0.039849
0.000000
0.000000
-0.000000
0.024110
0.000000
0.000000
-0.000000
0.015223
0.00000
0.00000
0.00000
Szulik, M.W.
Pallan, P.
Egli, M.
Stone, M.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
25.095
41.476
65.692
C10 H14 N3 O8 P
335.207
n
5-FORMYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2'-DEOXY-5-FORMYLCYTIDINE-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
N
1
N
P
N
2
N
O
N
3
N
O
N
4
N
O
N
5
N
N
N
6
N
C
N
7
N
C
N
8
N
O
N
9
N
N
N
10
N
C
N
11
N
N
N
12
N
C
N
13
N
C
N
14
N
C
N
15
R
C
N
16
N
O
N
17
R
C
N
18
S
C
N
19
N
O
N
20
N
C
N
21
N
O
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
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
Y
49
N
N
Y
50
N
C
Y
51
N
N
Y
52
N
C
Y
53
N
C
N
54
N
N
Y
55
N
N
Y
56
N
C
Y
57
N
N
Y
58
N
C
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
H
N
73
N
O
N
74
N
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
C
N
79
R
C
N
80
N
O
N
81
S
C
N
82
N
O
N
83
N
C
N
84
R
C
N
85
N
N
N
86
N
C
N
87
N
O
N
88
N
N
N
89
N
C
N
90
N
N
N
91
N
C
N
92
N
C
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
H
N
107
N
O
N
108
N
P
N
109
N
O
N
110
N
O
N
111
N
O
N
112
N
C
N
113
R
C
N
114
N
O
N
115
S
C
N
116
N
O
N
117
N
C
N
118
R
C
Y
119
N
N
Y
120
N
C
Y
121
N
N
Y
122
N
C
N
123
N
C
N
124
N
O
N
125
N
N
N
126
N
C
N
127
N
N
N
128
N
N
Y
129
N
C
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
H
N
144
N
O
N
145
N
P
N
146
N
O
N
147
N
O
N
148
N
O
N
149
N
C
N
150
R
C
N
151
N
O
N
152
S
C
N
153
N
O
N
154
N
C
N
155
R
C
N
156
N
N
N
157
N
C
N
158
N
O
N
159
N
N
N
160
N
C
N
161
N
O
N
162
N
C
N
163
N
C
N
164
N
C
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
H
N
180
N
O
N
181
N
H
N
182
N
H
N
1
N
sing
N
2
N
doub
N
3
N
sing
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
doub
N
11
N
sing
N
12
N
doub
N
13
N
sing
N
14
N
doub
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
sing
N
35
N
doub
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
doub
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
N
60
N
sing
Y
61
N
sing
Y
62
N
sing
Y
63
N
doub
N
64
N
sing
Y
65
N
sing
Y
66
N
sing
Y
67
N
doub
N
68
N
sing
Y
69
N
doub
N
70
N
sing
N
71
N
sing
Y
72
N
sing
Y
73
N
doub
N
74
N
sing
Y
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
doub
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
sing
N
101
N
doub
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
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
N
133
N
sing
Y
134
N
sing
Y
135
N
sing
Y
136
N
doub
N
137
N
sing
Y
138
N
sing
N
139
N
sing
Y
140
N
doub
N
141
N
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
doub
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
sing
N
175
N
doub
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
doub
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
54
1294
1305
10.1021/bi501534x
25632825
Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.
