1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Subramaniam, G.
Paz, M.M.
Kumar, G.S.
Das, A.
Palom, Y.
Clement, C.C.
Patel, D.J.
Tomasz, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C13 H16 N3 O2 1
246.285
DECARBAMOYL-2,7-DIAMINOMITOSENE
non-polymer
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
10473
10484
10.1021/bi010965a
11523988
Solution structure of a guanine-N7-linked complex of the mitomycin C metabolite 2,7-diaminomitosene and DNA. Basis of sequence selectivity.
2001
10.2210/pdb1jo1/pdb
pdb_00001jo1
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
3662.404
5'-D(*GP*TP*GP*(DAJ)GP*TP*AP*TP*AP*CP*CP*AP*C)-3'
2
syn
polymer
246.285
DECARBAMOYL-2,7-DIAMINOMITOSENE
2
syn
non-polymer
no
no
(DG)(DT)(DG)(DG)(DT)(DA)(DT)(DA)(DC)(DC)(DA)(DC)
GTGGTATACCAC
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
16.720
1
19
A
1
B
12
2.902
A_DG1:DC12_B
1
0.748
-1.162
0.561
-0.319
1.397
1
20
A
2
B
11
-0.418
A_DT2:DA11_B
2
-11.578
-0.244
0.224
-0.247
16.186
1
19
A
3
B
10
-0.207
A_DG3:DC10_B
3
2.519
-0.644
0.936
-0.408
-28.666
1
19
A
4
B
9
-1.918
A_DG4:DC9_B
4
-20.654
-0.234
-0.138
-0.129
-11.445
1
20
A
5
B
8
7.407
A_DT5:DA8_B
5
4.696
-0.017
0.226
-0.093
-6.187
1
20
A
6
B
7
5.702
A_DA6:DT7_B
6
-5.988
0.174
-1.021
-0.505
6.159
1
20
A
7
B
6
5.708
A_DT7:DA6_B
7
-5.977
-0.175
-1.021
-0.504
11.440
1
20
A
8
B
5
7.400
A_DA8:DT5_B
8
4.719
0.018
0.225
-0.091
28.677
1
19
A
9
B
4
-1.895
A_DC9:DG4_B
9
-20.594
0.236
-0.139
-0.127
-16.164
1
19
A
10
B
3
-0.205
A_DC10:DG3_B
10
2.533
0.649
0.937
-0.410
-1.358
1
20
A
11
B
2
-0.418
A_DA11:DT2_B
11
-11.575
0.249
0.225
-0.252
-16.703
1
19
A
12
B
1
2.897
A_DC12:DG1_B
12
0.731
1.161
0.559
-0.326
3.623
38.501
A
A
1
2
-3.136
B
B
12
11
3.589
-2.066
-0.303
-1.140
AA_DG1DT2:DA11DC12_BB
1
2.065
-3.134
38.394
-1.446
0.742
2.623
33.272
A
A
2
3
-10.209
B
B
11
10
2.779
-5.768
0.880
-0.892
AA_DT2DG3:DC10DA11_BB
2
-7.622
13.492
31.906
-0.745
-2.611
4.738
40.423
A
A
3
4
-4.093
B
B
10
9
4.733
-2.759
0.581
-2.077
AA_DG3DG4:DC9DC10_BB
3
15.501
-22.995
37.349
-2.538
1.790
2.675
31.783
A
A
4
5
8.468
B
B
9
8
2.711
4.618
-0.203
-0.114
AA_DG4DT5:DA8DC9_BB
4
-2.193
4.022
31.379
-0.908
0.038
3.211
42.792
A
A
5
6
11.532
B
B
8
7
3.020
8.255
0.635
1.011
AA_DT5DA6:DT7DA8_BB
5
12.299
-17.181
40.260
0.573
0.340
2.410
33.332
A
A
6
7
10.637
B
B
7
6
2.566
6.069
0.000
-0.650
AA_DA6DT7:DA6DT7_BB
6
0.002
-0.003
32.790
-1.908
0.000
3.210
42.787
A
A
7
8
11.535
B
B
6
5
3.019
8.256
-0.636
1.011
AA_DT7DA8:DT5DA6_BB
7
-12.298
17.182
40.254
0.574
-0.339
2.675
31.774
A
A
8
9
8.476
B
B
5
4
2.711
4.621
0.204
-0.113
AA_DA8DC9:DG4DT5_BB
8
2.189
-4.015
31.370
-0.908
-0.040
4.739
40.436
A
A
9
10
-4.097
B
B
4
3
4.734
-2.763
-0.581
-2.077
AA_DC9DC10:DG3DG4_BB
9
-15.509
22.999
37.360
-2.536
-1.790
2.623
33.274
A
A
10
11
-10.206
B
B
3
2
2.779
-5.766
-0.880
-0.892
AA_DC10DA11:DT2DG3_BB
10
7.613
-13.474
31.911
-0.745
2.609
3.624
38.483
A
A
11
12
-3.144
B
B
2
1
3.590
-2.070
0.302
-1.141
AA_DA11DC12:DG1DT2_BB
11
-2.049
3.111
38.377
-1.447
-0.740
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2001-09-12
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
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_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_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2001-07-26
REL
REL
DAJ
DECARBAMOYL-2,7-DIAMINOMITOSENE
synthesized using ABI-380B synthesizer
sample
This structure was determined using standard 2d-NOE buildup studies in H2O and D2O buffers.
