0.041322
0.000000
0.000000
0.000000
0.023443
0.000000
0.000000
0.000000
0.020278
0.00000
0.00000
0.00000
Robinson, H.
Gao, Y.-G.
Sanishvili, R.
Joachimiak, A.
Wang, A.H.-J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
24.200
42.656
49.315
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
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
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA 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
R
C
N
12
N
O
N
13
R
C
N
14
N
N
N
15
N
C
N
16
N
O
N
17
N
N
N
18
N
C
N
19
N
N
N
20
N
C
N
21
N
C
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
O
N
37
N
P
N
38
N
O
N
39
N
O
N
40
N
O
N
41
N
C
N
42
R
C
N
43
N
O
N
44
S
C
N
45
N
O
N
46
N
C
N
47
R
C
Y
48
N
N
Y
49
N
C
Y
50
N
N
Y
51
N
C
Y
52
N
C
N
53
N
N
Y
54
N
N
Y
55
N
C
Y
56
N
N
Y
57
N
C
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
O
N
73
N
P
N
74
N
O
N
75
N
O
N
76
N
O
N
77
N
C
N
78
R
C
N
79
N
O
N
80
S
C
N
81
N
O
N
82
N
C
N
83
R
C
N
84
N
N
N
85
N
C
N
86
N
O
N
87
N
N
N
88
N
C
N
89
N
N
N
90
N
C
N
91
N
C
N
92
N
H
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
O
N
107
N
P
N
108
N
O
N
109
N
O
N
110
N
O
N
111
N
C
N
112
R
C
N
113
N
O
N
114
S
C
N
115
N
O
N
116
N
C
N
117
R
C
Y
118
N
N
Y
119
N
C
Y
120
N
N
Y
121
N
C
N
122
N
C
N
123
N
O
N
124
N
N
N
125
N
C
N
126
N
N
N
127
N
N
Y
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
O
N
144
N
P
N
145
N
O
N
146
N
O
N
147
N
O
N
148
N
C
N
149
R
C
N
150
N
O
N
151
S
C
N
152
N
O
N
153
N
C
N
154
R
C
N
155
N
N
N
156
N
C
N
157
N
O
N
158
N
N
N
159
N
C
N
160
N
O
N
161
N
C
N
162
N
C
N
163
N
C
N
164
N
H
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
O
N
180
N
P
N
181
N
O
N
182
N
O
N
183
N
O
N
184
N
C
N
185
R
C
N
186
N
O
N
187
S
C
N
188
N
O
N
189
R
C
N
190
N
O
N
191
R
C
Y
192
N
N
Y
193
N
C
Y
194
N
N
Y
195
N
C
N
196
N
C
N
197
N
O
N
198
N
N
N
199
N
C
N
200
N
N
N
201
N
N
Y
202
N
C
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
O
N
218
N
H
N
219
N
H
N
220
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
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
doub
N
28
N
sing
N
29
N
doub
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
doub
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
doub
N
40
N
sing
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
Y
60
N
sing
Y
61
N
sing
Y
62
N
doub
N
63
N
sing
Y
64
N
sing
Y
65
N
sing
Y
66
N
doub
N
67
N
sing
Y
68
N
doub
N
69
N
sing
N
70
N
sing
Y
71
N
sing
Y
72
N
doub
N
73
N
sing
Y
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
doub
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
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
doub
N
101
N
sing
N
102
N
doub
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
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
Y
133
N
sing
Y
134
N
sing
Y
135
N
doub
N
136
N
sing
Y
137
N
sing
N
138
N
sing
Y
139
N
doub
N
140
N
doub
N
141
N
sing
N
142
N
sing
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
doub
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
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
doub
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
doub
N
179
N
sing
N
180
N
sing
N
181
N
doub
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
doub
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
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
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
Y
210
N
sing
Y
211
N
sing
Y
212
N
doub
N
213
N
sing
Y
214
N
sing
N
215
N
sing
Y
216
N
doub
N
217
N
doub
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
doub
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
28
1760
1766
10.1093/nar/28.8.1760
10734195
Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.
