1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Bae, S.-H.
Cheong, H.-K.
Kang, S.
Hwang, D.S.
Cheong, C.
Choi, B.-S.
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
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
278
45987
45993
10.1074/jbc.M306038200
12944412
Structure and dynamics of hemimethylated GATC sites: implications for DNA-SeqA recognition
2003
10.2210/pdb1opq/pdb
pdb_00001opq
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
3703.416
5'-D(*GP*CP*GP*AP*GP*AP*TP*CP*TP*GP*CP*G)-3'
1
syn
polymer
3623.368
5'-D(*CP*GP*CP*AP*GP*AP*TP*CP*TP*CP*GP*C)-3'
1
syn
polymer
no
no
(DG)(DC)(DG)(DA)(DG)(DA)(DT)(DC)(DT)(DG)(DC)(DG)
GCGAGATCTGCG
A
polydeoxyribonucleotide
no
no
(DC)(DG)(DC)(DA)(DG)(DA)(DT)(DC)(DT)(DC)(DG)(DC)
CGCAGATCTCGC
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
-8.465
1
19
A
1
B
24
-0.449
A_DG1:DC24_B
1
0.372
-0.432
0.057
-0.267
-2.162
1
19
A
2
B
23
-4.226
A_DC2:DG23_B
2
-4.605
-0.015
0.552
-0.174
1.083
1
19
A
3
B
22
-3.697
A_DG3:DC22_B
3
-1.851
0.411
0.850
-0.299
-13.280
1
20
A
4
B
21
3.177
A_DA4:DT21_B
4
-2.017
-0.419
-0.470
-0.249
-13.858
1
19
A
5
B
20
-0.378
A_DG5:DC20_B
5
-0.249
-0.225
-0.656
-0.295
-5.286
1
20
A
6
B
19
-8.691
A_DA6:DT19_B
6
11.038
-0.216
-0.588
-0.368
13.285
1
20
A
7
B
18
-9.711
A_DT7:DA18_B
7
10.959
0.094
-0.756
-0.289
17.110
1
19
A
8
B
17
-3.247
A_DC8:DG17_B
8
-1.492
-0.300
-1.313
-0.419
-9.292
1
20
A
9
B
16
0.621
A_DT9:DA16_B
9
-2.804
0.124
0.143
-0.284
4.427
1
19
A
10
B
15
-1.066
A_DG10:DC15_B
10
3.800
0.215
0.361
-0.190
-14.927
1
19
A
11
B
14
3.502
A_DC11:DG14_B
11
21.766
0.378
0.602
-0.324
7.648
1
19
A
12
B
13
0.447
A_DG12:DC13_B
12
10.574
-0.175
-0.182
-0.168
3.329
37.992
A
A
1
2
-1.576
B
B
24
23
3.314
-1.025
-0.730
1.137
AA_DG1DC2:DG23DC24_BB
1
-3.014
4.635
37.863
1.880
0.730
3.329
37.646
A
A
2
3
19.540
B
B
23
22
3.344
12.387
0.394
0.556
AA_DC2DG3:DC22DG23_BB
2
-1.529
2.412
35.588
-0.829
-0.819
3.976
37.025
A
A
3
4
13.135
B
B
22
21
4.044
8.249
1.069
-0.370
AA_DG3DA4:DT21DC22_BB
3
5.238
-8.340
35.756
-1.966
-0.804
3.327
32.919
A
A
4
5
3.371
B
B
21
20
3.354
1.909
-0.732
-0.159
AA_DA4DG5:DC20DT21_BB
4
0.567
-1.002
32.860
-0.613
1.390
2.957
38.058
A
A
5
6
2.425
B
B
20
19
2.970
1.580
-0.314
-0.545
AA_DG5DA6:DT19DC20_BB
5
-1.718
2.637
37.989
-1.018
0.284
3.101
37.739
A
A
6
7
-19.440
B
B
19
18
3.210
-12.345
0.194
-0.163
AA_DA6DT7:DA18DT19_BB
6
3.089
-4.864
35.602
1.335
0.097
3.089
32.616
A
A
7
8
2.528
B
B
18
17
3.075
1.412
0.574
-0.857
AA_DT7DC8:DG17DA18_BB
7
5.836
-10.448
32.074
-1.760
-0.059
3.920
39.032
A
A
8
9
15.971
B
B
17
16
4.331
10.523
0.360
-0.724
AA_DC8DT9:DA16DG17_BB
8
-4.787
7.266
37.344
-2.724
-1.284
3.305
29.596
A
A
9
10
6.007
B
B
16
15
3.274
3.059
0.197
0.437
AA_DT9DG10:DC15DA16_BB
9
2.880
-5.656
29.303
0.202
0.231
4.463
38.522
A
A
10
11
12.818
B
B
15
14
4.658
8.376
0.628
0.031
AA_DG10DC11:DG14DC15_BB
10
-4.409
6.747
37.384
-1.424
-1.725
3.133
31.414
A
A
11
12
-12.215
B
B
14
13
3.045
-6.493
0.150
-1.067
AA_DC11DG12:DC13DG14_BB
11
8.194
-15.415
29.664
-0.785
1.218
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2004-04-27
1
1
2008-04-29
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
