0.040667
0.000000
0.000000
0.000000
0.024728
0.000000
0.000000
0.000000
0.015207
0.00000
0.00000
0.00000
Czarny, A.
Boykin, D.W.
Wood, A.A.
Nunn, C.M.
Neidle, S.
Zhao, M.
Wilson, W.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
24.590
40.440
65.760
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
C23 H20 N6 O
396.445
5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE
non-polymer
Mg 2
24.305
MAGNESIUM ION
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
C
N
149
N
C
Y
150
N
C
Y
151
N
C
Y
152
N
C
Y
153
N
C
Y
154
N
C
Y
155
N
C
Y
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
Y
163
N
C
Y
164
N
C
Y
165
N
C
Y
166
N
C
Y
167
N
C
Y
168
N
C
Y
169
N
C
N
170
N
N
N
171
N
N
Y
172
N
N
Y
173
N
N
Y
174
N
N
Y
175
N
N
N
176
N
O
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
196
N
H
N
197
N
MG
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
sing
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
Y
163
N
sing
Y
164
N
doub
Y
165
N
doub
N
166
N
sing
Y
167
N
sing
N
168
N
sing
Y
169
N
doub
Y
170
N
sing
Y
171
N
sing
Y
172
N
sing
N
173
N
sing
Y
174
N
sing
Y
175
N
sing
Y
176
N
doub
Y
177
N
doub
Y
178
N
sing
Y
179
N
sing
Y
180
N
sing
Y
181
N
sing
Y
182
N
doub
N
183
N
sing
Y
184
N
sing
N
185
N
sing
Y
186
N
sing
Y
187
N
doub
Y
188
N
sing
Y
189
N
sing
Y
190
N
doub
Y
191
N
doub
N
192
N
sing
Y
193
N
sing
N
194
N
sing
Y
195
N
doub
N
196
N
sing
Y
197
N
sing
N
198
N
sing
N
199
N
sing
Y
200
N
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
23
3678
3684
10.1093/nar/23.18.3678
7478996
Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2.
1995
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
117
4716
4717
Analysis of Van Der Waals and Electrostatic Contributions in the Interactions of Minor Groove Binding Benzimidazoles with DNA
1995
US
Biochemistry
BICHAW
0033
0006-2960
30
10294
Low Temperature Crystallographic Analyses of the Binding of Hoechst 33258 to the Double Helical DNA Dodecamer C-G-C-G-A-A-T-T-C-G-C-G
1991
10.2210/pdb109d/pdb
pdb_0000109d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
AREA DETECTOR
XENTRONICS
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
ENRAF-NONIUS
3663.392
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
2
syn
polymer
396.445
5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE
1
syn
non-polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
90
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
2.23
44.88
5.955
1
19
A
1
B
24
