0.015163
0.000000
0.005511
0.000000
0.042095
0.000000
0.000000
0.000000
0.028599
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
109.98
90.00
65.949
23.756
37.204
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/pdb1nt8/pdb
pdb_00001nt8
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
2002-05-16
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
0.811
1.0
X11
EMBL/DESY, HAMBURG
0.811
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X11
3045.992
5'-d(CpCpGpGpTpApCpCpGpG)-3'
2
syn
polymer
40.078
CALCIUM ION
2
syn
non-polymer
18.015
water
37
nat
water
no
no
(DC)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DG)
CCGGTACCGG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
2.15
42.70
VAPOR DIFFUSION, HANGING DROP
6.5
MPD, Calcium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
290
-6.419
1
19
A
1
B
20
-2.443
A_DC1:DG20_B
1
-12.651
0.234
0.355
-0.259
0.629
1
19
A
2
B
19
-8.176
A_DC2:DG19_B
2
-5.970
-0.166
0.244
-0.122
7.214
1
19
A
3
B
18
-0.987
A_DG3:DC18_B
3
7.598
-0.334
0.328
-0.160
1.689
1
19
A
4
B
17
0.022
A_DG4:DC17_B
4
-19.638
-0.409
0.249
-0.098
-13.410
1
20
A
5
B
16
-3.981
A_DT5:DA16_B
5
-11.556
-0.585
0.136
0.314
7.637
1
20
A
6
B
15
-2.690
A_DA6:DT15_B
6
-13.589
0.013
0.252
-0.040
3.500
34.665
A
A
1
2
5.747
B
B
20
19
3.379
3.403
-0.225
2.294
AA_DC1DC2:DG19DG20_BB
1
5.848
-9.874
34.018
3.296
1.332
3.002
39.635
A
A
2
3
-4.904
B
B
19
18
3.241
-3.319
0.246
2.542
AA_DC2DG3:DC18DG19_BB
2
-2.732
4.037
39.410
4.121
-0.669
3.885
38.542
A
A
3
4
10.673
B
B
18
17
3.583
6.998
-1.257
1.449
AA_DG3DG4:DC17DC18_BB
3
-3.839
5.855
37.737
1.196
1.356
3.570
38.033
A
A
4
5
-8.018
B
B
17
16
3.674
-5.208
0.503
0.682
AA_DG4DT5:DA16DC17_BB
4
1.717
-2.643
37.650
1.783
-0.529
3.116
35.259
A
A
5
6
11.381
B
B
16
15
2.927
6.850
0.022
1.301
AA_DT5DA6:DT15DA16_BB
5
-1.664
2.764
34.569
1.200
-0.266
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
2003-02-11
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_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Holliday junction formed by the sequence TCGGTACCGA in the presence of one calcium ion
Holliday junction formed by TCGGTACCGA in presence of Na and Ca ions
Holliday junction formed by TCGGTACCGA with a spine of Sr ions
Holliday junction formed by CCGGTACCGG in the more symmetrical form
Holliday junction formed by CCGGTACmCGG with a methylated base
Holliay junction formed by CCGGTACGG in presnece of a Na ion
