0.016556
0.000000
0.000000
0.000000
0.016556
0.000000
0.000000
0.000000
0.040479
0.00000
0.00000
0.00000
Vargason, J.M.
Eichman, B.F.
Ho, P.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
90.00
90.00
60.400
60.400
24.704
C9 H13 Br N3 O7 P
386.093
n
5-BROMO-2'-DEOXY-CYTIDINE-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
H2 O
18.015
WATER
non-polymer
N
1
N
BR
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
N
N
7
N
C
N
8
N
C
N
9
N
O
N
10
N
N
N
11
N
C
N
12
N
N
N
13
N
C
N
14
N
C
N
15
N
C
N
16
R
C
N
17
N
O
N
18
R
C
N
19
S
C
N
20
N
O
N
21
N
O
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
O
N
36
N
P
N
37
N
O
N
38
N
O
N
39
N
O
N
40
N
C
N
41
R
C
N
42
N
O
N
43
S
C
N
44
N
O
N
45
N
C
N
46
R
C
N
47
N
N
N
48
N
C
N
49
N
O
N
50
N
N
N
51
N
C
N
52
N
N
N
53
N
C
N
54
N
C
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
O
N
70
N
P
N
71
N
O
N
72
N
O
N
73
N
O
N
74
N
C
N
75
R
C
N
76
N
O
N
77
S
C
N
78
N
O
N
79
N
C
N
80
R
C
Y
81
N
N
Y
82
N
C
Y
83
N
N
Y
84
N
C
N
85
N
C
N
86
N
O
N
87
N
N
N
88
N
C
N
89
N
N
N
90
N
N
Y
91
N
C
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
O
N
107
N
H
N
108
N
H
N
1
N
sing
N
2
N
doub
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
doub
N
12
N
sing
N
13
N
doub
N
14
N
sing
N
15
N
doub
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
doub
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
doub
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
doub
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
doub
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
Y
94
N
sing
Y
95
N
sing
Y
96
N
doub
N
97
N
sing
Y
98
N
sing
N
99
N
sing
Y
100
N
doub
N
101
N
doub
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
doub
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
US
Nat.Struct.Biol.
NSBIEW
2024
1072-8368
7
758
761
10.1038/78985
10966645
The extended and eccentric E-DNA structure induced by cytosine methylation or bromination.
2000
10.2210/pdb1f6j/pdb
pdb_00001f6j
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
298
1
IMAGE PLATE
1999-03-05
RIGAKU RAXIS IV
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU300
1889.101
DNA (5'-D(*GP*GP*CP*GP*(CBR)P*C)-3')
2
syn
polymer
18.015
water
28
nat
water
no
yes
(DG)(DG)(DC)(DG)(CBR)(DC)
GGCGCC
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
1
2.95
58.37
VAPOR DIFFUSION, SITTING DROP
6.0
MGCL2, SPERMINE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
SODIUM CACODYLATE
1
SPERMINE
1
MGCL2
1
MGCL2
2
-4.408
1
19
A
1
B
12
3.260
A_DG1:DC12_B
1
5.668
-0.471
0.229
-0.230
-2.126
1
19
A
2
B
11
5.060
A_DG2:CBR11_B
2
-8.479
-0.297
-0.018
-0.255
-0.340
1
19
A
3
B
10
4.883
A_DC3:DG10_B
3
0.916
0.022
-0.101
-0.222
-7.327
1
19
A
4
B
9
8.181
A_DG4:DC9_B
4
-7.305
-0.685
-0.075
-0.018
-2.194
1
19
A
5
B
8
2.770
A_CBR5:DG8_B
5
-11.728
0.216
0.156
-0.237
7.425
1
19
A
6
B
7
2.396
A_DC6:DG7_B
6
-7.452
0.570
-0.133
-0.418
2.952
32.849
A
A
1
2
10.298
B
B
12
11
3.314
5.793
-0.197
-1.762
AA_DG1DG2:CBR11DC12_BB
1
1.314
-2.335
32.322
-4.075
0.566
3.230
32.722
A
A
2
3
2.552
B
B
11
10
3.316
1.437
0.636
-1.970
AA_DG2DC3:DG10CBR11_BB
2
0.080
-0.143
32.691
-3.745
-1.115
3.854
22.802
A
A
3
4
-5.579
B
B
10
9
3.661
-2.202
-0.229
-2.176
AA_DC3DG4:DC9DG10_BB
3
-0.278
0.704
22.695
-4.596
0.466
3.404
36.627
A
A
4
5
0.453
B
B
9
8
3.311
0.284
-1.323
-1.990
AA_DG4CBR5:DG8DC9_BB
4
-3.524
5.616
36.462
