0.031249
0.000000
0.013252
0.000000
0.039418
0.000000
0.000000
0.000000
0.032296
0.000000
0.000000
0.000000
Chiu, T.K.
Dickerson, R.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
112.98
90.00
32.001
25.369
33.633
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
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
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
301
915
945
10.1006/jmbi.2000.4012
10966796
1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium.
2000
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
292
589
608
10.1006/jmbi.1999.3075
Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG.
1999
10.2210/pdb1en3/pdb
pdb_00001en3
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
IMAGE PLATE
1998-11-19
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
0.9500
1.0
X8C
NSLS
0.9500
SYNCHROTRON
NSLS BEAMLINE X8C
3045.004
DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*GP*G)-3')
1
syn
polymer
24.305
MAGNESIUM ION
4
syn
non-polymer
18.015
water
76
nat
water
no
no
(DC)(DC)(DA)(DA)(DC)(DG)(DT)(DT)(DG)(DG)
CCAACGTTGG
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
2.08
37.90
VAPOR DIFFUSION, SITTING DROP
INITIAL CONCENTRATION IN DROPLET: 0.24 MM DNA, 8.57 MM MAGNESIUM ACETATE, 0.11 MM STREPTONIGRIN, 10-15% MPD, 45% FINAL MPD CONCENTRATION IN RESERVOIR. SOLUTIONS WERE UNBUFFERED, VAPOR DIFFUSION, SITTING DROP, temperature 275.0K
275.0
MAGNESIUM ACETATE
1
STREPTONIGRIN
1
MPD
1
MPD
2
-6.248
1
19
A
1
A
10
0.513
A_DC1:DG10_A
1
-12.791
0.200
0.141
-0.150
0.588
1
19
A
2
A
9
-1.360
A_DC2:DG9_A
2
-7.659
0.190
-0.019
-0.187
3.969
1
20
A
3
A
8
1.420
A_DA3:DT8_A
3
-7.323
-0.041
0.075
-0.162
7.371
1
20
A
4
A
7
4.883
A_DA4:DT7_A
4
-12.300
0.075
0.216
-0.181
12.456
1
19
A
5
A
6
2.054
A_DC5:DG6_A
5
-12.628
0.149
-0.129
-0.101
-12.456
1
19
A
6
A
5
2.054
A_DG6:DC5_A
6
-12.628
-0.149
-0.129
-0.101
-7.371
1
20
A
7
A
4
4.883
A_DT7:DA4_A
7
-12.300
-0.075
0.216
-0.181
-3.969
1
20
A
8
A
3
1.420
A_DT8:DA3_A
8
-7.323
0.041
0.075
-0.162
-0.588
1
19
A
9
A
2
-1.360
A_DG9:DC2_A
9
-7.659
-0.190
-0.019
-0.187
6.248
1
19
A
10
A
1
0.513
A_DG10:DC1_A
10
-12.791
-0.200
0.141
-0.150
3.129
27.688
A
A
1
2
17.307
A
A
10
9
3.156
8.142
-0.395
0.628
AA_DC1DC2:DG9DG10_AA
1
3.487
-7.411
26.259
-0.633
1.658
2.780
50.700
A
A
2
3
-8.461
A
A
9
8
3.169
-7.223
0.320
2.751
AA_DC2DA3:DT8DG9_AA
2
1.229
-1.439
50.203
3.678
-0.295
3.178
30.425
A
A
3
4
15.013
A
A
8
7
3.227
7.789
0.444
0.364
AA_DA3DA4:DT7DT8_AA
3
-2.092
4.032
29.361
-0.861
-1.263
3.159
30.070
A
A
4
5
-2.004
A
A
7
6
3.131
-1.039
0.340
-0.374
AA_DA4DC5:DG6DT7_AA
4
2.352
-4.539
29.962
-0.516
-0.192
3.672
44.742
A
A
5
6
11.502
A
A
6
5
3.762
8.705
0.000
-0.134
