0.039526
0.000000
0.000000
0.000000
0.024832
0.000000
0.000000
0.000000
0.015413
0.00000
0.00000
0.00000
McDonough, M.
El-Sagheer, A.H.
Brown, T.
Schofield, C.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
25.300
40.270
64.880
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
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
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
Chem. Commun. (Camb.)
1364-548X
50
1794
1796
10.1039/c3cc48151d
24287551
Structural insights into how 5-hydroxymethylation influences transcription factor binding.
2014
10.2210/pdb4c5x/pdb
pdb_00004c5x
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
PIXEL
2011-07-24
DECTRIS PILATUS 2M
SI (111) DOUBLE CRYSTAL
SINGLE WAVELENGTH
M
x-ray
1
0.917300
1.0
I04-1
Diamond
0.917300
SYNCHROTRON
DIAMOND BEAMLINE I04-1
3693.418
5'-D(CP*GP*CP*GP*AP*AP*TP*TP*5HCP*GP*CP*GP)-3'
DICKERSON-DREW SEQUENCE DODECAMER
2
syn
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
136
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
2.02
39
NONE
7.5
40% MPD, SPERMINE, MAGNESIUM CHLORIDE, SODIUM CACODYLATE PH 7.5
3.091
1
19
A
1
B
24
0.439
A_DC1:DG24_B
1
-15.782
0.225
0.128
-0.120
4.303
1
19
A
2
B
23
-2.879
A_DG2:DC23_B
2
-15.308
-0.185
0.461
-0.170
-2.183
1
19
A
3
B
22
-0.668
A_DC3:DG22_B
3
-1.685
0.170
0.009
-0.168
13.886
1
19
A
4
B
21
-0.372
A_DG4:5HC21_B
4
-9.088
-0.286
0.053
-0.150
7.473
1
20
A
5
B
20
1.748
A_DA5:DT20_B
5
-16.447
0.021
0.005
-0.109
1.935
1
20
A
6
B
19
4.163
A_DA6:DT19_B
6
-15.937
0.041
0.076
-0.068
-0.190
1
20
A
7
B
18
4.282
A_DT7:DA18_B
7
-17.927
-0.010
0.103
-0.103
-2.709
1
20
A
8
B
17
3.434
A_DT8:DA17_B
8
-13.438
-0.079
0.012
-0.175
-9.340
1
19
A
9
B
16
-1.119
A_5HC9:DG16_B
9
-11.130
0.213
-0.108
-0.138
5.365
1
19
A
10
B
15
3.096
A_DG10:DC15_B
10
-9.142
-0.142
0.203
-0.098
4.090
1
19
A
11
B
14
-2.345
A_DC11:DG14_B
11
-17.682
0.148
0.102
-0.181
5.075
1
19
A
12
B
13
-0.238
A_DG12:DC13_B
12
-7.070
-0.130
0.389
-0.053
3.213
35.573
A
A
1
2
10.557
B
B
24
23
3.236
6.411
-0.139
0.151
AA_DC1DG2:DC23DG24_BB
1
-2.788
4.591
34.901
-0.682
-0.177
3.443
42.167
A
A
2
3
-10.962
B
B
23
22
3.537
-7.835
0.745
0.502
AA_DG2DC3:DG22DC23_BB
2
3.848
-5.385
41.294
1.568
-0.608
2.971
25.003
A
A
3
4
18.045
B
B
22
21
3.027
7.689
0.086
0.285
AA_DC3DG4:5HC21DG22_BB
3
-0.213
0.501
23.808
-1.491
-0.259
3.438
38.531
A
A
4
5
0.500
B
B
21
20
3.424
0.330
-0.506
-0.018
AA_DG4DA5:DT205HC21_BB
4
-1.267
1.920
38.510
-0.070
0.603
3.294
39.452
A
A
5
6
1.601
B
B
20
19
3.303
1.081
-0.005
-0.212
AA_DA5DA6:DT19DT20_BB
5
-1.434
2.124
39.413
-0.443
-0.164
3.280
31.977
A
A
6
7
-4.527
B
B
19
18
3.246
-2.492
-0.023
-0.577
AA_DA6DT7:DA18DT19_BB
6
-0.045
0.082
31.882
-0.598
0.034
3.248
34.973
A
A
7
8
-1.135
