0.039006
0.000000
0.000000
0.000000
0.023942
0.000000
0.000000
0.000000
0.015626
0.00000
0.00000
0.00000
Spingler, B.
Renciuk, D.
Vorlickova, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
25.637
41.767
63.997
C10 H16 N3 O8 P
337.223
n
2'-deoxy-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)
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
K 1
39.098
POTASSIUM ION
non-polymer
N
1
N
P
N
2
N
O
N
3
N
O
N
4
N
O
N
5
N
C
N
6
R
C
N
7
N
O
N
8
S
C
N
9
N
O
N
10
N
C
N
11
R
C
N
12
N
N
N
13
N
C
N
14
N
O
N
15
N
N
N
16
N
C
N
17
N
N
N
18
N
C
N
19
N
C
N
20
N
O
N
21
N
C
N
22
N
O
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
H
N
39
N
O
N
40
N
P
N
41
N
O
N
42
N
O
N
43
N
O
N
44
N
C
N
45
R
C
N
46
N
O
N
47
S
C
N
48
N
O
N
49
N
C
N
50
R
C
Y
51
N
N
Y
52
N
C
Y
53
N
N
Y
54
N
C
Y
55
N
C
N
56
N
N
Y
57
N
N
Y
58
N
C
Y
59
N
N
Y
60
N
C
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
H
N
75
N
O
N
76
N
P
N
77
N
O
N
78
N
O
N
79
N
O
N
80
N
C
N
81
R
C
N
82
N
O
N
83
S
C
N
84
N
O
N
85
N
C
N
86
R
C
N
87
N
N
N
88
N
C
N
89
N
O
N
90
N
N
N
91
N
C
N
92
N
N
N
93
N
C
N
94
N
C
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
H
N
109
N
O
N
110
N
P
N
111
N
O
N
112
N
O
N
113
N
O
N
114
N
C
N
115
R
C
N
116
N
O
N
117
S
C
N
118
N
O
N
119
N
C
N
120
R
C
Y
121
N
N
Y
122
N
C
Y
123
N
N
Y
124
N
C
N
125
N
C
N
126
N
O
N
127
N
N
N
128
N
C
N
129
N
N
N
130
N
N
Y
131
N
C
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
H
N
146
N
O
N
147
N
P
N
148
N
O
N
149
N
O
N
150
N
O
N
151
N
C
N
152
R
C
N
153
N
O
N
154
S
C
N
155
N
O
N
156
N
C
N
157
R
C
N
158
N
N
N
159
N
C
N
160
N
O
N
161
N
N
N
162
N
C
N
163
N
O
N
164
N
C
N
165
N
C
N
166
N
C
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
H
N
182
N
O
N
183
N
H
N
184
N
H
N
185
N
K
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
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
doub
N
13
N
sing
N
14
N
sing
N
15
N
doub
N
16
N
sing
N
17
N
doub
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
sing
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
sing
N
42
N
doub
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
Y
63
N
sing
Y
64
N
sing
Y
65
N
doub
N
66
N
sing
Y
67
N
sing
Y
68
N
sing
Y
69
N
doub
N
70
N
sing
Y
71
N
doub
N
72
N
sing
N
73
N
sing
Y
74
N
sing
Y
75
N
doub
N
76
N
sing
Y
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
doub
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
sing
N
103
N
doub
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
doub
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
Y
136
N
sing
Y
137
N
sing
Y
138
N
doub
N
139
N
sing
Y
140
N
sing
N
141
N
sing
Y
142
N
doub
N
143
N
doub
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
doub
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
sing
N
177
N
doub
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
doub
N
182
N
sing
N
183
N
sing
N
184
N
doub
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
41
9891
9900
10.1093/nar/gkt738
23963698
Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine.