-3.207
1.607
2.618
28.721
A
A
5
6
13.504
B
B
8
7
3.014
6.609
0.708
-1.744
AA_CBR5DC6:DG7DG8_BB
5
4.865
-9.941
27.547
-4.823
-0.465
chem_comp_atom
chem_comp_bond
database_2
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-08-28
1
1
2008-04-27
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE
B-DNA HEXAMER GGCGCC WITH SPERMINE
A-DNA HEXAMER GGCGM5CC
E-DNA HEXAMER GGCGM5CC
NDB
Y
NDB
2000-06-21
REL
REL
HOH
water
HOH
23
2
HOH
HOH
23
A
HOH
24
2
HOH
HOH
24
A
HOH
26
2
HOH
HOH
26
A
HOH
35
2
HOH
HOH
35
A
HOH
38
2
HOH
HOH
38
A
HOH
40
2
HOH
HOH
40
A
HOH
13
2
HOH
HOH
13
B
HOH
14
2
HOH
HOH
14
B
HOH
15
2
HOH
HOH
15
B
HOH
16
2
HOH
HOH
16
B
HOH
17
2
HOH
HOH
17
B
HOH
18
2
HOH
HOH
18
B
HOH
19
2
HOH
HOH
19
B
HOH
20
2
HOH
HOH
20
B
HOH
21
2
HOH
HOH
21
B
HOH
22
2
HOH
HOH
22
B
HOH
25
2
HOH
HOH
25
B
HOH
27
2
HOH
HOH
27
B
HOH
28
2
HOH
HOH
28
B
HOH
29
2
HOH
HOH
29
B
HOH
30
2
HOH
HOH
30
B
HOH
31
2
HOH
HOH
31
B
HOH
32
2
HOH
HOH
32
B
HOH
33
2
HOH
HOH
33
B
HOH
34
2
HOH
HOH
34
B
HOH
36
2
HOH
HOH
36
B
HOH
37
2
HOH
HOH
37
B
HOH
39
2
HOH
HOH
39
B
G
1
n
1
DG
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
BRO
5
n
5
CBR
5
A
C
6
n
6
DC
6
A
G
7
n
1
DG
7
B
G
8
n
2
DG
8
B
C
9
n
3
DC
9
B
G
10
n
4
DG
10
B
BRO
11
n
5
CBR
11
B
C
12
n
6
DC
12
B
author_defined_assembly
2
dimeric
A
CBR
5
A
CBR
5
DC
B
CBR
11
B
CBR
5
DC
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
0.256
0.193
0.2
0.2
2.25
8.0
226
2324
2324
9.7
RANDOM
1
THROUGHOUT
0.0
0.0
MOLECULAR REPLACEMENT
PARKINSON ET AL.
2.25
8.0
28
270
2
240
0
0.004
0.9
36.3
2.25
500
1F6J
2393
2393
0.0
0.0
0.05
1
39.3
12.9
99.9
0.347
2.25
2.33
12.0
99.9
phasing
AMoRE
refinement
X-PLOR
3.851
data reduction
d*TREK
data scaling
d*TREK
CRYSTAL STRUCTURE OF THE E-DNA HEXAMER GGCGBR5CC
1
N
N
1
N
N
2
N
N
2
N
N
covale
1.605
both
A
DG
4
A
O3'
DG
4
1_555
A
CBR
5
A
P
CBR
5
1_555
covale
1.604
both
A
CBR
5
A
O3'
CBR
5
1_555
A
DC
6
A
P
DC
6
1_555
covale
1.603
both
B
DG
10
B
O3'
DG
4
1_555
B
CBR
11
B
P
CBR
5
1_555
covale
1.597
both
B
CBR
11
B
O3'
CBR
5
1_555
B
DC
12
B
P
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
B
DC
12
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
B
DC
12
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
B
DC
12
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
CBR
11
B
N3
CBR
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
CBR
11
B
O2
CBR
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
CBR
11
B
N4
CBR
5
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
10
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
10
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
10
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
9
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
9
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
9
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
CBR
5
A
N3
CBR
5
1_555
B
DG
8
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
CBR
5
A
N4
CBR
5
1_555
B
DG
8
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
CBR
5
A
O2
CBR
5
1_555
B
DG
8
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
B
DG
7
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
B
DG
7
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
B
DG
7
B
N2
DG
1
1_555
DNA
E-DNA, DOUBLE HELIX, METHYLATION, DNA
1F6J
PDB
1
1F6J
1
6
1F6J
1
6
1F6J
A
1
1
6
7
12
1F6J
7
12
1F6J
B
1
1
6
96
tetragonal
P 43 21 2