2015
10.2210/pdb4qc7/pdb
pdb_00004qc7
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
IMAGE PLATE
2014-04-10
MAR scanner 300 mm plate
Si(111)
SINGLE WAVELENGTH
M
x-ray
1
1.000
1.0
21-ID-D
APS
1.000
SYNCHROTRON
APS BEAMLINE 21-ID-D
3691.402
short DNA strands
2
syn
polymer
18.015
water
17
nat
water
no
yes
(DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(5FC)(DG)(DC)(DG)
CGCGAATTCGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
1
2.32
46.88
VAPOR DIFFUSION, HANGING DROP
6.0
5% MPD, 20 mM Na Cacodylate, 6 mM Spermine tetra-HCl, 6 mM NaCl, 40 mM KCl , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
2.144
1
19
A
1
B
24
0.810
A_DC1:DG24_B
1
-4.019
0.338
0.026
-0.144
0.256
1
19
A
2
B
23
-4.213
A_DG2:DC23_B
2
-10.889
-0.144
0.416
-0.204
0.830
1
19
A
3
B
22
0.118
A_DC3:DG22_B
3
-4.831
0.237
-0.051
-0.152
10.648
1
19
A
4
B
21
2.220
A_DG4:5FC21_B
4
-9.423
-0.327
-0.040
-0.078
5.610
1
20
A
5
B
20
0.772
A_DA5:DT20_B
5
-15.046
0.047
-0.145
-0.040
2.004
1
20
A
6
B
19
3.924
A_DA6:DT19_B
6
-16.463
-0.170
0.118
-0.136
0.152
1
20
A
7
B
18
4.420
A_DT7:DA18_B
7
-17.844
0.039
0.103
-0.030
-3.608
1
20
A
8
B
17
4.886
A_DT8:DA17_B
8
-15.476
0.035
0.008
-0.142
-10.262
1
19
A
9
B
16
-1.552
A_5FC9:DG16_B
9
-7.640
0.335
0.044
-0.129
3.816
1
19
A
10
B
15
2.595
A_DG10:DC15_B
10
-2.026
-0.348
0.133
-0.168
1.657
1
19
A
11
B
14
-1.651
A_DC11:DG14_B
11
-14.458
0.085
0.325
-0.237
4.178
1
19
A
12
B
13
-2.409
A_DG12:DC13_B
12
-1.164
-0.210
-0.084
-0.260
3.508
36.502
A
A
1
2
-4.821
B
B
24
23
3.390
-3.003
-0.982
-0.188
AA_DC1DG2:DC23DG24_BB
1
-6.061
9.730
35.891
0.142
0.677
3.388
39.056
A
A
2
3
-2.956
B
B
23
22
3.354
-1.972
0.653
0.163
AA_DG2DC3:DG22DC23_BB
2
3.850
-5.770
38.825
0.489
-0.497
3.218
28.769
A
A
3
4
18.194
B
B
22
21
3.223
8.895
-0.360
0.541
AA_DC3DG4:5FC21DG22_BB
3
1.160
-2.374
27.363
-0.925
0.988
3.395
34.069
A
A
4
5
2.386
B
B
21
20
3.410
1.397
-0.148
-0.234
AA_DG4DA5:DT205FC21_BB
4
0.603
-1.030
34.036
-0.630
0.352
3.240
37.786
A
A
5
6
0.940
B
B
20
19
3.249
0.608
-0.064
-0.289
AA_DA5DA6:DT19DT20_BB
5
-2.917
4.509
37.673
-0.525
-0.274
3.254
35.106
A
A
6
7
-4.051
B
B
19
18
3.229
-2.442
-0.053
-0.487
AA_DA6DT7:DA18DT19_BB
6
0.147
-0.244
35.023
-0.445
0.109
3.279
36.910
A
A
7
8
-3.342
B
B
18
17
3.278
-2.114
-0.068
-0.218
AA_DT7DT8:DA17DA18_BB
7
1.581
-2.499
36.819
-0.058
0.322
3.387
40.279
A
A
8
9
-0.971
B
B
17
16
3.384
-0.669
-0.012
-0.308
AA_DT85FC9:DG16DA17_BB
8
1.003
-1.457
40.262
-0.369
0.135
3.090
26.427
A
A
9
10
6.754
B
B
16
15
3.087
3.078
0.635
0.669
AA_5FC9DG10:DC15DG16_BB
9
-1.916
4.203
26.181
0.687
-1.873
3.385
43.400
A
A
10
11
-8.978
B
B
15
14
3.389
-6.607
-1.429
0.550
AA_DG10DC11:DG14DC15_BB
10
-3.964
5.386
42.743
1.413
1.531
3.444
35.897
A
A
11
12
-2.906
B
B
14
13
3.392
-1.785
0.977
0.805
AA_DC11DG12:DC13DG14_BB
11
4.634
-7.542
35.563
1.574
-0.889
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2015-02-11
1
1
2015-02-25
1
2
2023-09-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
RCSB
Y
RCSB
2014-05-09
REL
REL
HOH
water
Chemically synthesized nucleic acid.