2013
10.2210/pdb4glh/pdb
pdb_00004glh
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
100
1
PIXEL
2012-06-09
DECTRIS PILATUS 2M-F
BARTELS MONOCHROMATOR
SINGLE WAVELENGTH
M
x-ray
1
1.00067
1.0
X06DA
SLS
1.00067
1.00067
SYNCHROTRON
SLS BEAMLINE X06DA
3693.418
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5HC)P*GP*CP*G)-3')
2
syn
polymer
39.098
POTASSIUM ION
2
syn
non-polymer
18.015
water
68
nat
water
no
yes
(DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(5HC)(DG)(DC)(DG)
CGCGAATTXGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
1
2.32
46.96
VAPOR DIFFUSION, HANGING DROP
7.0
0.04M sodium cacodylate buffer, 0.08M potassium chloride, 0.012M sodium chloride, 0.012M spermine tetra hydrochloride, 37% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
298.0
-1.203
1
19
A
1
B
12
-0.237
A_DC1:DG12_B
1
-0.678
0.303
0.296
-0.208
6.391
1
19
A
2
B
11
-5.353
A_DG2:DC11_B
2
-15.892
-0.192
0.587
-0.297
-1.757
1
19
A
3
B
10
-1.532
A_DC3:DG10_B
3
0.879
0.148
0.063
-0.119
7.986
1
20
A
5
B
8
4.257
A_DA5:DT8_B
4
-19.396
0.079
0.014
-0.146
1.165
1
20
A
6
B
7
4.064
A_DA6:DT7_B
5
-19.548
0.049
0.158
-0.129
-1.362
1
20
A
7
B
6
4.136
A_DT7:DA6_B
6
-17.917
-0.038
0.217
-0.088
-5.056
1
20
A
8
B
5
4.360
A_DT8:DA5_B
7
-12.885
-0.106
0.175
-0.186
11.672
1
19
A
10
B
3
1.246
A_DG10:DC3_B
8
-3.475
-0.201
0.457
-0.098
4.298
1
19
A
11
B
2
-1.543
A_DC11:DG2_B
9
-20.035
0.179
0.293
-0.184
5.442
1
19
A
12
B
1
-5.068
A_DG12:DC1_B
10
-3.562
-0.218
0.178
-0.217
3.210
38.089
A
A
1
2
-6.684
B
B
12
11
3.167
-4.343
-0.870
0.166
AA_DC1DG2:DC11DG12_BB
1
-4.708
7.246
37.566
0.795
0.747
3.615
40.582
A
A
2
3
-10.807
B
B
11
10
3.612
-7.438
0.887
0.122
AA_DG2DC3:DG10DC11_BB
2
5.150
-7.483
39.602
1.104
-0.637
6.496
63.980
A
A
3
5
3.141
B
B
10
8
6.504
3.327
-0.508
-0.041
AA_DC3DA5:DT8DG10_BB
3
-0.159
0.150
63.902
-0.324
0.466
3.322
38.783
A
A
5
6
0.167
B
B
8
7
3.332
0.111
0.067
-0.214
AA_DA5DA6:DT7DT8_BB
4
-2.274
3.426
38.719
-0.336
-0.384
3.274
31.933
A
A
6
7
-3.333
B
B
7
6
3.247
-1.832
0.079
-0.574
AA_DA6DT7:DA6DT7_BB
5
-0.032
0.058
31.882
-0.711
-0.149
3.272
36.211
A
A
7
8
-4.118
B
B
6
5
3.252
-2.557
0.002
-0.420
AA_DT7DT8:DA5DA6_BB
6
0.761
-1.226
36.116
-0.317
0.104
6.231
67.710
A
A
8
10
-3.203
B
B
5
3
6.251
-3.568
0.030
0.229
AA_DT8DG10:DC3DA5_BB
7
-1.913
1.717
67.603
0.465
-0.166
3.419
43.728
A
A
10
11
-13.130
B
B
3
2
3.589
-9.705
-1.326
0.516
AA_DG10DC11:DG2DC3_BB
8
-0.722
0.977
42.684
1.699
1.705
3.382
34.999
A
A
11
12
3.818
B
B
2
1
3.336
2.294
0.598
0.514
AA_DC11DG12:DC1DG2_BB
9
1.299
-2.162
34.902
0.500
-0.793
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Database references
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-08-28
1
1
2013-09-04
1
2
2013-12-04
1
3
2023-09-13
_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_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_seq_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.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2012-08-14