AA_DC5DG6:DC5DG6_AA
5
0.000
0.000
43.930
-1.087
0.000
3.159
30.070
A
A
6
7
-2.004
A
A
5
4
3.131
-1.039
-0.340
-0.374
AA_DG6DT7:DA4DC5_AA
6
-2.352
4.539
29.962
-0.516
0.192
3.178
30.425
A
A
7
8
15.013
A
A
4
3
3.227
7.789
-0.444
0.364
AA_DT7DT8:DA3DA4_AA
7
2.092
-4.032
29.361
-0.861
1.263
2.780
50.700
A
A
8
9
-8.461
A
A
3
2
3.169
-7.223
-0.320
2.751
AA_DT8DG9:DC2DA3_AA
8
-1.229
1.439
50.203
3.678
0.295
3.129
27.688
A
A
9
10
17.307
A
A
2
1
3.156
8.142
0.395
0.628
AA_DG9DG10:DC1DC2_AA
9
-3.487
7.411
26.259
-0.633
-1.658
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2000-09-25
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
1
4
2024-04-03
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_alt_id
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_alt_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_alt_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
NDB
Y
NDB
2000-03-20
REL
REL
MG
MAGNESIUM ION
HOH
water
5DNB
BDJ019
PDB
experimental model
MO3
111
2
MG
MG
111
A
MO6
112
2
MG
MG
112
A
MO6
114
2
MG
MG
114
A
MO6
113
2
MG
MG
113
A
HOH
201
3
HOH
HOH
201
A
HOH
202
3
HOH
HOH
202
A
HOH
203
3
HOH
HOH
203
A
HOH
204
3
HOH
HOH
204
A
HOH
205
3
HOH
HOH
205
A
HOH
206
3
HOH
HOH
206
A
HOH
207
3
HOH
HOH
207
A
HOH
208
3
HOH
HOH
208
A
HOH
209
3
HOH
HOH
209
A
HOH
210
3
HOH
HOH
210
A
HOH
211
3
HOH
HOH
211
A
HOH
212
3
HOH
HOH
212
A
HOH
213
3
HOH
HOH
213
A
HOH
214
3
HOH
HOH
214
A
HOH
215
3
HOH
HOH
215
A
HOH
216
3
HOH
HOH
216
A
HOH
217
3
HOH
HOH
217
A
HOH
218
3
HOH
HOH
218
A
HOH
219
3
HOH
HOH
219
A
HOH
220
3
HOH
HOH
220
A
HOH
221
3
HOH
HOH
221
A
HOH
222
3
HOH
HOH
222
A
HOH
223
3
HOH
HOH
223
A
HOH
224
3
HOH
HOH
224
A
HOH
225
3
HOH
HOH
225
A
HOH
226
3
HOH
HOH
226
A
HOH
227
3
HOH
HOH
227
A
HOH
228
3
HOH
HOH
228
A
HOH
229
3
HOH
HOH
229
A
HOH
230
3
HOH
HOH
230
A
HOH
231
3
HOH
HOH
231
A
HOH
232
3
HOH
HOH
232
A
HOH
233
3
HOH
HOH
233
A
HOH
234
3
HOH
HOH
234
A
HOH
235
3
HOH
HOH
235
A
HOH
238
3
HOH
HOH
238
A
HOH
239
3
HOH
HOH
239
A
HOH
240
3
HOH
HOH
240
A
HOH
242
3
HOH
HOH
242
A
HOH
243
3
HOH
HOH
243
A
HOH
245
3
HOH
HOH
245
A
HOH
247
3
HOH
HOH
247
A
HOH
248
3
HOH
HOH
248
A
HOH
250
3
HOH
HOH
250
A
HOH
251
3
HOH
HOH
251
A
HOH
252
3
HOH
HOH
252
A
HOH
254
3
HOH
HOH
254
A
HOH
256
3
HOH
HOH
256
A
HOH
259
3
HOH
HOH
259
A
HOH
262
3
HOH
HOH
262
A
HOH
266
3
HOH
HOH
266
A
HOH
1210
3
HOH
HOH
1210
A
HOH
1271
3
HOH
HOH
1271
A
HOH
1281
3
HOH
HOH
1281
A
HOH
1317
3
HOH
HOH
1317
A
MO3
111
3
HOH
HOH
1318
A
MO3
111
3
HOH
HOH
1319
A
MO3
111
3
HOH
HOH
1320
A
MO6
112
3
HOH
HOH
1321
A
MO6
112
3
HOH
HOH
1322
A
MO6
112
3
HOH
HOH
1323
A
MO6
112
3
HOH
HOH
1324
A
MO6
112
3
HOH
HOH
1325
A
MO6
112
3
HOH
HOH
1326
A
MO6
114
3
HOH
HOH
1327
A
MO6
114
3
