1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Mao, H.
Deng, Z.
Wang, F.
Harris, T.M.
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
C27 H28 N5 O15 P
693.509
[1',2'-DIDEOXY[2-AMINO-5-([9-HYDROXY-AFLATOXINB2-8-YL]-FORMYL-AMINO)-6-OXO-1,6-IHYDRO-PYRIMIDIN-4-YLAMINO]-RIBOFURANOSE]-5-MONOPHOSPHATE GROUP
DNA linking
US
Biochemistry
BICHAW
0033
0006-2960
37
4374
4387
10.1021/bi9718292
9521757
An intercalated and thermally stable FAPY adduct of aflatoxin B1 in a DNA duplex: structural refinement from 1H NMR.
1998
10.2210/pdb1hm1/pdb
pdb_00001hm1
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
CHAIN A, GUA 5 -> FAG, FAPY ADDUCT OF
3365.292
DNA (5'-D(*CP*TP*AP*TP*(FAG)P*AP*TP*TP*CP*A)-3')
1
syn
polymer
3068.042
DNA (5'-D(TP*GP*AP*AP*TP*CP*AP*TP*AP*G)-3')
1
syn
polymer
no
yes
(DC)(DT)(DA)(DT)(FAG)(DA)(DT)(DT)(DC)(DA)
CTATNATTCA
A
polydeoxyribonucleotide
no
no
(DT)(DG)(DA)(DA)(DT)(DC)(DA)(DT)(DA)(DG)
TGAATCATAG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-2.415
1
19
A
1
B
20
-2.206
A_DC1:DG20_B
1
-1.972
0.283
-0.058
-0.207
10.507
1
20
A
2
B
19
1.980
A_DT2:DA19_B
2
-12.803
0.213
-0.091
-0.119
34.127
1
20
A
3
B
18
0.238
A_DA3:DT18_B
3
1.165
0.035
0.240
-0.111
27.814
1
20
A
4
B
17
11.670
A_DT4:DA17_B
4
10.063
0.243
-0.391
0.051
7.291
1
20
A
6
B
15
-2.178
A_DA6:DT15_B
5
2.141
-0.095
0.570
-0.104
-11.030
1
20
A
7
B
14
-3.080
A_DT7:DA14_B
6
-10.858
-0.373
0.153
-0.087
-18.463
1
20
A
8
B
13
-1.582
A_DT8:DA13_B
7
-5.215
0.016
0.189
-0.180
-7.679
1
19
A
9
B
12
-0.200
A_DC9:DG12_B
8
2.457
0.503
0.020
-0.193
20.119
1
20
A
10
B
11
1.254
A_DA10:DT11_B
9
3.305
0.069
0.295
-0.042
3.033
33.096
A
A
1
2
15.403
B
B
20
19
3.064
8.662
0.285
0.227
AA_DC1DT2:DA19DG20_BB
1
3.403
-6.050
31.795
-0.993
0.046
2.785
41.233
A
A
2
3
-7.371
B
B
19
18
2.985
-5.171
0.429
1.055
AA_DT2DA3:DT18DA19_BB
2
-3.907
5.569
40.742
1.993
-0.983
4.152
32.373
A
A
3
4
11.896
B
B
18
17
4.227
6.581
0.741
-0.190
AA_DA3DT4:DA17DT18_BB
3
2.745
-4.961
31.599
-1.846
-0.701
4.476
35.038
A
A
6
7
-10.551
B
B
15
14
4.403
-6.319
0.275
-0.782
AA_DA6DT7:DA14DT15_BB
4
0.610
-1.018
34.476
0.000
-0.331
3.535
37.059
A
A
7
8
-1.519
B
B
14
13
3.517
-0.965
-0.063
-0.777
AA_DT7DT8:DA13DA14_BB
5
-0.183
0.288
37.047
-1.083
0.072
3.318
36.450
A
A
8
9
6.663
B
B
13
12
3.298
4.155
-0.097
0.384
AA_DT8DC9:DG12DA13_BB
6
-2.828
4.535
36.113
0.029
-0.243
2.161
30.150
A
A
9
10
23.634
B
B
12
11
2.479
11.965
0.176
-0.286
AA_DC9DA10:DT11DG12_BB
7
-1.397
2.759
27.690
-2.358
-0.549
database_2
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
1
0
1998-10-14
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_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
Y
BNL
1998-05-11
REL
REL
MINIMIZED AVERAGE
1
1
NOESY
TOCSY
DQF-COSY
6.80
1
atm
298.00
K
REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATED ANNEALING
0.1 M NACL,10 MM NAH2PO4, 0.05 MM NA2(EDTA)
BRUNGER
refinement
X-PLOR
2.4
structure solution
Felix
structure solution
Insight II
structure solution
X-PLOR
750
Bruker
DMX750
C
1
n
1
DC
1
A
T
2
n
2
DT
2
A
A
3
n
3
DA
3
A
T
4
n
4
DT
4
A
FAG
5
n
5
FAG
5
A
A
6
n
6
DA
6
A
T
7
n
7
DT
7
A
T
8
n
8
DT
8
A
C
9
n
9
DC
9
A
A
10
n
10
DA
10
A
T
11
n
1
DT
11
B
G
12
n
2
DG
12
B
A
13
n
3
DA
13
B
A
14
n
4
DA
14
B
T
15
n
5
DT
15
B
C
16
n
6
DC
16
B
A
17
n
7
DA
17
B
T
18
n
8
DT
18
B
A
19
n
9
DA
19
B
G
20
n
10
DG
20
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
DT
4
0.079
SIDE CHAIN
1
4.12
0.30
108.30
112.42
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
3.32
0.30
108.30
111.62
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
1
-4.99
0.60
122.90
117.91
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
1
3.49
0.30
108.30
111.79
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
1
3.76
0.50
113.80
117.56
A
A
A
N7
C8
N9
DA
DA
DA
3
3
3
N
1
-2.47
0.40
105.80
103.33
A
A
A
C8
N9
C4
DA
DA
DA
3
3
3
N
1
-4.30
0.60
122.90
118.60
A
A
A
C6
C5
C7
DT
DT
DT
4
4
4
N
1
3.36
0.30
108.30
111.66