sample
436D
PDB ID 436D
PDB
experimental model
HOH
1
2
HOH
HOH
101
A
HOH
3
2
HOH
HOH
102
A
HOH
4
2
HOH
HOH
103
A
HOH
5
2
HOH
HOH
104
A
HOH
8
2
HOH
HOH
105
A
HOH
23
2
HOH
HOH
106
A
HOH
24
2
HOH
HOH
107
A
HOH
2
2
HOH
HOH
101
B
HOH
6
2
HOH
HOH
102
B
HOH
7
2
HOH
HOH
103
B
HOH
9
2
HOH
HOH
104
B
HOH
15
2
HOH
HOH
105
B
HOH
20
2
HOH
HOH
106
B
HOH
21
2
HOH
HOH
107
B
HOH
22
2
HOH
HOH
108
B
HOH
27
2
HOH
HOH
109
B
HOH
28
2
HOH
HOH
110
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
5FC
9
n
9
5FC
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
DC
15
n
3
DC
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
5FC
21
n
9
5FC
21
B
DG
22
n
10
DG
22
B
DC
23
n
11
DC
23
B
DG
24
n
12
DG
24
B
author_and_software_defined_assembly
PISA
2
dimeric
2410
3
4260
A
5FC
9
A
5FC
9
DC
B
5FC
21
B
5FC
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
0.970
0.967
0.24529
0.22637
0.22767
1.90
35.07
413
5842
5362
7.2
99.35
4.094
0.117
RANDOM
1
THROUGHOUT
5
MOLECULAR REPLACEMENT
0.172
0.147
0.80
0.80
1.20
PDB ID 436D
MAXIMUM LIKELIHOOD
MASK
1.90
35.07
17
507
0
490
0
0.011
0.011
548
0.002
0.020
268
1.333
1.295
842
1.467
3.000
634
0.080
0.200
72
0.026
0.020
292
0.003
0.020
118
5.987
4.947
548
5.991
4.948
547
7.896
7.424
843
7.725
46.792
786
7.721
46.813
780
0.337
0.314
1.947
33
380
380
20
99.04
1.9
50
4QC7
5842
5801
0.064
1
60
10.2
99.3
0.738
1.90
1.93
3.25
1
6.7
100
data collection
MD2
diffractometer software from EMBL (with LS-CAT developed extensions)
phasing
MOLREP
refinement
REFMAC
5.8.0069
data reduction
HKL-2000
data scaling
HKL-2000
Dodecamer structure of 5-formylcytosine containing DNA
1
N
N
1
N
N
2
N
N
2
N
N
covale
1.588
both
A
DT
8
A
O3'
DT
8
1_555
A
5FC
9
A
P
5FC
9
1_555
covale
1.589
both
A
5FC
9
A
O3'
5FC
9
1_555
A
DG
10
A
P
DG
10
1_555
covale
1.588
both
B
DT
20
B
O3'
DT
8
1_555
B
5FC
21
B
P
5FC
9
1_555
covale
1.607
both
B
5FC
21
B
O3'
5FC
9
1_555
B
DG
22
B
P
DG
10
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
DC
3
A
N3
DC
3
1_555
B
DG
22
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
22
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
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
5FC
21
B
N3
5FC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
5FC
21
B
O2
5FC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
5FC
21
B
N4
5FC
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
5FC
9
A
N3
5FC
9
1_555
B
DG
16
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
5FC
9
A
N4
5FC
9
1_555
B
DG
16
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
5FC
9
A
O2
5FC
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
DC
15
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
15
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
15
B
N4
DC
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
double helix, B-form DNA, 5-formylcytosine, DNA
4QC7
PDB
1
4QC7
CGCGAATTCGCG
1
12
4QC7
1
12
4QC7
A
1
1
12
13
24
4QC7
13
24
4QC7
B
1
1
12
19
P 21 21 21