0.015247
0.000000
0.005898
0.000000
0.042323
0.000000
0.000000
0.000000
0.028805
0.00000
0.00000
0.00000
Cardin, C.J.
Gale, B.C.
Thorpe, J.H.
Texieira, S.C.M.
Gan, Y.
Moraes, M.I.A.A.
Brogden, A.L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
111.15
90.00
65.588
23.628
37.223
Ca 2
40.078
CALCIUM 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
CA
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
Structural Analysis of two Holliday junctions formed by the sequences TCGGTACCGA and CCGGTACCGG
10.2210/pdb1nqs/pdb
pdb_00001nqs
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
CCD
2002-05-15
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
0.811
1.0
X11
EMBL/DESY, HAMBURG
0.811
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X11
3045.005
5'-d(TpCpGpGpTpApCpCpGpA)-3'
2
syn
polymer
40.078
CALCIUM ION
1
syn
non-polymer
18.015
water
42
nat
water
no
no
(DT)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DA)
TCGGTACCGA
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
2.12
41.96
VAPOR DIFFUSION, SITTING DROP
6.5
MPD, calcium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
290
0.069
1
20
A
1
B
20
3.795
A_DT1:DA20_B
1
-11.987
0.147
0.272
-0.057
1.223
1
19
A
2
B
19
-2.239
A_DC2:DG19_B
2
-2.105
0.210
0.141
-0.183
3.977
1
19
A
3
B
18
-3.466
A_DG3:DC18_B
3
-4.854
-0.463
-0.283
-0.395
0.390
1
19
A
4
B
17
-2.569
A_DG4:DC17_B
4
-12.614
-0.464
0.241
-0.295
-8.288
1
20
A
5
B
16
-1.388
A_DT5:DA16_B
5
-11.199
-0.419
0.059
0.163
1.568
1
20
A
6
B
15
-3.192
A_DA6:DT15_B
6
-10.709
0.055
0.105
-0.095
3.761
40.890
A
A
1
2
5.104
B
B
20
19
3.559
3.554
0.384
2.329
AA_DT1DC2:DG19DA20_BB
1
4.606
-6.614
40.491
2.895
0.019
3.549
33.492
A
A
2
3
6.643
B
B
19
18
3.325
3.818
-0.081
2.284
AA_DC2DG3:DC18DG19_BB
2
1.814
-3.156
33.231
3.300
0.456
3.240
43.343
A
A
3
4
-3.703
B
B
18
17
3.269
-2.723
-0.843
1.883
AA_DG3DG4:DC17DC18_BB
3
-6.855
9.322
42.740
2.816
0.472
3.757
33.731
A
A
4
5
3.301
B
B
17
16
3.737
1.912
0.172
0.414
AA_DG4DT5:DA16DC17_BB
4
2.565
-4.426
33.583
0.358
0.181
3.028
43.458
A
A
5
6
0.947
B
B
16
15
3.007
0.701
0.075
1.525
AA_DT5DA6:DT15DA16_BB
5
-0.875
1.182
43.444
1.996
-0.180
chem_comp_atom
chem_comp_bond
database_2
diffrn_source
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
2003-02-04
1
1
2008-04-29
1
2
2011-07-13
1
3
2024-02-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_diffrn_source.pdbx_synchrotron_site
_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
Holliday junction formed by sequence TCGGTACCGA in presence of Na ion and Ca ions
Holliday junction formed by TCGGTACCGA with a spine of strontium ions
Holliday junction formed by CCGGTACCGG in the more symmetrical form
Holliday junction formed by CCGGTACmCGG with a methylated base
Holliday junction formed by CCGGTACCGG in presence of a Na ion
Holliday junction formed by teh mismatched sequence TCGGGACCGG
RCSB
Y
RCSB
2003-01-22
REL
REL
CA
CALCIUM ION
HOH
water
Chemically synthesized
sample
CA
101
2
CA
CA
101
B
HOH
6
3
HOH
HOH
11
A
HOH
7
3
HOH
HOH
12
A
HOH
8
3
HOH
HOH
13
A
HOH
14
3
HOH
HOH
14
A
HOH
17
3
HOH
HOH
15
A
HOH
18
3
HOH
HOH
16
A
HOH
20
3
HOH
HOH
17
A
HOH
21
3
HOH
HOH
18
A
HOH
22
3
HOH
HOH
19
A
HOH
26
3
HOH
HOH
20
A
HOH
28
3
HOH
HOH
21
A
HOH
31
3
HOH
HOH
22
A
HOH
33
3
HOH
HOH
23
A
HOH
34
3
HOH
HOH
24
A
HOH
40
3
HOH
HOH
25
A
HOH
41
3
HOH
HOH
26
A
HOH
42
3
HOH
HOH
27
A
HOH
1
3
HOH
HOH
102
B
HOH
2
3
HOH
HOH
103
B
HOH
3
3
HOH
HOH
104
B
HOH
4
3
HOH
HOH
105
B
HOH
5
3
HOH
HOH
106
B
HOH
9
3
HOH
HOH
107
B
HOH
10
3
HOH
HOH
108
B
HOH
11
3
HOH
HOH
109
B
HOH
12
3
HOH
HOH
110
B
HOH
13
3
HOH
HOH
111
B
HOH
15
3
HOH
HOH
112
B
HOH
16
3
HOH
HOH
113
B
HOH
19
3
HOH
HOH
114
B
HOH
23
3
HOH
HOH
115
B
HOH
24
3
HOH
HOH
116
B
HOH
25
3
HOH
HOH
117
B
HOH
27
3
HOH
HOH
118
B
HOH
29
3
HOH
HOH
119
B
HOH
30
3
HOH
HOH
120
B
HOH
32
3
HOH
HOH
121
B
HOH
35
3
HOH
HOH
122
B
HOH
36
3
HOH
HOH
123
B
HOH
37
3
HOH
HOH
124
