0.039401
0.000000
0.000000
0.000000
0.024830
0.000000
0.000000
0.000000
0.015289
0.00000
0.00000
0.00000
Yin, Y.W.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
25.380
40.274
65.405
C10 H16 N3 O7 P
321.224
n
5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
DNA 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
H2 O
18.015
WATER
non-polymer
Mg 2
24.305
MAGNESIUM ION
non-polymer
N
1
N
N
N
2
N
C
N
3
N
N
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
O
N
9
N
N
N
10
R
C
N
11
N
C
N
12
S
C
N
13
R
C
N
14
N
O
N
15
N
O
N
16
N
C
N
17
N
O
N
18
N
P
N
19
N
O
N
20
N
O
N
21
N
O
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
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
N
C
N
49
R
C
Y
50
N
N
Y
51
N
C
Y
52
N
N
Y
53
N
C
Y
54
N
C
N
55
N
N
Y
56
N
N
Y
57
N
C
Y
58
N
N
Y
59
N
C
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
H
N
74
N
O
N
75
N
P
N
76
N
O
N
77
N
O
N
78
N
O
N
79
N
C
N
80
R
C
N
81
N
O
N
82
S
C
N
83
N
O
N
84
N
C
N
85
R
C
N
86
N
N
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
C
N
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
Y
120
N
N
Y
121
N
C
Y
122
N
N
Y
123
N
C
N
124
N
C
N
125
N
O
N
126
N
N
N
127
N
C
N
128
N
N
N
129
N
N
Y
130
N
C
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
H
N
145
N
O
N
146
N
P
N
147
N
O
N
148
N
O
N
149
N
O
N
150
N
C
N
151
R
C
N
152
N
O
N
153
S
C
N
154
N
O
N
155
N
C
N
156
R
C
N
157
N
N
N
158
N
C
N
159
N
O
N
160
N
N
N
161
N
C
N
162
N
O
N
163
N
C
N
164
N
C
N
165
N
C
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
H
N
181
N
O
N
182
N
H
N
183
N
H
N
184
N
MG
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
N
6
N
doub
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
doub
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
sing
N
28
N
sing
N
29
N
sing
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
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
Y
62
N
sing
Y
63
N
sing
Y
64
N
doub
N
65
N
sing
Y
66
N
sing
Y
67
N
sing
Y
68
N
doub
N
69
N
sing
Y
70
N
doub
N
71
N
sing
N
72
N
sing
Y
73
N
sing
Y
74
N
doub
N
75
N
sing
Y
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
doub
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
sing
N
102
N
doub
N
103
N
sing
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
doub
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
N
134
N
sing
Y
135
N
sing
Y
136
N
sing
Y
137
N
doub
N
138
N
sing
Y
139
N
sing
N
140
N
sing
Y
141
N
doub
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
doub
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
doub
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
sing
N
176
N
doub
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
doub
N
181
N
sing
N
182
N
sing
N
183
N
doub
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
52
8590
8598
10.1021/bi400980c
24147911
Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence.