B
B
18
17
3.244
-0.682
-0.006
-0.388
AA_DT7DT8:DA17DA18_BB
7
1.404
-2.336
34.940
-0.544
0.220
3.390
42.181
A
A
8
9
-2.818
B
B
17
16
3.396
-2.026
-0.128
-0.240
AA_DT85HC9:DG16DA17_BB
8
2.693
-3.746
42.052
-0.117
0.466
3.029
26.168
A
A
9
10
13.357
B
B
16
15
3.051
5.972
0.629
0.838
AA_5HC9DG10:DC15DG16_BB
9
-4.044
9.045
25.172
0.314
-2.429
3.190
44.853
A
A
10
11
-13.160
B
B
15
14
3.348
-9.962
-1.259
0.631
AA_DG10DC11:DG14DC15_BB
10
-2.022
2.671
43.744
1.742
1.465
3.217
32.889
A
A
11
12
11.071
B
B
14
13
3.214
6.230
-0.036
0.327
AA_DC11DG12:DC13DG14_BB
11
-1.700
3.022
32.266
-0.479
-0.225
citation
citation_author
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Database references
Database references
Database references
Data collection
Database references
Derived calculations
Other
Refinement description
1
0
2013-10-02
1
1
2013-12-11
1
2
2014-02-12
1
3
2018-02-21
1
4
2023-12-20
_citation.journal_abbrev
_citation.journal_id_ISSN
_citation.page_last
_citation.pdbx_database_id_DOI
_citation.title
_citation_author.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_sf
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.conn_type_id
_struct_conn.id
_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
ULTRA HIGH RESOLUTION DICKERSON-DREW DODECAMER B-DNA WITH 5-METHYLCYSTOSINE MODIFICATION
ULTRA HIGH RESOLUTION DICKERSON-DREW DODECAMER B-DNA
PDBE
Y
PDBE
2013-09-16
REL
REL
MG
MAGNESIUM ION
HOH
water
32630
SYNTHETIC CONSTRUCT
sample
1BNA
PDB ENRTY 1BNA
PDB
experimental model
MG
101
2
MG
MG
101
A
HOH
2001
3
HOH
HOH
2001
A
HOH
2002
3
HOH
HOH
2002
A
HOH
2003
3
HOH
HOH
2003
A
HOH
2004
3
HOH
HOH
2004
A
HOH
2005
3
HOH
HOH
2005
A
HOH
2006
3
HOH
HOH
2006
A
HOH
2007
3
HOH
HOH
2007
A
HOH
2008
3
HOH
HOH
2008
A
HOH
2009
3
HOH
HOH
2009
A
HOH
2010
3
HOH
HOH
2010
A
HOH
2011
3
HOH
HOH
2011
A
HOH
2012
3
HOH
HOH
2012
A
HOH
2013
3
HOH
HOH
2013
A
HOH
2014
3
HOH
HOH
2014
A
HOH
2015
3
HOH
HOH
2015
A
HOH
2016
3
HOH
HOH
2016
A
HOH
2017
3
HOH
HOH
2017
A
HOH
2018
3
HOH
HOH
2018
A
HOH
2019
3
HOH
HOH
2019
A
HOH
2020
3
HOH
HOH
2020
A
HOH
2021
3
HOH
HOH
2021
A
HOH
2022
3
HOH
HOH
2022
A
HOH
2023
3
HOH
HOH
2023
A
HOH
2024
3
HOH
HOH
2024
A
HOH
2025
3
HOH
HOH
2025
A
HOH
2026
3
HOH
HOH
2026
A
HOH
2027
3
HOH
HOH
2027
A
HOH
2028
3
HOH
HOH
2028
A
HOH
2029
3
HOH
HOH
2029
A
HOH
2030
3
HOH
HOH
2030
A
HOH
2031
3
HOH
HOH
2031
A
HOH
2032
3
HOH
HOH
2032
A
HOH
2033
3
HOH
HOH
2033
A
HOH
2034
3
HOH
HOH
2034
A
HOH
2035
3
HOH
HOH
2035
A
HOH
2036
3
HOH
HOH
2036
A
HOH
2037
3
HOH
HOH
2037
A
HOH
2038
3
HOH
HOH
2038
A
HOH
2039
3
HOH
HOH
2039
A
HOH
2040
3
HOH
HOH
2040
A
HOH
2041
3
HOH
HOH
2041
A
HOH
2042
3
HOH
HOH
2042
A
HOH
2043
3
HOH
HOH
2043
A
HOH
2044
3
HOH
HOH
2044
A
HOH
2045
3
HOH
HOH
2045
A
HOH
