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/pdb1agz/pdb
pdb_00001agz
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-RAS61-3 DNA ADDUCT
3536.411
DNA (5'-D(*CP*GP*GP*AP*CP*AP*RP*GP*AP*AP*G)-3')
1
syn
polymer
(R)-(N6-ADENYL)-STYRENE OXIDE-RAS61-3 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)(DA)(R)(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
12.722
1
19
A
1
B
22
4.549
A_DC1:DG22_B
1
-17.379
0.773
-0.669
-0.541
-0.711
1
19
A
2
B
21
0.467
A_DG2:DC21_B
2
-10.463
-0.843
0.064
-0.361
-6.416
1
19
A
3
B
20
0.269
A_DG3:DC20_B
3
-8.917
-0.730
-0.274
-0.258
1.036
1
20
A
4
B
19
-1.306
A_DA4:DT19_B
4
-11.005
0.281
0.069
-0.101
4.156
1
19
A
5
B
18
-1.525
A_DC5:DG18_B
5
-8.158
0.735
-0.091
-0.273
3.815
1
20
A
6
B
17
-4.701
A_DA6:DT17_B
6
-0.420
0.111
0.088
-0.218
-1.173
1
20
A
7
B
16
2.123
A_R7:DT16_B
7
-16.644
-0.279
-0.146
-0.091
-6.139
1
19
A
8
B
15
2.476
A_DG8:DC15_B
8
-0.343
-0.791
-0.234
-0.209
6.027
1
20
A
9
B
14
-5.757
A_DA9:DT14_B
9
-9.944
0.242
-0.304
-0.155
9.565
1
20
A
10
B
13
-2.638
A_DA10:DT13_B
10
-6.579
0.464
0.076
-0.141
21.480
1
19
A
11
B
12
5.108
A_DG11:DC12_B
11
2.101
-0.946
0.579
-0.221
3.657
28.130
A
A
1
2
12.730
B
B
22
21
3.742
6.093
-0.485
-0.074
AA_DC1DG2:DC21DG22_BB
1
-5.990
12.515
26.826
-1.808
-0.630
3.637
36.335
A
A
2
3
-6.141
B
B
21
20
3.605
-3.823
-0.371
-0.506
AA_DG2DG3:DC20DC21_BB
2
0.132
-0.213
36.140
-0.220
0.615
2.919
39.218
A
A
3
4
2.114
B
B
20
19
2.936
1.419
0.324
-0.259
AA_DG3DA4:DT19DC20_BB
3
-0.724
1.079
39.187
-0.538
-0.559
3.194
35.234
A
A
4
5
-6.581
B
B
19
18
3.096
-3.975
0.022
-1.071
AA_DA4DC5:DG18DT19_BB
4
0.971
-1.608
35.003
-1.199
0.102
3.707
32.804
A
A
5
6
-11.949
B
B
18
17
3.553
-6.676
-0.664
-0.837
AA_DC5DA6:DT17DG18_BB
5
-5.191
9.291
31.724
-0.187
0.168
3.446
31.105
A
A
6
7
0.405
B
B
17
16
3.401
0.217
0.888
-1.166
AA_DA6R7:DT16DT17_BB
6
2.178
-4.064
31.030
-2.217
-1.220
2.814
27.959
A
A
7
8
13.050
B
B
16
15
3.166
6.253
-0.209
-1.277
AA_R7DG8:DC15DT16_BB
7
-1.000
2.086
27.247
-4.018
0.213
2.980
39.510
A
A
8
9
7.069
B
B
15
14
3.005
4.767
-0.536
0.036
AA_DG8DA9:DT14DC15_BB
8
0.666
-0.987
39.227
-0.462
0.865
2.626
31.666
A
A
9
10
15.852
B
B
14
13
2.987
8.546
0.668
-0.861
AA_DA9DA10:DT13DT14_BB
9
-1.293
2.399
30.493
-2.958
-1.433
2.279
28.102
A
A
10
11
14.923
B
B
13
12
2.697
7.143
0.319
-1.024
AA_DA10DG11:DC12DT13_BB
10
-4.197
8.768
26.877
-3.415
-1.425
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
1997-03-26
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
A
6
n
6
DA
6
A
R
7
n
7
R
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
7
A
R
7
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
2.93
0.30
108.30
111.23
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
2.83
0.30
108.30
111.13
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.46
0.50
113.10
117.56
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
-2.57
0.40
106.40
103.83
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
3.22
0.30
108.30
111.52
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
4.42
0.50
113.10
117.52
A
A
A
N7
C8
N9
DG
DG
DG
3
3
3
N
1
-2.71
0.40
106.40
103.69
A
A
A
C8
N9
C4
DG
DG
DG
3
3
3
N
1
2.70
0.30
108.30
111.00
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