2013
10.2210/pdb4mkw/pdb
pdb_00004mkw
Chirality error at C3' of 5CM B 15
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
CCD
ADSC QUANTUM 315r
SINGLE WAVELENGTH
M
x-ray
1
1.0
19-ID
APS
SYNCHROTRON
APS BEAMLINE 19-ID
3677.419
5methylC DNA dodecamer
2
syn
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
193
nat
water
no
yes
(DC)(DG)(5CM)(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
2.27
45.87
EVAPORATION
7
hanging drop, pH 7, EVAPORATION, temperature 290K
290
2.127
1
19
A
1
B
24
-0.863
A_DC1:DG24_B
1
-13.864
0.232
0.214
-0.178
8.194
1
19
A
2
B
23
-2.363
A_DG2:DC23_B
2
-12.514
-0.256
0.518
-0.199
-3.083
1
19
A
3
B
22
0.386
A_5CM3:DG22_B
3
-8.050
0.205
0.178
-0.117
12.999
1
19
A
4
B
21
-0.045
A_DG4:DC21_B
4
-8.258
-0.268
0.020
-0.178
5.752
1
20
A
5
B
20
2.757
A_DA5:DT20_B
5
-14.732
0.028
-0.055
-0.119
1.255
1
20
A
6
B
19
3.665
A_DA6:DT19_B
6
-16.824
0.023
0.131
-0.137
-1.010
1
20
A
7
B
18
3.244
A_DT7:DA18_B
7
-16.286
-0.039
0.087
-0.123
-1.560
1
20
A
8
B
17
3.587
A_DT8:DA17_B
8
-12.457
-0.074
-0.006
-0.174
-12.540
1
19
A
9
B
16
-2.210
A_DC9:DG16_B
9
-8.036
0.203
0.078
-0.150
4.984
1
19
A
10
B
15
2.741
A_DG10:5CM15_B
10
-6.693
-0.160
0.186
-0.102
1.967
1
19
A
11
B
14
-2.687
A_DC11:DG14_B
11
-16.061
0.117
0.155
-0.240
8.907
1
19
A
12
B
13
-9.793
A_DG12:DC13_B
12
25.520
-0.139
-0.554
-0.484
3.074
35.104
A
A
1
2
9.369
B
B
24
23
3.100
5.621
-0.155
0.061
AA_DC1DG2:DC23DG24_BB
1
-3.013
5.022
34.538
-0.699
-0.172
3.516
43.699
A
A
2
3
-11.648
B
B
23
22
3.646
-8.608
0.665
0.576
AA_DG25CM3:DG22DC23_BB
2
3.898
-5.274
42.714
1.687
-0.479
2.966
26.734
A
A
3
4
24.206
B
B
22
21
3.001
10.876
-0.270
0.567
AA_5CM3DG4:DC21DG22_BB
3
0.905
-2.014
24.442
-1.472
0.809
3.379
38.523
A
A
4
5
4.719
B
B
21
20
3.389
3.110
-0.268
-0.054
AA_DG4DA5:DT20DC21_BB
4
-0.616
0.934
38.397
-0.481
0.327
3.236
36.716
A
A
5
6
2.130
B
B
20
19
3.257
1.341
0.064
-0.356
AA_DA5DA6:DT19DT20_BB
5
-1.643
2.610
36.657
-0.746
-0.325
3.279
32.457
A
A
6
7
-3.799
B
B
19
18
3.247
-2.122
0.037
-0.607
AA_DA6DT7:DA18DT19_BB
6
0.653
-1.170
32.383
-0.714
0.048
3.211
34.676
A
A
7
8
-3.104
B
B
18
17
3.199
-1.849
-0.071
-0.396
AA_DT7DT8:DA17DA18_BB
7
1.177
-1.977
34.609
-0.387
0.296
3.497
42.557
A
A
8
9
-3.034
B
B
17
16
3.491
-2.201
-0.192
-0.259
AA_DT8DC9:DG16DA17_BB
8
0.484
-0.667
42.500
-0.120
0.316
2.993
25.329
A
A
9
10
7.924
B
B
16
15
3.001
3.460
0.693
0.627
AA_DC9DG10:5CM15DG16_BB
9
-2.055
4.707
25.013
0.505
-2.130
3.333
43.670
A
A
10
11
-10.984
B
B
15
14
3.406
-8.122
-1.221
0.503
AA_DG10DC11:DG145CM15_BB
10
-2.882
3.898
42.852
1.487
1.354
3.361
38.570
A
A
11
12
-16.723
B
B
14
13
3.639
-10.902
0.334
0.555
AA_DC11DG12:DC13DG14_BB
11
1.904
-2.920
37.006
2.315
-0.249
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
1
0
2013-11-06
1
1
2013-12-11
1
2
2024-02-28
_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.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.pdbx_leaving_atom_flag
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Different modification of the same DNA.
