0.023480
0.000000
0.000000
0.000000
0.023480
0.000000
0.000000
0.000000
0.015798
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
42.590
42.590
63.300
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
Co H18 N6 3
161.116
COBALT HEXAMMINE(III)
non-polymer
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
N
C
N
12
R
C
N
13
N
N
N
14
N
C
N
15
N
O
N
16
N
N
N
17
N
C
N
18
N
N
N
19
N
C
N
20
N
C
N
21
N
H
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
Y
47
N
N
Y
48
N
C
Y
49
N
N
Y
50
N
C
N
51
N
C
N
52
N
O
N
53
N
N
N
54
N
C
N
55
N
N
N
56
N
N
Y
57
N
C
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
H
N
70
N
H
N
71
N
H
N
72
N
O
N
73
N
H
N
74
N
H
N
75
N
MG
N
76
N
CO
N
77
N
N
N
78
N
N
N
79
N
N
N
80
N
N
N
81
N
N
N
82
N
N
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
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
1
N
sing
N
2
N
sing
N
3
N
doub
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
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
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
doub
N
27
N
sing
N
28
N
doub
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
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
Y
59
N
sing
Y
60
N
sing
Y
61
N
doub
N
62
N
sing
Y
63
N
sing
N
64
N
sing
Y
65
N
doub
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
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
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
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/pdb1f69/pdb
pdb_00001f69
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
1999-01-27
RIGAKU RAXIS IV
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU300
1810.205
DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
2
syn
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
161.116
COBALT HEXAMMINE(III)
1
syn
non-polymer
18.015
water
18
nat
water
no
no
(DG)(DG)(DC)(DG)(DC)(DC)
GGCGCC
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
1
3.76
67.33
VAPOR DIFFUSION, SITTING DROP
6.0
MGCL2, CO(NH3)6, SPERMINE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
MGCL2
1
CO(NH3)6
1
SPERMINE
1
SODIUM CACODYLATE
1
MGCL2
2
1.550
1
19
A
1
B
12
-0.671
A_DG1:DC12_B
1
-4.824
0.012
0.244
-0.407
3.872
1
19
A
2
B
11
-2.851
A_DG2:DC11_B
2
-1.000
0.323
0.254
-0.445
-0.524
1
19
A
3
B
10
-3.903
A_DC3:DG10_B
3
-14.341
-0.229
0.308
-0.320
1.145
1
19
A
4
B
9
-5.938
A_DG4:DC9_B
4
0.981
0.208
-0.262
-0.527
3.336
1
19
A
5
B
8
-0.854
A_DC5:DG8_B
5
-9.321
-0.223
0.108
-0.013
2.696
1
19
A
6
B
7
0.813
A_DC6:DG7_B
6
-6.631
0.643
0.109
-0.616
3.297
32.095
A
A
1
2
9.767
B
B
12
11
3.341
5.375
0.410
0.065
AA_DG1DG2:DC11DC12_BB
1
-0.737
1.339
31.645
-0.869
-0.877
3.562
33.943
A
A
2
3
-6.541
B
B
11
10
3.521
-3.809
-0.806
-0.196
AA_DG2DC3:DG10DC11_BB
2
-2.037
3.499
33.675
0.328
1.026
3.581
39.508
A
A
3
4
3.390
B
B
10
9
3.511
2.284
0.407
0.942
AA_DC3DG4:DC9DG10_BB
3
5.527
-8.205
39.071
1.101
0.107
3.352
31.216
A
A
4
5
1.289
B
B
9
8
3.333
0.692
-0.331
0.258
AA_DG4DC5:DG8DC9_BB
4
-4.231
7.886
30.928
0.345
-0.209
3.277
41.383
A
A
5
6
9.109
B
B
8
7
3.315
6.412
0.444
-0.109
AA_DC5DC6:DG7DG8_BB
5
1.674
-2.378
40.872
-0.850
-0.446
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
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
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr2_auth_comp_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr2_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_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.ptnr1_symmetry
_struct_conn.ptnr2_auth_asym_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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
B-DNA HEXAMER GGCGCC WITH SPERMINE
A-DNA HEXAMER GGCGM5CC
E-DNA HEXAMER GGCGM5CC
E-DNA HEXAMER GGCGBR5CC
RCSB
Y
RCSB
2000-06-20
REL
REL
MG
MAGNESIUM ION
NCO
COBALT HEXAMMINE(III)
HOH
water
MO6
13
2
MG
MG
13
A
NCO
14
3
NCO
NCO
14
A
HOH
15
4
HOH
HOH
15
A
HOH
20
4
HOH
HOH
20
A
HOH
22
4
HOH
HOH
22
A
HOH
24
4
HOH
HOH
24
A
HOH
25
4
HOH
HOH
25
A
HOH
26
4
HOH
HOH
26
A
MO6
13
4
HOH
HOH
28
A
MO6
13
4
HOH
HOH
32
A
HOH
16
4
HOH
HOH
16
B
HOH
17
4
HOH
HOH
17
B
HOH
18
4
HOH
