0.015266
0.000000
0.005558
0.000000
0.040479
0.000000
0.000000
0.000000
0.028782
0.00000
0.00000
0.00000
Vargason, J.M.
Ho, P.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
110.01
90.00
65.503
24.704
36.975
C10 H16 N3 O7 P
321.224
n
5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
DNA linking
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
N
N
2
N
C
N
3
N
N
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
O
N
9
N
N
N
10
R
C
N
11
N
C
N
12
S
C
N
13
R
C
N
14
N
O
N
15
N
O
N
16
N
C
N
17
N
O
N
18
N
P
N
19
N
O
N
20
N
O
N
21
N
O
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
H
N
36
N
H
N
37
N
H
N
38
N
CA
N
39
N
O
N
40
N
P
N
41
N
O
N
42
N
O
N
43
N
O
N
44
N
C
N
45
R
C
N
46
N
O
N
47
S
C
N
48
N
O
N
49
N
C
N
50
R
C
Y
51
N
N
Y
52
N
C
Y
53
N
N
Y
54
N
C
Y
55
N
C
N
56
N
N
Y
57
N
N
Y
58
N
C
Y
59
N
N
Y
60
N
C
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
H
N
73
N
H
N
74
N
H
N
75
N
O
N
76
N
P
N
77
N
O
N
78
N
O
N
79
N
O
N
80
N
C
N
81
R
C
N
82
N
O
N
83
S
C
N
84
N
O
N
85
N
C
N
86
R
C
N
87
N
N
N
88
N
C
N
89
N
O
N
90
N
N
N
91
N
C
N
92
N
N
N
93
N
C
N
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
Y
121
N
N
Y
122
N
C
Y
123
N
N
Y
124
N
C
N
125
N
C
N
126
N
O
N
127
N
N
N
128
N
C
N
129
N
N
N
130
N
N
Y
131
N
C
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
H
N
146
N
O
N
147
N
P
N
148
N
O
N
149
N
O
N
150
N
O
N
151
N
C
N
152
R
C
N
153
N
O
N
154
S
C
N
155
N
O
N
156
N
C
N
157
R
C
N
158
N
N
N
159
N
C
N
160
N
O
N
161
N
N
N
162
N
C
N
163
N
O
N
164
N
C
N
165
N
C
N
166
N
C
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
O
N
183
N
H
N
184
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
doub
N
6
N
doub
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
doub
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
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
doub
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
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
Y
62
N
sing
Y
63
N
sing
Y
64
N
doub
N
65
N
sing
Y
66
N
sing
Y
67
N
sing
Y
68
N
doub
N
69
N
sing
Y
70
N
doub
N
71
N
sing
N
72
N
sing
Y
73
N
sing
Y
74
N
doub
N
75
N
sing
Y
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
doub
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
N
101
N
sing
N
102
N
doub
N
103
N
sing
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
doub
N
115
N
sing
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
Y
135
N
sing
Y
136
N
sing
Y
137
N
doub
N
138
N
sing
Y
139
N
sing
N
140
N
sing
Y
141
N
doub
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
doub
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
doub
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
doub
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
doub
N
181
N
sing
N
182
N
sing
N
183
N
doub
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
277
21041
21049
10.1074/jbc.M201357200
11919197
The effect of cytosine methylation on the structure and geometry of the Holliday junction: the structure of d(CCGGTACm5CGG) at 1.5 A resolution.