REL
REL
K
POTASSIUM ION
HOH
water
32630
Synthetic construct
sample
1DPN
PDB ENTRY 1DPN
PDB
experimental model
K
51
2
K
K
101
A
K
52
2
K
K
101
B
HOH
104
3
HOH
HOH
201
A
HOH
105
3
HOH
HOH
202
A
HOH
108
3
HOH
HOH
203
A
HOH
112
3
HOH
HOH
204
A
HOH
116
3
HOH
HOH
205
A
HOH
118
3
HOH
HOH
206
A
HOH
123
3
HOH
HOH
207
A
HOH
124
3
HOH
HOH
208
A
HOH
127
3
HOH
HOH
209
A
HOH
128
3
HOH
HOH
210
A
HOH
129
3
HOH
HOH
211
A
HOH
131
3
HOH
HOH
212
A
HOH
132
3
HOH
HOH
213
A
HOH
133
3
HOH
HOH
214
A
HOH
134
3
HOH
HOH
215
A
HOH
135
3
HOH
HOH
216
A
HOH
137
3
HOH
HOH
217
A
HOH
138
3
HOH
HOH
218
A
HOH
139
3
HOH
HOH
219
A
HOH
140
3
HOH
HOH
220
A
HOH
145
3
HOH
HOH
221
A
HOH
146
3
HOH
HOH
222
A
HOH
150
3
HOH
HOH
223
A
HOH
152
3
HOH
HOH
224
A
HOH
153
3
HOH
HOH
225
A
HOH
156
3
HOH
HOH
226
A
HOH
157
3
HOH
HOH
227
A
HOH
159
3
HOH
HOH
228
A
HOH
160
3
HOH
HOH
229
A
HOH
162
3
HOH
HOH
230
A
HOH
164
3
HOH
HOH
231
A
HOH
166
3
HOH
HOH
232
A
HOH
167
3
HOH
HOH
233
A
HOH
168
3
HOH
HOH
234
A
HOH
101
3
HOH
HOH
201
B
HOH
102
3
HOH
HOH
202
B
HOH
103
3
HOH
HOH
203
B
HOH
106
3
HOH
HOH
204
B
HOH
107
3
HOH
HOH
205
B
HOH
109
3
HOH
HOH
206
B
HOH
110
3
HOH
HOH
207
B
HOH
111
3
HOH
HOH
208
B
HOH
113
3
HOH
HOH
209
B
HOH
114
3
HOH
HOH
210
B
HOH
115
3
HOH
HOH
211
B
HOH
117
3
HOH
HOH
212
B
HOH
119
3
HOH
HOH
213
B
HOH
120
3
HOH
HOH
214
B
HOH
121
3
HOH
HOH
215
B
HOH
122
3
HOH
HOH
216
B
HOH
125
3
HOH
HOH
217
B
HOH
126
3
HOH
HOH
218
B
HOH
130
3
HOH
HOH
219
B
HOH
136
3
HOH
HOH
220
B
HOH
141
3
HOH
HOH
221
B
HOH
142
3
HOH
HOH
222
B
HOH
143
3
HOH
HOH
223
B
HOH
144
3
HOH
HOH
224
B
HOH
147
3
HOH
HOH
225
B
HOH
148
3
HOH
HOH
226
B
HOH
149
3
HOH
HOH
227
B
HOH
151
3
HOH
HOH
228
B
HOH
154
3
HOH
HOH
229
B
HOH
155
3
HOH
HOH
230
B
HOH
158
3
HOH
HOH
231
B
HOH
161
3
HOH
HOH
232
B
HOH
163
3
HOH
HOH
233
B
HOH
165
3
HOH
HOH
234
B
DC
1
n
1
DC
1
A
DG
2
n
2
DG
2
A
DC
3
n
3
DC
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
5HC
9
n
9
5HC
9
A
DG
10
n
10
DG
10
A
DC
11
n
11
DC
11
A
DG
12
n
12
DG
12
A
DC
1
n
1
DC
1
B
DG
2
n
2
DG
2
B
DC
3
n
3
DC
3
B
DG
4
n
4
DG
4
B
DA
5
n
5
DA
5
B
DA
6
n
6
DA
6
B
DT
7
n
7
DT
7
B
DT
8
n
8
DT
8
B
5HC
9
n
9
5HC
9
B
DG
10
n
10
DG
10
B
DC
11
n
11
DC
11
B
DG
12
n
12
DG
12
B
0.232
0.237
0.232
0.237
0.272
0.276
399
427
5.115
4.999
7800
author_and_software_defined_assembly
PISA
2
dimeric
1480
-3
4490
A
DT
7
A
O2
DT
7
1_555
A
K
101
C
K
K
1_555
A
DT
8
A
O4'
DT
8
1_555
67.4
A
DT
7
A
O2
DT
7
1_555
A
K
101
C
K
K
1_555
B
DT
7
B
O2
DT
7
1_555
84.6
A
DT
8
A
O4'
DT
8
1_555
A
K
101
C
K
K
1_555
B
DT
7
B
O2
DT
7
1_555
141.0
A
DT
7
A
O2
DT
7
1_555
A
K
101
C
K
K
1_555
B
DT
8
B
O4'
DT
8
1_555
134.2
A
DT
8
A
O4'
DT
8
1_555
A
K
101
C
K
K
1_555
B
DT
8
B
O4'
DT
8
1_555
153.0
B
DT
7
B
O2
DT
7
1_555
A
K
101
C
K
K
1_555
B
DT
8
B
O4'
DT
8
1_555
65.4
A
DT
7
A
O2
DT
7
1_555
A
K
101
C
K
K
1_555
B
HOH
204
F
O
HOH
1_555
123.8
A
DT
8
A
O4'
DT
8
1_555
A
K
101
C
K
K
1_555
B
HOH
204
F
O
HOH
1_555
79.8