RCSB
Y
RCSB
2003-01-29
REL
REL
CA
CALCIUM ION
HOH
water
Chemically synthesized
sample
CA
2
2
CA
CA
102
A
CA
1
2
CA
CA
101
B
HOH
5
3
HOH
HOH
103
A
HOH
8
3
HOH
HOH
104
A
HOH
9
3
HOH
HOH
105
A
HOH
11
3
HOH
HOH
106
A
HOH
12
3
HOH
HOH
107
A
HOH
13
3
HOH
HOH
108
A
HOH
15
3
HOH
HOH
109
A
HOH
16
3
HOH
HOH
110
A
HOH
17
3
HOH
HOH
111
A
HOH
29
3
HOH
HOH
112
A
HOH
45
3
HOH
HOH
113
A
HOH
53
3
HOH
HOH
114
A
HOH
54
3
HOH
HOH
115
A
HOH
55
3
HOH
HOH
116
A
HOH
57
3
HOH
HOH
117
A
HOH
59
3
HOH
HOH
118
A
HOH
1
3
HOH
HOH
102
B
HOH
4
3
HOH
HOH
103
B
HOH
6
3
HOH
HOH
104
B
HOH
7
3
HOH
HOH
105
B
HOH
20
3
HOH
HOH
106
B
HOH
22
3
HOH
HOH
107
B
HOH
23
3
HOH
HOH
108
B
HOH
26
3
HOH
HOH
109
B
HOH
28
3
HOH
HOH
110
B
HOH
30
3
HOH
HOH
111
B
HOH
34
3
HOH
HOH
112
B
HOH
35
3
HOH
HOH
113
B
HOH
38
3
HOH
HOH
114
B
HOH
41
3
HOH
HOH
115
B
HOH
42
3
HOH
HOH
116
B
HOH
49
3
HOH
HOH
117
B
HOH
52
3
HOH
HOH
118
B
HOH
56
3
HOH
HOH
119
B
HOH
61
3
HOH
HOH
120
B
HOH
62
3
HOH
HOH
121
B
HOH
63
3
HOH
HOH
122
B
C
1
n
1
DC
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
G
10
n
10
DG
10
A
C
11
n
1
DC
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
G
20
n
10
DG
20
B
author_defined_assembly
4
tetrameric
A
HOH
103
E
O
HOH
1_555
A
CA
102
C
CA
CA
1_555
A
HOH
114
E
O
HOH
1_555
58.5
A
HOH
103
E
O
HOH
1_555
A
CA
102
C
CA
CA
1_555
A
HOH
115
E
O
HOH
1_555
82.4
A
HOH
114
E
O
HOH
1_555
A
CA
102
C
CA
CA
1_555
A
HOH
115
E
O
HOH
1_555
75.0
A
HOH
103
E
O
HOH
1_555
A
CA
102
C
CA
CA
1_555
A
HOH
116
E
O
HOH
1_555
83.4
A
HOH
114
E
O
HOH
1_555
A
CA
102
C
CA
CA
1_555
A
HOH
116
E
O
HOH
1_555
141.5
A
HOH
115
E
O
HOH
1_555
A
CA
102
C
CA
CA
1_555
A
HOH
116
E
O
HOH
1_555
96.5
A
HOH
103
E
O
HOH
1_555
A
CA
102
C
CA
CA
1_555
B
HOH
103
F
O
HOH
1_555
101.8
A
HOH
114
E
O
HOH
1_555
A
CA
102
C
CA
CA
1_555
B
HOH
103
F
O
HOH
1_555
111.0
A
HOH
115
E
O
HOH
1_555
A
CA
102
C
CA
CA
1_555
B
HOH
103
F
O
HOH
1_555
173.9
A
HOH
116
E
O
HOH
1_555
A
CA
102
C
CA
CA
1_555
B
HOH
103
F
O
HOH
1_555
79.7
B
HOH
102
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
104
F
O
HOH
1_555
131.6
B
HOH
102
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
105
F
O
HOH
1_555
110.4
B
HOH
104
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
105
F
O
HOH
1_555
113.9
B
HOH
102
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
110
F
O
HOH
1_555
80.7
B
HOH
104
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
110
F
O
HOH
1_555
140.6
B
HOH
105