HOH
HOH
1328
A
MO6
114
3
HOH
HOH
1329
A
MO6
114
3
HOH
HOH
1330
A
MO6
114
3
HOH
HOH
1331
A
MO6
114
3
HOH
HOH
1332
A
MO6
113
3
HOH
HOH
1333
A
MO6
113
3
HOH
HOH
1334
A
MO6
113
3
HOH
HOH
1335
A
MO6
113
3
HOH
HOH
1336
A
MO6
113
3
HOH
HOH
1337
A
MO6
113
3
HOH
HOH
1338
A
C
1
n
1
DC
1
A
C
2
n
2
DC
2
A
A
3
n
3
DA
3
A
A
4
n
4
DA
4
A
C
5
n
5
DC
5
A
G
6
n
6
DG
6
A
T
7
n
7
DT
7
A
T
8
n
8
DT
8
A
G
9
n
9
DG
9
A
G
10
n
10
DG
10
A
0.1391000
0.1545000
592
5
12786
author_defined_assembly
2
dimeric
A
HOH
1318
F
O
HOH
1_555
A
MG
111
B
MG
MG
1_555
A
HOH
1318
F
O
HOH
2_655
179.8
A
HOH
1318
F
O
HOH
1_555
A
MG
111
B
MG
MG
1_555
A
HOH
1319
F
O
HOH
1_555
89.8
A
HOH
1318
F
O
HOH
2_655
A
MG
111
B
MG
MG
1_555
A
HOH
1319
F
O
HOH
1_555
90.1
A
HOH
1318
F
O
HOH
1_555
A
MG
111
B
MG
MG
1_555
A
HOH
1319
F
O
HOH
2_655
90.1
A
HOH
1318
F
O
HOH
2_655
A
MG
111
B
MG
MG
1_555
A
HOH
1319
F
O
HOH
2_655
89.8
A
HOH
1319
F
O
HOH
1_555
A
MG
111
B
MG
MG
1_555
A
HOH
1319
F
O
HOH
2_655
90.0
A
HOH
1318
F
O
HOH
1_555
A
MG
111
B
MG
MG
1_555
A
HOH
1320
F
O
HOH
1_555
89.7
A
HOH
1318
F
O
HOH
2_655
A
MG
111
B
MG
MG
1_555
A
HOH
1320
F
O
HOH
1_555
90.4
A
HOH
1319
F
O
HOH
1_555
A
MG
111
B
MG
MG
1_555
A
HOH
1320
F
O
HOH
1_555
87.3
A
HOH
1319
F
O
HOH
2_655
A
MG
111
B
MG
MG
1_555
A
HOH
1320
F
O
HOH
1_555
177.4
A
HOH
1318
F
O
HOH
1_555
A
MG
111
B
MG
MG
1_555
A
HOH
1320
F
O
HOH
2_655
90.4
A
HOH
1318
F
O
HOH
2_655
A
MG
111
B
MG
MG
1_555
A
HOH
1320
F
O
HOH
2_655
89.7
A
HOH
1319
F
O
HOH
1_555
A
MG
111
B
MG
MG
1_555
A
HOH
1320
F
O
HOH
2_655
177.3
A
HOH
1319
F
O
HOH
2_655
A
MG
111
B
MG
MG
1_555
A
HOH
1320
F
O
HOH
2_655
87.3
A
HOH
1320
F
O
HOH
1_555
A
MG
111
B
MG
MG
1_555
A
HOH
1320
F
O
HOH
2_655
95.3
A
HOH
1321
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1322
A
F
O
HOH
1_555
176.9
A
HOH
1321
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1323
A
F
O
HOH
1_555
90.6
A
HOH
1322
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1323
A
F
O
HOH
1_555
90.8
A
HOH
1321
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1324
A
F
O
HOH
1_555
89.4
A
HOH
1322
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1324
A
F
O
HOH
1_555
89.3
A
HOH
1323
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1324
A
F
O
HOH
1_555
175.8
A
HOH
1321
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1325
A
F
O
HOH
1_555
92.5
A
HOH
1322
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1325
A
F
O
HOH
1_555
90.3
A
HOH
1323
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1325
A
F
O
HOH
1_555
86.4
A
HOH
1324
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1325
A
F
O
HOH
1_555
89.4
A
HOH
1321
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1326
A
F
O
HOH
1_555
87.7
A
HOH
