0.040795
0.000000
0.000000
0.000000
0.024037
0.000000
0.000000
0.000000
0.015141
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
24.513
41.602
66.044
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
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
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/pdb4glc/pdb
pdb_00004glc
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
BARTELS MONOCHROMATOR
SINGLE WAVELENGTH
M
x-ray
1
1.00067
1.0
X06DA
SLS
1.00067
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
18.015
water
40
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
1.98
46.04
7.0
0.04M sodium cacodylate buffer, 0.08M sodium chloride, 0.012M spermine tetra hydrochloride, 30% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
5.148
1
19
A
1
B
12
-0.440
A_DC1:DG12_B
1
12.788
0.153
-0.660
-0.239
-12.471
1
19
A
2
B
11
-5.540
A_DG2:DC11_B
2
-16.269
-0.320
0.413
-0.233
7.422
1
19
A
4
B
9
0.225
A_DG4:DC9_B
3
-6.877
-0.192
0.030
-0.140
5.553
1
20
A
5
B
8
0.997
A_DA5:DT8_B
4
-16.534
0.013
0.002
-0.141
4.367
1
20
A
6
B
7
4.571
A_DA6:DT7_B
5
-17.190
0.299
0.163
-0.098
0.287
1
20
A
7
B
6
2.958
A_DT7:DA6_B
6
-15.979
0.061
0.032
-0.088
0.636
1
20
A
8
B
5
4.124
A_DT8:DA5_B
7
-17.388
0.098
-0.160
-0.144
-13.463
1
19
A
9
B
4
-0.283
A_DC9:DG4_B
8
-9.727
0.297
-0.077
-0.145
4.279
1
19
A
11
B
2
-2.869
A_DC11:DG2_B
9
-18.864
0.285
0.333
-0.162
20.815
1
19
A
12
B
1
0.318
A_DG12:DC1_B
10
-4.207
-0.423
0.552
-0.201
3.974
39.707
A
A
1
2
-26.358
B
B
12
11
4.078
-17.191
-1.367
-0.195
AA_DC1DG2:DC11DG12_BB
1
-9.014
13.820
34.808
2.357
0.626
6.314
69.093
A
A
2
4
10.453
B
B
11
9
6.393
11.809
-0.120
-0.017
AA_DG2DG4:DC9DC11_BB
2
1.842
-1.631
68.179
-0.862
0.238
3.369
35.622
A
A
4
5
-2.645
B
B
9
8
3.368
-1.618
0.026
-0.099
AA_DG4DA5:DT8DC9_BB
3
1.010
-1.652
35.572
0.080
0.109
3.195
40.349
A
A
5
6
-1.734
B
B
8
7
3.199
-1.195
0.172
-0.293
AA_DA5DA6:DT7DT8_BB
4
-1.877
2.723
40.290
-0.294
-0.456
3.380
32.163
A
A
6
7
-5.178
B
B
7
6
3.346
-2.865
0.030
-0.554
AA_DA6DT7:DA6DT7_BB
5
1.231
-2.226
32.016
-0.472
0.172
3.133
35.906
A
A
7
8
-0.518
B
B
6
5
3.135
-0.319
0.066
-0.297
AA_DT7DT8:DA5DA6_BB
6
2.808
-4.560
35.798
-0.438
0.278
3.533
41.737
A
A
8
9
-0.738
B
B
5
4
3.532
-0.526
-0.078
-0.156
AA_DT8DC9:DG4DA5_BB
7
0.258
-0.362
41.733
-0.159
0.139
6.238
70.398
A
A
9
11
-3.524
B
B
4
2
6.265
-4.060
-0.295
0.512
AA_DC9DC11:DG2DG4_BB
8
-3.168
2.750
70.234
0.717
0.043
3.003
31.357
A
A
11
12
-2.430
B
B
2
1
3.088
-1.312
1.302
0.506
AA_DC11DG12:DC1DG2_BB
9
-1.464
2.711
31.297
1.167
-2.665
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
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
_struct_conn.pdbx_leaving_atom_flag
RCSB
Y
RCSB
2012-08-14
REL
REL
HOH
water
32630
Synthetic construct
sample
1DPN
PDB ENTRY 1DPN
PDB
experimental model
HOH
102
2
HOH
HOH
101
A
HOH
103
2
HOH
HOH
102
A
HOH
104
2
HOH
HOH
103
A
HOH
106
2
HOH
HOH
104
A
HOH
111
2
HOH
HOH
105
A
HOH
114
2
HOH
HOH
106
A
HOH
115
2
HOH
HOH
107
A
HOH
117
2
HOH