-0.490
A_DC1:DG24_B
1
-13.604
0.227
-0.224
-0.183
-0.896
1
19
A
2
B
23
-3.452
A_DG2:DC23_B
2
-8.828
-0.035
0.260
-0.233
-0.627
1
19
A
3
B
22
-1.400
A_DC3:DG22_B
3
-5.057
0.013
-0.005
-0.140
11.866
1
19
A
4
B
21
-2.655
A_DG4:DC21_B
4
-4.328
-0.152
-0.025
-0.038
6.887
1
20
A
5
B
20
0.156
A_DA5:DT20_B
5
-19.745
0.096
-0.197
-0.068
-6.398
1
20
A
6
B
19
2.897
A_DA6:DT19_B
6
-17.803
0.047
0.554
-0.226
0.750
1
20
A
7
B
18
18.116
A_DT7:DA18_B
7
-7.168
-0.656
0.761
-0.184
-7.253
1
20
A
8
B
17
-2.478
A_DT8:DA17_B
8
-18.250
-0.151
-0.063
-0.194
-10.992
1
19
A
9
B
16
-1.696
A_DC9:DG16_B
9
-8.317
-0.013
-0.006
-0.113
4.340
1
19
A
10
B
15
-0.710
A_DG10:DC15_B
10
-1.819
-0.011
0.087
-0.210
5.431
1
19
A
11
B
14
-2.624
A_DC11:DG14_B
11
-19.539
0.076
0.098
-0.146
4.047
1
19
A
12
B
13
-4.384
A_DG12:DC13_B
12
8.262
-0.154
-0.283
-0.212
3.541
38.145
A
A
1
2
14.228
B
B
24
23
3.562
9.194
-0.289
0.288
AA_DC1DG2:DC23DG24_BB
1
-4.363
6.753
36.811
-0.845
-0.168
3.360
39.416
A
A
2
3
-9.569
B
B
23
22
3.438
-6.420
0.633
0.487
AA_DG2DC3:DG22DC23_BB
2
3.367
-5.019
38.769
1.517
-0.521
3.211
30.555
A
A
3
4
14.162
B
B
22
21
3.158
7.390
-0.189
0.650
AA_DC3DG4:DC21DG22_BB
3
1.357
-2.600
29.638
-0.217
0.625
3.495
36.576
A
A
4
5
2.863
B
B
21
20
3.495
1.794
0.041
0.217
AA_DG4DA5:DT20DC21_BB
4
2.883
-4.599
36.423
0.081
0.359
3.233
39.587
A
A
5
6
9.496
B
B
20
19
3.505
6.367
0.315
-0.697
AA_DA5DA6:DT19DT20_BB
5
-7.700
11.483
38.355
-1.811
-1.410
3.006
28.417
A
A
6
7
-22.765
B
B
19
18
3.120
-10.896
0.833
-0.212
AA_DA6DT7:DA18DT19_BB
6
1.365
-2.853
26.250
2.009
-1.391
2.877
41.805
A
A
7
8
14.494
B
B
18
17
3.311
10.172
-0.831
-0.433
AA_DT7DT8:DA17DA18_BB
7
8.910
-12.695
39.651
-1.645
2.073
3.497
41.032
A
A
8
9
0.495
B
B
17
16
3.494
0.347
-0.016
0.373
AA_DT8DC9:DG16DA17_BB
8
-0.219
0.312
41.030
0.492
-0.003
3.280
29.819
A
A
9
10
6.499
B
B
16
15
3.202
3.333
0.182
1.181
AA_DC9DG10:DC15DG16_BB
9
-2.888
5.632
29.498
1.604
-0.952
3.019
41.392
A
A
10
11
-19.159
B
B
15
14
3.445
-13.319
-0.913
0.915
AA_DG10DC11:DG14DC15_BB
10
-1.243
1.788
39.261
2.744
1.156
3.601
39.989
A
A
11
12
-6.238
B
B
14
13
3.637
-4.249
0.879
0.906
AA_DC11DG12:DC13DG14_BB
11
4.677
-6.865
39.507
1.867
-0.687
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1995-05-08
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr2_auth_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
NDB
1995-02-15
REL
REL
IBB
5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE
MG
MAGNESIUM ION