2002
10.2210/pdb1l6b/pdb
pdb_00001l6b
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
2001-01-22
ADSC QUANTUM 4
Si 111 Chanel
SINGLE WAVELENGTH
M
x-ray
1
1.150
1.0
5.0.2
ALS
1.150
SYNCHROTRON
ALS BEAMLINE 5.0.2
3060.020
5'-D(*CP*CP*GP*GP*TP*AP*CP*(5CM)P*GP*G)-3'
2
syn
polymer
40.078
CALCIUM ION
1
syn
non-polymer
18.015
water
95
nat
water
no
yes
(DC)(DC)(DG)(DG)(DT)(DA)(DC)(5CM)(DG)(DG)
CCGGTACCGG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
1
2.45
49.84
VAPOR DIFFUSION, SITTING DROP
7.0
Sodium Cacodylate, CaCl2, Spermine tetrahydrochloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
Sodium Cacodylate
1
CaCl2
1
Spermine tetrahydrochloride
1
CaCl2
2
-3.619
1
19
A
1
B
20
2.943
A_DC1:DG20_B
1
-12.774
0.644
0.088
-0.082
-0.676
1
19
A
2
B
19
-0.141
A_DC2:DG19_B
2
-2.438
0.289
0.159
-0.222
2.922
1
19
A
3
B
18
-6.680
A_DG3:5CM18_B
3
-1.025
-0.328
0.141
-0.286
0.230
1
19
A
4
B
17
4.350
A_DG4:DC17_B
4
-12.149
-0.203
0.111
0.006
-2.699
1
20
A
5
B
16
1.008
A_DT5:DA16_B
5
-16.581
0.063
0.062
-0.080
-2.500
1
20
A
6
B
15
2.117
A_DA6:DT15_B
6
-10.310
0.030
0.105
-0.164
3.837
38.045
A
A
1
2
8.777
B
B
20
19
3.507
5.693
0.155
2.546
AA_DC1DC2:DG19DG20_BB
1
3.728
-5.747
37.453
3.086
0.298
3.201
37.042
A
A
2
3
-1.609
B
B
19
18
3.269
-1.022
0.018
2.488
AA_DC2DG3:5CM18DG19_BB
2
0.021
-0.034
37.028
4.052
-0.025
3.678
38.477
A
A
3
4
5.616
B
B
18
17
3.500
3.688
-0.579
1.623
AA_DG3DG4:DC175CM18_BB
3
-4.596
6.999
38.041
1.957
0.249
3.399
37.589
A
A
4
5
-2.171
B
B
17
16
3.429
-1.398
-0.302
0.618
AA_DG4DT5:DA16DC17_BB
4
0.655
-1.017
37.559
1.149
0.557
3.359
41.550
A
A
5
6
1.536
B
B
16
15
3.295
1.089
0.897
1.353
AA_DT5DA6:DT15DA16_BB
5
1.597
-2.252
41.507
1.790
-1.092
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_conn_type
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-08-07
1
1
2008-04-28
1
2
2011-07-13
1
3
2024-02-14
_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.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_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.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_conn.ptnr2_label_seq_id
_struct_conn_type.id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2002-03-08
REL
REL
CA
CALCIUM ION
HOH
water
The sequence is chemically synthesized.
sample
CA
21
2
CA
CA
21
B
HOH
22