B
DT
7
B
O2
DT
7
1_555
A
K
101
C
K
K
1_555
B
HOH
204
F
O
HOH
1_555
95.4
B
DT
8
B
O4'
DT
8
1_555
A
K
101
C
K
K
1_555
B
HOH
204
F
O
HOH
1_555
94.1
A
DT
7
A
O2
DT
7
1_555
A
K
101
C
K
K
1_555
B
HOH
205
F
O
HOH
1_555
95.2
A
DT
8
A
O4'
DT
8
1_555
A
K
101
C
K
K
1_555
B
HOH
205
F
O
HOH
1_555
94.1
B
DT
7
B
O2
DT
7
1_555
A
K
101
C
K
K
1_555
B
HOH
205
F
O
HOH
1_555
115.8
B
DT
8
B
O4'
DT
8
1_555
A
K
101
C
K
K
1_555
B
HOH
205
F
O
HOH
1_555
70.6
B
HOH
204
F
O
HOH
1_555
A
K
101
C
K
K
1_555
B
HOH
205
F
O
HOH
1_555
132.7
A
DT
8
A
O2
DT
8
1_555
B
K
101
D
K
K
1_555
A
5HC
9
A
O4'
5HC
9
1_555
62.8
A
DT
8
A
O2
DT
8
1_555
B
K
101
D
K
K
1_555
B
DT
7
B
O4'
DT
7
1_555
140.8
A
5HC
9
A
O4'
5HC
9
1_555
B
K
101
D
K
K
1_555
B
DT
7
B
O4'
DT
7
1_555
156.3
A
DT
8
A
O2
DT
8
1_555
B
K
101
D
K
K
1_555
B
HOH
204
F
O
HOH
1_555
103.2
A
5HC
9
A
O4'
5HC
9
1_555
B
K
101
D
K
K
1_555
B
HOH
204
F
O
HOH
1_555
102.0
B
DT
7
B
O4'
DT
7
1_555
B
K
101
D
K
K
1_555
B
HOH
204
F
O
HOH
1_555
74.1
A
DT
8
A
O2
DT
8
1_555
B
K
101
D
K
K
1_555
B
HOH
208
F
O
HOH
1_555
119.2
A
5HC
9
A
O4'
5HC
9
1_555
B
K
101
D
K
K
1_555
B
HOH
208
F
O
HOH
1_555
79.1
B
DT
7
B
O4'
DT
7
1_555
B
K
101
D
K
K
1_555
B
HOH
208
F
O
HOH
1_555
86.1
B
HOH
204
F
O
HOH
1_555
B
K
101
D
K
K
1_555
B
HOH
208
F
O
HOH
1_555
131.1
A
5HC
9
A
5HC
9
DC
B
5HC
9
B
5HC
9
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
-5.06
0.70
108.00
102.94
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
-6.37
0.80
102.40
96.03
A
A
A
C3'
C2'
C1'
DG
DG
DG
4
4
4
N
1
-5.18
0.70
108.00
102.82
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
7.55
1.20
119.70
127.25
A
A
A
C3'
O3'
P
DT
DT
DT
7
7
8
Y
1
-5.70
0.70
108.00
102.30
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
-4.95
0.80
102.40
97.45
A
A
A
C3'
C2'
C1'
DG
DG
DG
10
10
10
N
1
-7.44
0.70
108.00
100.56
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
-5.34
0.70
108.00
102.66
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
-3.60
0.60
128.60
125.00
A
A
A
C5
C6
O6
DG
DG
DG
12
12
12
N
1
2.38
0.30
108.30
110.68
B
B
B
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
2.79
0.30
108.30
111.09
B
B
B
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
-5.51
0.70
108.00
102.49
B
B
B
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
4.02
0.60
118.60
122.62
B
B
B
C6
N1
C2
DA
DA
DA
6
6
6
N
1
-3.22
0.50
110.60
107.38
B
B
B
C2
N3
C4
DA
DA
DA
6
6
6
N
1
-4.97
0.70
108.00
103.03
B
B
B
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
9.42
1.40
114.30
123.72
B
B
B
N1
C1'
C2'
DT
DT
DT
8
8
8
N
1
-8.65
0.70
108.00
99.35
B
B
B
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
-6.71
0.80
102.40
95.69
B
B
B
C3'
C2'
C1'
DG
DG
DG
10
10
10
N
1
7.61
1.20
119.70
127.31
B
B
B
C3'
O3'
P
DC
DC
DG
11
11
12
Y
ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
0.276
0.237
0.237
1.662
41.78
4703
427
8542
7781
10869
4.999
99.7
RANDOM
1
FREE R
0.0
MOLECULAR REPLACEMENT
PDB ENTRY 1DPN
ENGH AND HUBER
0
0.