2000
10.2210/pdb1dno/pdb
pdb_00001dno
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
110
1
CCD
1999-11-16
CUSTOM-MADE
SINGLE WAVELENGTH
M
x-ray
1
1.03321
1.0
19-ID
APS
1.03321
SYNCHROTRON
APS BEAMLINE 19-ID
3093.005
DNA/RNA (5'-R(*GP*CP*GP)-D(*TP*AP*TP*AP*CP*GP*C)-3')
2
syn
polymer
24.305
MAGNESIUM ION
4
syn
non-polymer
18.015
water
120
nat
water
no
no
GCG(DT)(DA)(DT)(DA)(DC)(DG)(DC)
GCGTATACGC
A,B
polydeoxyribonucleotide/polyribonucleotide hybrid
n
n
n
n
n
n
n
n
n
n
1
1.87
34.0
VAPOR DIFFUSION, SITTING DROP
6.5
2-MPD, CACODYLATE, SPERMINE, MGCL2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
CACODYLATE
1
SPERMINE
1
MGCL2
1
MPD
1
MPD
2
3.180
1
19
A
1
B
20
-3.804
A_G1:DC20_B
1
-6.173
-0.092
0.113
-0.112
4.319
1
19
A
2
B
19
1.118
A_C2:DG19_B
2
-13.011
0.205
-0.019
-0.138
-11.408
1
19
A
3
B
18
0.375
A_G3:DC18_B
3
-15.384
-0.217
-0.054
-0.090
-4.502
1
20
A
4
B
17
-0.917
A_DT4:DA17_B
4
-9.488
-0.129
0.170
-0.092
1.052
1
20
A
5
B
16
3.360
A_DA5:DT16_B
5
-15.087
-0.020
0.186
-0.109
8.772
1
20
A
6
B
15
12.181
A_DT6:DA15_B
6
-14.410
0.032
0.270
0.005
10.106
1
20
A
7
B
14
5.009
A_DA7:DT14_B
7
-12.218
-0.039
0.118
-0.085
10.667
1
19
A
8
B
13
0.426
A_DC8:G13_B
8
-18.872
0.164
-0.132
-0.162
-2.757
1
19
A
9
B
12
0.504
A_DG9:C12_B
9
-13.106
-0.135
0.156
-0.225
-2.976
1
19
A
10
B
11
-2.813
A_DC10:G11_B
10
-0.345
0.270
0.220
-0.090
3.124
38.380
A
A
1
2
3.231
B
B
20
19
3.205
2.123
0.542
-1.718
AA_G1C2:DG19DC20_BB
1
1.218
-1.854
38.305
-2.870
-0.677
2.065
32.468
A
A
2
3
30.499
B
B
19
18
3.421
16.303
-0.594
-1.913
AA_C2G3:DC18DG19_BB
2
-1.902
3.558
28.110
-6.005
0.762
2.960
32.086
A
A
3
4
8.603
B
B
18
17
3.125
4.731
-0.502
-1.156
AA_G3DT4:DA17DC18_BB
3
-3.139
5.707
31.593
-2.889
0.380
2.244
32.554
A
A
4
5
25.507
B
B
17
16
3.007
13.861
0.450
-1.212
AA_DT4DA5:DT16DA17_BB
4
1.250
-2.300
29.502
-4.205
-0.619
2.716
33.668
A
A
5
6
14.407
B
B
16
15
3.092
8.264
0.897
-1.214
AA_DA5DT6:DA15DT16_BB
5
0.126
-0.219
32.666
-3.310
-1.531
2.183
33.548
A
A
6
7
29.002
B
B
15
14
3.062
16.087
-0.775
-1.114
AA_DT6DA7:DT14DA15_BB
6
-0.056
0.102
29.537
-4.192
1.335
3.033
32.150
A
A
7
8
9.113
B
B
14
13
3.283
5.024
-0.351
-1.206
AA_DA7DC8:G13DT14_BB
7
2.066
-3.748
31.700
-3.053
0.993
2.626
34.691
A
A
8
9
23.332
B
B
13
12
3.475
13.535
-0.124
-1.526
AA_DC8DG9:C12G13_BB
8
-3.774
6.505
31.798
-4.586
-0.356
3.402
36.020
A
A
9
10
-0.662
B
B
12
11
3.357
-0.409
0.453
-1.894
AA_DG9DC10:G11C12_BB
9
2.779
-4.498
35.914
-3.003
-0.325
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_keywords
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Structure summary
1
0
2000-04-10
1
1
2008-04-27
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.ptnr2_auth_asym_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_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.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_keywords.text
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
1999-12-16
REL
REL
MG
MAGNESIUM ION
HOH
water
MO6
24
2
MG
MG
24
A
MO6
21
2
MG
