0.057000
0.000000
0.000000
0.000000
0.032774
0.000000
0.000000
0.000000
0.022619
0.00000
0.00000
0.00000
Mandal, P.K.
Venkadesh, S.
Vinayak, N.
Gautham, N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
17.544
30.512
44.210
Ba 2
137.327
BARIUM ION
non-polymer
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
H2 O
18.015
WATER
non-polymer
N
1
N
BA
N
2
N
O
N
3
N
P
N
4
N
O
N
5
N
O
N
6
N
O
N
7
N
C
N
8
R
C
N
9
N
O
N
10
S
C
N
11
N
O
N
12
N
C
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
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
H
N
36
N
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
N
C
N
49
R
C
N
50
N
N
N
51
N
C
N
52
N
O
N
53
N
N
N
54
N
C
N
55
N
N
N
56
N
C
N
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
P
N
74
N
O
N
75
N
O
N
76
N
O
N
77
N
C
N
78
R
C
N
79
N
O
N
80
S
C
N
81
N
O
N
82
N
C
N
83
R
C
Y
84
N
N
Y
85
N
C
Y
86
N
N
Y
87
N
C
N
88
N
C
N
89
N
O
N
90
N
N
N
91
N
C
N
92
N
N
N
93
N
N
Y
94
N
C
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
H
N
107
N
H
N
108
N
H
N
109
N
O
N
110
N
P
N
111
N
O
N
112
N
O
N
113
N
O
N
114
N
C
N
115
R
C
N
116
N
O
N
117
S
C
N
118
N
O
N
119
N
C
N
120
R
C
N
121
N
N
N
122
N
C
N
123
N
O
N
124
N
N
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
C
N
129
N
C
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
O
N
146
N
H
N
147
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
Y
24
N
sing
Y
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
sing
Y
30
N
doub
N
31
N
sing
Y
32
N
doub
N
33
N
sing
N
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
doub
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
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
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
doub
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
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
To be published
0353
Barium-DNA interactions
10.2210/pdb3fqb/pdb
pdb_00003fqb
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
mirrors
IMAGE PLATE
2008-09-17
MARRESEARCH
mirrors
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
BRUKER AXS MICROSTAR
1794.206
5'-D(*CP*AP*CP*GP*CP*G)-3'
1
syn
polymer
1825.216
5'-D(*CP*GP*CP*GP*TP*G)-3'
1
syn
polymer
137.327
BARIUM ION
1
syn
non-polymer
18.015
water
39
nat
water
no
no
(DC)(DA)(DC)(DG)(DC)(DG)
CACGCG
A
polydeoxyribonucleotide
no
no
(DC)(DG)(DC)(DG)(DT)(DG)
CGCGTG
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
1
1.63
24.75
VAPOR DIFFUSION, HANGING DROP
6.99
50mM Sodium cacoldylate, 10mM Barium chloride, 0.5mM Spermine, 30% (v/v) Methyl pentane diol , pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
Sodium cacoldylate
1
Barium chloride
1
Spermine
1
MPD
1
Sodium cacoldylate
2
Barium chloride
2
MPD
2
2.429
1
19
A
1
B
12
-0.919
A_DC1:DG12_B
1
-2.584
-0.321
-0.073
-0.070
-6.443
1
20
A
2
B
11
2.687
A_DA2:DT11_B
2
-4.232
0.040
0.207
-0.171
2.468
1
19
A
3
B
10
2.892
A_DC3:DG10_B
3
1.489
-0.208
0.111
-0.240
-7.852
1
19
A
4
B
9
4.793
A_DG4:DC9_B
4
-1.095
0.256
0.059
-0.136
6.098
1
19
A
5
B
8
2.263
A_DC5:DG8_B
5
-1.651
-0.413
0.248
-0.241
-5.472
1
19
A
6
B
7
3.549
A_DG6:DC7_B
6
4.933
0.348
-0.026
-0.259
4.844
-12.072
A
A
1
2
13.995
B
B
12
11
3.710
-2.901
-0.083
5.449
AA_DC1DA2:DT11DG12_BB
1
-1.954
-9.428
-11.556
-20.931
-3.750
3.116
-50.914
A
A
2
3
3.925
B
B
11
10
3.181
-3.372
0.202
-0.888
AA_DA2DC3:DG10DT11_BB
2
0.922
1.073
-50.802
1.259
0.296
5.549
-8.043
A
A
3
4
24.439
B
B
10
9
3.728
-3.318
0.044
5.269
AA_DC3DG4:DC9DG10_BB
3
-0.869
-6.399
-7.276
-23.259
-3.429
3.010
-52.873
A
A
4
5
4.148
B
B
9
8
3.079
-3.691
-0.079
-0.935
AA_DG4DC5:DG8DC9_BB
4
-1.185
-1.332
-52.741
1.272
-0.160
5.121
-6.405
A
A
5
6
28.368
B
B
8
7
3.764
-2.889
0.066
5.264
AA_DC5DG6:DC7DG8_BB
5
3.210
31.522
-4.731
-26.499
23.493
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
1
0
2009-02-10
1
1
2011-07-13
1
2