1322
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1326
A
F
O
HOH
1_555
89.6
A
HOH
1323
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1326
A
F
O
HOH
1_555
90.9
A
HOH
1324
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1326
A
F
O
HOH
1_555
93.3
A
HOH
1325
A
F
O
HOH
1_555
A
MG
112
A
C
MG
MG
1_555
A
HOH
1326
A
F
O
HOH
1_555
177.3
A
HOH
1333
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1334
A
F
O
HOH
1_555
178.0
A
HOH
1333
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1335
A
F
O
HOH
1_555
92.6
A
HOH
1334
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1335
A
F
O
HOH
1_555
88.9
A
HOH
1333
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1336
A
F
O
HOH
1_555
90.7
A
HOH
1334
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1336
A
F
O
HOH
1_555
87.8
A
HOH
1335
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1336
A
F
O
HOH
1_555
176.0
A
HOH
1333
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1337
A
F
O
HOH
1_555
90.7
A
HOH
1334
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1337
A
F
O
HOH
1_555
90.7
A
HOH
1335
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1337
A
F
O
HOH
1_555
87.8
A
HOH
1336
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1337
A
F
O
HOH
1_555
94.4
A
HOH
1333
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1338
A
F
O
HOH
1_555
88.9
A
HOH
1334
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1338
A
F
O
HOH
1_555
89.8
A
HOH
1335
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1338
A
F
O
HOH
1_555
90.6
A
HOH
1336
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1338
A
F
O
HOH
1_555
87.2
A
HOH
1337
A
F
O
HOH
1_555
A
MG
113
A
E
MG
MG
1_555
A
HOH
1338
A
F
O
HOH
1_555
178.3
A
HOH
1333
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1334
B
F
O
HOH
1_555
179.6
A
HOH
1333
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1335
B
F
O
HOH
1_555
90.8
A
HOH
1334
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1335
B
F
O
HOH
1_555
89.3
A
HOH
1333
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1336
B
F
O
HOH
1_555
89.8
A
HOH
1334
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1336
B
F
O
HOH
1_555
90.1
A
HOH
1335
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1336
B
F
O
HOH
1_555
178.6
A
HOH
1333
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1337
B
F
O
HOH
1_555
91.7
A
HOH
1334
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1337
B
F
O
HOH
1_555
87.9
A
HOH
1335
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1337
B
F
O
HOH
1_555
89.2
A
HOH
1336
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1337
B
F
O
HOH
1_555
89.6
A
HOH
1333
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1338
