1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Maufrais, C.
Fazakerley, G.V.
Cadet, J.
Boulard, Y.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C6 H12 N O7 P
241.136
N-(2-DEOXY-BETA-D-ERYTHO-PENTOFURANOSYL-5-PHOSPHATE) FORMAMIDE
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
N
1
N
P
N
2
N
O
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
R
C
N
10
N
N
N
11
N
C
N
12
N
O
N
13
S
C
N
14
N
C
N
15
N
O
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
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
O
N
29
N
P
N
30
N
O
N
31
N
O
N
32
N
O
N
33
N
C
N
34
R
C
N
35
N
O
N
36
S
C
N
37
N
O
N
38
N
C
N
39
R
C
Y
40
N
N
Y
41
N
C
Y
42
N
N
Y
43
N
C
Y
44
N
C
N
45
N
N
Y
46
N
N
Y
47
N
C
Y
48
N
N
Y
49
N
C
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
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
O
N
65
N
P
N
66
N
O
N
67
N
O
N
68
N
O
N
69
N
C
N
70
R
C
N
71
N
O
N
72
S
C
N
73
N
O
N
74
N
C
N
75
R
C
N
76
N
N
N
77
N
C
N
78
N
O
N
79
N
N
N
80
N
C
N
81
N
N
N
82
N
C
N
83
N
C
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
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
O
N
99
N
P
N
100
N
O
N
101
N
O
N
102
N
O
N
103
N
C
N
104
R
C
N
105
N
O
N
106
S
C
N
107
N
O
N
108
N
C
N
109
R
C
Y
110
N
N
Y
111
N
C
Y
112
N
N
Y
113
N
C
N
114
N
C
N
115
N
O
N
116
N
N
N
117
N
C
N
118
N
N
N
119
N
N
Y
120
N
C
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
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
O
N
136
N
P
N
137
N
O
N
138
N
O
N
139
N
O
N
140
N
C
N
141
R
C
N
142
N
O
N
143
S
C
N
144
N
O
N
145
N
C
N
146
R
C
N
147
N
N
N
148
N
C
N
149
N
O
N
150
N
N
N
151
N
C
N
152
N
O
N
153
N
C
N
154
N
C
N
155
N
C
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
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
1
N
doub
N
2
N
sing
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
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
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
doub
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
doub
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
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
Y
51
N
sing
Y
52
N
sing
Y
53
N
doub
N
54
N
sing
Y
55
N
sing
Y
56
N
sing
Y
57
N
doub
N
58
N
sing
Y
59
N
doub
N
60
N
sing
N
61
N
sing
Y
62
N
sing
Y
63
N
doub
N
64
N
sing
Y
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
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
doub
N
92
N
sing
N
93
N
doub
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
doub
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
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
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
Y
124
N
sing
Y
125
N
sing
Y
126
N
doub
N
127
N
sing
Y
128
N
sing
N
129
N
sing
Y
130
N
doub
N
131
N
doub
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
doub
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
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
doub
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
doub
N
170
N
sing
N
171
N
sing
N
172
N
doub
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
31
5930
5940
10.1093/nar/gkg803
14530441
Structural study of DNA duplex containing an N-(2-deoxy-beta-D-erythro-pentofuranosyl) formamide
frameshift by NMR and restrained molecular dynamics.
