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
C11 H16 N5 O6 P
345.248
n
N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE
DNA linking
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/pdb1oq2/pdb
pdb_00001oq2
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
3637.394
5'-D(*CP*GP*CP*AP*GP*(6MA)P*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
yes
(DC)(DG)(DC)(DA)(DG)(6MA)(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
8.500
1
19
A
1
B
24
-1.872
A_DG1:DC24_B
1
-6.180
-0.205
0.678
-0.346
-18.082
1
19
A
2
B
23
1.667
A_DC2:DG23_B
2
11.737
1.054
0.052
-0.390
-6.300
1
19
A
3
B
22
8.818
A_DG3:DC22_B
3
14.307
-0.183
1.020
-0.539
0.528
1
20
A
4
B
21
0.241
A_DA4:DT21_B
4
15.422
0.154
0.513
-0.277
5.627
1
19
A
5
B
20
-1.221
A_DG5:DC20_B
5
5.343
-0.161
0.312
-0.250
7.286
1
20
A
6
B
19
-15.518
A_DA6:DT19_B
6
1.656
0.213
0.161
0.139
-7.394
1
19
A
8
B
17
0.075
A_DC8:DG17_B
7
-6.755
-0.209
0.273
-0.176
-7.348
1
20
A
9
B
16
6.118
A_DT9:DA16_B
8
17.871
0.250
0.025
-0.260
0.596
1
19
A
10
B
15
0.096
A_DG10:DC15_B
9
32.381
0.272
-0.058
-0.224
-0.275
1
19
A
11
B
14
-4.557
A_DC11:DG14_B
10
16.719
0.073
-0.617
-0.373
16.712
1
19
A
12
B
13
-7.377
A_DG12:DC13_B
11
12.459
0.291
-0.377
-0.124
4.514
48.283
A
A
1
2
26.389
B
B
24
23
4.777
20.946
0.663
0.379
AA_DG1DC2:DG23DC24_BB
1
0.444
-0.559
43.747
-1.989
-0.759
3.384
46.622
A
A
2
3
-52.998
B
B
23
22
4.065
-36.458
-0.167
-1.151
AA_DC2DG3:DC22DG23_BB
2
-10.038
14.591
27.786
3.035
-1.025
3.191
35.586
A
A
3
4
-1.600
B
B
22
21
3.280
-0.973
-0.477
-1.645
AA_DG3DA4:DT21DC22_BB
3
6.318
-10.391
35.025
-2.550
1.698
3.447
30.775
A
A
4
5
18.002
B
B
21
20
3.580
9.404
-0.821
-0.008
AA_DA4DG5:DC20DT21_BB
4
-1.396
2.672
29.303
-2.041
1.245
2.851
37.971
A
A
5
6
20.384
B
B
20
19
3.395
13.007
-1.351
-0.832
AA_DG5DA6:DT19DC20_BB
5
2.080
-3.260
35.692
-2.917
2.338
7.069
69.035
A
A
6
8
-0.765
B
B
19
17
7.085
-0.867
0.673
-0.008
AA_DA6DC8:DG17DT19_BB
6
-1.607
1.418
69.013
0.062
-0.721
4.024
40.969
A
A
8
9
-30.029
B
B
17
16
4.225
-20.132
0.151
-0.734
AA_DC8DT9:DA16DG17_BB
7
-4.402
6.567
35.603
1.942
-0.870
2.773
35.067
A
A
9
10
18.306
B
B
16
15
3.204
10.859
-0.507
-0.951
AA_DT9DG10:DC15DA16_BB
8
-0.271
0.457
33.392
-3.106
0.803
3.690
32.799
A
A
10
11
15.867
B
B
15
14
3.982
8.839
-0.567
-0.281
AA_DG10DC11:DG14DC15_BB
9
3.404
-6.110
31.438
-2.319
1.706
3.089
28.437
A
A
11
12
12.199
B
B
14
13
3.123
5.950
-0.261
0.135
AA_DC11DG12:DC13DG14_BB
10
-0.491
1.007
27.816
-1.035
0.424
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
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
_struct_conn.pdbx_leaving_atom_flag
NMR structure of unmethylated GATC site
NMR structure of hemimethylated GATC site, N6-methyl in trans(respect to N1) configuration
RCSB
Y
PDBJ
2003-03-07
REL
REL
Chemical Synthesis
sample
Chemical Synthesis
sample
structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
100
17
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
6MA
18
n
6
6MA
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
B
6MA
18
B
6MA
6
A
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
3
A
B
H21
O2
DG
DC
1
24
1.54
4
A
B
H21
O2
DG
DC
1
24
1.59
7
A
B
H21
O2
DG
DC
1
24
1.56
9
A
B
H21
O2
DG
DC
1
24
1.59
10
A
B
H21
O2
DG
DC
1
24
1.60
11
A
B
H21
O2
DG
DC
1
24
1.59
12
A
B
H21
O2
DG
DC
1
24
1.55
14
A
B
H21
O2
DG
DC
1
24
1.55
minimized average
NMR structure of hemimethylated GATC site
1
N
N
2
N
N
covale
1.608
both
B
DG
17
B
O3'
DG
5
1_555
B
6MA
18
B
P
6MA
6
1_555
covale
1.611
both
B
6MA
18
B
O3'
6MA
6
1_555
B
DT
19
B
P
DT
7
1_555
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
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, hemimethylation, SeqA, MutH, N6-methyl, Dam (DNA adenine methyltransferase), DNA
1OQ2
PDB
1
1OQ2
1OQ2
PDB
2
1OQ2
1
12
1OQ2
1
12
1OQ2
A
1
1
12
13
24
1OQ2
13
24
1OQ2
B
2
1
12
1
P 1