B
F
O
HOH
1_555
89.7
A
HOH
1334
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1338
B
F
O
HOH
1_555
90.7
A
HOH
1335
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1338
B
F
O
HOH
1_555
91.7
A
HOH
1336
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1338
B
F
O
HOH
1_555
89.5
A
HOH
1337
B
F
O
HOH
1_555
A
MG
113
B
E
MG
MG
1_555
A
HOH
1338
B
F
O
HOH
1_555
178.3
A
HOH
1327
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1328
B
F
O
HOH
1_555
176.7
A
HOH
1327
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1329
B
F
O
HOH
1_555
92.1
A
HOH
1328
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1329
B
F
O
HOH
1_555
89.6
A
HOH
1327
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1330
B
F
O
HOH
1_555
88.5
A
HOH
1328
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1330
B
F
O
HOH
1_555
90.3
A
HOH
1329
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1330
B
F
O
HOH
1_555
172.4
A
HOH
1327
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1331
B
F
O
HOH
1_555
91.6
A
HOH
1328
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1331
B
F
O
HOH
1_555
85.3
A
HOH
1329
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1331
B
F
O
HOH
1_555
94.3
A
HOH
1330
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1331
B
F
O
HOH
1_555
93.2
A
HOH
1327
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1332
B
F
O
HOH
1_555
89.4
A
HOH
1328
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1332
B
F
O
HOH
1_555
93.6
A
HOH
1329
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1332
B
F
O
HOH
1_555
87.3
A
HOH
1330
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1332
B
F
O
HOH
1_555
85.1
A
HOH
1331
B
F
O
HOH
1_555
A
MG
114
B
D
MG
MG
1_555
A
HOH
1332
B
F
O
HOH
1_555
178.0
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_656
-x+1,y,-z+1
crystal symmetry operation
18.8703476042
0.0000000000
30.9639250848
1
A
MG
111
B
MG
1
A
HOH
217
F
HOH
1
A
HOH
219
F
HOH
1
A
DA
3
A
0.072
SIDE CHAIN
1
A
DC
5
0.064
SIDE CHAIN
1
A
DT
7
A
0.075
SIDE CHAIN
1
A
DG
9
0.069
SIDE CHAIN
1
-7.80
0.80
109.40
101.60
A
A
A
O5'
C5'
C4'
DA
DA
DA
3
3
3
B
B
B
N
1
-16.33
2.50
109.70
93.37
A
A
A
C4'
C3'
O3'
DA
DA
DA
3
3
3
B
N
1
3.83
0.50
103.90
107.73
A
A
A
C5
N7
C8
DA
DA
DA
3
3
3
N
1
-2.55
0.40
105.80
103.25
A
A
A
N9
C4
C5
DA
DA
DA
3
3
3
N
1
16.32
1.40
114.30
130.62
A
A
A
N9
C1'
C2'
DA
DA
DA
4
4
4
N
1
6.31
0.50
129.30
135.61
A
A
A
N1
C2
N3
DA
DA
DA
4
4
4
N
1
-3.92
0.50
110.60
106.68
A
A
A
C2
N3
C4
DA
DA
DA
4
4
4
N
1
-3.24
0.50
117.00
113.76
A
A
A
C4
C5
C6
DA
DA
DA
4
4
4
N
1
4.35
0.50
110.70
115.05
A
A
A
C4
C5
N7
DA
DA
DA
4
4
4
N
1
-4.95
0.50
103.90
98.95
A
A
A
C5
N7
C8
DA
DA
DA
4
4
4
N
1
4.22
0.50
113.80