MG
21
B
MO6
22
2
MG
MG
22
B
MO6
23
2
MG
MG
23
B
HOH
102
3
HOH
HOH
102
A
HOH
104
3
HOH
HOH
104
A
HOH
105
3
HOH
HOH
105
A
HOH
107
3
HOH
HOH
107
A
HOH
111
3
HOH
HOH
111
A
HOH
113
3
HOH
HOH
113
A
HOH
114
3
HOH
HOH
114
A
HOH
117
3
HOH
HOH
117
A
HOH
120
3
HOH
HOH
120
A
HOH
121
3
HOH
HOH
121
A
HOH
122
3
HOH
HOH
122
A
HOH
123
3
HOH
HOH
123
A
HOH
125
3
HOH
HOH
125
A
HOH
126
3
HOH
HOH
126
A
HOH
127
3
HOH
HOH
127
A
HOH
128
3
HOH
HOH
128
A
HOH
130
3
HOH
HOH
130
A
HOH
131
3
HOH
HOH
131
A
HOH
136
3
HOH
HOH
136
A
HOH
137
3
HOH
HOH
137
A
HOH
139
3
HOH
HOH
139
A
HOH
141
3
HOH
HOH
141
A
HOH
145
3
HOH
HOH
145
A
HOH
150
3
HOH
HOH
150
A
HOH
154
3
HOH
HOH
154
A
HOH
156
3
HOH
HOH
156
A
HOH
158
3
HOH
HOH
158
A
HOH
161
3
HOH
HOH
161
A
HOH
164
3
HOH
HOH
164
A
HOH
172
3
HOH
HOH
172
A
HOH
173
3
HOH
HOH
173
A
HOH
177
3
HOH
HOH
177
A
HOH
178
3
HOH
HOH
178
A
HOH
179
3
HOH
HOH
179
A
HOH
183
3
HOH
HOH
183
A
HOH
184
3
HOH
HOH
184
A
HOH
188
3
HOH
HOH
188
A
HOH
189
3
HOH
HOH
189
A
HOH
190
3
HOH
HOH
190
A
HOH
192
3
HOH
HOH
192
A
HOH
193
3
HOH
HOH
193
A
MO6
22
3
HOH
HOH
205
A
MO6
24
3
HOH
HOH
215
A
MO6
24
3
HOH
HOH
216
A
MO6
24
3
HOH
HOH
217
A
MO6
24
3
HOH
HOH
218
A
HOH
101
3
HOH
HOH
101
B
HOH
103
3
HOH
HOH
103
B
HOH
106
3
HOH
HOH
106
B
HOH
108
3
HOH
HOH
108
B
HOH
109
3
HOH
HOH
109
B
HOH
110
3
HOH
HOH
110
B
HOH
112
3
HOH
HOH
112
B
HOH
115
3
HOH
HOH
115
B
HOH
116
3
HOH
HOH
116
B
HOH
118
3
HOH
HOH
118
B
HOH
119
3
HOH
HOH
119
B
HOH
124
3
HOH
HOH
124
B
HOH
129
3
HOH
HOH
129
B
HOH
132
3
HOH
HOH
132
B
HOH
133
3
HOH
HOH
133
B
HOH
134
3
HOH
HOH
134
B
HOH
135
3
HOH
HOH
135
B
HOH
138
3
HOH
HOH
138
B
HOH
140
3
HOH
HOH
140
B
HOH
142
3
HOH
HOH
142
B
HOH
143
3
HOH
HOH
143
B
HOH
144
3
HOH
HOH
144
B
HOH
146
3
HOH
HOH
146
B
HOH
147
3
HOH
HOH
147
B
HOH
148
3
HOH
HOH
148
B
HOH
149
3
HOH
HOH
149
B
HOH
151
3
HOH
HOH
151
B
HOH
152
3
HOH
HOH
152
B
HOH
153
3
HOH
HOH
153
B
HOH
155
3
HOH
HOH
155
B
HOH
157
3
HOH
HOH
157
B
HOH
159
3
HOH
HOH
159
B
HOH
160
3
HOH
HOH
160
B
HOH
162
3
HOH
HOH
162
B
HOH
163
3
HOH
HOH
163
B
HOH
165
3
HOH
HOH
165
B
HOH
166
3
HOH
HOH
166
B
HOH
167
3
HOH
HOH
167
B
HOH
168
3
HOH
HOH
168
B
HOH
169
3
HOH
HOH
169
B
HOH
170
3
HOH
HOH
170
B
HOH
171
3
HOH
HOH
171
B
HOH
174
3
HOH
HOH
174
B
HOH
175
3
HOH
HOH
175
B
HOH
176
3
HOH
HOH
176
B
HOH
180
3
HOH
HOH
180
B
HOH
181
3
HOH
HOH
181
B
HOH
182
3
HOH
HOH
182
B
HOH
185
3
HOH
HOH
185
B
HOH
186
3
HOH
HOH
186
B
HOH
187
3
HOH
HOH
187
B
HOH
191
3
HOH
HOH
191
B
HOH
194
3
HOH
HOH
194
B
HOH
195
3
HOH
HOH
195
B
HOH
196
3
HOH
HOH
196
B
MO6
21
3
HOH
HOH
197
B
MO6
21
3
HOH
HOH
198
B
MO6
21
3
HOH
HOH
199
B
MO6
21
3
HOH
HOH
200
B
MO6
21
3
HOH
HOH
201
B
MO6
21
3
HOH
HOH
202
B
MO6
22
3
HOH
HOH
203
B
MO6
22
3
HOH
HOH
204
B
MO6
22
3
HOH
HOH
206
B
MO6
22
3
HOH
HOH
207
B
MO6
22
3
HOH
HOH
208
B
MO6
23
3
HOH
HOH
209
B
MO6
23
3
HOH
HOH
210
B
MO6
23
3
HOH
HOH
211
B
MO6
23
3
HOH
HOH
212
B
MO6
23
3
HOH
HOH
213
B
MO6
23
3
HOH
HOH
214
B
MO6
24
3
HOH
HOH
219
B
MO6
24
3
HOH
HOH
220
B
G
1
n
1
G
1
A
C
2
n
2
C
2
A
G
3
n
3
G
3
A
T
4
n
4
DT
4
A
A
5
n
5
DA
5