HOH
water
IBB
25
2
IBB
IBB
25
A
MO6
26
3
MG
MG
26
A
HOH
29
4
HOH
HOH
29
A
HOH
30
4
HOH
HOH
30
A
HOH
31
4
HOH
HOH
31
A
HOH
33
4
HOH
HOH
33
A
HOH
34
4
HOH
HOH
34
A
HOH
37
4
HOH
HOH
37
A
HOH
38
4
HOH
HOH
38
A
HOH
40
4
HOH
HOH
40
A
HOH
41
4
HOH
HOH
41
A
HOH
42
4
HOH
HOH
42
A
HOH
43
4
HOH
HOH
43
A
HOH
44
4
HOH
HOH
44
A
HOH
45
4
HOH
HOH
45
A
HOH
47
4
HOH
HOH
47
A
HOH
49
4
HOH
HOH
49
A
HOH
50
4
HOH
HOH
50
A
HOH
52
4
HOH
HOH
52
A
HOH
54
4
HOH
HOH
54
A
HOH
55
4
HOH
HOH
55
A
HOH
58
4
HOH
HOH
58
A
HOH
60
4
HOH
HOH
60
A
HOH
62
4
HOH
HOH
62
A
HOH
63
4
HOH
HOH
63
A
HOH
65
4
HOH
HOH
65
A
HOH
66
4
HOH
HOH
66
A
HOH
67
4
HOH
HOH
67
A
HOH
69
4
HOH
HOH
69
A
HOH
70
4
HOH
HOH
70
A
HOH
72
4
HOH
HOH
72
A
HOH
75
4
HOH
HOH
75
A
HOH
76
4
HOH
HOH
76
A
HOH
78
4
HOH
HOH
78
A
HOH
79
4
HOH
HOH
79
A
HOH
80
4
HOH
HOH
80
A
HOH
83
4
HOH
HOH
83
A
HOH
86
4
HOH
HOH
86
A
HOH
87
4
HOH
HOH
87
A
HOH
88
4
HOH
HOH
88
A
HOH
89
4
HOH
HOH
89
A
HOH
90
4
HOH
HOH
90
A
HOH
91
4
HOH
HOH
91
A
HOH
92
4
HOH
HOH
92
A
HOH
93
4
HOH
HOH
93
A
HOH
94
4
HOH
HOH
94
A
HOH
95
4
HOH
HOH
95
A
HOH
100
4
HOH
HOH
100
A
HOH
101
4
HOH
HOH
101
A
HOH
102
4
HOH
HOH
102
A
HOH
103
4
HOH
HOH
103
A
HOH
104
4
HOH
HOH
104
A
HOH
105
4
HOH
HOH
105
A
HOH
106
4
HOH
HOH
106
A
HOH
107
4
HOH
HOH
107
A
HOH
108
4
HOH
HOH
108
A
HOH
109
4
HOH
HOH
109
A
MO6
26
4
HOH
HOH
111
A
MO6
26
4
HOH
HOH
112
A
MO6
26
4
HOH
HOH
113
A
MO6
26
4
HOH
HOH
114
A
MO6
26
4
HOH
HOH
115
A
MO6
26
4
HOH
HOH
116
A
HOH
27
4
HOH
HOH
27
B
HOH
28
4
HOH
HOH
28
B
HOH
32
4
HOH
HOH
32
B
HOH
35
4
HOH
HOH
35
B
HOH
36
4
HOH
HOH
36
B
HOH
39
4
HOH
HOH
39
B
HOH
46
4
HOH
HOH
46
B
HOH
48
4
HOH
HOH
48
B
HOH
51
4
HOH
HOH
51
B
HOH
53
4
HOH
HOH
53
B
HOH
56
4
HOH
HOH
56
B
HOH
57
4
HOH
HOH
57
B
HOH
59
4
HOH
HOH
59
B
HOH
61
4
HOH
HOH
61
B
HOH
64
4
HOH
HOH
64
B
HOH
68
4
HOH
HOH
68
B
HOH
71
4
HOH
HOH
71
B
HOH
73
4
HOH
HOH
73
B
HOH
74
4
HOH
HOH
74
B
HOH
77
4
HOH
HOH
77
B
HOH
81
4
HOH
HOH
81
B
HOH
82
4
HOH
HOH
82
B
HOH
84
4
HOH
HOH
84
B
HOH
85
4
HOH
HOH
85
B
HOH
96
4
HOH
HOH
96
B
HOH
97
4
HOH
HOH
97
B
HOH
98
4
HOH
HOH
98
B
HOH
99
4
HOH
HOH
99
B
HOH
110
4
HOH
HOH
110
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
A
HOH
111
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
112
E
O
HOH
1_555
93.1
A
HOH
111
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
113
E
O
HOH
1_555
95.5
A
HOH
112
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
113
E
O
HOH
1_555
87.0
A
HOH
111
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