RCSB
Y
RCSB
2013-09-05
REL
REL
MG
MAGNESIUM ION
HOH
water
synthetic DNA oligos
sample
MG
25
2
MG
MG
101
A
HOH
1
3
HOH
HOH
201
A
HOH
3
3
HOH
HOH
202
A
HOH
4
3
HOH
HOH
203
A
HOH
7
3
HOH
HOH
204
A
HOH
8
3
HOH
HOH
205
A
HOH
9
3
HOH
HOH
206
A
HOH
11
3
HOH
HOH
207
A
HOH
12
3
HOH
HOH
208
A
HOH
13
3
HOH
HOH
209
A
HOH
14
3
HOH
HOH
210
A
HOH
18
3
HOH
HOH
211
A
HOH
21
3
HOH
HOH
212
A
HOH
22
3
HOH
HOH
213
A
HOH
23
3
HOH
HOH
214
A
HOH
25
3
HOH
HOH
215
A
HOH
26
3
HOH
HOH
216
A
HOH
27
3
HOH
HOH
217
A
HOH
28
3
HOH
HOH
218
A
HOH
30
3
HOH
HOH
219
A
HOH
31
3
HOH
HOH
220
A
HOH
32
3
HOH
HOH
221
A
HOH
36
3
HOH
HOH
222
A
HOH
38
3
HOH
HOH
223
A
HOH
40
3
HOH
HOH
224
A
HOH
41
3
HOH
HOH
225
A
HOH
42
3
HOH
HOH
226
A
HOH
43
3
HOH
HOH
227
A
HOH
45
3
HOH
HOH
228
A
HOH
47
3
HOH
HOH
229
A
HOH
48
3
HOH
HOH
230
A
HOH
49
3
HOH
HOH
231
A
HOH
53
3
HOH
HOH
232
A
HOH
54
3
HOH
HOH
233
A
HOH
57
3
HOH
HOH
234
A
HOH
58
3
HOH
HOH
235
A
HOH
61
3
HOH
HOH
236
A
HOH
62
3
HOH
HOH
237
A
HOH
64
3
HOH
HOH
238
A
HOH
65
3
HOH
HOH
239
A
HOH
70
3
HOH
HOH
240
A
HOH
71
3
HOH
HOH
241
A
HOH
73
3
HOH
HOH
242
A
HOH
75
3
HOH
HOH
243
A
HOH
77
3
HOH
HOH
244
A
HOH
78
3
HOH
HOH
245
A
HOH
79
3
HOH
HOH
246
A
HOH
80
3
HOH
HOH
247
A
HOH
82
3
HOH
HOH
248
A
HOH
83
3
HOH
HOH
249
A
HOH
85
3
HOH
HOH
250
A
HOH
86
3
HOH
HOH
251
A
HOH
89
3
HOH
HOH
252
A
HOH
91
3
HOH
HOH
253
A
HOH
93
3
HOH
HOH
254
A
HOH
94
3
HOH
HOH
255
A
HOH
95
3
HOH
HOH
256
A
HOH
99
3
HOH
HOH
257
A
HOH
101
3
HOH
HOH
258
A
HOH
107
3
HOH
HOH
259
A
HOH
108
3
HOH
HOH
260
A
HOH
110
3
HOH
HOH
261
A
HOH
111
3
HOH
HOH
262
A
HOH
112
3
HOH
HOH
263
A
HOH
115
3
HOH
HOH
264
A
HOH
116
3
HOH
HOH
265
A
HOH
117
3
HOH
HOH
266
A
HOH
118
3
HOH
HOH
267
A
HOH
120
3
HOH
HOH
268
A
HOH
121
3
HOH
HOH
269
A
HOH
122
3
HOH
HOH
270
A
HOH
123
3
HOH
HOH
271
A
HOH
124
3
HOH
HOH
272
A
HOH
126
3
HOH
HOH
273
A
HOH
127
3
HOH
HOH
274
A
HOH
128
3
HOH
HOH
275
A
HOH
129
3
HOH
HOH
276
A
HOH
131
3
HOH
HOH
277
A
HOH
134
3
HOH
HOH
278
A
HOH
135
3
HOH
HOH
279
A
HOH
136
3
HOH
HOH
280
A
HOH
138
3
HOH
HOH
281
A
HOH
139
3
HOH
HOH
282
A
HOH
141
3
HOH
HOH
283
A
HOH
142
3
HOH
HOH
284
A
HOH
143
3
HOH
HOH
285
A
HOH
145
3
HOH
HOH
286
A
HOH
147
3
HOH
HOH
287
A
HOH
148
3
HOH
HOH
288
A
HOH
149
3
HOH
HOH
289
A
HOH
153
3
HOH
HOH
290
A
HOH
157
3
HOH
HOH
291
A
HOH
158
3
HOH
HOH
292
A
HOH
162
3
HOH
HOH
293
A
HOH
163
3
HOH
HOH
294
A
HOH
168
3
HOH
HOH
295
A
HOH
169
3
HOH
HOH
296
A
HOH
170
3
HOH
HOH
297
A
HOH
171
3
HOH
HOH
298
A
HOH
172
3
HOH
HOH
299
A
HOH
175
3
HOH
HOH
300
A
HOH
178
3
HOH
HOH
301
A
HOH
179
3
HOH
HOH
302
A
HOH
181
3
HOH
HOH
303
A
HOH
182
3
HOH
HOH
304
A
HOH
