1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Feng, B.
Stone, M.P.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
C18 H22 N5 O7 P
451.370
n
2'-DEOXY-N6-(R)STYRENE OXIDE ADENOSINE MONOPHOSPHATE
DNA linking
US
Biochemistry
BICHAW
0033
0006-2960
34
14021
14036
10.1021/bi00043a008
7578000
Major groove (R)-alpha-(N6-adenyl)styrene oxide adducts in an oligodeoxynucleotide containing the human N-ras codon 61 sequence: conformations of the R(61,2) and R(61,3) sequence isomers from 1H NMR.
1995
US
Chem.Res.Toxicol.
CRTOEC
2140
0893-228X
8
821
Solution Structure of an Oligodeoxynucleotide Containing the Human N-Ras Codon 61 Sequence Refined from 1H NMR Using Molecular Dynamics Restrained by Nuclear Overhauser Effects
1995
10.2210/pdb1agk/pdb
pdb_00001agk
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
(R)-(N6-ADENYL)-STYRENE OXIDE-RAS61-2 DNA ADDUCT
3536.411
DNA (5'-D(*CP*GP*GP*AP*CP*RP*AP*GP*AP*AP*G)-3')
1
syn
polymer
(R)-(N6-ADENYL)-STYRENE OXIDE-RAS61-2 DNA ADDUCT
3291.145
DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3')
1
syn
polymer
no
yes
(DC)(DG)(DG)(DA)(DC)(R)(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
-17.225
1
19
A
1
B
22
-2.180
A_DC1:DG22_B
1
-1.455
0.730
0.180
-0.369
-0.316
1
19
A
2
B
21
-0.132
A_DG2:DC21_B
2
-9.939
-0.761
0.025
-0.380
5.462
1
19
A
3
B
20
0.644
A_DG3:DC20_B
3
-7.830
-0.626
0.075
-0.221
0.714
1
20
A
4
B
19
3.227
A_DA4:DT19_B
4
-14.796
0.744
-0.597
-0.212
-11.411
1
19
A
5
B
18
-4.028
A_DC5:DG18_B
5
5.596
-0.341
-0.192
-0.172
3.436
1
20
A
6
B
17
-0.247
A_R6:DT17_B
6
-3.064
0.169
0.049
-0.056
12.139
1
20
A
7
B
16
-2.513
A_DA7:DT16_B
7
-13.973
0.525
0.048
-0.138
7.801
1
19
A
8
B
15
-2.424
A_DG8:DC15_B
8
-8.808
-0.599
0.223
-0.185
3.028
1
20
A
9
B
14
-3.417
A_DA9:DT14_B
9
-18.771
0.189
-0.123
-0.229
10.055
1
20
A
10
B
13
-2.873
A_DA10:DT13_B
10
-6.829
0.285
0.084
-0.213
29.256
1
19
A
11
B
12
2.211
A_DG11:DC12_B
11
4.463
-0.831
0.796
-0.257
2.442
30.653
A
A
1
2
24.151
B
B
22
21
2.633
12.413
0.342
0.034
AA_DC1DG2:DC21DG22_BB
1
1.289
-2.507
28.053
-1.922
-0.441
3.057
33.095
A
A
2
3
1.648
B
B
21
20
3.048
0.938
-0.365
0.039
AA_DG2DG3:DC20DC21_BB
2
-0.991
1.741
33.067
-0.080
0.484
3.596
40.636
A
A
3
4
-5.411
B
B
20
19
3.601
-3.749
0.444
0.181
AA_DG3DA4:DT19DC20_BB
3
3.611
-5.214
40.315
0.721
-0.196
3.414
37.242
A
A
4
5
8.778
B
B
19
18
3.335
5.542
-1.320
-0.637
AA_DA4DC5:DG18DT19_BB
4
-8.304
13.152
35.925
-1.771
0.908
3.263
34.017
A
A
5
6
-3.423
B
B
18
17
3.270
-2.000
-0.045
-0.204
AA_DC5R6:DT17DG18_BB
5
2.712
-4.643
33.855
-0.029
0.510
2.916
36.849
A
A
6
7
6.662
B
B
17
16
2.904
4.203
-0.394
0.303
AA_R6DA7:DT16DT17_BB
6
0.345
-0.547
36.616
-0.029
0.664
3.180
30.747
A
A
7
8
1.181
B
B
16
15
3.185
0.626
-0.077
-0.155
AA_DA7DG8:DC15DT16_BB
7
-1.932
3.646
30.681
-0.411
-0.223
3.373
40.597
A
A
8
9
-7.065
B
B
15
14
3.420
-4.885
-0.189
-0.030
AA_DG8DA9:DT14DC15_BB
8
3.543
-5.124
40.165
0.524
0.685
2.866
37.017
A
A
9
10
-3.631
B
B
14
13
2.882
-2.303
0.092
0.057
AA_DA9DA10:DT13DT14_BB
9
-1.797
2.834
36.905
0.363
-0.357
2.571
26.796
A
A
10
11
11.708
B
B
13
12
2.696
5.364
0.480
0.239
AA_DA10DG11:DC12DT13_BB
10
-4.559
9.950
25.871
-0.621
-2.001
database_2
entity_poly
pdbx_database_status
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