114
E
O
HOH
1_555
174.7
A
HOH
112
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
114
E
O
HOH
1_555
91.3
A
HOH
113
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
114
E
O
HOH
1_555
87.5
A
HOH
111
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
115
E
O
HOH
1_555
90.9
A
HOH
112
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
115
E
O
HOH
1_555
171.6
A
HOH
113
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
115
E
O
HOH
1_555
85.3
A
HOH
114
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
115
E
O
HOH
1_555
85.0
A
HOH
111
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
116
E
O
HOH
1_555
93.6
A
HOH
112
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
116
E
O
HOH
1_555
91.1
A
HOH
113
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
116
E
O
HOH
1_555
170.7
A
HOH
114
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
116
E
O
HOH
1_555
83.5
A
HOH
115
E
O
HOH
1_555
A
MG
26
D
MG
MG
1_555
A
HOH
116
E
O
HOH
1_555
96.0
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
-4.54
0.70
108.00
103.46
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
8.87
1.20
119.70
128.57
A
A
A
C3'
O3'
P
DG
DG
DC
2
2
3
Y
1
-11.22
1.60
120.90
109.68
A
A
A
P
O5'
C5'
DC
DC
DC
3
3
3
N
1
-6.00
0.80
105.90
99.90
A
A
A
O4'
C1'
C2'
DC
DC
DC
3
3
3
N
1
4.96
0.30
108.30
113.26
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
-3.48
0.40
104.50
101.02
A
A
A
O4'
C4'
C3'
DA
DA
DA
6
6
6
N
1
6.59
0.70
110.30
116.89
A
A
A
C1'
O4'
C4'
DA
DA
DA
6
6
6
N
1
-6.03
0.80
105.90
99.87
A
A
A
O4'
C1'
C2'
DA
DA
DA
6
6
6
N
1
3.09
0.30
108.30
111.39
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
-13.10
0.60
118.60
105.50
A
A
A
C6
N1
C2
DA
DA
DA
6
6
6
N
1
7.42
0.50
129.30
136.72
A
A
A
N1
C2
N3
DA
DA
DA
6
6
6
N
1
-4.87
0.70
126.80
121.93
A
A
A
N3
C4
C5
DA
DA
DA
6
6
6
N
1
6.76
0.50
117.70
124.46
A
A
A
C5
C6
N1
DA
DA
DA
6
6
6
N
1
3.51
0.50
103.90
107.41
A
A
A
C5
N7
C8
DA
DA
DA
6
6
6
N
1
2.40
0.40
105.80
108.20
A
A
A
N9
C4
C5
DA
DA
DA
6
6
6
N
1
-6.34
0.80
123.70
117.36
A
A
A
C5
C6
N6
DA
DA
DA
6
6
6
N
1
9.65
1.20
119.70
129.35
A
A
A
C3'
O3'
P
DA
DA
DT
6
6
7
Y
1
-3.46
0.40
104.50
101.04
A
A
A
O4'
C4'
C3'
DT
DT
DT
7
7
7
N
1
5.23
0.30
108.30
113.53
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
-3.25
0.50
121.30
118.05
A
A
A
C6
N1
C2
DT
DT
DT
7
7
7
N
1
-5.71
0.60
115.20
109.49
A
A
A
N3
C4
C5
DT
DT
DT
7
7
7
N
1
6.03
0.60
118.00
124.03
A
A
A
C4
C5
C6
DT
DT
DT
7
7
7
N
1
-6.57
0.60
122.30
115.73
A
