0.040584
0.000000
0.000000
0.000000
0.024625
0.000000
0.000000
0.000000
0.015368
0.00000
0.00000
0.00000
Brown, D.G.
Sanderson, M.R.
Garman, E.
Neidle, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
24.640
40.610
65.070
C14 H15 N7
281.316
BERENIL
DIMINAZINE ACETURATE; 1,3-TRIS-(4'AMIDINOPHENYL)TRIAZINE
non-polymer
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
Y
1
N
C
Y
2
N
C
Y
3
N
C
Y
4
N
C
Y
5
N
C
Y
6
N
C
N
7
N
C
N
8
N
N
N
9
N
N
N
10
N
N
N
11
N
N
N
12
N
N
Y
13
N
C
Y
14
N
C
Y
15
N
C
Y
16
N
C
Y
17
N
C
Y
18
N
C
N
19
N
C
N
20
N
N
N
21
N
N
N
22
N
H
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
Y
49
N
N
Y
50
N
C
Y
51
N
N
Y
52
N
C
Y
53
N
C
N
54
N
N
Y
55
N
N
Y
56
N
C
Y
57
N
N
Y
58
N
C
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
183
N
MG
Y
1
N
doub
Y
2
N
sing
N
3
N
sing
Y
4
N
sing
N
5
N
sing
Y
6
N
doub
N
7
N
sing
Y
8
N
sing
N
9
N
sing
Y
10
N
doub
N
11
N
sing
N
12
N
sing
N
13
N
doub
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
E
doub
N
21
N
sing
Y
22
N
doub
Y
23
N
sing
Y
24
N
sing
N
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
N
29
N
sing
Y
30
N
doub
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
doub
N
41
N
sing
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
Y
61
N
sing
Y
62
N
sing
Y
63
N
doub
N
64
N
sing
Y
65
N
sing
Y
66
N
sing
Y
67
N
doub
N
68
N
sing
Y
69
N
doub
N
70
N
sing
N
71
N
sing
Y
72
N
sing
Y
73
N
doub
N
74
N
sing
Y
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
doub
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
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
doub
N
102
N
sing
N
103
N
doub
N
104
N
sing
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
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
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
Y
134
N
sing
Y
135
N
sing
Y
136
N
doub
N
137
N
sing
Y
138
N
sing
N
139
N
sing
Y
140
N
doub
N
141
N
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
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
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
doub
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
doub
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
226
481
490
10.1016/0022-2836(92)90962-J
1640462
Crystal structure of a berenil-d(CGCAAATTTGCG) complex. An example of drug-DNA recognition based on sequence-dependent structural features.
1992
UK
Embo J.
EMJODG
0897
0261-4189
9
1329
1334
Crystal Structure of a Berenil-Dodecanucleotide Complex: The Role of Water in Sequence-Specific Ligand Binding
1990
10.2210/pdb1d63/pdb
pdb_00001d63
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
291.00
1
AREA DETECTOR
XENTRONICS
x-ray
1
1.0
ROTATING ANODE
RIGAKU RU200
3662.404
DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')
2
syn
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
281.316
BERENIL
1
syn
non-polymer
18.015
water
65
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
2.22
44.65
VAPOR DIFFUSION, HANGING DROP
7.00
pH 7.00, VAPOR DIFFUSION, HANGING DROP
ROOM TEMPERATURE
WATER
1
MPD
1
MGCL2
1
NA CACODYLATE
1
AZIDE
1
WATER
2
MPD
2
6.727
1
19
A
1
B
24
-0.903
A_DC1:DG24_B
1
-12.201
0.138
-0.142
-0.127
0.535
1
19
A
2
B
23
-3.691
A_DG2:DC23_B
2
-12.462
-0.223
0.248
-0.196
-5.475
1
19
A
3
B
22
0.505
A_DC3:DG22_B
3
-7.477
-0.215
0.279
-0.059
10.114
1
20
A
4
B
21
0.377
A_DA4:DT21_B
4
-12.592
-0.245
-0.139
-0.130
11.099
1
20
A
5
B
20
0.709
A_DA5:DT20_B
5
-22.653
0.167
-0.096
-0.095
5.412
1
20
A
6
B
19
2.006
A_DA6:DT19_B
6
-18.310
0.116
0.328
-0.137
-0.972
1
20
A
7
B
18
0.360
A_DT7:DA18_B
7
-18.450
-0.098
0.147
-0.096
-8.982
1
20
A
8
B
17
-3.099
A_DT8:DA17_B
8
-18.084
-0.166
0.177
-0.088
-9.769
1
20
A
9
B
16
-3.461
A_DT9:DA16_B
9
-12.111
-0.103
0.044
-0.038
8.007
1
19
A
10
B
15
0.345
A_DG10:DC15_B
10
-5.137
-0.081
0.018
-0.076
3.967
1
19
A
11
B
14
-4.154
A_DC11:DG14_B
11
-21.588
0.005
0.420
-0.181
7.707
1
19
A
12
B
13
-3.391
A_DG12:DC13_B
12
11.556
-0.146
-0.048
-0.152
3.540
36.607
A
A
1
2
6.114
B
B
24
23
3.531
3.832
0.041
0.315
AA_DC1DG2:DC23DG24_BB
1
-1.564
2.495
36.380
-0.070
-0.298
3.510
38.671
A
A
2
3
-5.977
B
B
23
22
3.518
-3.950
0.597
0.152
AA_DG2DC3:DG22DC23_BB
2
1.856
-2.809
38.433
0.752
-0.655
3.094
29.007
A
A
3
4
11.696
B
B
22
21
3.083
5.797
-0.146
0.660
AA_DC3DA4:DT21DG22_BB
3
4.525
-9.130
28.079
0.092
1.248
3.323
37.608
A
A
4
5
3.507
B
B
21
20
3.316
2.259
0.011
0.223
AA_DA4DA5:DT20DT21_BB
4
0.499
-0.775
37.539
0.047
0.048
3.153
38.287
A
A
5
6
5.593
B
B
20
19
3.252
3.655
0.239
-0.361
AA_DA5DA6:DT19DT20_BB
5
-4.708
7.206
37.838
-1.002
-0.947
3.374
30.164
A
A
6
7
3.859
B
B
19
18
3.452
2.006
-0.163
-0.902
AA_DA6DT7:DA18DT19_BB
6
1.547
-2.975
30.060
-2.161
0.642
3.415
38.495
A
A
7
8
2.391
B
B
18
17
3.426
1.576
-0.333
-0.200
AA_DT7DT8:DA17DA18_BB
7
0.134
-0.203
38.464
-0.508
0.523
3.267
35.970
A
A
8
9
-6.643
B
B
17
16
3.299
-4.091
-0.005
0.050
AA_DT8DT9:DA16DA17_BB
8
2.191
-3.557
35.679
0.668
0.323
3.152
32.778
A
A
9
10
1.433
B
B
16
15
3.106
0.808
0.658
1.391
AA_DT9DG10:DC15DA16_BB
9
0.730
-1.294
32.761
2.332
-1.046
3.384
42.031
A
A
10
11
-12.014
B
B
15
14
3.491
-8.548
-0.981
0.624
AA_DG10DC11:DG14DC15_BB
10
-4.399
6.183
40.966
1.814
0.882
3.369
38.923
A
A
11
12
-9.588
B
B
14
13
3.451
-6.350
0.709
0.602
AA_DC11DG12:DC13DG14_BB
11
4.280
-6.462
38.191
1.715
-0.517
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
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
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_symmetry