118.02
A
A
A
N7
C8
N9
DA
DA
DA
4
4
4
N
1
-5.99
0.40
105.80
99.81
A
A
A
C8
N9
C4
DA
DA
DA
4
4
4
N
1
3.95
0.60
118.60
122.55
A
A
A
N1
C6
N6
DA
DA
DA
4
4
4
N
1
11.82
1.80
126.30
138.12
A
A
A
C4
N9
C1'
DA
DA
DA
4
4
4
N
1
-6.66
1.00
110.10
103.44
A
A
A
C1'
O4'
C4'
DC
DC
DC
5
5
5
N
1
-7.57
0.70
108.00
100.43
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
3.32
0.40
120.30
123.62
A
A
A
C6
N1
C2
DC
DC
DC
5
5
5
N
1
-8.90
0.70
119.20
110.30
A
A
A
N1
C2
N3
DC
DC
DC
5
5
5
N
1
6.66
0.50
119.90
126.56
A
A
A
C2
N3
C4
DC
DC
DC
5
5
5
N
1
7.96
0.70
121.90
129.86
A
A
A
N3
C2
O2
DC
DC
DC
5
5
5
N
1
9.45
1.20
119.70
129.15
A
A
A
C3'
O3'
P
DC
DC
DG
5
5
6
Y
1
-4.49
0.60
125.10
120.61
A
A
A
C6
N1
C2
DG
DG
DG
6
6
6
N
1
-2.91
0.40
110.80
107.89
A
A
A
C4
C5
N7
DG
DG
DG
6
6
6
N
1
3.90
0.50
104.30
108.20
A
A
A
C5
N7
C8
DG
DG
DG
6
6
6
N
1
-3.10
0.50
113.10
110.00
A
A
A
N7
C8
N9
DG
DG
DG
6
6
6
N
1
-3.44
0.40
106.40
102.96
A
A
A
C8
N9
C4
DG
DG
DG
6
6
6
N
1
5.52
0.40
105.40
110.92
A
A
A
N9
C4
C5
DG
DG
DG
6
6
6
N
1
-3.92
0.60
123.70
119.78
A
A
A
C5
C6
N1
DT
DT
DT
7
7
7
N
1
-5.16
0.80
109.40
104.24
A
A
A
O5'
C5'
C4'
DT
DT
DT
8
8
8
B
B
B
N
1
A
A
C4
C5
DC
DC
2
2
-0.061
0.008
1.425
1.364
N
1
A
A
N3
C4
DA
DA
3
3
-0.052
0.006
1.344
1.292
N
1
A
A
C5
N7
DA
DA
3
3
-0.046
0.006
1.388
1.342
N
1
A
A
N7
C8
DA
DA
3
3
-0.072
0.007
1.311
1.239
N
1
A
A
C8
N9
DA
DA
3
3
0.068
0.008
1.373
1.441
N
1
A
A
C1'
N9
DA
DA
4
4
-0.220
0.014
1.468
1.248
N
1
A
A
C4
C5
DA
DA
4
4
0.047
0.007
1.383
1.430
N
1
A
A
C5
C6
DA
DA
4
4
0.072
0.009
1.406
1.478
N
1
A
A
C5
N7
DA
DA
4
4
-0.114
0.006
1.388
1.274
N
1
A
A
N7
C8
DA
DA
4
4
0.077
0.007
1.311
1.388
N
1
A
A
C1'
N1
DC
DC
5
5
0.143
0.013
1.488
1.631
N
1
A
A
C2
O2
DC
DC
5
5
-0.078
0.009
1.240
1.162
N
1
A
A
N1
C2
DC
DC
5
5
0.085
0.010
1.397
1.482
N
1
A
A
N1
C6
DC
DC
5
5
-0.099
0.006
1.367
1.268
N
1
A
A
N3
C4
DC
DC
5
5
-0.057
0.007
1.335
1.278
N
1
A
A
N3
C4
DG
DG
6
6
0.055
0.007
1.350
1.405
N
1
A
A
C5
N7
DG
DG
6
6
-0.042
0.006
1.388
1.346
N
1
A
A
C8
N9
DG
DG
6
6
0.044
0.007
1.374
1.418
N
1
A
A
C2
N2
DG
DG
6
6
-0.064
0.010
1.341
1.277
N
1
A
A
C5
C7
DT
DT
7
7
0.042
0.006
1.496
1.538
N
1
A
A
N1
C2
DT
DT
8
8
-0.048
0.008
1.376
1.328
N
1
A
A
C5
C7
DT
DT
8
8
0.038
0.006
1.496
1.534
N
1
A
A
C4
C5
DG
DG
9
9
0.052
0.007
1.379
1.431
N
1
A
A
C5
N7
DG
DG
9
9
-0.037
0.006
1.388
1.351
N
REFINEMENT STARTED IN X-PLOR 3.843 WITH DNA MODEL FROM BDJ019. AFTER ALL DATA HAS BEEN ADDED AND REFINED BY SIMULATED ANNEALING IN X-PLOR 3.843, REFINEMENT CONTINUED BY CONJUGATE GRADIENT LEAST-SQUARES IN SHELXL-97. THE TOP 50 MOST DISAGREEABLE REFLECTIONS WERE REJECTED TOWARDS THE LATTER STAGES OF REFINEMENT BUT THESE ARE STILL INCLUDED IN THE RELEASED DATA.