HOH
18
B
HOH
19
4
HOH
HOH
19
B
HOH
21
4
HOH
HOH
21
B
HOH
23
4
HOH
HOH
23
B
MO6
13
4
HOH
HOH
27
B
MO6
13
4
HOH
HOH
29
B
MO6
13
4
HOH
HOH
30
B
MO6
13
4
HOH
HOH
31
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
C
5
n
5
DC
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
C
11
n
5
DC
11
B
C
12
n
6
DC
12
B
author_defined_assembly
2
dimeric
A
DG
1
A
N7
DG
1
1_555
A
NCO
14
D
CO
NCO
1_555
A
NCO
14
D
N1
NCO
1_555
164.8
A
DG
1
A
N7
DG
1
1_555
A
NCO
14
D
CO
NCO
1_555
A
NCO
14
D
N2
NCO
1_555
90.5
A
NCO
14
D
N1
NCO
1_555
A
NCO
14
D
CO
NCO
1_555
A
NCO
14
D
N2
NCO
1_555
85.0
A
DG
1
A
N7
DG
1
1_555
A
NCO
14
D
CO
NCO
1_555
A
DG
1
A
N7
DG
1
7_554
108.7
A
NCO
14
D
N1
NCO
1_555
A
NCO
14
D
CO
NCO
1_555
A
DG
1
A
N7
DG
1
7_554
86.4
A
NCO
14
D
N2
NCO
1_555
A
NCO
14
D
CO
NCO
1_555
A
DG
1
A
N7
DG
1
7_554
103.4
A
HOH
28
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
A
HOH
32
E
O
HOH
1_555
89.7
A
HOH
28
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
27
F
O
HOH
1_555
179.6
A
HOH
32
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
27
F
O
HOH
1_555
89.9
A
HOH
28
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
29
F
O
HOH
1_555
89.8
A
HOH
32
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
29
F
O
HOH
1_555
90.5
B
HOH
27
F
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
29
F
O
HOH
1_555
90.3
A
HOH
28
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
30
F
O
HOH
1_555
90.2
A
HOH
32
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
30
F
O
HOH
1_555
89.8
B
HOH
27
F
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
30
F
O
HOH
1_555
89.6
B
HOH
29
F
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
30
F
O
HOH
1_555
179.7
A
HOH
28
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
31
F
O
HOH
1_555
90.2
A
HOH
32
E
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
31
F
O
HOH
1_555
179.8
B
HOH
27
F
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
31
F
O
HOH
1_555
90.2
B
HOH
29
F
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
31
F
O
HOH
1_555
89.7
B
HOH
30
F
O
HOH
1_555
A
MG
13
C
MG
MG
1_555
B
HOH
31
F
O
HOH
1_555
90.0
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
NCO
14
D
NCO
1
A
HOH
15
E
HOH
1
B
HOH
21
F
HOH
0.2790000
0.2050000
0.2136000
0.2134000
2.6
8.0
214
1938
1937
11.
RANDOM
1
THROUGHOUT
2.0
MOLECULAR REPLACEMENT, REAL SPACE TRANSLATION/ROTATION/RIGID BODY SEARCH USING A CUSTOM X-PLOR 3.851 SCRIPT
PARKINSON ET AL.
2.6
8.0
12
262
10
240
0
0.005
1.1
42.5
2.6
500
1F69
2026
2026
0.0
0.0
0.0610000
1
27.0
9.5
99.9
0.2510000
2.60
2.72
9.7
99.9
model building
X-PLOR
refinement
X-PLOR
3.851
data reduction
d*TREK
data scaling
d*TREK
phasing
X-PLOR
CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
metalc
1.944
A
DG
1
A
N7
DG
1
1_555
A
NCO
14
D
CO
NCO
1_555
metalc
1.947
A
DG
1
A
N7
DG
1
7_554
A
NCO
14
D
CO
NCO
1_555
metalc
2.022
A
MG
13
C
MG
MG
1_555
A
HOH
28
E
O
HOH
1_555
metalc
2.017
A
MG
13
C
MG
MG
1_555
A
HOH
32
E
O
HOH
1_555
metalc
2.021
A
MG
13
C
MG
MG
1_555
B
HOH
27
F
O
HOH
1_555
metalc
2.025
A
MG
13
C
MG
MG
1_555
B
HOH
29
F
O
HOH
1_555
metalc
2.012
A
MG
13
C
MG
MG
1_555
B
HOH
30
F
O
HOH
1_555
metalc
2.012
A
MG
13
C
MG
MG
1_555
B
HOH
31
F
O
HOH
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
DC
11
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
11
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
11
B
N4
DC
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
DC
5
A
N3
DC
5
1_555
B
DG
8
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
8
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
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
B-DNA, E-DNA, DOUBLE HELIX, DNA
1F69
PDB
1
1F69
1
6
1F69
1
6
1F69
A
1
1
6
7
12
1F69
7
12
1F69
B
1
1
6
BINDING SITE FOR RESIDUE MG A 13
A
MG
13
Software
7
BINDING SITE FOR RESIDUE NCO A 14
A
NCO
14
Software
4
A
DG
4
A
DG
4
7
1_555
A
HOH
28
E
HOH
7
1_555
A
HOH
32
E
HOH
7
1_555
B
HOH
27
F
HOH
7
1_555
B
HOH
29
F
HOH
7
1_555
B
HOH
30
F
HOH
7
1_555
B
HOH
31
F
HOH
7
1_555
A
DG
1
A
DG
1
4
7_554
A
DG
1
A
DG
1
4
1_555
A
DG
2
A
DG
2
4
1_555
B
DC
11
B
DC
5
4
1_555
91
tetragonal
P 41 2 2