0.039546
0.000000
0.000000
0.000000
0.024865
0.000000
0.000000
0.000000
0.015274
0.00000
0.00000
0.00000
Szulik, M.W.
Nocek, B.
Joachimiak, A.
Stone, M.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
25.287
40.217
65.471
C9 H14 N3 O8 P
323.197
2'-deoxy-5-hydroxycytidine 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
Mg 2
24.305
MAGNESIUM ION
non-polymer
N
1
N
P
N
2
N
N
N
3
N
C
N
4
N
O
N
5
N
N
N
6
N
C
N
7
N
N
N
8
N
C
N
9
N
O
N
10
N
C
N
11
R
C
N
12
N
C
N
13
S
C
N
14
N
O
N
15
R
C
N
16
N
O
N
17
N
C
N
18
N
O
N
19
N
O
N
20
N
O
N
21
N
H
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
O
N
34
N
H
N
35
N
H
N
36
N
O
N
37
N
P
N
38
N
O
N
39
N
O
N
40
N
O
N
41
N
C
N
42
R
C
N
43
N
O
N
44
S
C
N
45
N
O
N
46
N
C
N
47
R
C
Y
48
N
N
Y
49
N
C
Y
50
N
N
Y
51
N
C
Y
52
N
C
N
53
N
N
Y
54
N
N
Y
55
N
C
Y
56
N
N
Y
57
N
C
N
58
N
H
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
O
N
73
N
P
N
74
N
O
N
75
N
O
N
76
N
O
N
77
N
C
N
78
R
C
N
79
N
O
N
80
S
C
N
81
N
O
N
82
N
C
N
83
R
C
N
84
N
N
N
85
N
C
N
86
N
O
N
87
N
N
N
88
N
C
N
89
N
N
N
90
N
C
N
91
N
C
N
92
N
H
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
O
N
107
N
P
N
108
N
O
N
109
N
O
N
110
N
O
N
111
N
C
N
112
R
C
N
113
N
O
N
114
S
C
N
115
N
O
N
116
N
C
N
117
R
C
Y
118
N
N
Y
119
N
C
Y
120
N
N
Y
121
N
C
N
122
N
C
N
123
N
O
N
124
N
N
N
125
N
C
N
126
N
N
N
127
N
N
Y
128
N
C
N
129
N
H
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
O
N
144
N
P
N
145
N
O
N
146
N
O
N
147
N
O
N
148
N
C
N
149
R
C
N
150
N
O
N
151
S
C
N
152
N
O
N
153
N
C
N
154
R
C
N
155
N
N
N
156
N
C
N
157
N
O
N
158
N
N
N
159
N
C
N
160
N
O
N
161
N
C
N
162
N
C
N
163
N
C
N
164
N
H
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
O
N
180
N
H
N
181
N
H
N
182
N
MG
N
1
N
sing
N
2
N
doub
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
doub
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
doub
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
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
doub
N
40
N
sing
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
Y
60
N
sing
Y
61
N
sing
Y
62
N
doub
N
63
N
sing
Y
64
N
sing
Y
65
N
sing
Y
66
N
doub
N
67
N
sing
Y
68
N
doub
N
69
N
sing
N
70
N
sing
Y
71
N
sing
Y
72
N
doub
N
73
N
sing
Y
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
doub
N
78
N
sing
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
doub
N
101
N
sing
N
102
N
doub
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
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
Y
133
N
sing
Y
134
N
sing
Y
135
N
doub
N
136
N
sing
Y
137
N
sing
N
138
N
sing
Y
139
N
doub
N
140
N
doub
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
doub
N
152
N
sing
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
doub
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
doub
N
179
N
sing
N
180
N
sing
N
181
N
doub
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
TO BE PUBLISHED
0353
Crystal structure of 5-hydroxy-2'-deoxycytidine base paired with 2'-deoxyguanosine in Dickerson Drew Dodecamer
10.2210/pdb4f3u/pdb
pdb_00004f3u