_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
MG
MAGNESIUM ION
BRN
BERENIL
HOH
water
MG
26
2
MG
MG
26
A
BRN
25
3
BRN
BRN
25
B
HOH
28
4
HOH
HOH
28
A
HOH
29
4
HOH
HOH
29
A
HOH
31
4
HOH
HOH
31
A
HOH
35
4
HOH
HOH
35
A
HOH
36
4
HOH
HOH
36
A
HOH
37
4
HOH
HOH
37
A
HOH
41
4
HOH
HOH
41
A
HOH
42
4
HOH
HOH
42
A
HOH
45
4
HOH
HOH
45
A
HOH
47
4
HOH
HOH
47
A
HOH
49
4
HOH
HOH
49
A
HOH
53
4
HOH
HOH
53
A
HOH
54
4
HOH
HOH
54
A
HOH
55
4
HOH
HOH
55
A
HOH
57
4
HOH
HOH
57
A
HOH
58
4
HOH
HOH
58
A
HOH
59
4
HOH
HOH
59
A
HOH
63
4
HOH
HOH
63
A
HOH
64
4
HOH
HOH
64
A
HOH
65
4
HOH
HOH
65
A
HOH
66
4
HOH
HOH
66
A
HOH
68
4
HOH
HOH
68
A
HOH
71
4
HOH
HOH
71
A
HOH
72
4
HOH
HOH
72
A
HOH
75
4
HOH
HOH
75
A
HOH
77
4
HOH
HOH
77
A
HOH
79
4
HOH
HOH
79
A
HOH
80
4
HOH
HOH
80
A
HOH
84
4
HOH
HOH
84
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
91
4
HOH
HOH
91
A
HOH
27
4
HOH
HOH
27
B
HOH
30
4
HOH
HOH
30
B
HOH
32
4
HOH
HOH
32
B
HOH
33
4
HOH
HOH
33
B
HOH
34
4
HOH
HOH
34
B
HOH
38
4
HOH
HOH
38
B
HOH
39
4
HOH
HOH
39
B
HOH
40
4
HOH
HOH
40
B
HOH
43
4
HOH
HOH
43
B
HOH
44
4
HOH
HOH
44
B
HOH
46
4
HOH
HOH
46
B
HOH
48
4
HOH
HOH
48
B
HOH
50
4
HOH
HOH
50
B
HOH
51
4
HOH
HOH
51
B
HOH
52
4
HOH
HOH
52
B
HOH
56
4
HOH
HOH
56
B
HOH
60
4
HOH
HOH
60
B
HOH
61
4
HOH
HOH
61
B
HOH
62
4
HOH
HOH
62
B
HOH
67
4
HOH
HOH
67
B
HOH
69
4
HOH
HOH
69
B
HOH
70
4
HOH
HOH
70
B
HOH
73
4
HOH
HOH
73
B
HOH
74
4
HOH
HOH
74
B
HOH
76
4
HOH
HOH
76
B
HOH
78
4
HOH
HOH
78
B
HOH
81
4
HOH
HOH
81
B
HOH
82
4
HOH
HOH
82
B
HOH
83
4
HOH
HOH
83
B
HOH
85
4
HOH
HOH
85
B
HOH
90
4
HOH
HOH
90
B
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
A
4
n
4
DA
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
T
9
n
9
DT
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
A
16
n
4
DA
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
T
21
n
9
DT
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
41
E
O
HOH
3_657
A
MG
26
C
MG
MG
1_555
A
HOH
54
E
O
HOH
1_555
69.3
A
HOH
41
E
O
HOH
3_657
A
MG
26
C
MG
MG
1_555
A
HOH
55
E
O
HOH
1_555
170.6
A
HOH
54
E
O
HOH
1_555
A
MG
26
C
MG
MG
1_555
A
HOH
55
E
O
HOH
1_555
117.4
A
HOH
41
E
O
HOH
3_657
A
MG
26
C
MG
MG
1_555
A
HOH
66
E
O
HOH
3_657
78.4
A
HOH
54
E
O
HOH
1_555
A
MG
26
C
MG
MG
1_555
A
HOH
66
E
O
HOH
3_657
81.6
A
HOH
55
E
O
HOH
1_555
A
MG
26
C
MG
MG
1_555
A
HOH
66
E
O
HOH
3_657
95.6
A
HOH
41
E
O
HOH
3_657
A
MG
26
C
MG
MG
1_555
B
HOH
83
F
O
HOH
1_555
81.1
A
HOH
54
E
O
HOH
1_555
A
MG
26
C
MG
MG
1_555
B
HOH
83
F
O
HOH
1_555
147.7
A
HOH
55
E
O
HOH
1_555
A
MG
26
C
MG
MG
1_555
B
HOH
83
F
O
HOH
1_555
90.8
A
HOH
66
E
O
HOH
3_657
A
MG
26
C
MG
MG
1_555
B
HOH
83
F
O
HOH
1_555
80.2
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
-2.50
0.40
121.90
119.40
A
A
A
N3
C4
C5
DC
DC
DC