A
T
6
n
6
DT
6
A
A
7
n
7
DA
7
A
C
8
n
8
DC
8
A
G
9
n
9
DG
9
A
C
10
n
10
DC
10
A
G
11
n
1
G
11
B
C
12
n
2
C
12
B
G
13
n
3
G
13
B
T
14
n
4
DT
14
B
A
15
n
5
DA
15
B
T
16
n
6
DT
16
B
A
17
n
7
DA
17
B
C
18
n
8
DC
18
B
G
19
n
9
DG
19
B
C
20
n
10
DC
20
B
0.193
0.191
0.239
507
5
10217
author_defined_assembly
2
dimeric
A
HOH
215
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
A
HOH
216
G
O
HOH
1_555
178.0
A
HOH
215
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
A
HOH
217
G
O
HOH
1_555
89.7
A
HOH
216
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
A
HOH
217
G
O
HOH
1_555
91.4
A
HOH
215
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
A
HOH
218
G
O
HOH
1_555
88.8
A
HOH
216
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
A
HOH
218
G
O
HOH
1_555
89.4
A
HOH
217
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
A
HOH
218
G
O
HOH
1_555
90.7
A
HOH
215
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
B
HOH
219
H
O
HOH
1_555
91.2
A
HOH
216
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
B
HOH
219
H
O
HOH
1_555
87.8
A
HOH
217
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
B
HOH
219
H
O
HOH
1_555
177.8
A
HOH
218
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
B
HOH
219
H
O
HOH
1_555
91.3
A
HOH
215
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
B
HOH
220
H
O
HOH
1_555
93.0
A
HOH
216
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
B
HOH
220
H
O
HOH
1_555
88.8
A
HOH
217
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
B
HOH
220
H
O
HOH
1_555
86.8
A
HOH
218
G
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
B
HOH
220
H
O
HOH
1_555
176.8
B
HOH
219
H
O
HOH
1_555
A
MG
24
C
MG
MG
1_555
B
HOH
220
H
O
HOH
1_555
91.2
A
HOH
205
G
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
203
H
O
HOH
1_555
91.4
A
HOH
205
G
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
204
H
O
HOH
1_555
89.2
B
HOH
203
H
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
204
H
O
HOH
1_555
176.8
A
HOH
205
G
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
206
H
O
HOH
1_555
90.0
B
HOH
203
H
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
206
H
O
HOH
1_555
88.1
B
HOH
204
H
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
206
H
O
HOH
1_555
88.7
A
HOH
205
G
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
207
H
O
HOH
1_555
176.6
B
HOH
203
H
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
207
H
O
HOH
1_555
91.3
B
HOH
204
H
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
207
H
O
HOH
1_555
88.2
B
HOH
206
H
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
207
H
O
HOH
1_555
92.1
A
HOH
205
G
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
208
H
O
HOH
1_555
89.8
B
HOH
203
H
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
208
H
O
HOH
1_555
89.9
B
HOH
204
H
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
208
H
O
HOH
1_555
93.2
B
HOH
206
H
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
208
H
O
HOH
1_555
178.0
B
HOH
207
H