HOH
108
A
HOH
121
2
HOH
HOH
109
A
HOH
124
2
HOH
HOH
110
A
HOH
126
2
HOH
HOH
111
A
HOH
128
2
HOH
HOH
112
A
HOH
130
2
HOH
HOH
113
A
HOH
134
2
HOH
HOH
114
A
HOH
137
2
HOH
HOH
115
A
HOH
138
2
HOH
HOH
116
A
HOH
101
2
HOH
HOH
101
B
HOH
105
2
HOH
HOH
102
B
HOH
107
2
HOH
HOH
103
B
HOH
108
2
HOH
HOH
104
B
HOH
109
2
HOH
HOH
105
B
HOH
110
2
HOH
HOH
106
B
HOH
112
2
HOH
HOH
107
B
HOH
113
2
HOH
HOH
108
B
HOH
116
2
HOH
HOH
109
B
HOH
118
2
HOH
HOH
110
B
HOH
119
2
HOH
HOH
111
B
HOH
120
2
HOH
HOH
112
B
HOH
122
2
HOH
HOH
113
B
HOH
123
2
HOH
HOH
114
B
HOH
125
2
HOH
HOH
115
B
HOH
127
2
HOH
HOH
116
B
HOH
129
2
HOH
HOH
117
B
HOH
131
2
HOH
HOH
118
B
HOH
132
2
HOH
HOH
119
B
HOH
133
2
HOH
HOH
120
B
HOH
135
2
HOH
HOH
121
B
HOH
136
2
HOH
HOH
122
B
HOH
139
2
HOH
HOH
123
B
HOH
140
2
HOH
HOH
124
B
DC
1
n
1
DC
1
A
DG
2
n
2
DG
2
A
5HC
3
n
3
5HC
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
1
n
1
DC
1
B
DG
2
n
2
DG
2
B
5HC
3
n
3
5HC
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
DC
9
n
9
DC
9
B
DG
10
n
10
DG
10
B
DC
11
n
11
DC
11
B
DG
12
n
12
DG
12
B
0.244
0.251
0.225
0.233
0.298
0.306
400
435
7.052
7.015
5672
author_and_software_defined_assembly
PISA
2
dimeric
1170
-5
4550
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
-5.17
0.70
108.00
102.83
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
-5.10
0.70
108.00
102.90
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
-5.62
0.70
108.00
102.38
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
-7.53
0.70
108.00
100.47
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
-7.16
0.80
102.40
95.24
A
A
A
C3'
C2'
C1'
DG
DG
DG
10
10
10
N
1
-5.26
0.70
108.00
102.74
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
-3.87
0.60
118.90
115.03
B
B
B
N1
C2
O2
DC
DC
DC
1
1
1
N
1
-5.80
0.70
108.00
102.20
B
B
B
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
-6.74
0.70
108.00
101.26
B
B
B
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
8.54
1.40
114.30
122.84
B
B
B
N1
C1'
C2'
DC
DC
DC
9
9
9
N
1
-7.29
0.70
108.00
100.71
B
B
B
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
-5.74
0.80
102.40
96.66
B
B
B
C3'
C2'
C1'
DG
DG
DG
10
10
10
N
0.306
0.233
0.251
0.233
1.831
35.2
2123
435
6201
6119
2406
7.015
97.5
RANDOM
1
FREE R
0.0
MOLECULAR REPLACEMENT
PDB ENTRY 1DPN
ENGH AND HUBER
0
0.00
528.60
1.831
35.2
40
530
0
490
0
0.007
0.028
0.000
0.012
0.000
0.006
0.008
0.000
0.070
0.000
1.831
41.60
4GLC
6201
0.034
0.021
1
24.06
3.68
97.5
0.216
1.831
1.94
6.65
1
3.62
96.6
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
2
N
N
covale
1.609
both
A
DG
2
A
O3'
DG
2
1_555
A
5HC
3
A
P
5HC
3
1_555
covale
1.613
both
A
5HC
3
A
O3'
5HC
3
1_555
A
DG
4
A
P
DG
4
1_555
covale
1.615
both
B
DG
2
B
O3'
DG
2
1_555
B
5HC
3
B
P
5HC
3
1_555
covale
1.603
both
B
5HC
3
B
O3'
5HC
3
1_555
B
DG
4
B
P
DG
4
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
4GLC
PDB
1
4GLC
1
12
4GLC
1
12
4GLC
A
1
1
12
1
12
4GLC
1
12
4GLC
B
1
1
12
19
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