B
HOH
38
3
HOH
HOH
125
B
HOH
39
3
HOH
HOH
126
B
T
1
n
1
DT
1
A
C
2
n
2
DC
2
A
G
3
n
3
DG
3
A
G
4
n
4
DG
4
A
T
5
n
5
DT
5
A
A
6
n
6
DA
6
A
C
7
n
7
DC
7
A
C
8
n
8
DC
8
A
G
9
n
9
DG
9
A
A
10
n
10
DA
10
A
T
11
n
1
DT
11
B
C
12
n
2
DC
12
B
G
13
n
3
DG
13
B
G
14
n
4
DG
14
B
T
15
n
5
DT
15
B
A
16
n
6
DA
16
B
C
17
n
7
DC
17
B
C
18
n
8
DC
18
B
G
19
n
9
DG
19
B
A
20
n
10
DA
20
B
author_defined_assembly
4
tetrameric
B
HOH
102
E
O
HOH
1_555
B
CA
101
C
CA
CA
1_555
B
HOH
109
E
O
HOH
1_555
81.6
B
HOH
102
E
O
HOH
1_555
B
CA
101
C
CA
CA
1_555
B
HOH
117
E
O
HOH
1_555
96.6
B
HOH
109
E
O
HOH
1_555
B
CA
101
C
CA
CA
1_555
B
HOH
117
E
O
HOH
1_555
76.4
B
HOH
102
E
O
HOH
1_555
B
CA
101
C
CA
CA
1_555
B
HOH
118
E
O
HOH
1_555
95.0
B
HOH
109
E
O
HOH
1_555
B
CA
101
C
CA
CA
1_555
B
HOH
118
E
O
HOH
1_555
79.0
B
HOH
117
E
O
HOH
1_555
B
CA
101
C
CA
CA
1_555
B
HOH
118
E
O
HOH
1_555
150.9
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_555
-x,y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1
A
HOH
18
D
HOH
1
B
HOH
123
E
HOH
1
-6.57
0.70
108.00
101.43
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
2.42
0.30
108.30
110.72
B
B
B
O4'
C1'
N1
DT
DT
DT
11
11
11
N
1
4.04
0.30
108.30
112.34
B
B
B
O4'
C1'
N1
DT
DT
DT
15
15
15
N
1
-4.12
0.60
122.90
118.78
B
B
B
C6
C5
C7
DT
DT
DT
15
15
15
N
1
2.89
0.30
108.30
111.19
B
B
B
O4'
C1'
N1
DC
DC
DC
17
17
17
N
1
B
B
O3'
C3'
DT
DT
15
15
-0.052
0.006
1.419
1.367
N
39.038
-0.39
0.00
-1.12
2.94
0.00
-3.36
0.959
0.903
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.27779
0.22304
0.22538
1.97
34.71
176
3728
3691
4.6
99.00
RANDOM
1
THROUGHOUT
1.0
1.0
MOLECULAR REPLACEMENT
0.80
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
1.97
34.71
42
447
1
404
0
0.009
0.021
452
0.003
0.020
192
1.982
3.000
694
1.649
3.000
484
0.065
0.200
60
0.010
0.020
210
0.001
0.020
4
0.153
0.200
51
0.210
0.200
197
0.089
0.200
102
0.241
0.200
28
0.070
0.200
3
0.082
0.200
12
0.339
0.200
18
0.104
0.200
15
2.894
3.000
452
4.414
4.500
694
0.347
0.339
2.021
9
263
20
39.038
1.97
34.71
1NQS
3906
3877
1.0
1.0
0.07
0.07
1
6.1
7.6
99.3
0.296
1.97
2.08
6.1
549
0.296
5.6
100
refinement
REFMAC
5.1.24
data reduction
MOSFLM
data scaling
CCP4
(SCALA)
refinement
XTALVIEW
Structural Characterisation of the Holliday Junction formed by the sequence d(TCGGTACCGA) at 1.97 A
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
metalc
2.374
B
CA
101
C
CA
CA
1_555
B
HOH
102
E
O
HOH
1_555
metalc
2.313
B
CA
101
C
CA
CA
1_555
B
HOH
109
E
O
HOH
1_555
metalc
2.382
B
CA
101
C
CA
CA
1_555
B
HOH
117
E
O
HOH
1_555
metalc
2.492
B
CA
101
C
CA
CA
1_555
B
HOH
118
E
O
HOH
1_555
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
B
DA
20
B
N1
DA
10
1_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
B
DA
20
B
N6
DA
10
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
19
B
N1
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
19
B
O6
DG
9
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
19
B
N2
DG
9
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
DC
18
B
N3
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
18
B
O2
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
18
B
N4
DC
8
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
17
B
N3
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
17
B
O2
DC
7
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
17
B
N4
DC
7
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
DA
16
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
DA
16
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
15
B
N3
DT
5
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
15
B
O4
DT
5
1_555
DNA
Holliday Junction, Calcium ion, DNA
1NQS
PDB
1
1NQS
1
10
1NQS
1
10
1NQS
A
1
1
10
11
20
1NQS
11
20
1NQS
B
1
1
10
BINDING SITE FOR RESIDUE CA B 101
B
CA
101
Software
4
B
HOH
102
E
HOH
4
1_555
B
HOH
109
E
HOH
4
1_555
B
HOH
117
E
HOH
4
1_555
B
HOH
118
E
HOH
4
1_555
5
C 1 2 1