3.63
0.50
113.80
117.43
A
A
A
N7
C8
N9
DA
DA
DA
4
4
4
N
1
2.99
0.30
108.30
111.29
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
2.00
0.30
108.30
110.30
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
3.78
0.50
113.80
117.58
A
A
A
N7
C8
N9
DA
DA
DA
6
6
6
N
1
2.56
0.30
108.30
110.86
A
A
A
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
4.39
0.50
113.10
117.49
A
A
A
N7
C8
N9
DG
DG
DG
8
8
8
N
1
-2.87
0.40
106.40
103.53
A
A
A
C8
N9
C4
DG
DG
DG
8
8
8
N
1
3.41
0.30
108.30
111.71
A
A
A
O4'
C1'
N9
DA
DA
DA
9
9
9
N
1
3.66
0.50
113.80
117.46
A
A
A
N7
C8
N9
DA
DA
DA
9
9
9
N
1
3.54
0.30
108.30
111.84
A
A
A
O4'
C1'
N9
DA
DA
DA
10
10
10
N
1
3.65
0.50
113.80
117.45
A
A
A
N7
C8
N9
DA
DA
DA
10
10
10
N
1
3.17
0.30
108.30
111.47
A
A
A
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
4.42
0.50
113.10
117.52
A
A
A
N7
C8
N9
DG
DG
DG
11
11
11
N
1
-2.62
0.40
106.40
103.78
A
A
A
C8
N9
C4
DG
DG
DG
11
11
11
N
1
3.29
0.30
108.30
111.59
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
-36.80
1.90
104.00
67.20
B
B
B
O3'
P
O5'
DC
DT
DT
12
13
13
Y
1
27.27
1.10
110.50
137.77
B
B
B
O3'
P
OP1
DC
DT
DT
12
13
13
Y
1
-13.41
1.50
119.60
106.19
B
B
B
OP1
P
OP2
DT
DT
DT
13
13
13
N
1
-34.80
0.90
105.70
70.90
B
B
B
O5'
P
OP1
DT
DT
DT
13
13
13
N
1
12.26
1.20
110.70
122.96
B
B
B
O5'
P
OP2
DT
DT
DT
13
13
13
N
1
2.91
0.30
108.30
111.21
B
B
B
O4'
C1'
N1
DT
DT
DT
13
13
13
N
1
-4.09
0.60
122.90
118.81
B
B
B
C6
C5
C7
DT
DT
DT
13
13
13
N
1
3.17
0.30
108.30
111.47
B
B
B
O4'
C1'
N1
DT
DT
DT
14
14
14
N
1
-3.72
0.60
122.90
119.18
B
B
B
C6
C5
C7
DT
DT
DT
14
14
14
N
1
2.19
0.30
108.30
110.49
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
3.55
0.30
108.30
111.85
B
B
B
O4'
C1'
N1
DT
DT
DT
16
16
16
N
1
-3.73
0.60
122.90
119.17
B
B
B
C6
C5
C7
DT
DT
DT
16
16
16
N
1
2.78
0.30
108.30
111.08
B
B
B
O4'
C1'
N1
DT
DT
DT
17
17
17
N
1
-3.67
0.60
122.90
119.23
B
B
B
C6
C5
C7
DT
DT
DT
17
17
17
N
1
3.55
0.30
108.30
111.85
B
B
B
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
4.24
0.50
113.10
117.34
B
B
B
N7
C8
N9
DG
DG
DG
18
18
18
N
1
-2.52
0.40
106.40
103.88
B
B
B
C8
N9
C4
DG
DG
DG
18
18
18
N
1
3.20
0.30
108.30
111.50
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
2.91
0.30
108.30
111.21
B
B
B
O4'
C1'
N1
DC
DC
DC
20
20
20
N
1
2.70
0.30
108.30
111.00
B
B
B
O4'
C1'
N1
DC
DC
DC
21
21
21
N
1
3.28
0.30
108.30
111.58
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
4.37
0.50
113.10
117.47
B
B
B
N7
C8
N9
DG
DG
DG
22
22
22
N
1
-2.54
0.40
106.40
103.86
B
B
B
C8
N9
C4
DG
DG
DG
22
22
22
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 THIRD POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE
1
N
N
2
N
N
covale
1.608
both
A
DA
6
A
O3'
DA
6
1_555
A
R
7
A
P
R
7
1_555
covale
1.604
both
A
R
7
A
O3'
R
7
1_555
A
DG
8
A
P
DG
8
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
DA
6
A
N1
DA
6
1_555
B
DT
17
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
17
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
R
7
A
N1
R
7
1_555
B
DT
16
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
R
7
A
N6
R
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
1AGZ
PDB
1
1AGZ
1AGZ
PDB
2
1AGZ
1
11
1AGZ
1
11
1AGZ
A
1
1
11
12
22
1AGZ
12
22
1AGZ
B
2
1
11
1
P 1