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
110
F
O
HOH
1_555
57.6
B
HOH
102
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
118
F
O
HOH
1_555
54.7
B
HOH
104
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
118
F
O
HOH
1_555
129.0
B
HOH
105
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
118
F
O
HOH
1_555
68.3
B
HOH
110
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
118
F
O
HOH
1_555
86.1
B
HOH
102
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
119
F
O
HOH
1_555
58.0
B
HOH
104
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
119
F
O
HOH
1_555
76.5
B
HOH
105
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
119
F
O
HOH
1_555
136.6
B
HOH
110
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
119
F
O
HOH
1_555
138.7
B
HOH
118
F
O
HOH
1_555
B
CA
101
D
CA
CA
1_555
B
HOH
119
F
O
HOH
1_555
73.1
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
110
E
HOH
1
2.43
0.30
108.30
110.73
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
-5.68
0.90
105.70
100.02
A
A
A
O5'
P
OP2
DC
DC
DC
2
2
2
N
1
-3.01
0.40
104.50
101.49
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
1
-5.09
0.80
102.40
97.31
A
A
A
C3'
C2'
C1'
DC
DC
DC
2
2
2
N
1
-6.72
0.80
105.90
99.18
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
1
-10.81
0.70
108.00
97.19
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
5.41
0.50
119.90
125.31
A
A
A
C2
N3
C4
DC
DC
DC
2
2
2
N
1
-2.80
0.40
104.50
101.70
A
A
A
O4'
C4'
C3'
DG
DG
DG
3
3
3
N
1
-4.51
0.70
108.00
103.49
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
1
-3.37
0.40
104.50
101.13
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
1
-5.80
0.70
108.00
102.20
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
-4.56
0.50
111.90
107.34
A
A
A
C2
N3
C4
DG
DG
DG
4
4
4
N
1
4.11
0.40
110.80
114.91
A
A
A
C4
C5
N7
DG
DG
DG
4
4
4
N
1
3.06
0.40
106.40
109.46
A
A
A
C8
N9
C4
DG
DG
DG
4
4
4
N
1
-4.53
0.40
105.40
100.87
A
A
A
N9
C4
C5
DG
DG
DG
4
4
4
N
1
-5.88
0.60
130.40
124.52
A
A
A
C6
C5
N7
DG
DG
DG
4
4
4
N
1
-9.45
0.90
116.20
106.75
A
A
A
N1
C2
N2
DG
DG
DG
4
4
4
N
1
8.90
0.70
119.90
128.80
A
A
A
N3
C2
N2
DG
DG
DG
4
4
4
N
1
-5.78
0.80
109.40
103.62
A
A
A
O5'
C5'
C4'
DT
DT
DT
5
5
5
N
1
5.79
0.30
108.30
114.09
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
4.82
0.60
119.00
123.82
A
A
A
C4
C5
C7
DT
DT
DT
5
5
5
N
1
-3.77
0.60
122.90
119.13
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
1
-15.09