186
3
HOH
HOH
305
A
HOH
188
3
HOH
HOH
306
A
HOH
189
3
HOH
HOH
307
A
HOH
191
3
HOH
HOH
308
A
HOH
192
3
HOH
HOH
309
A
HOH
193
3
HOH
HOH
310
A
HOH
2
3
HOH
HOH
101
B
HOH
5
3
HOH
HOH
102
B
HOH
6
3
HOH
HOH
103
B
HOH
10
3
HOH
HOH
104
B
HOH
15
3
HOH
HOH
105
B
HOH
16
3
HOH
HOH
106
B
HOH
17
3
HOH
HOH
107
B
HOH
19
3
HOH
HOH
108
B
HOH
20
3
HOH
HOH
109
B
HOH
24
3
HOH
HOH
110
B
HOH
29
3
HOH
HOH
111
B
HOH
33
3
HOH
HOH
112
B
HOH
34
3
HOH
HOH
113
B
HOH
35
3
HOH
HOH
114
B
HOH
37
3
HOH
HOH
115
B
HOH
39
3
HOH
HOH
116
B
HOH
44
3
HOH
HOH
117
B
HOH
46
3
HOH
HOH
118
B
HOH
50
3
HOH
HOH
119
B
HOH
51
3
HOH
HOH
120
B
HOH
52
3
HOH
HOH
121
B
HOH
55
3
HOH
HOH
122
B
HOH
56
3
HOH
HOH
123
B
HOH
59
3
HOH
HOH
124
B
HOH
60
3
HOH
HOH
125
B
HOH
63
3
HOH
HOH
126
B
HOH
66
3
HOH
HOH
127
B
HOH
67
3
HOH
HOH
128
B
HOH
68
3
HOH
HOH
129
B
HOH
69
3
HOH
HOH
130
B
HOH
72
3
HOH
HOH
131
B
HOH
74
3
HOH
HOH
132
B
HOH
76
3
HOH
HOH
133
B
HOH
81
3
HOH
HOH
134
B
HOH
84
3
HOH
HOH
135
B
HOH
87
3
HOH
HOH
136
B
HOH
88
3
HOH
HOH
137
B
HOH
90
3
HOH
HOH
138
B
HOH
92
3
HOH
HOH
139
B
HOH
96
3
HOH
HOH
140
B
HOH
97
3
HOH
HOH
141
B
HOH
98
3
HOH
HOH
142
B
HOH
100
3
HOH
HOH
143
B
HOH
102
3
HOH
HOH
144
B
HOH
103
3
HOH
HOH
145
B
HOH
104
3
HOH
HOH
146
B
HOH
105
3
HOH
HOH
147
B
HOH
106
3
HOH
HOH
148
B
HOH
109
3
HOH
HOH
149
B
HOH
113
3
HOH
HOH
150
B
HOH
114
3
HOH
HOH
151
B
HOH
119
3
HOH
HOH
152
B
HOH
125
3
HOH
HOH
153
B
HOH
130
3
HOH
HOH
154
B
HOH
132
3
HOH
HOH
155
B
HOH
133
3
HOH
HOH
156
B
HOH
137
3
HOH
HOH
157
B
HOH
140
3
HOH
HOH
158
B
HOH
144
3
HOH
HOH
159
B
HOH
146
3
HOH
HOH
160
B
HOH
150
3
HOH
HOH
161
B
HOH
151
3
HOH
HOH
162
B
HOH
152
3
HOH
HOH
163
B
HOH
154
3
HOH
HOH
164
B
HOH
155
3
HOH
HOH
165
B
HOH
156
3
HOH
HOH
166
B
HOH
159
3
HOH
HOH
167
B
HOH
160
3
HOH
HOH
168
B
HOH
161
3
HOH
HOH
169
B
HOH
164
3
HOH
HOH
170
B
HOH
165
3
HOH
HOH
171
B
HOH
166
3
HOH
HOH
172
B
HOH
167
3
HOH
HOH
173
B
HOH
173
3
HOH
HOH
174
B
HOH
174
3
HOH
HOH
175
B
HOH
176
3
HOH
HOH
176
B
HOH
177
3
HOH
HOH
177
B
HOH
180
3
HOH
HOH
178
B
HOH
183
3
HOH
HOH
179
B
HOH
184
3
HOH
HOH
180
B
HOH
185
3
HOH
HOH
181
B
HOH
187
3
HOH
HOH
182
B
HOH
190
3
HOH
HOH
183
B
DC
1
n
1
DC
1
A
DG
2
n
2
DG
2
A
5CM
3
n
3
5CM
3
A
DG
4
n
4
DG
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
DC
9
n
9
DC
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
5CM
15
n
3
5CM
15
B
DG
16
n
4
DG
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
DC
21
n
9
DC
21
B
DG
22
n
10
DG
22
B
DC
23
n
11
DC
23
B
DG
24
n
12
DG
24
B
0.1275
0.1388
0.5881
0.6043
-0.9972
1.5483
0.0896
0.0407
-0.0097
0.0763
0.0944
0.1500
-0.0977
-0.0297
-0.0970