3
HOH
HOH
22
A
HOH
23
3
HOH
HOH
23
A
HOH
24
3
HOH
HOH
24
A
HOH
28
3
HOH
HOH
28
A
HOH
29
3
HOH
HOH
29
A
HOH
30
3
HOH
HOH
30
A
HOH
31
3
HOH
HOH
31
A
HOH
32
3
HOH
HOH
32
A
HOH
33
3
HOH
HOH
33
A
HOH
34
3
HOH
HOH
34
A
HOH
35
3
HOH
HOH
35
A
HOH
36
3
HOH
HOH
36
A
HOH
39
3
HOH
HOH
39
A
HOH
40
3
HOH
HOH
40
A
HOH
54
3
HOH
HOH
54
A
HOH
61
3
HOH
HOH
61
A
HOH
64
3
HOH
HOH
64
A
HOH
65
3
HOH
HOH
65
A
HOH
67
3
HOH
HOH
67
A
HOH
68
3
HOH
HOH
68
A
HOH
70
3
HOH
HOH
70
A
HOH
75
3
HOH
HOH
75
A
HOH
78
3
HOH
HOH
78
A
HOH
85
3
HOH
HOH
85
A
HOH
86
3
HOH
HOH
86
A
HOH
87
3
HOH
HOH
87
A
HOH
88
3
HOH
HOH
88
A
HOH
90
3
HOH
HOH
90
A
HOH
91
3
HOH
HOH
91
A
HOH
93
3
HOH
HOH
93
A
HOH
94
3
HOH
HOH
94
A
HOH
96
3
HOH
HOH
96
A
HOH
99
3
HOH
HOH
99
A
HOH
100
3
HOH
HOH
100
A
HOH
101
3
HOH
HOH
101
A
HOH
102
3
HOH
HOH
102
A
HOH
103
3
HOH
HOH
103
A
HOH
108
3
HOH
HOH
108
A
HOH
109
3
HOH
HOH
109
A
HOH
110
3
HOH
HOH
110
A
HOH
113
3
HOH
HOH
113
A
HOH
114
3
HOH
HOH
114
A
HOH
115
3
HOH
HOH
115
A
HOH
25
3
HOH
HOH
25
B
HOH
26
3
HOH
HOH
26
B
HOH
27
3
HOH
HOH
27
B
HOH
37
3
HOH
HOH
37
B
HOH
38
3
HOH
HOH
38
B
HOH
41
3
HOH
HOH
41
B
HOH
42
3
HOH
HOH
42
B
HOH
43
3
HOH
HOH
43
B
HOH
44
3
HOH
HOH
44
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
51
3
HOH
HOH
51
B
HOH
52
3
HOH
HOH
52
B
HOH
53
3
HOH
HOH
53
B
HOH
55
3
HOH
HOH
55
B
HOH
56
3
HOH
HOH
56
B
HOH
57
3
HOH
HOH
57
B
HOH
58
3
HOH
HOH
58
B
HOH
59
3
HOH
HOH
59
B
HOH
60
3
HOH
HOH
60
B
HOH
62
3
HOH
HOH
62
B
HOH
63
3
HOH
HOH
63
B
HOH
66
3
HOH
HOH
66
B
HOH
69
3
HOH
HOH
69
B
HOH
71
3
HOH
HOH
71
B
HOH
72
3
HOH
HOH
72
B
HOH
73
3
HOH
HOH
73
B
HOH
74
3
HOH
HOH
74
B
HOH
76
3
HOH
HOH
76
B
HOH
77
3
HOH
HOH
77
B
HOH
79
3
HOH
HOH
79
B
HOH
80
3
HOH
HOH
80
B
HOH
81
3
HOH
HOH
81
B
HOH
82
3
HOH
HOH
82
B
HOH
83
3
HOH
HOH
83
B
HOH
84
3
HOH
HOH
84
B
HOH
89
3
HOH
HOH
89
B
HOH
92
3
HOH
HOH
92
B
HOH
95
3
HOH
HOH
95
B
HOH
97
3
HOH
HOH
97
B
HOH
98
3
HOH
HOH
98
B
HOH
104
3
HOH
HOH
104
B
HOH
105
3
HOH
HOH
105
B
HOH
106
3
HOH
HOH
106
B
HOH
107
3
HOH
HOH
107
B
HOH
111
3
HOH
HOH
111
B
HOH
112
3
HOH
HOH
112
B
HOH
116
3
HOH
HOH
116
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
5CM
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
5CM
18
B
G
19
n
9
DG
19
B
G
20
n
10
DG
20
B
39.6562
-65.3704
-3.5173
65.7801
-27.2352
-30.5233
-0.0841
-0.9030
-0.5051
0.3513
0.1557
0.6348