0.1592000
0.1409000
0.1409000
0.985
8.0
17441
631
13464
13464
2945
5
95
RANDOM
1
THROUGHOUT
0
0
MOLECULAR REPLACEMENT
BDJ019
PARKINSON ET AL.
SWAT 0.814695 0.4550
14
114.0
272.84
0.985
8.0
61
457
32
364
0
0.018
0.049
0.019
0.006
0.026
0.072
5.3
0.985
8.0
1EN3
13464
13464
-1.0
0.0470000
1
21.6
5.75
95.0
0.1230000
0.985
1.016
7.4
90.7
model building
X-PLOR
refinement
SHELXL-97
data reduction
DENZO
data scaling
SCALEPACK
phasing
X-PLOR
1A CRYSTAL STRUCTURES OF B-DNA REVEAL SEQUENCE-SPECIFIC BINDING AND GROOVE-SPECIFIC BENDING OF DNA BY MAGNESIUM AND CALCIUM
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
metalc
2.047
A
MG
111
B
MG
MG
1_555
A
HOH
1318
F
O
HOH
1_555
metalc
2.046
A
MG
111
B
MG
MG
1_555
A
HOH
1318
F
O
HOH
2_655
metalc
2.090
A
MG
111
B
MG
MG
1_555
A
HOH
1319
F
O
HOH
1_555
metalc
2.091
A
MG
111
B
MG
MG
1_555
A
HOH
1319
F
O
HOH
2_655
metalc
2.120
A
MG
111
B
MG
MG
1_555
A
HOH
1320
F
O
HOH
1_555
metalc
2.120
A
MG
111
B
MG
MG
1_555
A
HOH
1320
F
O
HOH
2_655
metalc
2.075
A
A
A
MG
112
C
MG
MG
1_555
A
HOH
1321
F
O
HOH
1_555
metalc
2.076
A
A
A
MG
112
C
MG
MG
1_555
A
HOH
1322
F
O
HOH
1_555
metalc
2.065
A
A
A
MG
112
C
MG
MG
1_555
A
HOH
1323
F
O
HOH
1_555
metalc
2.065
A
A
A
MG
112
C
MG
MG
1_555
A
HOH
1324
F
O
HOH
1_555
metalc
2.094
A
A
A
MG
112
C
MG
MG
1_555
A
HOH
1325
F
O
HOH
1_555
metalc
2.071
A
A
A
MG
112
C
MG
MG
1_555
A
HOH
1326
F
O
HOH
1_555
metalc
2.080
A
A
A
MG
113
E
MG
MG
1_555
A
HOH
1333
F
O
HOH
1_555
metalc
2.077
B
B
A
MG
113
E
MG
MG
1_555
A
HOH
1333
F
O
HOH
1_555
metalc
2.073
A
A
A
MG
113
E
MG
MG
1_555
A
HOH
1334
F
O
HOH
1_555
metalc
2.086
B
B
A
MG
113
E
MG
MG
1_555
A
HOH
1334
F
O
HOH
1_555
metalc
2.064
A
A
A
MG
113
E
MG
MG
1_555
A
HOH
1335
F
O
HOH
1_555
metalc
2.088
B
B
A
MG
113
E
MG
MG
1_555
A
HOH
1335
F
O
HOH
1_555
metalc
2.073
A
A
A
MG
113
E
MG
MG
1_555
A
HOH
1336
F
O
HOH
1_555
metalc
2.084
B
B
A
MG
113
E
MG
MG
1_555
A
HOH
1336
F
O
HOH
1_555
metalc
2.131
A
A
A
MG
113
E
MG
MG
1_555
A
HOH
1337
F
O
HOH
1_555
metalc
2.084
B
B
A
MG
113
E
MG
MG
1_555
A
HOH
1337
F
O
HOH
1_555
metalc
2.091
A
A
A
MG
113
E
MG
MG
1_555
A
HOH
1338
F
O
HOH
1_555
metalc
2.082
B
B
A
MG
113
E
MG
MG
1_555
A
HOH
1338
F
O
HOH
1_555
metalc
2.065
B
B
A
MG
114
D
MG
MG
1_555
A
HOH
1327
F
O
HOH
1_555
metalc
2.052
B
B
A
MG
114
D
MG
MG
1_555
A
HOH
1328
F
O
HOH
1_555
metalc
2.062
B
B
A
MG
114
D
MG
MG
1_555
A
HOH
1329
F
O
HOH
1_555
metalc
2.087
B
B
A
MG
114
D
MG
MG
1_555
A
HOH
1330
F
O
HOH
1_555
metalc
2.087
B
B
A
MG
114
D
MG
MG
1_555
A
HOH
1331
F
O
HOH
1_555
metalc
2.107
B
B
A
MG
114
D
MG
MG
1_555
A
HOH
1332
F
O
HOH
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
A
DG
10
A
N1
DG
10
2_656
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
A
DG
10
A
O6
DG
10
2_656
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
A