0.1691
0.0145
0.0056
0.1760
0.0075
0.1810
refined
10.4426
0.8733
24.0836
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
all
author_and_software_defined_assembly
PISA
2
dimeric
2360
2
4350
A
HOH
211
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
263
D
O
HOH
1_555
91.3
A
HOH
211
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
108
E
O
HOH
1_555
91.6
A
HOH
263
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
108
E
O
HOH
1_555
91.6
A
HOH
211
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
109
E
O
HOH
1_555
176.6
A
HOH
263
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
109
E
O
HOH
1_555
87.0
B
HOH
108
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
109
E
O
HOH
1_555
85.5
A
HOH
211
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
150
E
O
HOH
1_555
91.6
A
HOH
263
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
150
E
O
HOH
1_555
86.6
B
HOH
108
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
150
E
O
HOH
1_555
176.4
B
HOH
109
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
150
E
O
HOH
1_555
91.3
A
HOH
211
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
152
E
O
HOH
1_555
89.0
A
HOH
263
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
152
E
O
HOH
1_555
177.1
B
HOH
108
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
152
E
O
HOH
1_555
91.2
B
HOH
109
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
152
E
O
HOH
1_555
92.9
B
HOH
150
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
152
E
O
HOH
1_555
90.5
A
5CM
3
A
5CM
3
DC
B
5CM
15
B
5CM
3
DC
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
B
C3'
5CM
15
PLANAR
1
A
B
O
O
HOH
HOH
268
171
1.85
1
A
A
OP1
O
DC
HOH
11
265
1.86
1
B
B
O
O
HOH
HOH
131
139
1.92
1
A
A
O
O
HOH
HOH
241
296
2.04
1
B
B
O
O
HOH
HOH
174
176
2.05
1
A
A
O
O
HOH
HOH
213
297
2.06
1
B
B
O
O
HOH
HOH
153
176
2.07
1
B
B
O
O
HOH
HOH
117
171
2.08
1
A
A
OP1
O
DG
HOH
10
296
2.09
1
A
A
OP1
O
DG
HOH
12
246
2.09
1
B
B
OP2
O
DG
HOH
14
140
2.15
1
A
A
O
O
HOH
HOH
249
297
2.16
1
A
A
O
O
HOH
HOH
295
304
2.16
1
A
A
O
O
HOH
HOH
256
258
2.16
1
B
B
OP2
O
DT
HOH
20
165
2.16
1
B
B
O5'
O
DG
HOH
22
162
2.17
1
-4.99
0.70
108.00
103.01
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
-5.13
0.80
102.40
97.27
A
A
A
C3'
C2'
C1'
DG
DG
DG
10
10
10
N
1
2.53
0.30
108.30
110.83
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
-5.51
0.70
108.00
102.49
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
-5.13
0.70
108.00
102.87
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
3.41
0.30
108.30
111.71