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
B
HOH
208
H
O
HOH
1_555
88.2
B
HOH
197
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
198
H
O
HOH
1_555
178.7
B
HOH
197
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
199
H
O
HOH
1_555
88.4
B
HOH
198
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
199
H
O
HOH
1_555
92.6
B
HOH
197
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
200
H
O
HOH
1_555
90.0
B
HOH
198
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
200
H
O
HOH
1_555
89.2
B
HOH
199
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
200
H
O
HOH
1_555
90.1
B
HOH
197
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
201
H
O
HOH
1_555
88.7
B
HOH
198
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
201
H
O
HOH
1_555
90.3
B
HOH
199
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
201
H
O
HOH
1_555
176.9
B
HOH
200
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
201
H
O
HOH
1_555
90.9
B
HOH
197
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
202
H
O
HOH
1_555
89.3
B
HOH
198
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
202
H
O
HOH
1_555
91.4
B
HOH
199
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
202
H
O
HOH
1_555
88.4
B
HOH
200
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
202
H
O
HOH
1_555
178.4
B
HOH
201
H
O
HOH
1_555
B
MG
21
D
MG
MG
1_555
B
HOH
202
H
O
HOH
1_555
90.6
B
HOH
209
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
210
H
O
HOH
1_555
177.6
B
HOH
209
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
211
H
O
HOH
1_555
88.8
B
HOH
210
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
211
H
O
HOH
1_555
89.3
B
HOH
209
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
212
H
O
HOH
1_555
88.3
B
HOH
210
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
212
H
O
HOH
1_555
90.2
B
HOH
211
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
212
H
O
HOH
1_555
89.5
B
HOH
209
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
213
H
O
HOH
1_555
89.8
B
HOH
210
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
213
H
O
HOH
1_555
92.0
B
HOH
211
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
213
H
O
HOH
1_555
178.5
B
HOH
212
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
213
H
O
HOH
1_555
89.8
B
HOH
209
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
214
H
O
HOH
1_555
90.0
B
HOH
210
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
214
H
O
HOH
1_555
91.4
B
HOH
211
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
214
H
O
HOH
1_555
89.5
B
HOH
212
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
214
H
O
HOH
1_555
178.1
B
HOH
213
H
O
HOH
1_555
B
MG
23
F
MG
MG
1_555
B
HOH
214
H
O
HOH
1_555
91.1
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
G
3
0.068
SIDE CHAIN
1
A
DA
7
0.063
SIDE CHAIN
1
B
G
11
0.073
SIDE CHAIN
1
B
DC
20
0.066
SIDE CHAIN
1
-4.46
0.70
109.70
105.24
A
A
A
C1'
O4'
C4'
C
C
C
2
2
2
N
1
-2.50
0.40
104.50
102.00
A
A
A
O4'
C4'
C3'
DT
DT
DT
4
4
4
N
1
3.83
0.60
118.60
122.43
A
A
A
C6
N1
C2
DA