2024-03-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
PDBJ
2009-01-07
REL
REL
BA
BARIUM ION
HOH
water
BA
1
3
BA
BA
7
A
HOH
2
4
HOH
HOH
8
A
HOH
9
4
HOH
HOH
9
A
HOH
10
4
HOH
HOH
10
A
HOH
7
4
HOH
HOH
11
A
HOH
12
4
HOH
HOH
12
A
HOH
13
4
HOH
HOH
13
A
HOH
14
4
HOH
HOH
14
A
HOH
15
4
HOH
HOH
15
A
HOH
17
4
HOH
HOH
17
A
HOH
18
4
HOH
HOH
18
A
HOH
19
4
HOH
HOH
19
A
HOH
20
4
HOH
HOH
20
A
HOH
25
4
HOH
HOH
25
A
HOH
28
4
HOH
HOH
28
A
HOH
29
4
HOH
HOH
29
A
HOH
30
4
HOH
HOH
30
A
HOH
31
4
HOH
HOH
31
A
HOH
34
4
HOH
HOH
34
A
HOH
35
4
HOH
HOH
35
A
HOH
37
4
HOH
HOH
37
A
HOH
39
4
HOH
HOH
39
A
HOH
1
4
HOH
HOH
1
B
HOH
3
4
HOH
HOH
3
B
HOH
4
4
HOH
HOH
4
B
HOH
5
4
HOH
HOH
5
B
HOH
6
4
HOH
HOH
6
B
HOH
8
4
HOH
HOH
14
B
HOH
11
4
HOH
HOH
15
B
HOH
16
4
HOH
HOH
16
B
HOH
21
4
HOH
HOH
21
B
HOH
22
4
HOH
HOH
22
B
HOH
23
4
HOH
HOH
23
B
HOH
24
4
HOH
HOH
24
B
HOH
26
4
HOH
HOH
26
B
HOH
27
4
HOH
HOH
27
B
HOH
32
4
HOH
HOH
32
B
HOH
33
4
HOH
HOH
33
B
HOH
36
4
HOH
HOH
36
B
HOH
38
4
HOH
HOH
38
B
C
1
n
1
DC
1
A
A
2
n
2
DA
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
C
5
n
5
DC
5
A
G
6
n
6
DG
6
A
C
7
n
1
DC
7
B
G
8
n
2
DG
8
B
C
9
n
3
DC
9
B
G
10
n
4
DG
10
B
T
11
n
5
DT
11
B
G
12
n
6
DG
12
B
author_and_software_defined_assembly
PISA
2
dimeric
860
-13
2310
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
4.05
0.30
108.30
112.35
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
3.59
0.50
106.80
110.39
A
A
A
O4'
C1'
C2'
DA
DA
DA
2
2
2
N
1
-3.32
0.50
129.30
125.98
A
A
A
N1
C2
N3
DA
DA
DA
2
2
2
N
1
7.77
1.20
119.70
127.47
A
A
A
C3'
O3'
P
DA
DA
DC
2
2
3
A
Y
1
-5.71
0.70
108.00
102.29
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
7.79
1.20
110.70
118.49
A
A
A
O5'
P
OP2
DC
DC
DC
5
5
5
N
1
3.18
0.30
108.30
111.48
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
1.84
0.30
108.30
110.14
B
B
B
O4'
C1'
N1
DC
DC
DC
7
7
7
N
1
3.50
0.50
106.80
110.30
B
B
B
O4'
C1'
C2'
DG
DG
DG
8
8
8
N
1
2.45
0.30
108.30
110.75
B
B
B
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
-6.09
0.70
108.00
101.91
B
B
B
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
2.51
0.40
110.80
113.31
B
B
B
C4
C5
N7
DG
DG
DG
10
10
10
N
1
2.35
0.30
108.30
110.65
B
B
B
O4'
C1'
N1
DT
DT
DT
11
11
11
N
1
-5.89
0.70
108.00
102.11
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
16.177
-0.05
0.00
0.00
0.05
0.00
0.00
0.942
0.950
0.22312
0.21689
0.21730
1.67
13.74
145
2427
2427
5.6
86.05
2.983
0.091
RANDOM
1
ISOTROPIC
THROUGHOUT
MOLECULAR REPLACEMENT
0.187
0.139
0.80
0.80
1.40
MAXIMUM LIKELIHOOD
MASK
0.224
1.67
13.74
39
290
2
249
0
0.016
0.021
280
2.247
3.000
434
0.094
0.200
49
0.011
0.020
125
0.212
0.200
112
0.274
0.200
163
0.257
0.200
18
0.400
0.200
3
0.167
0.200
20
0.214
0.200
3
1.925
3.000
309
2.583
4.500
431
0.245
0.320
1.716
12
183
12
20
94.20
26.6
1.67
30
3FQB
3037
2791
0.0882
0.0635
1
6.1
4.54
91.9
0.2711
1.67
1.73
1.7
183
0.2330
4.37
89.6
data collection
MAR345dtb
phasing
PHASER
refinement
REFMAC
5.2.0019
data reduction
AUTOMAR
data scaling
SCALEPACK
N
Barium interactions with Z-DNA
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
12
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
12
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
12
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N1
DA
2
1_555
B
DT
11
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N6
DA
2
1_555
B
DT
11
B
O4
DT
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
DG
6
A
N1
DG
6
1_555
B
DC
7
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
7
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
7
B
N4
DC
1
1_555
DNA
Z-DNA Double Helix, DNA
3FQB
PDB
1
3FQB
3FQB
PDB
2
3FQB
1
6
3FQB
1
6
3FQB
A
1
1
6
7
12
3FQB
7
12
3FQB
B
2
1
6
BINDING SITE FOR RESIDUE BA A 7
A
BA
7
Software
4
A
DC
3
A
DC
3
4
1_555
A
DG
4
A
DG
4
4
1_555
A
DG
6
A
DG
6
4
4_455
A
HOH
30
D
HOH
4
1_555
19
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