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
mirrors
CCD
2012-02-05
ADSC QUANTUM 315r
double crystal
SINGLE WAVELENGTH
M
x-ray
1
0.9794
1.0
19-ID
APS
0.9794
SYNCHROTRON
APS BEAMLINE 19-ID
3679.392
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5OC)P*GP*CP*G)-3')
2
syn
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
94
nat
water
no
yes
(DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(5OC)(DG)(DC)(DG)
CGCGAATTXGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
1
2.26
45.62
VAPOR DIFFUSION, HANGING DROP
7.0
10% MPD, 40mM sodium cacodylate, 12 mM spermine-tetra-HCl, 80mM sodium chloride, 20mM magnesium chloride., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
5.508
1
19
A
1
B
24
0.176
A_DC1:DG24_B
1
-15.184
0.190
0.133
-0.121
7.215
1
19
A
2
B
23
-1.769
A_DG2:DC23_B
2
-11.875
-0.234
0.399
-0.197
-0.562
1
19
A
3
B
22
-1.193
A_DC3:DG22_B
3
-5.860
0.124
0.097
-0.164
5.862
1
20
A
5
B
20
3.888
A_DA5:DT20_B
4
-16.356
-0.020
-0.071
-0.084
2.175
1
20
A
6
B
19
4.404
A_DA6:DT19_B
5
-15.357
0.051
0.142
-0.103
-1.242
1
20
A
7
B
18
3.716
A_DT7:DA18_B
6
-16.394
-0.046
0.094
-0.141
-0.613
1
20
A
8
B
17
3.819
A_DT8:DA17_B
7
-13.579
-0.073
-0.112
-0.154
4.802
1
19
A
10
B
15
2.717
A_DG10:DC15_B
8
-9.236
-0.113
0.254
-0.088
3.262
1
19
A
11
B
14
-3.576
A_DC11:DG14_B
9
-16.058
0.112
0.173
-0.180
6.240
1
19
A
12
B
13
-1.687
A_DG12:DC13_B
10
-6.562
-0.182
0.207
-0.095
3.181
34.969
A
A
1
2
10.186
B
B
24
23
3.222
6.088
-0.063
0.042
AA_DC1DG2:DC23DG24_BB
1
-2.175
3.638
34.384
-0.837
-0.220
3.441
42.132
A
A
2
3
-8.495
B
B
23
22
3.521
-6.084
0.540
0.509
AA_DG2DC3:DG22DC23_BB
2
2.349
-3.280
41.646
1.380
-0.492
6.471
65.062
A
A
3
5
10.282
B
B
22
20
6.488
11.012
0.014
0.423
AA_DC3DA5:DT20DG22_BB
3
3.423
-3.196
64.142
-0.524
0.272
3.251
36.767
A
A
5
6
0.413
B
B
20
19
3.260
0.260
0.014
-0.292
AA_DA5DA6:DT19DT20_BB
4
-2.393
3.796
36.691
-0.498
-0.347
3.275
32.350
A
A
6
7
-2.020
B
B
19
18
3.257
-1.125
0.015
-0.579
AA_DA6DT7:DA18DT19_BB
5
0.709
-1.273
32.324
-0.841
0.098
3.189
34.326
A
A
7
8
-2.361
B
B
18
17
3.185
-1.392
-0.078
-0.358
AA_DT7DT8:DA17DA18_BB
6
1.787
-3.030
34.253
-0.394
0.406
6.480
69.095
A
A
8
10
1.376
B
B
17
15
6.476
1.560
-0.058
0.675
AA_DT8DG10:DC15DA17_BB
7
-4.700
4.146
68.939
0.482
-0.290
3.256
43.019
A
A
10
11
-12.171
B
B
15
14
3.348
-8.861
-1.308
0.514
AA_DG10DC11:DG14DC15_BB
8
-2.790
3.831
42.050
1.596
1.502
3.237
34.010
A
A
11
12
9.673
B
B
14
13
3.225
5.633
-0.032
0.338
AA_DC11DG12:DC13DG14_BB
9
-0.294
0.505
33.553
-0.317
0.009
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
pdbx_validate_polymer_linkage
struct_conn
struct_site
repository
Initial release
Refinement description
Advisory
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-06-05
1
1
2017-11-15
1
2
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.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
RCSB
Y
RCSB
2012-05-09
REL
REL
MG
MAGNESIUM ION
HOH
water
32630
synthetic
sample
436D
PDB ENTRY 436D
PDB
experimental model
MG
45
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