lowest number of NOE violations
12
1
2D NOESY
2D NOESY
P-COSY
HOHAHA
P-COSY
2D NOESY
0.1 M NaCl
6.8
ambient
278
K
0.1 M NaCl
6.8
ambient
303
K
The structure is based on 126 intramolecular DNA constraints, 30 H-bonding constraints, 48 intermolecular drug-DNA constraints, and 48 dihedral constraints
distance geometry and molecular dynamics
1.2 mM d(GTG(+G)TATACCAC) duplex in 0.01 M sodium phosphate, 0.1 M NaCl, 0.001M EDTA
90% H2O/10% D2O
1.2 mM d(GTG(+G)TATACCAC) duplex in 0.01 M sodium phosphate, 0.1 M NaCl, 0.001M EDTA
100% D2O
Varian Instruments
collection
VNMR
6.1
MSI
data analysis
Felix
3.0
A. Brunger
structure solution
X-PLOR
3.01
A. Brunger
refinement
X-PLOR
3.01
500
Varian
UNITYPLUS
600
Varian
UNITYPLUS
DAM
13
2
DAJ
DAJ
13
A
DAM
13
2
DAJ
DAJ
13
B
G
1
n
1
DG
1
A
T
2
n
2
DT
2
A
G
3
n
3
DG
3
A
+G
4
n
4
DG
4
A
T
5
n
5
DT
5
A
A
6
n
6
DA
6
A
T
7
n
7
DT
7
A
A
8
n
8
DA
8
A
C
9
n
9
DC
9
A
C
10
n
10
DC
10
A
A
11
n
11
DA
11
A
C
12
n
12
DC
12
A
G
1
n
1
DG
1
B
T
2
n
2
DT
2
B
G
3
n
3
DG
3
B
+G
4
n
4
DG
4
B
T
5
n
5
DT
5
B
A
6
n
6
DA
6
B
T
7
n
7
DT
7
B
A
8
n
8
DA
8
B
C
9
n
9
DC
9
B
C
10
n
10
DC
10
B
A
11
n
11
DA
11
B
C
12
n
12
DC
12
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
B
A
O4
HN1
DT
DAJ
7
13
1.48
1
A
B
O4
HN1
DT
DAJ
7
13
1.48
1
3.99
0.30
108.30
112.29
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
3.81
0.50
113.10
116.91
A
A
A
N7
C8
N9
DG
DG
DG
1
1
1
N
1
3.35
0.30
108.30
111.65
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
1
7.29
0.30
108.30
115.59
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
-4.73
0.70
102.20
97.47
A
A
A
C4'
C3'
C2'
DG
DG
DG
4
4
4
N
1
5.22
0.30
108.30
113.52
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
2.81
0.40
105.40
108.21
A
A
A
N9
C4
C5
DG
DG
DG
4
4
4
N
1
5.51
0.60
119.00
124.51
A
A
A
C4
C5
C7
DT
DT
DT
5
5
5
N
1
-6.81
0.60
122.90
116.09
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
1
2.65
0.30
108.30
110.95
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
-6.76
0.80
105.90
99.14
A
A
A
O4'
C1'
C2'
DC
DC
DC
9
9
9
N
1
6.43
0.30
108.30
114.73
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
3.80
0.60
118.90
122.70
A
A
A
N1
C2
O2
DC
DC
DC
9
9
9
N
1
2.07
0.30
108.30
110.37
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
3.60
0.60
118.90
122.50
A
A
A
N1
C2
O2
DC
DC
DC
10
10
10
N
1
3.37
0.30
108.30
111.67
A
A
A
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
4.02
0.30
108.30
112.32
B
B
B
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
3.80
0.50
113.10
116.90
B
B
B
N7
C8
N9
DG
DG
DG
1
1
1
N
1
3.30
0.30
108.30
111.60
B
B
B
O4'
C1'
N1
DT
DT
DT
2
2
2
N
1
7.27
0.30
108.30
115.57
B
B
B
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
-4.75
0.70
102.20
97.45
B
B
B
C4'
C3'
C2'
DG
DG
DG
4
4
4
N
1
5.28
0.30
108.30
113.58
B
B
B
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
2.87
0.40
105.40
108.27
B
B
B
N9
C4
C5
DG
DG
DG
4
4
4
N
1
5.57
0.60
119.00
124.57
B
B
B
C4
C5
C7
DT
DT
DT
5
5
5
N
1
-6.84
0.60
122.90
116.06
B
B
B
C6
C5
C7
DT
DT
DT
5
5
5
N
1
2.69
0.30
108.30
110.99
B
B
B
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
-3.63
0.60
122.30
118.67
B
B
B
N3
C2
O2
DT
DT
DT
7
7
7
N
1
-6.73
0.80
105.90
99.17
B
B
B
O4'
C1'
C2'
DC
DC
DC
9
9
9
N
1
6.37
0.30
108.30
114.67
B
B
B
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
3.78
0.60
118.90
122.68
B
B
B
N1
C2
O2
DC
DC
DC
9