1.90
104.00
88.91
A
A
A
O3'
P
O5'
DT
DA
DA
5
6
6
Y
1
3.00
0.30
108.30
111.30
A
A
A
O4'
C1'
N9
DA
DA
DA
6
6
6
N
1
4.11
0.60
118.60
122.71
A
A
A
C6
N1
C2
DA
DA
DA
6
6
6
N
1
3.52
0.50
110.70
114.22
A
A
A
C4
C5
N7
DA
DA
DA
6
6
6
N
1
-3.75
0.50
103.90
100.15
A
A
A
C5
N7
C8
DA
DA
DA
6
6
6
N
1
-3.70
0.40
105.80
102.10
A
A
A
N9
C4
C5
DA
DA
DA
6
6
6
N
1
5.33
0.30
108.30
113.63
A
A
A
O4'
C1'
N1
DC
DC
DC
7
7
7
N
1
-9.84
1.20
119.70
109.86
A
A
A
C3'
O3'
P
DC
DC
DC
7
7
8
Y
1
-5.40
0.80
105.90
100.50
A
A
A
O4'
C1'
C2'
DC
DC
DC
8
8
8
N
1
4.69
0.70
119.90
124.59
A
A
A
N3
C2
N2
DG
DG
DG
9
9
9
N
1
-5.14
0.60
119.90
114.76
A
A
A
N1
C6
O6
DG
DG
DG
9
9
9
N
1
5.52
0.60
128.60
134.12
A
A
A
C5
C6
O6
DG
DG
DG
9
9
9
N
1
10.28
1.20
119.70
129.98
A
A
A
C3'
O3'
P
DG
DG
DG
9
9
10
Y
1
9.79
1.50
119.60
129.39
A
A
A
OP1
P
OP2
DG
DG
DG
10
10
10
N
1
-7.58
1.00
110.10
102.52
B
B
B
C1'
O4'
C4'
DC
DC
DC
11
11
11
N
1
-6.78
0.70
108.00
101.22
B
B
B
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
4.71
0.40
120.30
125.01
B
B
B
C6
N1
C2
DC
DC
DC
11
11
11
N
1
4.03
0.40
121.90
125.93
B
B
B
N3
C4
C5
DC
DC
DC
11
11
11
N
1
-3.35
0.50
121.00
117.65
B
B
B
C5
C6
N1
DC
DC
DC
11
11
11
N
1
5.18
0.60
118.90
124.08
B
B
B
N1
C2
O2
DC
DC
DC
11
11
11
N
1
-6.33
0.90
105.70
99.36
B
B
B
O5'
P
OP2
DC
DC
DC
12
12
12
N
1
4.62
0.40
120.30
124.92
B
B
B
C6
N1
C2
DC
DC
DC
12
12
12
N
1
-3.48
0.50
119.90
116.42
B
B
B
C2
N3
C4
DC
DC
DC
12
12
12
N
1
4.37
0.40
121.90
126.27
B
B
B
N3
C4
C5
DC
DC
DC
12
12
12
N
1
4.27
0.70
121.90
126.17
B
B
B
N3
C2
O2
DC
DC
DC
12
12
12
N
1
-7.42
0.70
120.20
112.78
B
B
B
C5
C4
N4
DC
DC
DC
12
12
12
N
1
11.30
1.50
119.60
130.90
B
B
B
OP1
P
OP2
DG
DG
DG
13
13
13
N
1
-3.28
0.50
111.90
108.62
B
B
B
C2
N3
C4
DG
DG
DG
13
13
13
N
1
3.82
0.60
119.90
123.72
B
B
B
N1
C6
O6
DG
DG
DG
13
13
13
N
1
-4.15
0.60
128.60
124.45
B
B
B
C5
C6
O6
DG
DG
DG
13
13
13
N
1
10.66
1.50
119.60
130.26
B
B
B
OP1
P
OP2
DG
DG
DG
14
14
14
N
1
-6.81
0.90
105.70
98.89
B
B
B
O5'
P
OP1
DG
DG
DG
14
14
14
N
1
7.84
1.20
110.70
118.54
B
B
B
O5'
P
OP2
DG
DG
DG
14
14
14
N
1
8.63
1.10
109.80
118.43
B
B
B
C5'
C4'
O4'
DG
DG
DG
14
14
14
N
1
1.89
0.30
108.30
110.19
B
B
B
O4'
C1'
N9
DG
DG
DG
14
14
14
N
1
-4.57
0.60
123.90
119.33
B
B
B
N1
C2
N3
DG
DG
DG
14
14
14
N
1
3.44
0.50
111.90
115.34
B
B
B
C2
N3
C4
DG
DG
DG
14
14
14
N
1
-2.62
0.40
106.40
103.78
B
B
B
C8
N9
C4
DG
DG
DG
14
14
14
N
1
7.92
1.20
119.70
127.62
B
B
B
C3'
O3'
P
DG
DG
DT
14
14
15
Y
1
2.49