1
1
1
N
1
3.87
0.30
108.30
112.17
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
11.99
1.20
119.70
131.69
A
A
A
C3'
O3'
P
DG
DG
DC
2
2
3
Y
1
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
4.79
0.60
118.60
123.39
A
A
A
C6
N1
C2
DA
DA
DA
4
4
4
N
1
-3.98
0.50
129.30
125.32
A
A
A
N1
C2
N3
DA
DA
DA
4
4
4
N
1
-3.87
0.50
117.70
113.83
A
A
A
C5
C6
N1
DA
DA
DA
4
4
4
N
1
-7.96
0.80
109.40
101.44
A
A
A
O5'
C5'
C4'
DA
DA
DA
5
5
5
N
1
-9.99
1.60
120.90
110.91
A
A
A
P
O5'
C5'
DA
DA
DA
5
5
5
N
1
3.80
0.60
118.60
122.40
A
A
A
C6
N1
C2
DA
DA
DA
5
5
5
N
1
-4.92
0.50
129.30
124.38
A
A
A
N1
C2
N3
DA
DA
DA
5
5
5
N
1
11.84
1.20
119.70
131.54
A
A
A
C3'
O3'
P
DA
DA
DA
5
5
6
Y
1
-6.58
0.80
109.40
102.82
A
A
A
O5'
C5'
C4'
DA
DA
DA
6
6
6
N
1
1.92
0.30
108.30
110.22
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
4.37
0.60
118.60
122.97
A
A
A
C6
N1
C2
DA
DA
DA
6
6
6
N
1
-4.16
0.50
129.30
125.14
A
A
A
N1
C2
N3
DA
DA
DA
6
6
6
N
1
-3.47
0.50
117.70
114.23
A
A
A
C5
C6
N1
DA
DA
DA
6
6
6
N
1
4.92
0.80
123.70
128.62
A
A
A
C5
C6
N6
DA
DA
DA
6
6
6
N
1
13.00
1.20
119.70
132.70
A
A
A
C3'
O3'
P
DA
DA
DT
6
6
7
Y
1
11.00
1.20
119.70
130.70
A
A
A
C3'
O3'
P
DT
DT
DT
7
7
8
Y
1
-5.75
0.80
109.40
103.65
A
A
A
O5'
C5'
C4'
DT
DT
DT
8
8
8
N
1
-3.71
0.60
127.20
123.49
A
A
A
C2
N3
C4
DT
DT
DT
8
8
8
N
1
-7.71
0.80
109.40
101.69
A
A
A
O5'
C5'
C4'
DT
DT
DT
9
9
9
N
1
-5.20
0.60
127.20
122.00
A
A
A
C2
N3
C4
DT
DT
DT
9
9
9
N
1
4.46
0.60
115.20
119.66
A
A
A
N3
C4
C5
DT
DT
DT
9
9
9
N
1
11.61
1.20
119.70
131.31
A
A
A
C3'
O3'
P
DT
DT
DG
9
9
10
Y
1
-5.85
0.80
109.40
103.55
A
A
A
O5'
C5'
C4'
DG
DG
DG
10
10
10
N
1
-8.32
0.80
102.40
94.08
A
A
A
C3'
C2'
C1'
DG
DG
DG
10
10
10
N
1
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
-4.14
0.60
125.10
120.96
A
A
A
C6
N1
C2
DG
DG
DG
10
10
10
N
1
3.93
0.50
111.50
115.43
A
A
A
C5
C6
N1
DG
DG
DG
10
10
10
N
1
-4.90
0.80
109.40
104.50
A
A
A
O5'
C5'
C4'
DC
DC
DC
11
11
11
N
1
-5.43
0.80
102.40
96.97
B
B
B
C3'
C2'
C1'
DC
DC
DC
13
13
13
N
1
-5.13
0.80
109.40
104.27
B
B
B
O5'
C5'
C4'
DA
DA
DA
16
16
16
N
1
-5.56
0.80
109.40
103.84
B
B
B
O5'
C5'
C4'
DA
DA
DA
17
17
17
N
1
-10.34
1.60
120.90
110.56
B
B
B
P
O5'
C5'
DA
DA
DA
17
17
17
N
1
2.51
0.30
108.30
110.81
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
-3.55
0.50
129.30
125.75
B
B
B
N1
C2
N3
DA
DA
DA
17
17
17
N
1
-5.43
0.80
109.40
103.97
B
B
B
O5'
C5'
C4'
DA
DA
DA
18
18
18
N
1
3.10
0.30
108.30
111.40
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
5.01
0.60
118.60
123.61
B
B
B
C6
N1
C2
DA
DA
DA
18
18
18
N
1
-4.01
0.50
129.30
125.29
B
B
B
N1
C2
N3
DA
DA
DA
18
18
18
N
1
-3.90
0.50
117.70
113.80
B
B
B
C5
C6
N1
DA
DA
DA
18
18
18
N
1
8.43
1.20
119.70
128.13
B
B
B
C3'
O3'
P
DA
DA
DT
18
18
19
Y
1