A
A
N3
C2
O2
DT
DT
DT
7
7
7
N
1
-6.15
0.60
122.90
116.75
A
A
A
C6
C5
C7
DT
DT
DT
7
7
7
N
1
-2.66
0.40
104.50
101.84
A
A
A
O4'
C4'
C3'
DT
DT
DT
8
8
8
N
1
3.81
0.60
114.60
118.41
A
A
A
N1
C2
N3
DT
DT
DT
8
8
8
N
1
4.77
0.60
118.00
122.77
A
A
A
C4
C5
C6
DT
DT
DT
8
8
8
N
1
-4.16
0.60
122.30
118.14
A
A
A
N3
C2
O2
DT
DT
DT
8
8
8
N
1
-6.93
0.70
108.00
101.07
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
-2.94
0.40
104.50
101.56
A
A
A
O4'
C4'
C3'
DG
DG
DG
12
12
12
N
1
7.86
1.20
119.70
127.56
B
B
B
C3'
O3'
P
DC
DC
DG
13
13
14
Y
1
-3.16
0.40
104.50
101.34
B
B
B
O4'
C4'
C3'
DC
DC
DC
15
15
15
N
1
-5.05
0.80
105.90
100.85
B
B
B
O4'
C1'
C2'
DC
DC
DC
15
15
15
N
1
2.58
0.30
108.30
110.88
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
4.12
0.50
119.90
124.02
B
B
B
C2
N3
C4
DC
DC
DC
15
15
15
N
1
-3.48
0.40
121.90
118.42
B
B
B
N3
C4
C5
DC
DC
DC
15
15
15
N
1
11.47
1.20
119.70
131.17
B
B
B
C3'
O3'
P
DA
DA
DA
17
17
18
Y
1
8.24
0.70
110.30
118.54
B
B
B
C1'
O4'
C4'
DA
DA
DA
18
18
18
N
1
-10.70
0.80
105.90
95.20
B
B
B
O4'
C1'
C2'
DA
DA
DA
18
18
18
N
1
14.36
0.60
118.60
132.96
B
B
B
C6
N1
C2
DA
DA
DA
18
18
18
N
1
-8.36
0.50
129.30
120.94
B
B
B
N1
C2
N3
DA
DA
DA
18
18
18
N
1
6.27
0.50
110.60
116.87
B
B
B
C2
N3
C4
DA
DA
DA
18
18
18
N
1
-5.39
0.70
126.80
121.41
B
B
B
N3
C4
C5
DA
DA
DA
18
18
18
N
1
-5.28
0.50
117.00
111.72
B
B
B
C4
C5
C6
DA
DA
DA
18
18
18
N
1
-5.47
0.40
105.80
100.33
B
B
B
N9
C4
C5
DA
DA
DA
18
18
18
N
1
10.84
0.80
127.40
138.24
B
B
B
N3
C4
N9
DA
DA
DA
18
18
18
N
1
-11.70
0.60
118.60
106.90
B
B
B
N1
C6
N6
DA
DA
DA
18
18
18
N
1
13.33
0.80
123.70
137.03
B
B
B
C5
C6
N6
DA
DA
DA
18
18
18
N
1
-12.64
1.60
120.90
108.26
B
B
B
P
O5'
C5'
DT
DT
DT
19
19
19
N
1
2.63
0.30
108.30
110.93
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
-4.55
0.60
115.20
110.65
B
B
B
N3
C4
C5
DT
DT
DT
19
19
19
N
1
4.15
0.60
118.00
122.15
B
B
B
C4
C5
C6
DT
DT
DT
19
19
19
N
1
-4.24
0.40
104.50
100.26
B
B
B
O4'
C4'
C3'
DT
DT
DT
20
20
20
N
1
-5.08
0.70
108.00
102.92
B
B
B
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
-9.71
1.60
120.90
111.19
B
B
B
P
O5'
C5'
DC
DC
DC
21
21
21
N
1
-5.37
0.70
108.00
102.63
B
B
B
O4'
C1'
N1
DC
DC
DC
21
21
21
N
1
3.61
0.60
118.90
122.51
B
B
B
N1
C2
O2
DC
DC
DC
21
21
21
N
1
2.91
0.30
108.30
111.21
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
3.66
0.30
108.30
111.96
B
B
B
O4'
C1'
N1
DC
DC
DC
23
23
23
N
1
-11.67
1.90
112.60
100.93
B
B
B
N9
C1'
C2'
DG
DG
DG
24
24
24
N
1
8.01
0.30
108.30