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
3.61
0.50
113.80
117.41
A
A
A
N7
C8
N9
DA
DA
DA
6
6
6
N
1
-2.49
0.40
105.80
103.31
A
A
A
C8
N9
C4
DA
DA
DA
6
6
6
N
1
5.98
0.30
108.30
114.28
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
3.74
0.30
108.30
112.04
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
-3.69
0.60
122.90
119.21
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
1
3.46
0.30
108.30
111.76
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
2.94
0.30
108.30
111.24
A
A
A
O4'
C1'
N9
DA
DA
DA
10
10
10
N
1
3.69
0.50
113.80
117.49
A
A
A
N7
C8
N9
DA
DA
DA
10
10
10
N
1
-2.64
0.40
105.80
103.16
A
A
A
C8
N9
C4
DA
DA
DA
10
10
10
N
1
3.73
0.30
108.30
112.03
B
B
B
O4'
C1'
N1
DT
DT
DT
11
11
11
N
1
4.02
0.30
108.30
112.32
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
4.61
0.50
113.10
117.71
B
B
B
N7
C8
N9
DG
DG
DG
12
12
12
N
1
-3.27
0.40
106.40
103.13
B
B
B
C8
N9
C4
DG
DG
DG
12
12
12
N
1
3.81
0.30
108.30
112.11
B
B
B
O4'
C1'
N9
DA
DA
DA
13
13
13
N
1
3.71
0.50
113.80
117.51
B
B
B
N7
C8
N9
DA
DA
DA
13
13
13
N
1
-2.73
0.40
105.80
103.07
B
B
B
C8
N9
C4
DA
DA
DA
13
13
13
N
1
6.65
0.30
108.30
114.95
B
B
B
O4'
C1'
N9
DA
DA
DA
14
14
14
N
1
3.70
0.50
113.80
117.50
B
B
B
N7
C8
N9
DA
DA
DA
14
14
14
N
1
3.04
0.30
108.30
111.34
B
B
B
O4'
C1'
N1
DT
DT
DT
15
15
15
N
1
-4.63
0.60
122.90
118.27
B
B
B
C6
C5
C7
DT
DT
DT
15
15
15
N
1
4.65
0.30
108.30
112.95
B
B
B
O4'
C1'
N1
DC
DC
DC
16
16
16
N
1
3.87
0.30
108.30
112.17
B
B
B
O4'
C1'
N9
DA
DA
DA
17
17
17
N
1
3.84
0.50
113.80
117.64
B
B
B
N7
C8
N9
DA
DA
DA
17
17
17
N
1
-2.41
0.40
105.80
103.39
B
B
B
C8
N9
C4
DA
DA
DA
17
17
17
N
1
3.38
0.30
108.30
111.68
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
1
4.16
0.30
108.30
112.46
B
B
B
O4'
C1'
N9
DA
DA
DA
19
19
19
N
1
4.02
0.50
113.80
117.82
B
B
B
N7
C8
N9
DA
DA
DA
19
19
19
N
1
-2.62
0.40
105.80
103.18
B
B
B
C8
N9
C4
DA
DA
DA
19
19
19
N
1
3.04
0.30
108.30
111.34
B
B
B
O4'
C1'
N9
DG
DG
DG
20
20
20
N
1
4.51
0.50
113.10
117.61
B
B
B
N7
C8
N9
DG
DG
DG
20
20
20
N
1
-2.92
0.40
106.40
103.48
B
B
B
C8
N9
C4
DG
DG
DG
20
20
20
N
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
THE SOLUTION NMR STRUCTURE OF A THERMALLY STABLE FAPY ADDUCT OF AFLATOXIN B1 IN AN OLIGODEOXYNUCLEOTIDE DUPLEX REFINED FROM DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATED ANNEALING, MINIMIZED AVERAGE STRUCTURE
1
N
N
2
N
N
covale
1.613
both
A
DT
4
A
O3'
DT
4
1_555
A
FAG
5
A
P
FAG
5
1_555
covale
1.619
one
A
FAG
5
A
O3'
FAG
5
1_555
A
DA
6
A
P
DA
6
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
20
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
20
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
20
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
B
DA
19
B
N1
DA
9
1_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
B
DA
19
B
N6
DA
9
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
18
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
18
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
DA
17
B
N1
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
DA
17
B
N6
DA
7
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
15
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
15
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
14
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
14
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
13
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
13
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
12
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
12
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
12
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N1
DA
10
1_555
B
DT
11
B
N3
DT
1
1_555
hydrog
WATSON-CRICK
A
DA
10
A
N6
DA
10
1_555
B
DT
11
B
O4
DT
1
1_555
DNA
AFLATOXIN B1, FAPY, FORMAMIDOPYRIMIDINE, INTERCALATION, DNA DUPLEX, SOLUTION STRUCTURE, DNA ADDUCT, DEOXYRIBONUCLEIC ACID, DNA
1HM1
PDB
1
1HM1
1HM1
PDB
2
1HM1
1
10
1HM1
1
10
1HM1
A
1
1
10
11
20
1HM1
11
20
1HM1
B
2
1
10
1
P 1