2046
3
HOH
HOH
2046
A
HOH
2047
3
HOH
HOH
2047
A
HOH
2048
3
HOH
HOH
2048
A
HOH
2049
3
HOH
HOH
2049
A
HOH
2050
3
HOH
HOH
2050
A
HOH
2051
3
HOH
HOH
2051
A
HOH
2052
3
HOH
HOH
2052
A
HOH
2053
3
HOH
HOH
2053
A
HOH
2054
3
HOH
HOH
2054
A
HOH
2055
3
HOH
HOH
2055
A
HOH
2056
3
HOH
HOH
2056
A
HOH
2057
3
HOH
HOH
2057
A
HOH
2058
3
HOH
HOH
2058
A
HOH
2059
3
HOH
HOH
2059
A
HOH
2060
3
HOH
HOH
2060
A
HOH
2061
3
HOH
HOH
2061
A
HOH
2062
3
HOH
HOH
2062
A
HOH
2063
3
HOH
HOH
2063
A
HOH
2064
3
HOH
HOH
2064
A
HOH
2065
3
HOH
HOH
2065
A
HOH
2066
3
HOH
HOH
2066
A
HOH
2067
3
HOH
HOH
2067
A
HOH
2068
3
HOH
HOH
2068
A
HOH
2069
3
HOH
HOH
2069
A
HOH
2070
3
HOH
HOH
2070
A
HOH
2071
3
HOH
HOH
2071
A
HOH
2072
3
HOH
HOH
2072
A
HOH
2073
3
HOH
HOH
2073
A
HOH
2001
3
HOH
HOH
2001
B
HOH
2002
3
HOH
HOH
2002
B
HOH
2003
3
HOH
HOH
2003
B
HOH
2004
3
HOH
HOH
2004
B
HOH
2005
3
HOH
HOH
2005
B
HOH
2006
3
HOH
HOH
2006
B
HOH
2007
3
HOH
HOH
2007
B
HOH
2008
3
HOH
HOH
2008
B
HOH
2009
3
HOH
HOH
2009
B
HOH
2010
3
HOH
HOH
2010
B
HOH
2011
3
HOH
HOH
2011
B
HOH
2012
3
HOH
HOH
2012
B
HOH
2013
3
HOH
HOH
2013
B
HOH
2014
3
HOH
HOH
2014
B
HOH
2015
3
HOH
HOH
2015
B
HOH
2016
3
HOH
HOH
2016
B
HOH
2017
3
HOH
HOH
2017
B
HOH
2018
3
HOH
HOH
2018
B
HOH
2019
3
HOH
HOH
2019
B
HOH
2020
3
HOH
HOH
2020
B
HOH
2021
3
HOH
HOH
2021
B
HOH
2022
3
HOH
HOH
2022
B
HOH
2023
3
HOH
HOH
2023
B
HOH
2024
3
HOH
HOH
2024
B
HOH
2025
3
HOH
HOH
2025
B
HOH
2026
3
HOH
HOH
2026
B
HOH
2027
3
HOH
HOH
2027
B
HOH
2028
3
HOH
HOH
2028
B
HOH
2029
3
HOH
HOH
2029
B
HOH
2030
3
HOH
HOH
2030
B
HOH
2031
3
HOH
HOH
2031
B
HOH
2032
3
HOH
HOH
2032
B
HOH
2033
3
HOH
HOH
2033
B
HOH
2034
3
HOH
HOH
2034
B
HOH
2035
3
HOH
HOH
2035
B
HOH
2036
3
HOH
HOH
2036
B
HOH
2037
3
HOH
HOH
2037
B
HOH
2038
3
HOH
HOH
2038
B
HOH
2039
3
HOH
HOH
2039
B
HOH
2040
3
HOH
HOH
2040
B
HOH
2041
3
HOH
HOH
2041
B
HOH
2042
3
HOH
HOH
2042
B
HOH
2043
3
HOH
HOH
2043
B
HOH
2044
3
HOH
HOH
2044
B
HOH
2045
3
HOH
HOH
2045
B
HOH
2046
3
HOH
HOH
2046
B
HOH
2047
3
HOH
HOH
2047
B
HOH
2048
3
HOH
HOH
2048
B
HOH
2049
3
HOH
HOH
2049
B
HOH
2050
3
HOH
HOH
2050
B
HOH
2051
3
HOH
HOH
2051
B
HOH
2052
3
HOH
HOH
2052
B
HOH
2053
3
HOH
HOH
2053
B
HOH
2054
3
HOH
HOH
2054
B
HOH
2055
3
HOH
HOH
2055
B
HOH
2056
3
HOH
HOH
2056
B
HOH
2057
3
HOH
HOH
2057
B
HOH
2058
3
HOH
HOH
2058
B
HOH
2059
3
HOH
HOH
2059
B
HOH
2060
3
HOH
HOH
2060
B
HOH
2061
3
HOH
HOH
2061
B
HOH
2062
3
HOH
HOH
2062
B
HOH
2063
3
HOH
HOH
2063
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
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
5HC
21
n
9
5HC
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
1180
-6.7
4590
A
HOH
2018
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2019
D
O
HOH
1_555
92.4
A
HOH
2018
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2029