Other
Polymer sequence
1
0
1997-08-20
1
1
2008-03-24
1
2
2011-07-13
2
0
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_database_status.process_site
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
MINIMIZED AVERAGE STRUCTURE
MINIMIZED AVERAGE STRUCTURE
Y
BNL
1997-03-25
REL
THIS STRUCTURE PROVIDED THE BEST-FIT FOR THE NOE DATA BASED ON THE RELAXATION MATRIX ANALYSIS USING CORMA
1
1
NOESY
2QF-COSY
AND TOCSY
: NOESY
2QF-COSY
AND(DO
05'-D
6.9
293
K
REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NOE-RESTRAINED MOLECULAR DYNAMICS/SIMULATED ANNEALING
BRUNGER
refinement
X-PLOR
3.1
structure solution
Felix
structure solution
X-PLOR
structure solution
MARDIGRAS
structure solution
CORMA
500
Bruker
AMX500
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
R
6
n
6
R
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
R
6
A
R
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
HB
O4
R
DT
6
16
1.55
1
4.23
0.30
108.30
112.53
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
-12.58
1.20
119.70
107.12
A
A
A
C3'
O3'
P
DC
DC
DG
1
1
2
Y
1
-30.88
1.90
104.00
73.12
A
A
A
O3'
P
O5'
DC
DG
DG
1
2
2
Y
1
20.82
1.10
110.50
131.32
A
A
A
O3'
P
OP1
DC
DG
DG
1
2
2
Y
1
-24.59
0.90
105.70
81.11
A
A
A
O5'
P
OP1
DG
DG
DG
2
2
2
N
1
2.34
0.30
108.30
110.64
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.54
0.50
113.10
117.64
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
-2.87
0.40
106.40
103.53
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
2.57
0.30
108.30
110.87
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
4.46
0.50
113.10
117.56
A
A
A
N7
C8
N9
DG
DG
DG
3
3
3
N
1
-2.64
0.40
106.40
103.76
A
A
A
C8
N9
C4
DG
DG
DG
3
3
3
N
1
3.30
0.30
108.30
111.60
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
3.65
0.50
113.80
117.45
A
A
A
N7
C8
N9
DA
DA
DA
4
4
4
N
1
-2.45
0.40
105.80
103.35
A
A
A
C8
N9
C4
DA
DA
DA
4
4
4
N
1
2.39
0.30
108.30
110.69
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
-3.16
0.50
129.30
126.14
A
A
A
N1
C2
N3
DA
DA
DA
7
7
7
N
1
4.03
0.50
113.80
117.83
A
A
A
N7
C8
N9
DA
DA
DA
7
7
7
N
1
-2.73
0.40
105.80
103.07
A
A
A
C8
N9
C4
DA
DA
DA
7
7
7
N
1
2.87
0.30
108.30
111.17
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
4.79
0.50
113.10
117.89
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
1
-2.85
0.40
106.40
103.55
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
1
1.83
0.30
108.30
110.13
A
A
A
O4'
C1'
N9
DA
DA
DA
9
9
9
N
1
3.85
0.50
113.80
117.65
A
A
A
N7
C8
N9
DA
DA
DA
9
9
9
N
1
-2.74
0.40
105.80
103.06
A
A
A
C8
N9
C4
DA
DA
DA
9
9
9
N
1
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N9
DA
DA
DA
10
10
10
N
1
3.91
0.50
113.80
117.71
A
A
A
N7
C8
N9
DA
DA
DA
10
10
10
N
1
-2.57
0.40
105.80
103.23
A
A
A
C8
N9
C4
DA
DA
DA
10
10
10
N
1
2.65
0.30
108.30
110.95
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
4.55
0.50
113.10
117.65
A
A
A
N7
C8
N9
DG
DG
DG
11
11
11
N
1
-2.87
0.40
106.40
103.53
A
A
A
C8
N9
C4
DG
DG
DG
11
11
11
N
1
3.24
0.30
108.30
111.54
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
-12.73
1.20
119.70
106.97
B
B
B
C3'
O3'
P
DC
DC
DT
12
12
13
Y
1
-27.29
1.90
104.00
76.71
B
B
B
O3'
P
O5'
DC
DT
DT
12
13
13
Y
1
16.88
1.10
110.50
127.38
B
B
B
O3'
P
OP1
DC
DT
DT
12