0.30
108.30
110.79
B
B
B
O4'
C1'
N1
DT
DT
DT
15
15
15
N
1
-5.17
0.60
122.30
117.13
B
B
B
N3
C2
O2
DT
DT
DT
15
15
15
N
1
4.47
0.60
119.00
123.47
B
B
B
C4
C5
C7
DT
DT
DT
15
15
15
N
1
-6.61
0.60
122.90
116.29
B
B
B
C6
C5
C7
DT
DT
DT
15
15
15
N
1
4.97
0.30
108.30
113.27
B
B
B
O4'
C1'
N9
DA
DA
DA
16
16
16
N
1
10.95
1.50
119.60
130.55
B
B
B
OP1
P
OP2
DC
DC
DC
17
17
17
N
1
4.60
0.50
119.90
124.50
B
B
B
C2
N3
C4
DC
DC
DC
17
17
17
N
1
5.74
0.60
118.90
124.64
B
B
B
N1
C2
O2
DC
DC
DC
17
17
17
N
1
-4.57
0.70
118.00
113.43
B
B
B
N3
C4
N4
DC
DC
DC
17
17
17
N
1
4.89
0.70
120.20
125.09
B
B
B
C5
C4
N4
DC
DC
DC
17
17
17
N
1
-8.16
0.90
105.70
97.54
B
B
B
O5'
P
OP1
DG
DG
DG
19
19
19
N
1
7.79
1.20
110.70
118.49
B
B
B
O5'
P
OP2
DG
DG
DG
19
19
19
N
1
2.92
0.40
110.80
113.72
B
B
B
C4
C5
N7
DG
DG
DG
19
19
19
N
1
3.82
0.60
126.00
129.82
B
B
B
N3
C4
N9
DG
DG
DG
19
19
19
N
1
-5.38
0.60
130.40
125.02
B
B
B
C6
C5
N7
DG
DG
DG
19
19
19
N
1
7.56
0.60
119.90
127.46
B
B
B
N1
C6
O6
DG
DG
DG
19
19
19
N
1
-9.83
0.60
128.60
118.77
B
B
B
C5
C6
O6
DG
DG
DG
19
19
19
N
1
2.92
0.30
108.30
111.22
B
B
B
O4'
C1'
N9
DG
DG
DG
20
20
20
N
1
4.04
0.50
111.90
115.94
B
B
B
C2
N3
C4
DG
DG
DG
20
20
20
N
1
-5.04
0.40
110.80
105.76
B
B
B
C4
C5
N7
DG
DG
DG
20
20
20
N
1
-4.80
0.40
106.40
101.60
B
B
B
C8
N9
C4
DG
DG
DG
20
20
20
N
1
6.65
0.40
105.40
112.05
B
B
B
N9
C4
C5
DG
DG
DG
20
20
20
N
1
-5.34
0.60
126.00
120.66
B
B
B
N3
C4
N9
DG
DG
DG
20
20
20
N
1
5.48
0.60
130.40
135.88
B
B
B
C6
C5
N7
DG
DG
DG
20
20
20
N
1
7.74
0.90
116.20
123.94
B
B
B
N1
C2
N2
DG
DG
DG
20
20
20
N
1
-7.65
0.70
119.90
112.25
B
B
B
N3
C2
N2
DG
DG
DG
20
20
20
N
1
9.13
1.30
127.00
136.13
B
B
B
C8
N9
C1'
DG
DG
DG
20
20
20
N
1
A
A
C2
N3
DC
DC
2
2
-0.049
0.008
1.353
1.304
N
1
A
A
O3'
C3'
DT
DT
5
5
-0.062
0.006
1.419
1.357
N
1
A
A
N3
C4
DA
DA
6
6
0.053
0.006
1.344
1.397
N
1
A
A
N9
C4
DA
DA
6
6
0.036
0.006
1.374
1.410
N
1
A
A
N3
C4
DG
DG
10
10
0.043
0.007
1.350
1.393
N
1
B
B
O3'
C3'
DC
DC
11
11
-0.062
0.006
1.419
1.357
N
1
B
B
O3'
P
DC
DC
11
12
-0.082
0.012
1.607
1.525
Y
1
B
B
C4
N4
DC
DC
12
12
-0.072
0.009
1.335
1.263
N
1
B
B
N1
C2
DG
DG
13
13
0.048
0.008
1.373
1.421
N
1
B
B
O3'
C3'
DG
DG
14
14
-0.106
0.006
1.419
1.313
N
1
B
B
N7
C8
DG
DG
14
14
0.043
0.006
1.305
1.348
N
1
B
B
C1'
N1
DT
DT
15
15
0.091
0.013
1.488
1.579
N
1
B
B
N1
C2
DT
DT
15
15
0.078
0.008
1.376
1.454
N
1
B
B
O3'
C3'
DA
DA
16
16
-0.038
0.006
1.419
1.381
N
1
B
B
C6
O6
DG
DG
19
19
0.064
0.009