NMR structure of hemimethylated GATC site, N6-methyl in cis(respect to N1) configuration
NMR structure of hemimethylated GATC site, N6-methyl in trans(respect to N1) configuration
RCSB
Y
PDBJ
2003-03-06
REL
REL
chemical synthesis (phosphoramidite method)
sample
chemical synthesis (phosphoramidite method)
sample
structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
100
19
1
minimized average structure
G
1
n
1
DG
1
A
C
2
n
2
DC
2
A
G
3
n
3
DG
3
A
A
4
n
4
DA
4
A
G
5
n
5
DG
5
A
A
6
n
6
DA
6
A
T
7
n
7
DT
7
A
C
8
n
8
DC
8
A
T
9
n
9
DT
9
A
G
10
n
10
DG
10
A
C
11
n
11
DC
11
A
G
12
n
12
DG
12
A
C
13
n
1
DC
13
B
G
14
n
2
DG
14
B
C
15
n
3
DC
15
B
A
16
n
4
DA
16
B
G
17
n
5
DG
17
B
A
18
n
6
DA
18
B
T
19
n
7
DT
19
B
C
20
n
8
DC
20
B
T
21
n
9
DT
21
B
C
22
n
10
DC
22
B
G
23
n
11
DG
23
B
C
24
n
12
DC
24
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
minimized average
NMR structure of unmethylated GATC site
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
B
DC
24
B
N3
DC
12
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
B
DC
24
B
O2
DC
12
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
B
DC
24
B
N4
DC
12
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
23
B
N1
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
23
B
O6
DG
11
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
23
B
N2
DG
11
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
DC
22
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
22
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
22
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
21
B
N3
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
21
B
O4
DT
9
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
B
DC
20
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
B
DC
20
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
B
DC
20
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
19
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
19
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
18
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
18
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N3
DC
8
1_555
B
DG
17
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
8
A
N4
DC
8
1_555
B
DG
17
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
8
A
O2
DC
8
1_555
B
DG
17
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
B
DA
16
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
16
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
15
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
15
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
15
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
14
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
14
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
14
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
B
DC
13
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
B
DC
13
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
B
DC
13
B
N4
DC
1
1_555
DNA
GATC, AGATCT, oriC, Dam (DNA adenine methyltransferase), SeqA, MutH, hemimethylation, DNA
1OPQ
PDB
1
1OPQ
1OPQ
PDB
2
1OPQ
1
12
1OPQ
1
12
1OPQ
A
1
1
12
13
24
1OPQ
13
24
1OPQ
B
2
1
12
1
P 1