6
3
HOH
HOH
204
A
HOH
7
3
HOH
HOH
205
A
HOH
11
3
HOH
HOH
206
A
HOH
12
3
HOH
HOH
207
A
HOH
14
3
HOH
HOH
208
A
HOH
15
3
HOH
HOH
209
A
HOH
20
3
HOH
HOH
210
A
HOH
23
3
HOH
HOH
211
A
HOH
24
3
HOH
HOH
212
A
HOH
26
3
HOH
HOH
213
A
HOH
27
3
HOH
HOH
214
A
HOH
29
3
HOH
HOH
215
A
HOH
30
3
HOH
HOH
216
A
HOH
33
3
HOH
HOH
217
A
HOH
35
3
HOH
HOH
218
A
HOH
36
3
HOH
HOH
219
A
HOH
40
3
HOH
HOH
220
A
HOH
42
3
HOH
HOH
221
A
HOH
43
3
HOH
HOH
222
A
HOH
44
3
HOH
HOH
223
A
HOH
45
3
HOH
HOH
224
A
HOH
47
3
HOH
HOH
225
A
HOH
50
3
HOH
HOH
226
A
HOH
51
3
HOH
HOH
227
A
HOH
54
3
HOH
HOH
228
A
HOH
57
3
HOH
HOH
229
A
HOH
58
3
HOH
HOH
230
A
HOH
59
3
HOH
HOH
231
A
HOH
61
3
HOH
HOH
232
A
HOH
63
3
HOH
HOH
233
A
HOH
64
3
HOH
HOH
234
A
HOH
68
3
HOH
HOH
235
A
HOH
69
3
HOH
HOH
236
A
HOH
70
3
HOH
HOH
237
A
HOH
71
3
HOH
HOH
238
A
HOH
72
3
HOH
HOH
239
A
HOH
73
3
HOH
HOH
240
A
HOH
74
3
HOH
HOH
241
A
HOH
83
3
HOH
HOH
242
A
HOH
90
3
HOH
HOH
243
A
HOH
92
3
HOH
HOH
244
A
HOH
93
3
HOH
HOH
245
A
HOH
97
3
HOH
HOH
246
A
HOH
2
3
HOH
HOH
101
B
HOH
5
3
HOH
HOH
102
B
HOH
9
3
HOH
HOH
103
B
HOH
10
3
HOH
HOH
104
B
HOH
13
3
HOH
HOH
105
B
HOH
16
3
HOH
HOH
106
B
HOH
17
3
HOH
HOH
107
B
HOH
18
3
HOH
HOH
108
B
HOH
19
3
HOH
HOH
109
B
HOH
21
3
HOH
HOH
110
B
HOH
22
3
HOH
HOH
111
B
HOH
25
3
HOH
HOH
112
B
HOH
28
3
HOH
HOH
113
B
HOH
31
3
HOH
HOH
114
B
HOH
32
3
HOH
HOH
115
B
HOH
34
3
HOH
HOH
116
B
HOH
37
3
HOH
HOH
117
B
HOH
38
3
HOH
HOH
118
B
HOH
39
3
HOH
HOH
119
B
HOH
41
3
HOH
HOH
120
B
HOH
46
3
HOH
HOH
121
B
HOH
48
3
HOH
HOH
122
B
HOH
49
3
HOH
HOH
123
B
HOH
52
3
HOH
HOH
124
B
HOH
53
3
HOH
HOH
125
B
HOH
55
3
HOH
HOH
126
B
HOH
56
3
HOH
HOH
127
B
HOH
60
3
HOH
HOH
128
B
HOH
65
3
HOH
HOH
129
B
HOH
66
3
HOH
HOH
130
B
HOH
67
3
HOH
HOH
131
B
HOH
77
3
HOH
HOH
132
B
HOH
78
3
HOH
HOH
133
B
HOH
79
3
HOH
HOH
134
B
HOH
80
3
HOH
HOH
135
B
HOH
81
3
HOH
HOH
136
B
HOH
82
3
HOH
HOH
137
B
HOH
84
3
HOH
HOH
138
B
HOH
85
3
HOH
HOH
139
B
HOH
86
3
HOH
HOH
140
B
HOH
87
3
HOH
HOH
141
B
HOH
88
3
HOH
HOH
142
B
HOH
89
3
HOH
HOH
143
B
HOH
91
3
HOH
HOH
144
B
HOH
94
3
HOH
HOH
145
B
HOH
95
3
HOH
HOH
146
B
HOH
96
3
HOH
HOH
147
B
HOH
98
3
HOH
HOH
148
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
5OC
9
n
9
5OC
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
5OC
21
n
9
5OC
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
1190
-7
4570
A
HOH
233
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
234
D
O
HOH
1_555
89.4
A
HOH
233
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
101
E
O
HOH
1_555
94.2
A
HOH
234
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
101
E
O
HOH
1_555
83.0
A
HOH
233
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
129
E
O
HOH
1_555
92.7
A
HOH
234
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
129
E
O
HOH
1_555
169.8
B
HOH
101
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
129
E
O
HOH
1_555
87.0
A
HOH
233
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
130
E
O
HOH
1_555
90.0
A
HOH
234
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
130
E
O
HOH
1_555
92.2
B
HOH
101