1.1211
-0.8730
-0.0716
0.2193
-0.0509
0.0226
0.2019
-0.0111
0.2009
refined
-23.5496
-4.0210
31.5800
X-RAY DIFFRACTION
19.0929
-34.1174
6.4047
7.7498
-3.7460
19.3486
-0.3929
0.5998
0.2261
0.1842
-0.5138
-0.2891
-0.4788
0.9031
0.9067
0.2135
-0.0682
-0.0104
0.2145
-0.0163
0.2316
refined
-24.3518
-2.2437
27.4043
X-RAY DIFFRACTION
73.6440
29.7510
-34.8349
-31.1825
-7.8896
12.6152
0.3110
-0.7572
-0.5078
0.9600
-1.0112
-0.4549
0.0084
0.5481
0.7002
0.2822
-0.0708
0.0029
0.2112
0.0620
0.3076
refined
-20.2174
-7.0259
31.7428
X-RAY DIFFRACTION
31.8458
-16.4704
-17.2257
60.7766
26.7388
15.3935
-0.3105
0.0076
-0.1267
0.0063
-0.1597
-0.6120
0.1935
-0.2728
0.4701
0.1780
-0.0714
0.0054
0.2284
0.0183
0.2290
refined
-19.7853
-2.7001
29.4324
X-RAY DIFFRACTION
25.8388
31.5804
-38.8855
140.7212
-1.7557
-49.6423
-1.0436
-2.1748
-2.3502
-1.1715
-0.0225
-2.8706
-0.2093
1.0938
1.0661
0.1361
0.0018
0.0531
0.1811
0.1867
0.5998
refined
-15.0534
-8.6311
29.9965
X-RAY DIFFRACTION
19.3127
-18.7803
27.7757
31.9537
-18.5586
39.3974
0.0925
-0.0749
0.2600
0.1104
0.0654
-0.0749
0.5252
0.3620
-0.1580
0.1474
-0.0708
0.0213
0.2107
0.0077
0.2390
refined
-15.7179
-3.6051
28.5235
X-RAY DIFFRACTION
-33.2176
35.6873
21.4316
97.4899
8.6115
9.6956
-0.4664
-0.8486
-0.6343
0.0611
1.8361
-0.9404
0.6118
0.1238
-1.3697
0.1127
0.0185
0.2925
0.0525
-0.0218
0.8587
refined
-11.8014
-8.9161
24.7459
X-RAY DIFFRACTION
-15.6948
6.3589
-5.6967
-1.1890
12.8826
17.7216
0.4353
0.2259
0.1550
-0.2832
-0.5064
-0.0562
0.4219
0.4380
0.0712
0.1603
-0.0487
0.0251
0.2080
0.0105
0.2461
refined
-12.2614
-3.8573
26.3341
X-RAY DIFFRACTION
10.1295
-5.6539
-56.9417
-170.7949
130.6918
39.3911
-0.8956
-0.3819
-1.8019
4.3522
-1.9174
2.0470
1.4498
-0.1603
2.8130
0.2247
-0.1052
0.0578
0.2145
-0.1042
0.4111
refined
-9.8904
-5.4184
20.2105
X-RAY DIFFRACTION
86.2189
-61.8312
116.8995
142.9202
-175.8928
172.1028
1.5859
-0.1292
0.1968
-0.3509
-1.6707
-1.1169
1.1662
-0.0665
0.0848
0.1104
-0.1023
0.0036
0.1680
-0.0212
0.2505
refined
-8.8316
-3.2726
24.3849
X-RAY DIFFRACTION
31.9197
24.2335
36.3879
-3.2971
-29.4735
37.5881
1.4370
-0.4494
-0.3081
-0.6766
-1.5241
-0.7593
1.5704
-0.0925
0.0871
0.2338
-0.0041
0.0037
0.2439
-0.0464
0.1803
refined
-8.7296
0.1935
18.4519
X-RAY DIFFRACTION
-18.6331
-13.4605
-29.3996
27.9050
13.8058
31.9223