DG
10
A
N2
DG
10
2_656
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
A
DG
9
A
N1
DG
9
2_656
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
A
DG
9
A
O6
DG
9
2_656
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
A
DG
9
A
N2
DG
9
2_656
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
A
DT
8
A
N3
DT
8
2_656
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
A
DT
8
A
O4
DT
8
2_656
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
A
DT
7
A
N3
DT
7
2_656
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
A
DT
7
A
O4
DT
7
2_656
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
A
DG
6
A
N1
DG
6
2_656
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
A
DG
6
A
O6
DG
6
2_656
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
A
DG
6
A
N2
DG
6
2_656
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
A
DC
5
A
N3
DC
5
2_656
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
A
DC
5
A
O2
DC
5
2_656
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
A
DC
5
A
N4
DC
5
2_656
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
A
DA
4
A
N1
DA
4
2_656
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
A
DA
4
A
N6
DA
4
2_656
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
A
DA
3
A
N1
DA
3
2_656
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
A
DA
3
A
N6
DA
3
2_656
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
A
DC
2
A
N3
DC
2
2_656
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
A
DC
2
A
O2
DC
2
2_656
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
A
DC
2
A
N4
DC
2
2_656
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
A
DC
1
A
N3
DC
1
2_656
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
A
DC
1
A
O2
DC
1
2_656
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
A
DC
1
A
N4
DC
1
2_656
DNA
DIVALENT CATIONS, DNA SEQUENCE-SPECIFIC BINDING, SHELXDNA, B-DNA, DNA
1EN3
PDB
1
1EN3
1
10
1EN3
1
10
1EN3
A
1
1
10
BINDING SITE FOR RESIDUE MG A 111
A
MG
111
Software
6
BINDING SITE FOR RESIDUE MG A 112
A
MG
112
Software
6
BINDING SITE FOR RESIDUE MG A 114
A
MG
114
Software
6
BINDING SITE FOR RESIDUE MG A 113
A
MG
113
Software
6
A
HOH
1318
F
HOH
6
1_555
A
HOH
1318
F
HOH
6
2_655
A
HOH
1319
F
HOH
6
1_555
A
HOH
1319
F
HOH
6
2_655
A
HOH
1320
F
HOH
6
2_655
A
HOH
1320
F
HOH
6
1_555
A
HOH
1321
F
HOH
6
1_555
A
HOH
1322
F
HOH
6
1_555
A
HOH
1323
F
HOH
6
1_555
A
HOH
1324
F
HOH
6
1_555
A
HOH
1325
F
HOH
6
1_555
A
HOH
1326
F
HOH
6
1_555
A
HOH
1327
F
HOH
6
1_555
A
HOH
1328
F
HOH
6
1_555
A
HOH
1329
F
HOH
6
1_555
A
HOH
1330
F
HOH
6
1_555
A
HOH
1331
F
HOH
6
1_555
A
HOH
1332
F
HOH
6
1_555
A
HOH
1333
F
HOH
6
1_555
A
HOH
1334
F
HOH
6
1_555
A
HOH
1335
F
HOH
6
1_555
A
HOH
1336
F
HOH
6
1_555
A
HOH
1337
F
HOH
6
1_555
A
HOH
1338
F
HOH
6
1_555
5
monoclinic
C 1 2 1