1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Hennard, C.
Finneman, J.
Harris, C.M.
Harris, T.M.
Stone, M.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C18 H22 N5 O7 P
451.370
n
(R)-(N-PHENYL-2-HYDROXY-ETHYL)-2'-DEOXY-ADENOSINE-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
US
Biochemistry
BICHAW
0033
0006-2960
40
9780
9791
10.1021/bi010564v
11502171
The nonmutagenic (R)- and (S)-beta-(N(6)-adenyl)styrene oxide adducts are oriented in the major groove and show little perturbation to DNA
structure.
2001
10.2210/pdb1k5e/pdb
pdb_00001k5e
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
N-RAS Protooncogene
3536.411
5'-D(*CP*GP*GP*AP*CP*(ABR)P*AP*GP*AP*AP*G)-3'
1
syn
polymer
N-RAS Protooncogene
3291.145
5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'
1
syn
polymer
no
yes
(DC)(DG)(DG)(DA)(DC)(ABR)(DA)(DG)(DA)(DA)(DG)
CGGACAAGAAG
A
polydeoxyribonucleotide
no
no
(DC)(DT)(DT)(DC)(DT)(DT)(DG)(DT)(DC)(DC)(DG)
CTTCTTGTCCG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-8.032
1
19
A
1
B
22
-2.802
A_DC1:DG22_B
1
-10.320
0.115
0.324
-0.122
-10.951
1
19
A
2
B
21
1.042
A_DG2:DC21_B
2
-9.208
-0.223
-0.232
-0.095
-10.182
1
19
A
3
B
20
0.655
A_DG3:DC20_B
3
-10.098
-0.195
-0.209
-0.105
-10.001
1
20
A
4
B
19
1.895
A_DA4:DT19_B
4
-2.904
0.101
0.399
-0.196
-6.305
1
19
A
5
B
18
1.607
A_DC5:DG18_B
5
7.304
0.318
0.119
-0.083
6.967
1
20
A
6
B
17
-1.586
A_ABR6:DT17_B
6
-12.813
-0.039
-0.300
-0.147
1.649
1
20
A
7
B
16
4.197
A_DA7:DT16_B
7
-11.783
-0.049
0.160
-0.170
-2.161
1
19
A
8
B
15
-3.323
A_DG8:DC15_B
8
-13.492
-0.065
-0.176
-0.179
-0.962
1
20
A
9
B
14
0.142
A_DA9:DT14_B
9
-2.256
-0.055
0.164
-0.123
3.950
1
20
A
10
B
13
2.190
A_DA10:DT13_B
10
-7.185
-0.031
-0.064
-0.118
1.145
1
19
A
11
B
12
-3.004
A_DG11:DC12_B
11
-14.343
-0.095
0.160
-0.162
2.656
31.342
A
A
1
2
22.167
B
B
22
21
3.098
11.695
0.047
-0.621
AA_DC1DG2:DC21DG22_BB
1
1.345
-2.549
29.098
-3.165
0.144
3.179
33.302
A
A
2
3
7.718
B
B
21
20
3.301
4.403
-0.039
-0.637
AA_DG2DG3:DC20DC21_BB
2
-3.411
5.979
32.846
-1.844
-0.499
3.135
33.931
A
A
3
4
0.238
B
B
20
19
3.262
0.138
0.353
-0.829
AA_DG3DA4:DT19DC20_BB
3
-6.529
11.254
33.315
-1.443
-1.639
3.085
32.409
A
A
4
5
3.348
B
B
19
18
3.180
1.862
-0.021
-1.079
AA_DA4DC5:DG18DT19_BB
4
4.330
-7.784
32.073
-2.249
0.771
2.462
31.192
A
A
5
6
6.960
B
B
18
17
2.745
3.705
-0.532
-0.755
AA_DC5ABR6:DT17DG18_BB
5
6.820
-12.812
30.234
-1.974
2.040
3.594
41.772
A
A
6
7
6.535
B
B
17
16
3.507
4.643
-0.383
0.807
AA_ABR6DA7:DT16DT17_BB
6
-4.363
6.141
41.305
0.600
0.037
3.213
33.775
A
A
7
8
8.719
B
B
16
15
3.291
5.042
-0.687
-0.595
AA_DA7DG8:DC15DT16_BB
7
-2.651
4.584
33.304
-1.841
0.753
2.575
35.531
A
A
8
9
6.152
B
B
15
14
2.744
3.729
0.179
-0.820
AA_DG8DA9:DT14DC15_BB
8
-6.287
10.371
34.795
-1.792
-1.048
3.256
35.053
A
A
9
10
-4.505
B
B
14
13
3.215
-2.710
-0.226
-0.776
AA_DA9DA10:DT13DT14_BB
9
1.092
-1.814
34.935
-0.886
0.538
3.545
30.469
A
A
10
11
-10.217
B
B
13
12
3.486
-5.343
-0.387
-0.692
AA_DA10DG11:DC12DT13_BB
10
0.539
-1.031
30.003
-0.161
0.854
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-01-23