13
13
Y
1
-20.44
0.90
105.70
85.26
B
B
B
O5'
P
OP1
DT
DT
DT
13
13
13
N
1
7.44
1.20
110.70
118.14
B
B
B
O5'
P
OP2
DT
DT
DT
13
13
13
N
1
1.93
0.30
108.30
110.23
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
1
-3.65
0.60
122.90
119.25
B
B
B
C6
C5
C7
DT
DT
DT
13
13
13
N
1
13.96
1.10
110.50
124.46
B
B
B
O3'
P
OP2
DT
DT
DT
13
14
14
Y
1
-10.98
0.90
105.70
94.72
B
B
B
O5'
P
OP2
DT
DT
DT
14
14
14
N
1
-36.71
1.90
104.00
67.29
B
B
B
O3'
P
O5'
DT
DC
DC
14
15
15
Y
1
-29.81
2.20
105.20
75.39
B
B
B
O3'
P
OP2
DT
DC
DC
14
15
15
Y
1
8.85
1.10
110.50
119.35
B
B
B
O3'
P
OP1
DT
DC
DC
14
15
15
Y
1
25.26
1.20
110.70
135.96
B
B
B
O5'
P
OP2
DC
DC
DC
15
15
15
N
1
2.87
0.30
108.30
111.17
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
2.60
0.30
108.30
110.90
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
1
1.86
0.30
108.30
110.16
B
B
B
O4'
C1'
N1
DT
DT
DT
17
17
17
N
1
2.78
0.30
108.30
111.08
B
B
B
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
4.44
0.50
113.10
117.54
B
B
B
N7
C8
N9
DG
DG
DG
18
18
18
N
1
-2.55
0.40
106.40
103.85
B
B
B
C8
N9
C4
DG
DG
DG
18
18
18
N
1
3.04
0.30
108.30
111.34
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
2.37
0.30
108.30
110.67
B
B
B
O4'
C1'
N1
DC
DC
DC
20
20
20
N
1
-31.66
1.90
104.00
72.34
B
B
B
O3'
P
O5'
DC
DC
DC
20
21
21
Y
1
-19.44
2.20
105.20
85.76
B
B
B
O3'
P
OP2
DC
DC
DC
20
21
21
Y
1
24.18
1.10
110.50
134.68
B
B
B
O3'
P
OP1
DC
DC
DC
20
21
21
Y
1
-25.57
1.50
119.60
94.03
B
B
B
OP1
P
OP2
DC
DC
DC
21
21
21
N
1
-32.67
0.90
105.70
73.03
B
B
B
O5'
P
OP1
DC
DC
DC
21
21
21
N
1
18.26
1.20
110.70
128.96
B
B
B
O5'
P
OP2
DC
DC
DC
21
21
21
N
1
5.22
0.30
108.30
113.52
B
B
B
O4'
C1'
N1
DC
DC
DC
21
21
21
N
1
-37.10
1.90
104.00
66.90
B
B
B
O3'
P
O5'
DC
DG
DG
21
22
22
Y
1
28.63
1.10
110.50
139.13
B
B
B
O3'
P
OP1
DC
DG
DG
21
22
22
Y
1
-12.51
1.50
119.60
107.09
B
B
B
OP1
P
OP2
DG
DG
DG
22
22
22
N
1
-33.44
0.90
105.70
72.26
B
B
B
O5'
P
OP1
DG
DG
DG
22
22
22
N
1
11.03
1.20
110.70
121.73
B
B
B
O5'
P
OP2
DG
DG
DG
22
22
22
N
1
4.65
0.50
113.10
117.75
B
B
B
N7
C8
N9
DG
DG
DG
22
22
22
N
1
-2.96
0.40
106.40
103.44
B
B
B
C8
N9
C4
DG
DG
DG
22
22
22
N
1
A
A
O3'
C3'
DC
DC
1
1
0.094
0.013
1.435
1.529
N
1
B
B
O3'
C3'
DC
DC
12
12
0.092
0.013
1.435
1.527
N
1
B
B
P
OP1
DT
DT
13
13
0.104
0.017
1.485
1.589
N
1
B
B
O5'
C5'
DT
DT
13
13
0.096
0.016
1.440
1.536
N
1
B
B
O3'
C3'
DT
DT
13
13
-0.130
0.006
1.419
1.289
N
1
B
B
O3'
C3'
DT
DT
14
14
0.107
0.013
1.435
1.542
N
1
B
B
P
O5'
DC
DC
20
20
0.061
0.010
1.593
1.654
N
1
B
B
C5'
C4'
DC
DC
20
20
0.044
0.007
1.512
1.556
N
1
B
B
P
O5'
DG
DG
22
22
0.064
0.010
1.593
1.657
N
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE SECOND POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE
1
N
N
2
N
N
covale
1.604
both
A
DC
5
A
O3'
DC
5
1_555
A
R
6
A
P
R
6
1_555
covale
1.619
both
A
R
6
A
O3'
R
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
R
6
A
N1
R
6
1_555
B
DT
17
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
R
6
A
N6
R
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
DNA DUPLEX, B-DNA, HUMAN N-RAS GENE, CODON 61 SEQUENCE, R-STYRENE OXIDE ADDUCT, N6-ADENINE, MAJOR GROOVE, DEOXYRIBONUCLEIC ACID, DNA
1AGK
PDB
1
1AGK
1AGK
PDB
2
1AGK
1
11
1AGK
1
11
1AGK
A
1
1
11
12
22
1AGK
12
22
1AGK
B
2
1
11
1
P 1