D
O
HOH
1_555
92.7
A
HOH
2019
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2029
D
O
HOH
1_555
85.9
A
HOH
2018
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2071
D
O
HOH
1_555
91.2
A
HOH
2019
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2071
D
O
HOH
1_555
173.3
A
HOH
2029
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2071
D
O
HOH
1_555
88.3
A
HOH
2018
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2072
D
O
HOH
1_555
177.2
A
HOH
2019
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2072
D
O
HOH
1_555
86.7
A
HOH
2029
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2072
D
O
HOH
1_555
89.9
A
HOH
2071
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2072
D
O
HOH
1_555
90.0
A
HOH
2018
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2073
D
O
HOH
1_555
89.6
A
HOH
2019
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2073
D
O
HOH
1_555
92.4
A
HOH
2029
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2073
D
O
HOH
1_555
177.1
A
HOH
2071
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2073
D
O
HOH
1_555
93.3
A
HOH
2072
D
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
2073
D
O
HOH
1_555
87.8
A
5HC
9
A
5HC
9
DC
B
5HC
21
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
A
A
O
O
HOH
HOH
2009
2038
2.03
1
A
A
O
O
HOH
HOH
2009
2034
2.15
1
A
DC
11
0.060
SIDE CHAIN
1
B
DC
23
0.095
SIDE CHAIN
1
-6.22
0.80
102.40
96.18
A
A
A
C3'
C2'
C1'
DG
DG
DG
4
4
4
N
1
-7.29
0.90
105.70
98.41
A
A
A
O5'
P
OP2
DA
DA
DA
6
6
6
N
1
-10.69
0.90
105.70
95.01
A
A
A
O5'
P
OP2
DG
DG
DG
10
10
10
N
1
-7.46
0.70
108.00
100.54
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
-2.52
0.40
110.80
108.28
A
A
A
C4
C5
N7
DG
DG
DG
12
12
12
N
1
3.06
0.40
105.40
108.46
A
A
A
N9
C4
C5
DG
DG
DG
12
12
12
N
1
-6.43
0.70
108.00
101.57
B
B
B
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
9.98
1.50
119.60
129.58
B
B
B
OP1
P
OP2
DG
DG
DG
14
14
14
N
1
-11.21
0.90
105.70
94.49
B
B
B
O5'
P
OP2
DG
DG
DG
14
14
14
N
1
-11.34
1.60
120.90
109.56
B
B
B
P
O5'
C5'
DG
DG
DG
14
14
14
N
1
-8.10
1.00
110.10
102.00
B
B
B
C1'
O4'
C4'
DG
DG
DG
14
14
14
N
1
-5.65
0.70
108.00
102.35
B
B
B
O4'
C1'
N9
DG
DG
DG
14
14
14
N
1
5.36
0.30
108.30
113.66
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
1
-3.41
0.50
129.30
125.89
B
B
B
N1
C2
N3
DA
DA
DA
17
17
17
N
1
2.13
0.30
108.30
110.43
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
-3.37
0.40
104.50
101.13
B
B
B
O4'
C4'
C3'
DC
DC
DC
23
23
23
N
1
B
B
C2
O2
DC
DC
13
13
-0.094
0.009
1.240
1.146
N
1
B
B
O3'
C3'
DG
DG
14
14
-0.055
0.006
1.419
1.364
N
22.06
7.7695
0.0000
0.0000
-6.7934
0.0000
-0.9761
0.1734
0.1421
0.1452
1.3
34.2
2971
17362
10.15
93.78
0.14
1
0.0
MOLECULAR REPLACEMENT
