0.047210
-0.000000
0.000000
0.000000
0.035257
0.000000
0.000000
0.000000
0.022502
0.00000
0.00000
0.00000
Thiyagarajan, S.
Satheesh Kumar, P.
Rajan, S.S.
Gautham, N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
21.182
28.363
44.440
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
Mg 2
24.305
MAGNESIUM ION
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
Y
13
N
N
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
N
18
N
N
Y
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
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
H
N
36
N
H
N
37
N
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
56
N
C
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
H
N
70
N
H
N
71
N
O
N
72
N
P
N
73
N
O
N
74
N
O
N
75
N
O
N
76
N
C
N
77
R
C
N
78
N
O
N
79
S
C
N
80
N
O
N
81
N
C
N
82
R
C
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
N
Y
93
N
C
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
H
N
107
N
H
N
108
N
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
N
C
N
119
R
C
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
C
N
129
N
H
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
O
N
145
N
H
N
146
N
H
N
147
N
MG
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
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
58
1381
1384
10.1107/S090744490200896X
12136163
Structure of d(TGCGCA)2 at 293 K: comparison of the effects of sequence and temperature.
2002
10.2210/pdb1ljx/pdb
pdb_00001ljx
SEVERAL CHIRALITY ERRORS
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
293
1
FRANK
AREA DETECTOR
1998-04-15
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
1809.218
5'-D(*TP*GP*CP*GP*CP*A)-3'
2
syn
polymer
24.305
MAGNESIUM ION
2
syn
non-polymer
18.015
water
58
nat
water
no
no
(DT)(DG)(DC)(DG)(DC)(DA)
TGCGCA
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
1
1.84
33.32
VAPOR DIFFUSION, HANGING DROP
7.0
cacodylate, MgCl2, cobalt hexaamine chloride, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
cacodylate
1
MgCl2
1
cobalt hexaamine chloride
1
MPD
1
8.125
1
20
A
1
B
12
-2.191
A_DT1:DA12_B
1
0.864
-0.181
0.049
-0.129
0.338
1
19
A
2
B
11
0.019
A_DG2:DC11_B
2
2.851
0.174
0.282
-0.127
-0.651
1
19
A
3
B
10
1.743
A_DC3:DG10_B
3
1.280
-0.082
0.321
-0.069
-3.865
1
19
A
4
B
9
1.120
A_DG4:DC9_B
4
0.556
0.197
0.108
-0.072
7.322
1
19
A
5
B
8
1.281
A_DC5:DG8_B
5
-3.475
-0.179
0.026
-0.109
-6.303
1
20
A
6
B
7
-1.697
A_DA6:DT7_B
6
0.776
0.059
0.142
-0.105
4.330
-14.256
A
A
1
2
5.231
B
B
12
11
3.875
-1.294
0.138
5.607
AA_DT1DG2:DC11DA12_BB
1
1.503
6.075
-14.118
-21.093
2.297
3.576
-53.165
A
A
2
3
-0.945
B
B
11
10
3.568
0.845
-0.129
-0.720
AA_DG2DC3:DG10DC11_BB
2
-0.745
-0.832
-53.154
0.745
-0.195
3.989
-9.317
A
A
3
4
2.724
B
B
10
9
3.743
-0.442
0.052
5.271
AA_DC3DG4:DC9DG10_BB
3
-0.252