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
130
E
O
HOH
1_555
173.5
B
HOH
129
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
130
E
O
HOH
1_555
97.7
A
HOH
233
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
131
E
O
HOH
1_555
175.4
A
HOH
234
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
131
E
O
HOH
1_555
86.0
B
HOH
101
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
131
E
O
HOH
1_555
86.0
B
HOH
129
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
131
E
O
HOH
1_555
91.9
B
HOH
130
E
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
B
HOH
131
E
O
HOH
1_555
89.3
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
A
A
OP2
P
5OC
DG
9
10
7.31
1
B
B
OP2
P
5OC
DG
21
22
7.03
1
-5.79
0.90
105.70
99.91
A
A
A
O5'
P
OP2
DC
DC
DC
3
3
3
N
1
-8.18
0.90
105.70
97.52
A
A
A
O5'
P
OP2
DA
DA
DA
6
6
6
N
1
-4.83
0.80
102.40
97.57
A
A
A
C3'
C2'
C1'
DG
DG
DG
10
10
10
N
1
-5.50
0.90
105.70
100.20
A
A
A
O5'
P
OP2
DG
DG
DG
12
12
12
N
1
8.19
1.20
119.70
127.89
B
B
B
C3'
O3'
P
DT
DT
5OC
20
20
21
Y
1
-12.07
1.90
104.00
91.93
B
B
B
O3'
P
O5'
DT
5OC
5OC
20
21
21
Y
27.000
3.09
0.00
0.00
-2.47
0.00
-0.62
0.970
0.956
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.23170
0.17234
0.18
0.17555
1.401
25.00
658
13382
12724
4.9
97.71
3.612
0.060
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.069
0.071
0.80
0.80
1.20
PDB ENTRY 436D
MAXIMUM LIKELIHOOD
MASK
1.401
25.00
94
583
1
488
0
0.019
0.011
546
0.003
0.020
256
2.400
1.479
840
6.219
3.000
610
0.327
0.200
74
0.036
0.020
290
0.027
0.020
122
7.478
3.000
802
35.672
5.000
20
19.925
5.000
819
0.273
0.233
1.438
58
778
20
93.83
1.40
25.0
4F3U
13718
13485
2.0
0.051
1
35.1
6.7
98.3
1.40
1.42
1
95.4
data collection
SBC-Collect
Collect
phasing
MOLREP
refinement
REFMAC
5.6.0117
data reduction
HKL-3000
data scaling
HKL-3000
Crystal structure of 5-hydroxy-2'-deoxycytidine base paired with 2'-deoxyguanosine in Dickerson Drew Dodecamer
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
covale
1.616
both
A
DT
8
A
O3'
DT
8
1_555
A
5OC
9
A
P
5OC
9
1_555
covale
1.629
both
B
DT
20
B
O3'
DT
8
1_555
B
5OC
21
B
P
5OC
9
1_555
metalc
2.103
A
MG
101
C
MG
MG
1_555
A
HOH
233
D
O
HOH
1_555
metalc
2.047
A
MG
101
C
MG
MG
1_555
A
HOH
234
D
O
HOH
1_555
metalc
2.101
A
MG
101
C
MG
MG
1_555
B
HOH
101
E
O
HOH
1_555
metalc
2.025
A
MG
101
C
MG
MG
1_555
B
HOH
129
E
O
HOH
1_555
metalc
2.019
A
MG
101
C
MG
MG
1_555
B
HOH
130
E
O
HOH
1_555
metalc
2.084
A
MG
101
C
MG
MG
1_555
B
HOH
131
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
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
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
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
5-hydroxy-dC, modified Dickerson, 5-hydroxy-2'-deoxycytidine, DNA
4F3U
PDB
1
4F3U
1
12
4F3U
1
12
4F3U
A
1
1
12
13
24
4F3U
13
24
4F3U
B
1
1
12
BINDING SITE FOR RESIDUE MG A 101
A
MG
101
Software
6
A
HOH
233
D
HOH
6
1_555
A
HOH
234
D
HOH
6
1_555
B
HOH
101
E
HOH
6
1_555
B
HOH
129
E
HOH
6
1_555
B
HOH
130
E
HOH
6
1_555
B
HOH
131
E
HOH
6
1_555
19
P 21 21 21