16.50
0.29
0.50
PDB ENRTY 1BNA
ML
FLAT BULK SOLVENT MODEL
48.272
0.442
1.3
34.2
136
627
1
490
0
0.022
555
2.486
858
30.110
226
0.124
94
0.041
24
0.2261
0.1948
1.3213
130
1167
84.00
0.2134
0.1855
1.3441
121
1149
85.00
0.2285
0.1809
1.3685
136
1180
89.00
0.2393
0.1621
1.3949
137
1240
91.00
0.2242
0.1664
1.4233
135
1214
92.00
0.2022
0.1503
1.4543
142
1259
94.00
0.2397
0.1595
1.4881
147
1296
94.00
0.1885
0.1401
1.5253
139
1201
91.00
0.1947
0.1195
1.5666
141
1300
96.00
0.1627
0.1129
1.6127
146
1291
95.00
0.1261
0.1001
1.6647
144
1284
95.00
0.1537
0.0979
1.7242
142
1299
97.00
0.1331
0.1065
1.7932
149
1330
97.00
0.1795
0.1243
1.8749
146
1312
98.00
0.1921
0.1294
1.9737
147
1322
98.00
0.1572
0.1325
2.0973
141
1237
92.00
0.1952
0.1357
2.2592
148
1318
98.00
0.2007
0.1655
2.4865
146
1324
97.00
0.1917
0.1505
2.8462
149
1300
97.00
0.1664
0.1645
3.5853
141
1286
95.00
0.1432
0.1385
34.2269
144
1288
96.00
15.58
1.21
34.22
4C5X
19814
1.0
0.02
1
26.20
5.3
95.8
0.52
1.21
1.24
2.40
1
4.3
79.4
refinement
PHENIX
(PHENIX.REFINE)
data reduction
xia2
data scaling
SCALA
phasing
PHASER
Ultra High Resolution Dickerson-Drew dodecamer B-DNA with 5-Hydroxymethyl-cytosine Modification
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
covale
1.639
both
A
DT
8
A
O3'
DT
8
1_555
A
5HC
9
A
P
5HC
9
1_555
covale
1.630
both
A
5HC
9
A
O3'
5HC
9
1_555
A
DG
10
A
P
DG
10
1_555
covale
1.595
both
B
DT
20
B
O3'
DT
8
1_555
B
5HC
21
B
P
5HC
9
1_555
covale
1.633
both
B
5HC
21
B
O3'
5HC
9
1_555
B
DG
22
B
P
DG
10
1_555
metalc
2.055
A
MG
101
C
MG
MG
1_555
A
HOH
2018
D
O
HOH
1_555
metalc
2.066
A
MG
101
C
MG
MG
1_555
A
HOH
2019
D
O
HOH
1_555
metalc
2.038
A
MG
101
C
MG
MG
1_555
A
HOH
2029
D
O
HOH
1_555
metalc
2.098
A
MG
101
C
MG
MG
1_555
A
HOH
2071
D
O
HOH
1_555
metalc
2.102
A
MG
101
C
MG
MG
1_555
A
HOH
2072
D
O
HOH
1_555
metalc
2.113
A
MG
101
C
MG
MG
1_555
A
HOH
2073
D
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
DG
4
A
N1
DG
4
1_555
B
5HC
21
B
N3
5HC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
5HC
21
B
O2
5HC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
5HC
21
B
N4
5HC
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
5HC
9
A
N3
5HC
9
1_555
B
DG
16
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
5HC
9
A
N4
5HC
9
1_555
B
DG
16
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
5HC
9
A
O2
5HC
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
DNA, CYTOSINE MODIFICATION
4C5X
PDB
1
4C5X
1
12
4C5X
1
12
4C5X
A
1
1
12
13
24
4C5X
13
24
4C5X
B
1
1
12
BINDING SITE FOR RESIDUE MG A 101
A
MG
101
Software
6
A
HOH
2018
D
HOH
6
1_555
A
HOH
2019
D
HOH
6
1_555
A
HOH
2029
D
HOH
6
1_555
A
HOH
2071
D
HOH
6
1_555
A
HOH
2072
D
HOH
6
1_555
A
HOH
2073
D
HOH
6
1_555
19
P 21 21 21