116.31
B
B
B
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
3.55
0.50
113.10
116.65
B
B
B
N7
C8
N9
DG
DG
DG
24
24
24
N
1
-3.10
0.40
106.40
103.30
B
B
B
C8
N9
C4
DG
DG
DG
24
24
24
N
1
-5.08
0.70
119.90
114.82
B
B
B
N3
C2
N2
DG
DG
DG
24
24
24
N
1
3.73
0.60
119.90
123.63
B
B
B
N1
C6
O6
DG
DG
DG
24
24
24
N
1
A
A
C3'
C2'
DC
DC
3
3
-0.052
0.008
1.516
1.464
N
1
A
A
C5
N7
DG
DG
4
4
-0.041
0.006
1.388
1.347
N
1
A
A
C6
N1
DA
DA
6
6
0.063
0.007
1.351
1.414
N
1
A
A
N9
C4
DA
DA
6
6
0.042
0.006
1.374
1.416
N
1
A
A
C5
N7
DG
DG
10
10
-0.037
0.006
1.388
1.351
N
1
B
B
N1
C2
DA
DA
18
18
-0.114
0.009
1.339
1.225
N
1
B
B
C2
N3
DA
DA
18
18
-0.157
0.009
1.331
1.174
N
1
B
B
N3
C4
DA
DA
18
18
0.126
0.006
1.344
1.470
N
1
B
B
C6
N1
DA
DA
18
18
-0.076
0.007
1.351
1.275
N
1
B
B
C5
N7
DA
DA
18
18
-0.040
0.006
1.388
1.348
N
1
B
B
N9
C4
DA
DA
18
18
0.099
0.006
1.374
1.473
N
1
B
B
C5
N7
DG
DG
22
22
-0.043
0.006
1.388
1.345
N
1
B
B
C5
N7
DG
DG
24
24
-0.043
0.006
1.388
1.345
N
0.1970000
0.1970000
2.000
8.000
4016
1
2.000
2.000
8.000
84
607
37
486
0
0.020
4.30
109D
1
87.000
refinement
X-PLOR
VARIABILITY IN DNA MINOR GROOVE WIDTH RECOGNISED BY LIGAND BINDING: THE CRYSTAL STRUCTURE OF A BIS-BENZIMIDAZOLE COMPOUND BOUND TO THE DNA DUPLEX D(CGCGAATTCGCG)2
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
metalc
2.179
A
MG
26
D
MG
MG
1_555
A
HOH
111
E
O
HOH
1_555
metalc
2.192
A
MG
26
D
MG
MG
1_555
A
HOH
112
E
O
HOH
1_555
metalc
2.200
A
MG
26
D
MG
MG
1_555
A
HOH
113
E
O
HOH
1_555
metalc
2.305
A
MG
26
D
MG
MG
1_555
A
HOH
114
E
O
HOH
1_555
metalc
2.206
A
MG
26
D
MG
MG
1_555
A
HOH
115
E
O
HOH
1_555
metalc
2.251
A
MG
26
D
MG
MG
1_555
A
HOH
116
E
O
HOH
1_555
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
DA-DA MISPAIR
A
DA
6
A
N6
DA
6
1_555
B
DA
18
B
N1
DA
6
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
109D
PDB
1
109D
1
12
109D
1
12
109D
A
1
1
12
13
24
109D
13
24
109D
B
1
1
12
BINDING SITE FOR RESIDUE IBB A 25
A
IBB
25
Software
12
BINDING SITE FOR RESIDUE MG A 26
A
MG
26
Software
6
A
DA
5
A
DA
5
12
1_555
A
DA
6
A
DA
6
12
1_555
A
DT
7
A
DT
7
12
1_555
A
DT
8
A
DT
8
12
1_555
A
DC
9
A
DC
9
12
1_555
A
HOH
40
E
HOH
12
1_555
A
HOH
62
E
HOH
12
1_555
A
HOH
66
E
HOH
12
1_555
B
DA
18
B
DA
6
12
1_555
B
DT
19
B
DT
7
12
1_555
B
DT
20
B
DT
8
12
1_555
B
DC
21
B
DC
9
12
1_555
A
HOH
111
E
HOH
6
1_555
A
HOH
112
E
HOH
6
1_555
A
HOH
113
E
HOH
6
1_555
A
HOH
114
E
HOH
6
1_555
A
HOH
115
E
HOH
6
1_555
A
HOH
116
E
HOH
6
1_555
19
P 21 21 21