0.039722
0.000000
0.000000
0.000000
0.024637
0.000000
0.000000
0.000000
0.015291
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
25.175
40.590
65.399
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
Mg 2
24.305
MAGNESIUM 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
186
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
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/pdb4hli/pdb
pdb_00004hli
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
1.000670
1.0
X06DA
SLS
1.00067
1.000670
SYNCHROTRON
SLS BEAMLINE X06DA
3693.418
DNA (5'-D(*CP*GP*(5HC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
2
syn
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
39.098
POTASSIUM ION
1
syn
non-polymer
18.015
water
29
nat
water
no
yes
(DC)(DG)(5HC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)
CGXGAATTCGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
1
2.27
45.73
VAPOR DIFFUSION, SITTING DROP
7.0
0.04m sodium cacodylate buffer, 0.08M NaCCl, 0.12m KCl, 0.02m MgCl2, 0.012m spermine tetra hydrochloride, 35% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
-5.343
1
19
A
1
B
12
-2.534
A_DC1:DG12_B
1
-4.489
0.076
0.576
-0.178
-0.280
1
19
A
2
B
11
0.027
A_DG2:DC11_B
2
-16.029
-0.396
0.302
-0.042
15.427
1
19
A
4
B
9
-3.836
A_DG4:DC9_B
3
-4.481
-0.710
-0.046
-0.108
4.870
1
20
A
5
B
8
2.021
A_DA5:DT8_B
4
-16.988
0.116
0.075
-0.256
6.074
1
20
A
6
B
7
0.749
A_DA6:DT7_B
5
-17.504
0.050
0.439
-0.265
-1.675
1
20
A
7
B
6
4.983
A_DT7:DA6_B
6
-22.231
0.115
0.224
-0.188
-5.236
1
20
A
8
B
5
4.739
A_DT8:DA5_B
7
-15.646
0.045
0.192
-0.080
-16.184
1
19
A
9
B
4
-2.285
A_DC9:DG4_B
8
-10.535
0.408
0.070
-0.134
9.181
1
19
A
11
B
2
-2.838
A_DC11:DG2_B
9
-21.989
0.325
-0.169
-0.169
10.500
1
19
A
12
B
1
2.410
A_DG12:DC1_B
10
-6.420
-0.154
0.248
0.038
3.277
35.219
A
A
1
2
-0.625
B
B
12
11
3.267
-0.378
-0.587
-0.141
AA_DC1DG2:DC11DG12_BB
1
-0.556
0.920
35.213
-0.177
0.887
6.454
66.039
A
A
2
4
-0.369
B
B
11
9
6.456
-0.402
-0.358
0.416
AA_DG2DG4:DC9DC11_BB
2
-0.012
0.011
66.038
0.414
0.327
3.451
39.117
A
A
4
5
4.133
B
B
9
8
3.491
2.764
0.095
-0.403
AA_DG4DA5:DT8DC9_BB
3
-1.274
1.905
39.003
-0.954
-0.304
3.034
37.381
A
A
5
6
-1.809
B
B
8
7
3.020
-1.158
-0.120
-0.514
AA_DA5DA6:DT7DT8_BB
4
-3.175
4.961
37.233
-0.660
-0.201
3.387
32.984
A
A
6
7
-1.174
B
B
7
6
3.370
-0.666
0.203
-0.713
AA_DA6DT7:DA6DT7_BB
5
3.275
-5.778
32.818
-1.138
0.219
3.239
34.277
A
A
7
8
-3.992
B
B
6
5
3.213
-2.350
-0.217
-0.403
AA_DT7DT8:DA5DA6_BB
6
-1.902
3.231
34.147
-0.319
0.072
3.503
42.469
A
A
8
9
-7.224
B
B
5
4
3.509
-5.219
-0.337
-0.306
AA_DT8DC9:DG4DA5_BB
7
1.879
-2.601
42.122
0.148
0.671
5.968
70.388
A
A
9
11
-4.708
B
B
4
2
6.031
-5.422
-0.077
0.683
AA_DC9DC11:DG2DG4_BB
8
1.928
-1.674
70.183
0.943
0.191
3.240
35.276
A
A
11
12
15.630
B
B
2
1
3.254
9.356
0.501
0.560
AA_DC11DG12:DC1DG2_BB
9
-2.799
4.675
33.939
-0.482
-1.247
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
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-09-04
1
1
2013-12-04
1
2
2023-09-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_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_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr2_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_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_comp_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