DA
DA
5
5
5
N
1
3.65
0.60
118.60
122.25
A
A
A
C6
N1
C2
DA
DA
DA
7
7
7
N
1
-3.06
0.50
117.70
114.64
A
A
A
C5
C6
N1
DA
DA
DA
7
7
7
N
1
5.29
0.80
123.70
128.99
A
A
A
C5
C6
N6
DA
DA
DA
7
7
7
N
1
-3.17
0.40
104.50
101.33
A
A
A
O4'
C4'
C3'
DC
DC
DC
8
8
8
N
1
-3.86
0.40
104.50
100.64
A
A
A
O4'
C4'
C3'
DC
DC
DC
10
10
10
N
1
2.87
0.30
108.30
111.17
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
4.10
0.40
120.30
124.40
A
A
A
C6
N1
C2
DC
DC
DC
10
10
10
N
1
-3.83
0.50
121.00
117.17
A
A
A
C5
C6
N1
DC
DC
DC
10
10
10
N
1
-5.02
0.70
120.20
115.18
A
A
A
C5
C4
N4
DC
DC
DC
10
10
10
N
1
-3.20
0.40
120.30
117.10
B
B
B
C6
N1
C2
C
C
C
12
12
12
N
1
5.06
0.50
121.00
126.06
B
B
B
C5
C6
N1
C
C
C
12
12
12
N
1
5.41
0.90
109.80
115.21
B
B
B
C5'
C4'
O4'
G
G
G
13
13
13
N
1
-3.71
0.60
119.90
116.19
B
B
B
N1
C6
O6
G
G
G
13
13
13
N
1
3.92
0.60
128.60
132.52
B
B
B
C5
C6
O6
G
G
G
13
13
13
N
1
-2.41
0.40
104.50
102.09
B
B
B
O4'
C4'
C3'
DA
DA
DA
15
15
15
N
1
-2.82
0.40
104.50
101.68
B
B
B
O4'
C4'
C3'
DT
DT
DT
16
16
16
N
1
-2.67
0.40
104.50
101.83
B
B
B
O4'
C4'
C3'
DA
DA
DA
17
17
17
N
1
-3.07
0.40
104.50
101.43
B
B
B
O4'
C4'
C3'
DC
DC
DC
18
18
18
N
1
1.89
0.30
108.30
110.19
B
B
B
O4'
C1'
N1
DC
DC
DC
18
18
18
N
0.242
0.193
0.195
0.193
1.40
20.0
2139
519
10433
10433
1830
5
98.7
RANDOM
1
A POSTERIORI
0.0
0.0
MOLECULAR REPLACEMENT
NDB ID ADJ043
G.PARKINSON ET AL.
SHELXL SWAT OPTION
0
0
534
1.40
20.0
96
534
28
410
0
0.011
0.027
0.070
0.006
0.032
22.2
1.40
20.0
1DNO
10433
10433
0.0
0.0
0.067
1
37.3
11.7
98.7
0.092
1.40
1.45
23.8
11.0
91.7
data scaling
d*TREK
data reduction
HKL-2000
model building
X-PLOR
refinement
SHELXL-97
data reduction
d*TREK
data scaling
HKL-2000
phasing
X-PLOR
A-DNA/RNA DODECAMER R(GCG)D(TATACGC) MG BINDING SITES
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
metalc
2.045
A
MG
24
C
MG
MG
1_555
A
HOH
215
G
O
HOH
1_555
metalc
2.050
A
MG
24
C
MG
MG
1_555
A
HOH
216
G
O
HOH
1_555
metalc
2.051
A
MG
24
C
MG
MG
1_555
A
HOH
217
G
O
HOH
1_555
metalc
2.065
A
MG
24
C
MG
MG
1_555
A
HOH
218
G
O
HOH
1_555
metalc
2.060
A
MG
24
C
MG
MG
1_555
B
HOH
219
H
O
HOH
1_555
metalc
2.081
A
MG
24
C
MG
MG
1_555
B
HOH
220
H
O
HOH
1_555
metalc
2.059
A
HOH
205
G
O
HOH
1_555
B
MG
22
E
MG
MG
1_555
metalc
2.067
B
MG
21
D
MG
MG
1_555
B
HOH
197
H
O
HOH
1_555
metalc
2.060
B
MG
21
D
MG
MG
1_555
B
HOH
198
H
O
HOH
1_555
metalc
2.072
B
MG
21
D
MG
MG
1_555
B
HOH
199
H
O
HOH
1_555
metalc
2.059
B
MG
21
D
MG
MG
1_555
B
HOH
200
H
O
HOH
1_555
metalc
2.061
B
MG
21
D
MG
MG
1_555
B
HOH
201
H
O
HOH
1_555
metalc
2.059
B
MG
21
D
MG
MG
1_555
B
HOH
202
H
O
HOH
1_555
metalc
2.053
B
MG
22
E
MG
MG
1_555
B
HOH
203
H
O
HOH
1_555
metalc
2.059
B
MG
22
E
MG
MG
1_555
B
HOH
204
H
O
HOH
1_555
metalc
2.059
B
MG
22
E
MG
MG
1_555
B
HOH
206
H
O
HOH
1_555
metalc
2.067
B
MG
22
E
MG
MG
1_555
B
HOH
207
H
O
HOH
1_555
metalc
2.053
B
MG
22
E
MG
MG
1_555
B
HOH
208
H
O
HOH
1_555
metalc
2.066
B
MG
23
F
MG
MG
1_555
B
HOH
209
H
O
HOH
1_555
metalc
2.057
B
MG
23
F
MG
MG
1_555
B
HOH
210
H
O
HOH
1_555
metalc
2.072
B