-0.1392
0.0019
0.0260
0.0020
-0.0358
-0.2992
0.2906
0.1245
0.1749
0.1604
-0.0896
-0.0044
0.2620
-0.0031
0.2816
refined
-6.3843
-0.5946
23.3958
X-RAY DIFFRACTION
37.7508
14.6060
-13.7286
4.5721
-32.8983
127.2733
0.8822
-0.5793
0.3741
0.2324
-0.1017
0.2333
-1.0202
0.6222
-0.7804
0.1646
0.0241
-0.0357
0.2349
-0.0592
0.2170
refined
-8.1580
4.9250
15.2207
X-RAY DIFFRACTION
-32.7401
11.3623
11.3356
55.2677
-12.4559
27.8329
0.0751
0.1836
-0.4812
-0.4189
-0.3610
0.1893
-0.1083
-0.0029
0.2859
0.1904
0.0547
-0.0007
0.2589
-0.0179
0.2635
refined
-8.9181
1.5595
11.8048
X-RAY DIFFRACTION
12.6731
-22.8190
-0.3025
42.1537
-45.6118
40.4101
-1.2262
1.3317
0.1101
1.9541
0.6642
-0.2658
-1.1482
1.4436
0.5620
0.2141
0.0013
-0.1155
0.1596
-0.0377
0.2842
refined
-8.7823
9.0508
11.5989
X-RAY DIFFRACTION
5.5263
10.7363
-24.5397
8.9619
33.2917
-59.8856
0.3400
-0.5365
-0.1510
0.1242
-0.3654
0.1300
0.2653
0.3460
0.0254
0.2353
0.0110
-0.0382
0.2294
0.0237
0.2299
refined
-11.9075
5.3907
12.2875
X-RAY DIFFRACTION
-8.0511
2.0084
-29.3745
2.3787
-0.4330
-38.5842
0.1117
-0.6018
0.0702
-0.2074
-0.7694
-0.7221
0.3514
0.0497
0.6577
0.3115
-0.0269
-0.0631
0.1570
0.0400
0.2908
refined
-12.1175
11.6276
7.4152
X-RAY DIFFRACTION
0.3359
4.8936
6.5259
3.5442
-2.4547
7.9459
-0.1593
0.0172
-0.0179
0.0270
0.3810
-0.3305
-0.1823
0.5346
-0.2217
0.2187
0.0208
-0.0081
0.2276
0.0094
0.2407
refined
-14.7532
7.8645
9.7921
X-RAY DIFFRACTION
14.6766
10.3688
-13.2883
57.6915
-0.2695
-6.0534
-0.2504
-1.0129
-0.7037
-1.1069
-0.8841
-1.5993
-1.2908
-1.2208
1.1345
0.2728
0.0084
-0.0414
0.2118
0.0882
0.2113
refined
-15.8403
10.9027
2.8171
X-RAY DIFFRACTION
-15.4863
-8.6937
-1.4508
61.2629
-19.7220
31.9492
-0.3364
0.1117
-0.1955
0.0340
0.4591
-0.2928
-0.2823
0.1434
-0.1227
0.1664
0.0389
-0.0065
0.2276
0.0002
0.2463
refined
-17.8822
9.2521
7.4232
X-RAY DIFFRACTION
27.0270
-16.3273
-73.2060
-78.9518
26.9969
64.0552
0.1635
0.0307
0.0330
0.1312
-0.0225
0.4782
1.1582
0.3953
-0.1409
0.2593
-0.0886
-0.0099
0.2301
-0.0165
0.2168
refined
7.4001
2.1815
21.4797
X-RAY DIFFRACTION
-26.6266
-19.5159
-3.5969
84.4258
-21.6730
48.1060
-0.0233
0.2363
0.3677
0.4446
-0.2828
-0.2385
-0.0441
-0.1182
0.3061
0.1629
-0.0792
-0.0027
0.2372
0.0083
0.2497
refined
6.0313
6.4583
22.4479
X-RAY DIFFRACTION
-38.2354
28.7267
31.0678
25.7498