-1.554
-9.303
-31.325
-0.320
3.061
-48.577
A
A
4
5
6.009
B
B
9
8
3.201
-4.936
0.006
-1.305
AA_DG4DC5:DG8DC9_BB
4
0.760
0.925
-48.336
1.951
0.063
6.017
-11.184
A
A
5
6
32.148
B
B
8
7
3.821
-5.908
-0.128
5.348
AA_DC5DA6:DT7DG8_BB
5
1.998
10.869
-9.288
-12.909
4.258
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2002-05-03
1
1
2008-04-28
1
2
2011-07-13
1
3
2017-10-11
1
4
2023-08-16
_software.classification
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr2_auth_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2002-04-23
REL
REL
MG
MAGNESIUM ION
HOH
water
1DCG
PDB entry 1DCG with its terminal bases modified
PDB
experimental model
MG
19
2
MG
MG
19
A
MG
18
2
MG
MG
18
B
HOH
14
3
HOH
HOH
14
A
HOH
17
3
HOH
HOH
17
A
HOH
20
3
HOH
HOH
20
A
HOH
22
3
HOH
HOH
22
A
HOH
23
3
HOH
HOH
23
A
HOH
24
3
HOH
HOH
24
A
HOH
25
3
HOH
HOH
25
A
HOH
26
3
HOH
HOH
26
A
HOH
30
3
HOH
HOH
30
A
HOH
36
3
HOH
HOH
36
A
HOH
38
3
HOH
HOH
38
A
HOH
39
3
HOH
HOH
39
A
HOH
40
3
HOH
HOH
40
A
HOH
44
3
HOH
HOH
44
A
HOH
51
3
HOH
HOH
51
A
HOH
55
3
HOH
HOH
55
A
HOH
56
3
HOH
HOH
56
A
HOH
59
3
HOH
HOH
59
A
HOH
63
3
HOH
HOH
63
A
HOH
67
3
HOH
HOH
67
A
HOH
13
3
HOH
HOH
13
B
HOH
15
3
HOH
HOH
15
B
HOH
16
3
HOH
HOH
16
B
HOH
21
3
HOH
HOH
21
B
HOH
27
3
HOH
HOH
27
B
HOH
28
3
HOH
HOH
28
B
HOH
29
3
HOH
HOH
29
B
HOH
31
3
HOH
HOH
31
B
HOH
32
3
HOH
HOH
32
B
HOH
33
3
HOH
HOH
33
B
HOH
34
3
HOH
HOH
34
B
HOH
35
3
HOH
HOH
35
B
HOH
37
3
HOH
HOH
37
B
HOH
41
3
HOH
HOH
41
B
HOH
42
3
HOH
HOH
42
B
HOH
43
3
HOH
HOH
43
B
HOH
45
3
HOH
HOH
45
B
HOH
46
3
HOH
HOH
46
B
HOH
47
3
HOH
HOH
47
B
HOH
48
3
HOH
HOH
48
B
HOH
49
3
HOH
HOH
49
B
HOH
50
3
HOH
HOH
50
B
HOH
52
3
HOH
HOH
52
B
HOH
53
3
HOH
HOH
53
B
HOH
54
3
HOH
HOH
54
B
HOH
57
3
HOH
HOH
57
B
HOH
58
3
HOH
HOH
58
B
HOH
60
3
HOH
HOH
60
B
HOH
61
3
HOH
HOH
61
B
HOH
62
3
HOH
HOH
62
B
HOH
64
3
HOH
HOH
64
B
HOH
65
3
HOH
HOH
65
B
HOH
66
3
HOH
HOH
66
B
HOH
68
3
HOH
HOH
68
B
HOH
69
3
HOH
HOH
69
B
HOH
70
3
HOH
HOH
70
B
HOH
71
3
HOH
HOH
71
B
HOH
72
3
HOH
HOH
72
B
T
1
n
1
DT
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
A
6
n
6
DA
6
A
T
7
n
1
DT
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
A
12
n
6
DA
12
B
author_defined_assembly
2
dimeric
A
HOH
23
E
O
HOH
1_555
A
MG
19
C
MG
MG
1_555
A
HOH
24
E
O
HOH
1_555
144.1
A
HOH
23
E
O
HOH
1_555
A
MG
19
C
MG
MG
1_555
A
HOH
25
E
O
HOH
1_555
97.7
A
HOH
24
E
O
HOH
1_555
A
MG
19
C
MG
MG
1_555
A
HOH
25
E
O
HOH
1_555
88.0
A
HOH
23
E
O
HOH
1_555
A
MG
19
C
MG
MG
1_555
A
HOH
63
E
O
HOH
1_555
79.6
A
HOH
24
E
O
HOH
1_555
A
MG
19
C
MG
MG
1_555
A
HOH
63
E
O
HOH
1_555
97.9
A
HOH
25
E
O
HOH
1_555
A
MG
19
C
MG
MG
1_555
A
HOH
63
E
O
HOH
1_555
173.1
B
HOH
34
F
O
HOH
1_555
B
MG
18
D
MG
MG
1_555
B
HOH
43
F
O
HOH
1_555
71.7
B
HOH
34
F
O
HOH
1_555
B
MG
18
D
MG
MG
1_555
B
HOH
46
F
O
HOH
1_555
97.5
B
HOH
43
F
O
HOH