1.237
1.301
N
34.530
-1.19
0.00
-0.77
2.84
0.00
-2.17
0.939
0.925
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.28262
0.24659
0.24834
2.00
34.92
167
4940
3539
4.5
97.37
4.868
0.136
RANDOM
1
THROUGHOUT
1.0
1.0
MOLECULAR REPLACEMENT
0.253
0.205
0.80
0.80
1.40
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
2.00
34.92
37
443
2
404
0
0.024
0.021
452
0.002
0.020
186
3.768
3.000
694
1.779
3.000
472
0.117
0.200
60
0.020
0.020
210
0.000
0.020
2
0.170
0.200
51
0.227
0.200
194
0.117
0.200
109
0.282
0.200
22
0.043
0.200
3
0.204
0.200
26
0.378
0.200
16
0.128
0.200
10
3.613
3.000
452
4.770
4.500
694
0.207
0.233
2.052
9
248
20
34.53
1.91
34.92
1NT8
6058
4276
1.0
1.0
0.103
0.106
1
4.18
4.0
97.6
0.849
1.91
2.01
0.8
624
0.849
3.9
97.4
refinement
REFMAC
5.1.24
data reduction
MOSFLM
data scaling
CCP4
(SCALA)
refinement
XTALVIEW
The structure is the more symmetrical form of the Holliday Junction with two calcium ions present
Structural Characterisation of the Holliday junction formed by the sequence CCGGTACCGG at 2.00 A
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
metalc
3.017
A
CA
102
C
CA
CA
1_555
A
HOH
103
E
O
HOH
1_555
metalc
2.604
A
CA
102
C
CA
CA
1_555
A
HOH
114
E
O
HOH
1_555
metalc
2.474
A
CA
102
C
CA
CA
1_555
A
HOH
115
E
O
HOH
1_555
metalc
2.408
A
CA
102
C
CA
CA
1_555
A
HOH
116
E
O
HOH
1_555
metalc
2.852
A
CA
102
C
CA
CA
1_555
B
HOH
103
F
O
HOH
1_555
metalc
2.414
B
CA
101
D
CA
CA
1_555
B
HOH
102
F
O
HOH
1_555
metalc
2.735
B
CA
101
D
CA
CA
1_555
B
HOH
104
F
O
HOH
1_555
metalc
3.242
B
CA
101
D
CA
CA
1_555
B
HOH
105
F
O
HOH
1_555
metalc
2.630
B
CA
101
D
CA
CA
1_555
B
HOH
110
F
O
HOH
1_555
metalc
2.443
B
CA
101
D
CA
CA
1_555
B
HOH
118
F
O
HOH
1_555
metalc
2.568
B
CA
101
D
CA
CA
1_555
B
HOH
119
F
O
HOH
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
20
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
20
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
20
B
N2
DG
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
1NT8
PDB
1
1NT8
1
10
1NT8
1
10
1NT8
A
1
1
10
11
20
1NT8
11
20
1NT8
B
1
1
10
BINDING SITE FOR RESIDUE CA B 101
B
CA
101
Software
5
BINDING SITE FOR RESIDUE CA A 102
A
CA
102
Software
5
B
HOH
102
F
HOH
5
1_555
B
HOH
104
F
HOH
5
1_555
B
HOH
110
F
HOH
5
1_555
B
HOH
118
F
HOH
5
1_555
B
HOH
119
F
HOH
5
1_555
A
HOH
103
E
HOH
5
1_555
A
HOH
114
E
HOH
5
1_555
A
HOH
115
E
HOH
5
1_555
A
HOH
116
E
HOH
5
1_555
B
HOH
103
F
HOH
5
1_555
5
C 1 2 1