2003
10.2210/pdb1osr/pdb
pdb_00001osr
2749.826
5'-D(*AP*GP*GP*AP*CP*CP*AP*CP*G)-3'
1
syn
polymer
2945.905
5'-D(*CP*GP*TP*GP*GP*(2DF)P*TP*CP*CP*T)-3'
1
syn
polymer
no
no
(DA)(DG)(DG)(DA)(DC)(DC)(DA)(DC)(DG)
AGGACCACG
A
polydeoxyribonucleotide
no
yes
(DC)(DG)(DT)(DG)(DG)(2DF)(DT)(DC)(DC)(DT)
CGTGGNTCCT
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-20.071
1
20
A
1
B
19
-10.630
A_DA1:DT19_B
1
-3.873
-0.563
-0.047
-0.192
-12.890
1
19
A
2
B
18
-6.941
A_DG2:DC18_B
2
-10.584
0.609
-0.318
-0.030
-4.452
1
19
A
3
B
17
-4.326
A_DG3:DC17_B
3
-6.491
0.079
0.105
-0.028
-5.201
1
20
A
4
B
16
-7.564
A_DA4:DT16_B
4
0.109
0.490
0.094
0.126
-3.299
1
19
A
5
B
14
-4.528
A_DC5:DG14_B
5
-4.383
-0.036
0.270
0.024
2.696
1
19
A
6
B
13
-3.681
A_DC6:DG13_B
6
-7.327
0.033
0.063
-0.024
7.486
1
20
A
7
B
12
-4.892
A_DA7:DT12_B
7
-3.196
0.168
0.419
0.026
4.372
1
19
A
8
B
11
-6.566
A_DC8:DG11_B
8
-6.209
-0.605
0.493
-0.080
22.312
1
19
A
9
B
10
-8.167
A_DG9:DC10_B
9
-5.550
0.688
1.024
-0.148
3.152
40.415
A
A
1
2
-1.462
B
B
19
18
3.189
-1.007
-0.178
-0.490
AA_DA1DG2:DC18DT19_BB
1
5.355
-7.774
40.062
-0.600
0.843
2.976
34.206
A
A
2
3
-6.132
B
B
18
17
2.995
-3.592
-0.033
-0.141
AA_DG2DG3:DC17DC18_BB
2
-4.191
7.154
33.771
0.280
-0.552
3.341
39.995
A
A
3
4
-8.891
B
B
17
16
3.312
-6.059
-0.051
-0.447
AA_DG3DA4:DT16DC17_BB
3
0.363
-0.533
39.550
0.057
0.118
3.284
32.727
A
A
4
5
2.033
B
B
16
14
3.304
1.145
0.056
-0.475
AA_DA4DC5:DG14DT16_BB
4
-0.450
0.799
32.705
-1.043
-0.178
3.227
36.053
A
A
5
6
-8.271
B
B
14
13
3.245
-5.102
0.237
-0.045
AA_DC5DC6:DG13DG14_BB
5
1.317
-2.135
35.678
0.647
-0.197
3.252
40.234
A
A
6
7
-4.737
B
B
13
12
3.249
-3.253
-0.078
-0.190
AA_DC6DA7:DT12DG13_BB
6
-2.824
4.112
40.013
0.092
-0.206
3.357
31.565
A
A
7
8
-1.729
B
B
12
11
3.342
-0.941
-0.155
-0.546
AA_DA7DC8:DG11DT12_BB
7
-0.107
0.197
31.551
-0.825
0.264
2.778
41.936
A
A
8
9
-12.295
B
B
11
10
2.782
-8.723
0.034
-0.359
AA_DC8DG9:DC10DG11_BB
8
-4.677
6.591
40.802
0.282
-0.467
database_2
pdbx_nmr_software
pdbx_nmr_spectrometer
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Data collection
1
0
2003-10-14
1
1
2008-04-29
1
2
2011-07-13
1
3
2022-02-23
1
4
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_struct_conn.pdbx_leaving_atom_flag
RCSB
Y
RCSB
2003-03-20
REL
THE STRUCTURES WERE DETERMINED USING PROTON NMR FOLLOWED BY DISTANCE
RESTRAINED MOLECULAR DYNAMICS SIMULATIONS. TWO REPRESENTATIVE
STRUCTURES OF THE TWO ISOMER CIS AND TRANS FOR THE FORMAMIDE RESIDUE
ARE PRESENTED.