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
1K5F is the SAME STRUCTURE WITH (S)-(N-PHENYL-2-HYDROXY-ETHYL)-2'-DEOXY-ADENOSINE-5'-MONOPHOSPHATE.
RCSB
Y
RCSB
2001-10-10
REL
This sequence was generated by an oligonucleotide synthesizer
sample
This sequence was generated by an oligonucleotide synthesizer
sample
NOESY at 100, 150 and 200 ms mixing time
back calculated data agree with experimental NOESY spectrum
50
1
Noesy
DQF-COSY
10mM phosphate buffer
6.9
1
atm
293
K
simulated annealing,
molecular dynamics,
matrix relaxation
1
minimized average structure
130 OD260 of double stranded oligodeoxynucleotide are dissolved in 0.5 ml nmr buffer containing 99.996% D2O.
The buffer is 10mM sodium phosphate pH 6.9 containing 100mM NaCl and 0.05mM Na2EDTA.
Molecular simulations
collection
Felix
97
James, TL
refinement
MARDIGRAS
3.0
Brunger
iterative matrix relaxation
X-PLOR
3.85
James
data analysis
CORMA
4.0
500
Bruker
DRX
C
1
n
1
DC
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
ABR
6
n
6
ABR
6
A
A
7
n
7
DA
7
A
G
8
n
8
DG
8
A
A
9
n
9
DA
9
A
A
10
n
10
DA
10
A
G
11
n
11
DG
11
A
C
12
n
1
DC
12
B
T
13
n
2
DT
13
B
T
14
n
3
DT
14
B
C
15
n
4
DC
15
B
T
16
n
5
DT
16
B
T
17
n
6
DT
17
B
G
18
n
7
DG
18
B
T
19
n
8
DT
19
B
C
20
n
9
DC
20
B
C
21
n
10
DC
21
B
G
22
n
11
DG
22
B
author_defined_assembly
2
dimeric
A
ABR
6
A
ABR
6
DA
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
B
HA
O4
ABR
DT
6
16
1.43
1
B
B
H2''
O5'
DC
DT
15
16
1.48
1
A
B
CA
O4
ABR
DT
6
16
2.15
1
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.48
0.50
113.10
117.58
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
-2.42
0.40
106.40
103.98
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
2.80
0.30
108.30
111.10
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
4.56
0.50
113.10
117.66
A
A
A
N7
C8
N9
DG
DG
DG
3
3
3
N
1
-2.51
0.40
106.40
103.89
A
A
A
C8
N9
C4
DG
DG
DG
3
3
3
N
1
3.83
0.50
113.80
117.63
A
A
A
N7
C8
N9
DA
DA
DA
4
4
4
N
1
2.47
0.30
108.30
110.77
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
1.83
0.30
108.30
110.13
A
A
A
O4'
C1'
N9
DA
DA
DA
7
7
7
N
1
3.85
0.50
113.80
117.65
A
A
A
N7
C8
N9
DA
DA
DA
7
7
7
N
1
2.00
0.30
108.30
110.30
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
4.68
0.50
113.10
117.78
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
1
-2.53
0.40
106.40
103.87
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
1
3.66
0.50
113.80
117.46
A
A
A
N7
C8
N9
DA
DA
DA
9
9
9
N
1
2.42
0.30
108.30
110.72
A
A
A
O4'
C1'
N9
DA
DA
DA
10
10
10
N
1
3.85
0.50
113.80
117.65
A
A
A
N7
C8
N9
DA
DA
DA
10
10
10
N
1
2.09
0.30
108.30
110.39
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
4.57
0.50
113.10
117.67
A
A
A
N7
C8
N9
DG
DG
DG
11
11
11
N
1
-2.52
0.40
106.40
103.88
A
A
A
C8
N9
C4
DG
DG
DG
11
11
11
N
1
2.03
0.30
108.30
110.33
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
2.65
0.30
108.30
110.95
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
1
2.80
0.30
108.30
111.10
B
B
B
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
2.55
0.30
108.30
110.85