MG
23
F
MG
MG
1_555
B
HOH
211
H
O
HOH
1_555
metalc
2.058
B
MG
23
F
MG
MG
1_555
B
HOH
212
H
O
HOH
1_555
metalc
2.048
B
MG
23
F
MG
MG
1_555
B
HOH
213
H
O
HOH
1_555
metalc
2.050
B
MG
23
F
MG
MG
1_555
B
HOH
214
H
O
HOH
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
DC
20
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
DC
20
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
DC
20
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
C
2
A
N3
C
2
1_555
B
DG
19
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
C
2
A
N4
C
2
1_555
B
DG
19
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
C
2
A
O2
C
2
1_555
B
DG
19
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
A
G
3
A
N1
G
3
1_555
B
DC
18
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
G
3
A
N2
G
3
1_555
B
DC
18
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
G
3
A
O6
G
3
1_555
B
DC
18
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
DA
17
B
N1
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
DA
17
B
N6
DA
7
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
16
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
16
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
15
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
15
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
B
DT
14
B
N3
DT
4
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
B
DT
14
B
O4
DT
4
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
G
13
B
N1
G
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
G
13
B
O6
G
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
G
13
B
N2
G
3
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
B
C
12
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
B
C
12
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
B
C
12
B
N4
C
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
G
11
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
G
11
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
G
11
B
N2
G
1
1_555
DNA-RNA HYBRID
DNA CONFORMATION, RNA/DNA HYBRID, METAL IONS, DNA-RNA COMPLEX, DNA-RNA HYBRID COMPLEX, DNA-RNA HYBRID
1DNO
PDB
1
1DNO
1
10
1DNO
1
10
1DNO
A
1
1
10
11
20
1DNO
11
20
1DNO
B
1
1
10
BINDING SITE FOR RESIDUE MG B 21
B
MG
21
Software
6
BINDING SITE FOR RESIDUE MG B 22
B
MG
22
Software
6
BINDING SITE FOR RESIDUE MG B 23
B
MG
23
Software
6
BINDING SITE FOR RESIDUE MG A 24
A
MG
24
Software
6
B
HOH
197
H
HOH
6
1_555
B
HOH
198
H
HOH
6
1_555
B
HOH
199
H
HOH
6
1_555
B
HOH
200
H
HOH
6
1_555
B
HOH
201
H
HOH
6
1_555
B
HOH
202
H
HOH
6
1_555
A
HOH
205
G
HOH
6
1_555
B
HOH
203
H
HOH
6
1_555
B
HOH
204
H
HOH
6
1_555
B
HOH
206
H
HOH
6
1_555
B
HOH
207
H
HOH
6
1_555
B
HOH
208
H
HOH
6
1_555
B
HOH
209
H
HOH
6
1_555
B
HOH
210
H
HOH
6
1_555
B
HOH
211
H
HOH
6
1_555
B
HOH
212
H
HOH
6
1_555
B
HOH
213
H
HOH
6
1_555
B
HOH
214
H
HOH
6
1_555
A
HOH
215
G
HOH
6
1_555
A
HOH
216
G
HOH
6
1_555
A
HOH
217
G
HOH
6
1_555
A
HOH
218
G
HOH
6
1_555
B
HOH
219
H
HOH
6
1_555
B
HOH
220
H
HOH
6
1_555
19
orthorhombic
P 21 21 21