-7.39
0.80
109.40
102.01
B
B
B
O5'
C5'
C4'
DT
DT
DT
19
19
19
N
1
-12.00
1.60
120.90
108.90
B
B
B
P
O5'
C5'
DT
DT
DT
19
19
19
N
1
1.83
0.30
108.30
110.13
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
11.66
1.20
119.70
131.36
B
B
B
C3'
O3'
P
DT
DT
DT
19
19
20
Y
1
8.74
1.20
119.70
128.44
B
B
B
C3'
O3'
P
DT
DT
DT
20
20
21
Y
1
-7.37
0.80
109.40
102.03
B
B
B
O5'
C5'
C4'
DT
DT
DT
21
21
21
N
1
-5.49
0.70
108.00
102.51
B
B
B
O4'
C1'
N1
DT
DT
DT
21
21
21
N
1
-5.30
0.60
127.20
121.90
B
B
B
C2
N3
C4
DT
DT
DT
21
21
21
N
1
4.16
0.60
115.20
119.36
B
B
B
N3
C4
C5
DT
DT
DT
21
21
21
N
1
-5.82
0.80
102.40
96.58
B
B
B
C3'
C2'
C1'
DG
DG
DG
22
22
22
N
1
5.26
0.30
108.30
113.56
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
-5.92
0.80
109.40
103.48
B
B
B
O5'
C5'
C4'
DC
DC
DC
23
23
23
N
1
-5.00
0.80
109.40
104.40
B
B
B
O5'
C5'
C4'
DG
DG
DG
24
24
24
N
1
2.08
0.30
108.30
110.38
B
B
B
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
3.03
0.50
111.50
114.53
B
B
B
C5
C6
N1
DG
DG
DG
24
24
24
N
1
A
A
O3'
P
DA
DT
6
7
-0.083
0.012
1.607
1.524
Y
1
A
A
O4'
C1'
DT
DT
8
8
0.070
0.011
1.420
1.490
N
1
B
B
OP2
O
DG
HOH
24
61
1.66
1_555
2_665
1
A
A
C5'
O
DC
HOH
1
64
1.93
1_555
3_657
1
A
A
O
O
HOH
HOH
86
91
1.97
1_555
2_664
1
A
B
O
O
HOH
HOH
45
70
2.04
1_555
2_564
1
A
B
O
O
HOH
HOH
57
46
2.09
1_555
2_665
0.1830000
2.000
7.000
3106
1
2.000
TR
isotropic
TR
isotropic
TR
isotropic
2.000
7.000
65
573
22
486
0
0.011
0.026
0.032
0.032
fix
fix
fix
2.000
1D63
12415
4067
0.0620000
1
refinement
NUCLSQ
CRYSTAL STRUCTURE OF A BERENIL-D(CGCAAATTTGCG) COMPLEX; AN EXAMPLE OF DRUG-DNA RECOGNITION BASED ON SEQUENCE-DEPENDENT STRUCTURAL FEATURES
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
metalc
1.984
A
MG
26
C
MG
MG
1_555
A
HOH
41
E
O
HOH
3_657
metalc
1.906
A
MG
26
C
MG
MG
1_555
A
HOH
54
E
O
HOH
1_555
metalc
1.985
A
MG
26
C
MG
MG
1_555
A
HOH
55
E
O
HOH
1_555
metalc
2.290
A
MG
26
C
MG
MG
1_555
A
HOH
66
E
O
HOH
3_657
metalc
2.330
A
MG
26
C
MG
MG
1_555
B
HOH
83
F
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
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
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
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
1D63
PDB
1
1D63
1
12
1D63
1
12
1D63
A
1
1
12
13
24
1D63
13
24
1D63
B
1
1
12
BINDING SITE FOR RESIDUE BRN B 25
B
BRN
25
Software
9
BINDING SITE FOR RESIDUE MG A 26
A
MG
26
Software
5
A
DA
6
A
DA
6
9
1_555
A
DT
7
A
DT
7
9
1_555
A
DT
8
A
DT
8
9
1_555
A
DT
9
A
DT
9
9
1_555
B
DA
18
B
DA
6
9
1_555
B
DT
19
B
DT
7
9
1_555
B
DT
20
B
DT
8
9
1_555
B
DT
21
B
DT
9
9
1_555
B
HOH
67
F
HOH
9
1_555
A
HOH
41
E
HOH
5
3_657
A
HOH
54
E
HOH
5
1_555
A
HOH
55
E
HOH
5
1_555
A
HOH
66
E
HOH
5
3_657
B
HOH
83
F
HOH
5
1_555
19
P 21 21 21