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
2.24
0.30
108.30
110.54
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
1
2.24
0.30
108.30
110.54
B
B
B
O4'
C1'
N1
DT
DT
DT
17
17
17
N
1
2.59
0.30
108.30
110.89
B
B
B
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
4.49
0.50
113.10
117.59
B
B
B
N7
C8
N9
DG
DG
DG
18
18
18
N
1
-2.60
0.40
106.40
103.80
B
B
B
C8
N9
C4
DG
DG
DG
18
18
18
N
1
2.47
0.30
108.30
110.77
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
2.89
0.30
108.30
111.19
B
B
B
O4'
C1'
N1
DC
DC
DC
20
20
20
N
1
2.72
0.30
108.30
111.02
B
B
B
O4'
C1'
N1
DC
DC
DC
21
21
21
N
1
2.87
0.30
108.30
111.17
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
4.53
0.50
113.10
117.63
B
B
B
N7
C8
N9
DG
DG
DG
22
22
22
N
1
-2.61
0.40
106.40
103.79
B
B
B
C8
N9
C4
DG
DG
DG
22
22
22
N
minimized average
Solution Structure of R-styrene Adduct in the Ras61 Sequence
1
N
N
2
N
N
covale
1.611
both
A
DC
5
A
O3'
DC
5
1_555
A
ABR
6
A
P
ABR
6
1_555
covale
1.613
both
A
ABR
6
A
O3'
ABR
6
1_555
A
DA
7
A
P
DA
7
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
22
B
N1
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
22
B
O6
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
22
B
N2
DG
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
21
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
21
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
21
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
DC
20
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
20
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
20
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
19
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
19
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
18
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
18
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
18
B
N2
DG
7
1_555
hydrog
WATSON-CRICK
A
ABR
6
A
N1
ABR
6
1_555
B
DT
17
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
ABR
6
A
N6
ABR
6
1_555
B
DT
17
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
B
DT
16
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
B
DT
16
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DG
8
A
N1
DG
8
1_555
B
DC
15
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
8
A
N2
DG
8
1_555
B
DC
15
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
8
A
O6
DG
8
1_555
B
DC
15
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DA
9
A
N1
DA
9
1_555
B
DT
14
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
9
A
N6
DA
9
1_555
B
DT
14
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N1
DA
10
1_555
B
DT
13
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N6
DA
10
1_555
B
DT
13
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N1
DG
11
1_555
B
DC
12
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
11
A
N2
DG
11
1_555
B
DC
12
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
11
A
O6
DG
11
1_555
B
DC
12
B
N4
DC
1
1_555
DNA
styrene, DNA adduct, solution structure of DNA, DNA
1K5E
PDB
1
1K5E
1K5E
PDB
2
1K5E
1
11
1K5E
1
11
1K5E
A
1
1
11
12
22
1K5E
12
22
1K5E
B
2
1
11