2
NOESY
COSY
DQFCOSY
TOCSY
HSQC 1H-31P
10 mM PHOSPHATE BUFFER, 150 mM NACL, 0.2 mM EDTA
6.5
AMBIENT
290
K
10 mM PHOSPHATE BUFFER, 150 mM NACL, 0.2 mM EDTA
5.5
AMBIENT
278
K
MOLECULAR MODELING; SIMULATED ANNEALING; RESTRAINED MOLECULAR DYNAMICS SIMULATIONS
2
those which were used to initiate molecular dynamic simulations
2 MM DNA, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.2 MM EDTA
99.9% D2O
2 MM DNA, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.2 MM EDTA
90% H2O/10% D2O
KOLLMAN
refinement
Amber
LEBRET
refinement
MORCAD
Koradi, Wuthrich
refinement
MOLMOL
2.6
BRUKER
processing
XwinNMR
2.5
600
Bruker
AVANCE
500
Bruker
AVANCE
A
1
n
1
DA
1
A
G
2
n
2
DG
2
A
G
3
n
3
DG
3
A
A
4
n
4
DA
4
A
C
5
n
5
DC
5
A
C
6
n
6
DC
6
A
A
7
n
7
DA
7
A
C
8
n
8
DC
8
A
G
9
n
9
DG
9
A
C
10
n
1
DC
10
B
G
11
n
2
DG
11
B
T
12
n
3
DT
12
B
G
13
n
4
DG
13
B
G
14
n
5
DG
14
B
2DF
15
n
6
2DF
15
B
T
16
n
7
DT
16
B
C
17
n
8
DC
17
B
C
18
n
9
DC
18
B
T
19
n
10
DT
19
B
author_defined_assembly
2
dimeric
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
DA
1
0.064
SIDE CHAIN
1
A
DG
9
0.059
SIDE CHAIN
1
B
DC
18
0.064
SIDE CHAIN
2
A
DA
1
0.078
SIDE CHAIN
1
3.09
0.30
108.30
111.39
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
1
1.94
0.30
108.30
110.24
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
1.92
0.30
108.30
110.22
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
1
2.39
0.30
108.30
110.69
B
B
B
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
2.39
0.30
108.30
110.69
B
B
B
O4'
C1'
N1
DT
DT
DT
12
12
12
N
1
-3.70
0.60
122.90
119.20
B
B
B
C6
C5
C7
DT
DT
DT
12
12
12
N
1
2.31
0.30
108.30
110.61
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
1
2.28
0.30
108.30
110.58
B
B
B
O4'
C1'
N1
DC
DC
DC
18
18
18
N
1
2.95
0.30
108.30
111.25
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
2
3.43
0.30
108.30
111.73
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
2
2.11
0.30
108.30
110.41
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
2
2.13
0.30
108.30
110.43
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
2
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
2
2.25
0.30
108.30
110.55
B
B
B
O4'
C1'
N1
DC
DC
DC
10
10
10
N
2
2.74
0.30
108.30
111.04
B
B
B
O4'
C1'
N1
DT
DT
DT
12
12
12
N
2
2.68
0.30
108.30
110.98
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
2
2.07
0.30
108.30
110.37
B
B
B
O4'
C1'
N1
DC
DC
DC
18
18
18
N
2
2.89
0.30
108.30
111.19
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
Structural study of dna duplex containaing a n-(2-deoxy-beta-erytho-pentofuranosyl) formamide frameshift by nmr and restrained molecular dynamics
1
N
N
2
N
N
covale
1.622
both
B
DG
14
B
O3'
DG
5
1_555
B
2DF
15
B
P
2DF
6
1_555
covale
1.611
both
B
2DF
15
B
O3'
2DF
6
1_555
B
DT
16
B
P
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N1
DA
1
1_555
B
DT
19
B
N3
DT
10
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N6
DA
1
1_555
B
DT
19
B
O4
DT
10
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
18
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
18
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
18
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
DC
17
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
17
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
17
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
16
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
16
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
14
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
14
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
14
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
B
DG
13
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
B
DG
13
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
B
DG
13
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
B
DT
12
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
B
DT
12
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
11
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
11
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
11
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N1
DG
9
1_555
B
DC
10
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
9
A
N2
DG
9
1_555
B
DC
10
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
9
A
O6
DG
9
1_555
B
DC
10
B
N4
DC
1
1_555
DNA
MODIFIED BASE, MUTAGENESIS, DEOXYRIBONUCLEIC ACID, DNA
1OSR
PDB
1
1OSR
1OSR
PDB
2
1OSR
1
9
1OSR
1
9
1OSR
A
1
1
9
10
19
1OSR
10
19
1OSR
B
2
1
10
1
P 1