1_555
B
MG
18
D
MG
MG
1_555
B
HOH
46
F
O
HOH
1_555
148.8
B
HOH
34
F
O
HOH
1_555
B
MG
18
D
MG
MG
1_555
B
HOH
49
F
O
HOH
1_555
99.9
B
HOH
43
F
O
HOH
1_555
B
MG
18
D
MG
MG
1_555
B
HOH
49
F
O
HOH
1_555
113.9
B
HOH
46
F
O
HOH
1_555
B
MG
18
D
MG
MG
1_555
B
HOH
49
F
O
HOH
1_555
96.6
B
HOH
34
F
O
HOH
1_555
B
MG
18
D
MG
MG
1_555
B
HOH
68
F
O
HOH
1_555
83.1
B
HOH
43
F
O
HOH
1_555
B
MG
18
D
MG
MG
1_555
B
HOH
68
F
O
HOH
1_555
70.1
B
HOH
46
F
O
HOH
1_555
B
MG
18
D
MG
MG
1_555
B
HOH
68
F
O
HOH
1_555
79.7
B
HOH
49
F
O
HOH
1_555
B
MG
18
D
MG
MG
1_555
B
HOH
68
F
O
HOH
1_555
175.5
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
C4'
DG
4
PLANAR
1
B
C4'
DG
8
PLANAR
1
B
C4'
DG
10
PLANAR
1
13.53
1.20
115.70
129.23
A
A
A
C5'
C4'
C3'
DG
DG
DG
4
4
4
N
1
11.70
1.10
109.80
121.50
A
A
A
C5'
C4'
O4'
DG
DG
DG
4
4
4
N
1
14.01
1.20
115.70
129.71
B
B
B
C5'
C4'
C3'
DG
DG
DG
8
8
8
N
1
11.09
1.10
109.80
120.89
B
B
B
C5'
C4'
O4'
DG
DG
DG
8
8
8
N
1
13.50
1.20
115.70
129.20
B
B
B
C5'
C4'
C3'
DG
DG
DG
10
10
10
N
1
11.57
1.10
109.80
121.37
B
B
B
C5'
C4'
O4'
DG
DG
DG
10
10
10
N
0.2670000
0.2120000
1.64
19.0
339
3824
3368
10
RANDOM
1
THROUGHOUT
1.0
MOLECULAR REPLACEMENT
PDB entry 1DCG with its terminal bases modified
1.64
19.0
58
300
2
240
0
1.64
19
1LJX
3564
3468
1.0
1.0
0.0450000
1
97.3
phasing
AMoRE
refinement
CNS
data collection
MAR345
data reduction
AUTOMAR
THE STRUCTURE OF D(TPGPCPGPCPA)2 AT 293K: COMPARISON OF THE EFFECT OF SEQUENCE AND TEMPERATURE
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
metalc
2.002
A
MG
19
C
MG
MG
1_555
A
HOH
23
E
O
HOH
1_555
metalc
1.829
A
MG
19
C
MG
MG
1_555
A
HOH
24
E
O
HOH
1_555
metalc
2.018
A
MG
19
C
MG
MG
1_555
A
HOH
25
E
O
HOH
1_555
metalc
1.884
A
MG
19
C
MG
MG
1_555
A
HOH
63
E
O
HOH
1_555
metalc
2.075
B
MG
18
D
MG
MG
1_555
B
HOH
34
F
O
HOH
1_555
metalc
2.252
B
MG
18
D
MG
MG
1_555
B
HOH
43
F
O
HOH
1_555
metalc
2.043
B
MG
18
D
MG
MG
1_555
B
HOH
46
F
O
HOH
1_555
metalc
1.819
B
MG
18
D
MG
MG
1_555
B
HOH
49
F
O
HOH
1_555
metalc
2.489
B
MG
18
D
MG
MG
1_555
B
HOH
68
F
O
HOH
1_555
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
B
DA
12
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
B
DA
12
B
N6
DA
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
DA
6
A
N1
DA
6
1_555
B
DT
7
B
N3
DT
1
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
7
B
O4
DT
1
1_555
DNA
Z-DNA hexamer with AT base pairs at the terminal, DNA
1LJX
PDB
1
1LJX
1
6
1LJX
1
6
1LJX
A
1
1
6
7
12
1LJX
7
12
1LJX
B
1
1
6
BINDING SITE FOR RESIDUE MG B 18
B
MG
18
Software
5
BINDING SITE FOR RESIDUE MG A 19
A
MG
19
Software
4
B
HOH
34
F
HOH
5
1_555
B
HOH
43
F
HOH
5
1_555
B
HOH
46
F
HOH
5
1_555
B
HOH
49
F
HOH
5
1_555
B
HOH
68
F
HOH
5
1_555
A
HOH
23
E
HOH
4
1_555
A
HOH
24
E
HOH
4
1_555
A
HOH
25
E
HOH
4
1_555
A
HOH
63
E
HOH
4
1_555
19
P 21 21 21