552.3
1.662
41.78
68
560
2
490
0
0.0087
0.0293
0.0000
0.0149
0.0000
0.0082
0.0080
0.0084
0.0267
0.0000
1.662
41.78
4GLH
8542
7781
4
2
0.025
0.0152
1
28.66
3.61
99.4
0.202
1.662
1.76
6.93
1
3.71
99.0
data collection
RemDAq
phasing
PHASER
refinement
SHELXL-97
data reduction
XDS
data scaling
XDS
DNA dodecamer containing 5-hydroxymethyl cytosine
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
covale
1.603
both
A
DT
8
A
O3'
DT
8
1_555
A
5HC
9
A
P
5HC
9
1_555
covale
1.598
both
A
5HC
9
A
O3'
5HC
9
1_555
A
DG
10
A
P
DG
10
1_555
covale
1.603
both
B
DT
8
B
O3'
DT
8
1_555
B
5HC
9
B
P
5HC
9
1_555
covale
1.597
both
B
5HC
9
B
O3'
5HC
9
1_555
B
DG
10
B
P
DG
10
1_555
metalc
2.677
A
DT
7
A
O2
DT
7
1_555
A
K
101
C
K
K
1_555
metalc
3.116
A
DT
8
A
O4'
DT
8
1_555
A
K
101
C
K
K
1_555
metalc
2.708
A
DT
8
A
O2
DT
8
1_555
B
K
101
D
K
K
1_555
metalc
3.177
A
5HC
9
A
O4'
5HC
9
1_555
B
K
101
D
K
K
1_555
metalc
2.703
A
K
101
C
K
K
1_555
B
DT
7
B
O2
DT
7
1_555
metalc
3.291
A
K
101
C
K
K
1_555
B
DT
8
B
O4'
DT
8
1_555
metalc
2.877
A
K
101
C
K
K
1_555
B
HOH
204
F
O
HOH
1_555
metalc
2.775
A
K
101
C
K
K
1_555
B
HOH
205
F
O
HOH
1_555
metalc
3.295
B
DT
7
B
O4'
DT
7
1_555
B
K
101
D
K
K
1_555
metalc
2.899
B
K
101
D
K
K
1_555
B
HOH
204
F
O
HOH
1_555
metalc
2.889
B
K
101
D
K
K
1_555
B
HOH
208
F
O
HOH
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
12
B
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
12
B
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
12
B
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
11
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
11
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
11
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
10
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
10
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
10
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
8
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
8
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
7
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
7
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
6
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
6
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
5
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
5
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
3
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
3
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
3
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
2
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
2
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
2
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
B
DC
1
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
B
DC
1
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
B
DC
1
B
N4
DC
1
1_555
DNA
B-DNA dodecamer, epigenetics, 5-hydroxymethyl cytosine, DNA
4GLH
PDB
1
4GLH
1
12
4GLH
1
12
4GLH
A
1
1
12
1
12
4GLH
1
12
4GLH
B
1
1
12
BINDING SITE FOR RESIDUE K A 101
A
K
101
Software
6
BINDING SITE FOR RESIDUE K B 101
B
K
101
Software
6
A
DT
7
A
DT
7
6
1_555
A
DT
8
A
DT
8
6
1_555
B
DT
7
B
DT
7
6
1_555
B
DT
8
B
DT
8
6
1_555
B
HOH
204
F
HOH
6
1_555
B
HOH
205
F
HOH
6
1_555
A
DT
8
A
DT
8
6
1_555
A
5HC
9
A
5HC
9
6
1_555
B
DA
6
B
DA
6
6
1_555
B
DT
7
B
DT
7
6
1_555
B
HOH
204
F
HOH
6
1_555
B
HOH
208
F
HOH
6
1_555
19
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