2012-10-17
REL
REL
MG
MAGNESIUM ION
K
POTASSIUM ION
HOH
water
9606
Homo sapiens
sample
1DPN
PDB ENTRY 1DPN
PDB
experimental model
MO6
51
2
MG
MG
101
A
K
52
3
K
K
102
A
MO6
51
4
HOH
HOH
201
A
MO6
51
4
HOH
HOH
202
A
MO6
51
4
HOH
HOH
203
A
MO6
51
4
HOH
HOH
204
A
MO6
51
4
HOH
HOH
205
A
MO6
51
4
HOH
HOH
206
A
HOH
102
4
HOH
HOH
207
A
HOH
103
4
HOH
HOH
208
A
HOH
104
4
HOH
HOH
209
A
HOH
110
4
HOH
HOH
210
A
HOH
111
4
HOH
HOH
211
A
HOH
112
4
HOH
HOH
212
A
HOH
113
4
HOH
HOH
213
A
HOH
114
4
HOH
HOH
214
A
HOH
116
4
HOH
HOH
215
A
HOH
117
4
HOH
HOH
216
A
HOH
119
4
HOH
HOH
217
A
HOH
121
4
HOH
HOH
218
A
HOH
122
4
HOH
HOH
219
A
HOH
101
4
HOH
HOH
101
B
HOH
105
4
HOH
HOH
102
B
HOH
106
4
HOH
HOH
103
B
HOH
107
4
HOH
HOH
104
B
HOH
108
4
HOH
HOH
105
B
HOH
109
4
HOH
HOH
106
B
HOH
115
4
HOH
HOH
107
B
HOH
118
4
HOH
HOH
108
B
HOH
120
4
HOH
HOH
109
B
HOH
123
4
HOH
HOH
110
B
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
5HC
3
n
3
5HC
3
A
G
4
n
4
DG
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
C
9
n
9
DC
9
A
G
10
n
10
DG
10
A
C
11
n
11
DC
11
A
G
12
n
12
DG
12
A
C
1
n
1
DC
1
B
G
2
n
2
DG
2
B
5HC
3
n
3
5HC
3
B
G
4
n
4
DG
4
B
A
5
n
5
DA
5
B
A
6
n
6
DA
6
B
T
7
n
7
DT
7
B
T
8
n
8
DT
8
B
C
9
n
9
DC
9
B
G
10
n
10
DG
10
B
C
11
n
11
DC
11
B
G
12
n
12
DG
12
B
0.2461
0.2548
0.2429
0.2518
0.3180
0.3281
308
334
7.14
6.99
4315
author_and_software_defined_assembly
PISA
2
dimeric
1540
-7
4470
A
DT
8
A
O2
DT
8
1_555
A
K
102
D
K
K
1_555
A
DC
9
A
O4'
DC
9
1_555
65.0
A
DT
8
A
O2
DT
8
1_555
A
K
102
D
K
K
1_555
B
DT
7
B
O4'
DT
7
1_555
139.8
A
DC
9
A
O4'
DC
9
1_555
A
K
102
D
K
K
1_555
B
DT
7
B
O4'
DT
7
1_555
155.2
A
DT
8
A
O2
DT
8
1_555
A
K
102
D
K
K
1_555
B
HOH
102
F
O
HOH
1_555
97.0
A
DC
9
A
O4'
DC
9
1_555
A
K
102
D
K
K
1_555
B
HOH
102
F
O
HOH
1_555
102.9
B
DT
7
B
O4'
DT
7
1_555
A
K
102
D
K
K
1_555
B
HOH
102
F
O
HOH
1_555
76.4
A
DT
8
A
O2
DT
8
1_555
A
K
102
D
K
K
1_555
B
HOH
104
F
O
HOH
1_555
119.5
A
DC
9
A
O4'
DC
9
1_555
A
K
102
D
K
K
1_555
B
HOH
104
F
O
HOH
1_555
78.6
B
DT
7
B
O4'
DT
7
1_555
A
K
102
D
K
K
1_555
B
HOH
104
F
O
HOH
1_555
85.9
B
HOH
102
F
O
HOH
1_555
A
K
102
D
K
K
1_555
B
HOH
104
F
O
HOH
1_555
138.7
A
HOH
201
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
202
E
O
HOH
1_555
72.5
A
HOH
201
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
203
E
O
HOH
1_555
109.8
A
HOH
202
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
203
E
O
HOH
1_555
173.1
A
HOH
201
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
204
E
O
HOH
1_555
173.2
A
HOH
202
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
204
E
O
HOH
1_555
108.1
A
HOH
203
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
204
E
O
HOH
1_555
70.5
A
HOH
201
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
205
E
O
HOH
1_555
86.6
A
HOH
202
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
205
E
O
HOH
1_555
93.2
A
HOH
203
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
205
E
O
HOH
1_555
93.4
A
HOH
204
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
205
E
O
HOH
1_555
86.7