9
9
N
1
2.07
0.30
108.30
110.37
B
B
B
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
3.60
0.60
118.90
122.50
B
B
B
N1
C2
O2
DC
DC
DC
10
10
10
N
1
3.43
0.30
108.30
111.73
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
A
A
C5
C7
DT
DT
2
2
0.041
0.006
1.496
1.537
N
1
A
A
N7
C8
DG
DG
4
4
0.068
0.006
1.305
1.373
N
1
A
A
C5
C7
DT
DT
5
5
0.051
0.006
1.496
1.547
N
1
A
A
C5
C7
DT
DT
7
7
0.038
0.006
1.496
1.534
N
1
B
B
C5
C7
DT
DT
2
2
0.041
0.006
1.496
1.537
N
1
B
B
N7
C8
DG
DG
4
4
0.068
0.006
1.305
1.373
N
1
B
B
C5
C7
DT
DT
5
5
0.051
0.006
1.496
1.547
N
1
B
B
C5
C7
DT
DT
7
7
0.037
0.006
1.496
1.533
N
N7-Guanine Adduct of 2,7-diaminomitosene with DNA
1
N
N
1
N
N
2
N
N
2
N
N
covale
1.503
none
A
DG
4
A
N7
DG
4
1_555
A
DAJ
13
C
C10
DAJ
1_555
covale
1.504
none
B
DG
4
B
N7
DG
4
1_555
B
DAJ
13
D
C10
DAJ
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
B
DC
12
B
N3
DC
12
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
B
DC
12
B
O2
DC
12
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
B
DC
12
B
N4
DC
12
1_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
B
DA
11
B
N1
DA
11
1_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
B
DA
11
B
N6
DA
11
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
DC
10
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
10
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
10
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
9
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
9
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
9
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
DA
8
B
N1
DA
8
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
DA
8
B
N6
DA
8
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
7
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
7
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
6
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
6
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N1
DA
8
1_555
B
DT
5
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N6
DA
8
1_555
B
DT
5
B
O4
DT
5
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
4
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
4
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
4
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
DG
3
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
DG
3
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
DG
3
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DA
11
A
N1
DA
11
1_555
B
DT
2
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
11
A
N6
DA
11
1_555
B
DT
2
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DC
12
A
N3
DC
12
1_555
B
DG
1
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
12
A
N4
DC
12
1_555
B
DG
1
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
12
A
O2
DC
12
1_555
B
DG
1
B
N2
DG
1
1_555
DNA
double helix, major groove binding drug, guanine-N7-alkylator, DNA
1JO1
PDB
1
1JO1
1
12
1JO1
1
12
1JO1
A
1
1
12
1
12
1JO1
1
12
1JO1
B
1
1
12
BINDING SITE FOR RESIDUE DAJ A 13
A
DAJ
13
Software
6
BINDING SITE FOR RESIDUE DAJ B 13
B
DAJ
13
Software
6
A
DG
3
A
DG
3
6
1_555
A
DG
4
A
DG
4
6
1_555
A
DT
5
A
DT
5
6
1_555
A
DA
6
A
DA
6
6
1_555
B
DA
6
B
DA
6
6
1_555
B
DT
7
B
DT
7
6
1_555
A
DA
6
A
DA
6
6
1_555
A
DT
7
A
DT
7
6
1_555
B
DG
3
B
DG
3
6
1_555
B
DG
4
B
DG
4
6
1_555
B
DT
5
B
DT
5
6
1_555
B
DA
6
B
DA
6
6
1_555