A
A
N1
C2
O2
DC
DC
DC
11
11
11
N
1
-6.07
0.70
121.90
115.83
A
A
A
N3
C2
O2
DC
DC
DC
11
11
11
N
1
2.40
0.30
108.30
110.70
B
B
B
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
6.34
0.60
118.90
125.24
B
B
B
N1
C2
O2
DC
DC
DC
13
13
13
N
1
-4.33
0.70
121.90
117.57
B
B
B
N3
C2
O2
DC
DC
DC
13
13
13
N
1
-3.02
0.50
104.30
101.28
B
B
B
C5
N7
C8
DG
DG
DG
14
14
14
N
1
3.42
0.50
113.10
116.52
B
B
B
N7
C8
N9
DG
DG
DG
14
14
14
N
1
8.31
1.20
119.70
128.01
B
B
B
C3'
O3'
P
DG
DG
DC
14
14
15
Y
1
4.18
0.60
118.90
123.08
B
B
B
N1
C2
O2
DC
DC
DC
15
15
15
N
1
-10.86
1.60
120.90
110.04
B
B
B
P
O5'
C5'
DA
DA
DA
17
17
17
N
1
5.98
0.70
110.30
116.28
B
B
B
C1'
O4'
C4'
DA
DA
DA
17
17
17
N
1
-11.33
0.80
105.90
94.57
B
B
B
O4'
C1'
C2'
DA
DA
DA
17
17
17
N
1
3.16
0.50
113.80
116.96
B
B
B
N7
C8
N9
DA
DA
DA
17
17
17
N
1
-5.19
0.80
105.90
100.71
B
B
B
O4'
C1'
C2'
DA
DA
DA
18
18
18
N
1
3.49
0.30
108.30
111.79
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
-3.25
0.40
105.80
102.55
B
B
B
C8
N9
C4
DA
DA
DA
18
18
18
N
1
-3.22
0.40
104.50
101.28
B
B
B
O4'
C4'
C3'
DT
DT
DT
19
19
19
N
1
-8.83
1.00
110.10
101.27
B
B
B
C1'
O4'
C4'
DT
DT
DT
19
19
19
N
1
-5.52
0.80
105.90
100.38
B
B
B
O4'
C1'
C2'
DT
DT
DT
19
19
19
N
1
-4.83
0.80
105.90
101.07
B
B
B
O4'
C1'
C2'
DT
DT
DT
20
20
20
N
1
-7.16
0.70
108.00
100.84
B
B
B
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
3.97
0.60
118.00
121.97
B
B
B
C4
C5
C6
DT
DT
DT
20
20
20
N
1
6.83
1.10
109.80
116.63
B
B
B
C5'
C4'
O4'
DT
DT
DT
21
21
21
N
1
-6.11
0.80
105.90
99.79
B
B
B
O4'
C1'
C2'
DT
DT
DT
21
21
21
N
1
12.18
0.30
108.30
120.48
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
3.76
0.50
113.10
116.86
B
B
B
N7
C8
N9
DG
DG
DG
22
22
22
N
1
-2.87
0.40
106.40
103.53
B
B
B
C8
N9
C4
DG
DG
DG
22
22
22
N
1
-11.69
1.90
104.00
92.31
B
B
B
O3'
P
O5'
DG
DC
DC
22
23
23
Y
1
4.02
0.60
106.00
110.02
B
B
B
O4'
C4'
C3'
DC
DC
DC
23
23
23
N
1
3.77
0.60
118.90
122.67
B
B
B
N1
C2
O2
DC
DC
DC
23
23
23
N
1
A
A
C5'
C4'
DC
DC
1
1
0.053
0.007
1.512
1.565
N
1
A
A
C3'
C2'
DG
DG
2
2
-0.050
0.008
1.516
1.466
N
1
A
A
O3'
C3'
DG
DG
2
2
-0.051
0.006
1.419
1.368
N
1
A
A
O4'
C4'
DC
DC
3
3
-0.064
0.010
1.446
1.382
N
1
A
A
C4'
C3'
DT
DT
7
7
-0.082
0.010
1.521
1.439
N
1
A
A
C5
C7
DT
DT
9
9
0.047
0.006
1.496
1.543
N
1
A
A
C5'
C4'
DG
DG
10
10
0.055
0.007
1.512
1.567
N
1
A
A
C6
N1
DG
DG
10
10
-0.051
0.007
1.391
1.340
N
1
B
B
C4'
C3'
DT
DT
21
21
-0.111
0.010
1.521
1.410
N
1
B
B
C5
C7
DT
DT
21
21
0.058
0.006
1.496
1.554
N
0.1980000
0.1980000
2.200
8.000
2348
1
2.000
TR
isotropic
TR
isotropic
2.200
8.000
47
564
31
486
0
0.021
4.10
fix
fix
2.100
15.000
121D
2348
2.000
1
refinement
X-PLOR
MOLECULAR STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN
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
DA
4
A
N1
DA
4
1_555
B
DT
21
B
N3
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
21
B
O4
DT
9
1_555
hydrog
DA-DT PAIR
A
DA
5
A
N6
DA
5
1_555
B
DT
19
B
O4
DT
7
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
DT-DA PAIR
A
DT
7
A
N3
DT
7
1_555
B
DA
18
B
N1
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
DT
9
A
N3
DT
9
1_555
B
DA
16
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
16
B
N6
DA
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
121D
PDB
1
121D
1
12
121D
1
12
121D
A
1
1
12
13
24
121D
13
24
121D
B
1
1
12
BINDING SITE FOR RESIDUE NT A 25
A
NT
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
DT
9
A
DT
9
10
1_555
A
DG
10
A
DG
10
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
DT
21
B
DT
9
10
1_555
19
P 21 21 21