A
HOH
201
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
206
E
O
HOH
1_555
93.0
A
HOH
202
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
206
E
O
HOH
1_555
86.6
A
HOH
203
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
206
E
O
HOH
1_555
86.8
A
HOH
204
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
206
E
O
HOH
1_555
93.8
A
HOH
205
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
206
E
O
HOH
1_555
179.5
A
5HC
3
A
5HC
3
DC
B
5HC
3
B
5HC
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
-4.40
0.70
108.00
103.60
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
-5.70
0.70
108.00
102.30
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
-6.75
0.80
102.40
95.65
A
A
A
C3'
C2'
C1'
DG
DG
DG
10
10
10
N
1
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
8.46
1.20
119.70
128.16
B
B
B
C3'
O3'
P
DT
DT
DC
8
8
9
Y
1
-5.52
0.80
102.40
96.88
B
B
B
C3'
C2'
C1'
DG
DG
DG
10
10
10
N
0.3281
0.2518
0.2548
0.2518
1.99
50.00
2099
334
4775
4315
2456
6.99
96.5
RANDOM
1
FREE R
0.0
MOLECULAR REPLACEMENT
PDB ENTRY 1DPN
ENGH AND HUBER
1
0.00
515.50
1.99
50.00
29
521
2
490
0
0.007
0.073
0.000
0.0005
0.000
0.006
0.005
0.000
0.075
0.000
1.99
50.0
4HLI
4775
4315
2
4
0.038
0.022
1
21.23
3.55
96.5
0.217
1.99
2.11
5.81
1
3.27
94.6
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
3
N
N
4
N
N
4
N
N
covale
1.617
both
A
DG
2
A
O3'
DG
2
1_555
A
5HC
3
A
P
5HC
3
1_555
covale
1.606
both
A
5HC
3
A
O3'
5HC
3
1_555
A
DG
4
A
P
DG
4
1_555
covale
1.606
both
B
DG
2
B
O3'
DG
2
1_555
B
5HC
3
B
P
5HC
3
1_555
covale
1.605
both
B
5HC
3
B
O3'
5HC
3
1_555
B
DG
4
B
P
DG
4
1_555
metalc
2.847
A
DT
8
A
O2
DT
8
1_555
A
K
102
D
K
K
1_555
metalc
2.987
A
DC
9
A
O4'
DC
9
1_555
A
K
102
D
K
K
1_555
metalc
2.091
A
MG
101
C
MG
MG
1_555
A
HOH
201
E
O
HOH
1_555
metalc
2.093
A
MG
101
C
MG
MG
1_555
A
HOH
202
E
O
HOH
1_555
metalc
2.088
A
MG
101
C
MG
MG
1_555
A
HOH
203
E
O
HOH
1_555
metalc
2.094
A
MG
101
C
MG
MG
1_555
A
HOH
204
E
O
HOH
1_555
metalc
2.130
A
MG
101
C
MG
MG
1_555
A
HOH
205
E
O
HOH
1_555
metalc
2.135
A
MG
101
C
MG
MG
1_555
A
HOH
206
E
O
HOH
1_555
metalc
3.158
A
K
102
D
K
K
1_555
B
DT
7
B
O4'
DT
7
1_555
metalc
2.641
A
K
102
D
K
K
1_555
B
HOH
102
F
O
HOH
1_555
metalc
2.711
A
K
102
D
K
K
1_555
B
HOH
104
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
DG
4
A
N1
DG
4
1_555
B
DC
9
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
9
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
9
B
N4
DC
9
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
DC
9
A
N3
DC
9
1_555
B
DG
4
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
4
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
4
B
N2
DG
4
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
4HLI
PDB
1
4HLI
1
12
4HLI
1
12
4HLI
A
1
1
12
1
12
4HLI
1
12
4HLI
B
1
1
12
BINDING SITE FOR RESIDUE MG A 101
A
MG
101
Software
6
BINDING SITE FOR RESIDUE K A 102
A
K
102
Software
6
A
HOH
201
E
HOH
6
1_555
A
HOH
202
E
HOH
6
1_555
A
HOH
203
E
HOH
6
1_555
A
HOH
204
E
HOH
6
1_555
A
HOH
205
E
HOH
6
1_555
A
HOH
206
E
HOH
6
1_555
A
DT
8
A
DT
8
6
1_555
A
DC
9
A
DC
9
6
1_555
B
DA
6
B
DA
6
6
1_555
B
DT
7
B
DT
7
6
1_555
B
HOH
102
F
HOH
6
1_555
B
HOH
104
F
HOH
6
1_555
19
P 21 21 21