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
1
-4.95
0.70
108.00
103.05
B
B
B
O4'
C1'
N9
DA
DA
DA
17
17
17
N
1
-5.45
0.70
108.00
102.55
B
B
B
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
A
B
O
O
HOH
HOH
300
183
1.81
1_555
3_645
1
A
A
O
O
HOH
HOH
294
295
2.09
1_555
3_555
0.2400
0.2101
0.2132
1.219
9.586
1736
17417
17380
9.99
84.24
0.14
10% random
1
1.36
MOLECULAR REPLACEMENT
26.64
0.90
1.11
ML
FLAT BULK SOLVENT MODEL
1.219
9.586
193
682
1
488
0
0.009
546
2.070
840
31.262
230
0.282
92
0.022
26
0.3594
0.3406
1.2549
63
571
38.00
0.3261
0.3223
1.2953
95
844
56.00
0.3112
0.3065
1.3415
129
1173
76.00
0.2724
0.2756
1.3951
162
1451
95.00
0.2715
0.2480
1.4584
166
1499
99.00
0.2512
0.2373
1.5350
171
1530
99.00
0.2272
0.2141
1.6307
165
1513
99.00
0.1970
0.1864
1.7559
169
1523
99.00
0.2193
0.1900
1.9313
173
1557
100.00
0.2021
0.1836
2.2078
171
1546
100.00
0.2394
0.1969
2.7704
174
1555
98.00
0.2859
0.2307
9.5866
98
882
53.00
1.219
10
4MKW
17417
17380
2.0
2.0
1
99
refinement
PHENIX
(phenix.refine: 1.8.2_1309)
Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
covale
1.607
both
A
DG
2
A
O3'
DG
2
1_555
A
5CM
3
A
P
5CM
3
1_555
covale
1.603
both
A
5CM
3
A
O3'
5CM
3
1_555
A
DG
4
A
P
DG
4
1_555
covale
1.601
both
B
DG
14
B
O3'
DG
2
1_555
B
5CM
15
B
P
5CM
3
1_555
covale
1.602
both
B
5CM
15
B
O3'
5CM
3
1_555
B
DG
16
B
P
DG
4
1_555
metalc
2.156
A
MG
101
C
MG
MG
1_555
A
HOH
211
D
O
HOH
1_555
metalc
2.034
A
MG
101
C
MG
MG
1_555
A
HOH
263
D
O
HOH
1_555
metalc
2.076
A
MG
101
C
MG
MG
1_555
B
HOH
108
E
O
HOH
1_555
metalc
2.130
A
MG
101
C
MG
MG
1_555
B
HOH
109
E
O
HOH
1_555
metalc
2.051
A
MG
101
C
MG
MG
1_555
B
HOH
150
E
O
HOH
1_555
metalc
2.120
A
MG
101
C
MG
MG
1_555
B
HOH
152
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
5CM
3
A
N3
5CM
3
1_555
B
DG
22
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
5CM
3
A
N4
5CM
3
1_555
B
DG
22
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
5CM
3
A
O2
5CM
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
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
5CM
15
B
N3
5CM
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
5CM
15
B
O2
5CM
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
5CM
15
B
N4
5CM
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
Modified DNA dodecamer, DNA
4MKW
PDB
1
4MKW
1
12
4MKW
1
12
4MKW
A
1
1
12
13
24
4MKW
13
24
4MKW
B
1
1
12
BINDING SITE FOR RESIDUE MG A 101
A
MG
101
Software
6
A
HOH
211
D
HOH
6
1_555
A
HOH
263
D
HOH
6
1_555
B
HOH
108
E
HOH
6
1_555
B
HOH
109
E
HOH
6
1_555
B
HOH
150
E
HOH
6
1_555
B
HOH
152
E
HOH
6
1_555
19
P 21 21 21