-4.4404
-8.0421
-1.5383
0.6958
-0.3909
0.1941
0.9944
0.1001
0.4676
0.4919
0.5439
0.2241
0.0043
0.0379
0.2499
-0.0342
0.1960
refined
6.3693
-0.7713
24.8018
X-RAY DIFFRACTION
-9.1722
-22.2466
-13.2270
21.3942
-26.4130
109.1286
-0.2350
0.2918
0.1452
0.5085
-0.2768
0.5082
-0.2947
0.1974
0.5119
0.1606
-0.0568
-0.0007
0.2508
-0.0243
0.2377
refined
3.0774
2.5364
23.1817
X-RAY DIFFRACTION
-37.0645
6.1146
18.2591
2.3341
16.3855
-18.4106
-0.7110
-0.6349
-0.1565
-0.3906
0.6335
-0.2130
1.2969
0.6083
0.0775
0.3833
0.0119
0.0861
0.1887
0.0383
0.2222
refined
2.8543
-2.5424
28.9653
X-RAY DIFFRACTION
6.8665
3.6303
15.8893
2.6342
-7.4169
-0.0140
-0.2463
0.2643
-0.1261
0.0614
0.3957
-0.1924
0.2585
0.7660
-0.1493
0.2269
-0.0339
0.0229
0.2339
0.0085
0.2251
refined
0.1425
0.6967
25.7545
X-RAY DIFFRACTION
-10.1660
-2.5773
7.4818
-24.2274
8.3416
47.9807
-0.7835
0.0564
-0.3690
0.1475
0.1313
-0.0198
0.1707
-0.6070
0.6523
0.2729
-0.0380
0.0321
0.2531
0.0577
0.1649
refined
-1.2412
-0.5688
33.1204
X-RAY DIFFRACTION
-3.7392
7.7900
1.0676
30.5541
-26.9825
50.4288
-0.3723
-0.0949
-0.3595
-0.0542
0.4762
0.6386
0.6481
-0.4029
-0.1039
0.1950
-0.0334
-0.0068
0.2160
0.0024
0.2190
refined
-3.0786
0.1943
28.2931
X-RAY DIFFRACTION
-16.0032
6.9011
-13.9362
3.4182
23.8670
-96.1209
-2.1464
-1.5257
-1.1615
0.8624
1.5533
0.4565
-1.0846
-0.7243
0.5931
0.3068
0.0557
0.0141
0.3860
0.0562
0.1338
refined
-6.1684
2.4174
33.3546
X-RAY DIFFRACTION
-1.2355
-39.6528
-24.7245
185.3272
12.4874
-7.8355
-0.2890
0.0847
0.0267
0.7800
0.0739
-0.8428
0.6503
-0.3484
0.2151
0.1800
-0.0669
-0.0044
0.2647
0.0120
0.2290
refined
-6.3392
-0.7438
29.3206
X-RAY DIFFRACTION
22.5462
-13.5500
36.6988
99.1579
-0.6837
8.0557
-1.0118
-1.1386
0.1943
0.1334
1.5176
0.0263
-1.2568
-0.3291
-0.5059
0.0939
-0.0736
0.0032
0.3073
-0.0715
0.1915
refined
-10.6693
5.5166
30.8363
X-RAY DIFFRACTION
5.0488
-44.3188
-17.9444
92.0636
17.8953
86.4322
-0.0407
0.0734
-0.1095
-0.0767
0.0550
0.1749
-0.0788
-0.5013
-0.0143
0.0834
-0.0804
-0.0113
0.2167
-0.0094
0.2562
refined
-10.5029
1.0916
28.2487
X-RAY DIFFRACTION
27.1955
-26.8394
0.6267
-39.9019
-40.7519
-26.2738
-1.2519
-0.8863
0.0119
-0.4573
-0.1782
2.2497
-0.9802
-0.0979
1.4300
0.1979
-0.0634
-0.0548
0.1369
-0.0060
0.3987
refined
-14.4433
6.1379
26.3795
X-RAY DIFFRACTION
-17.6817
14.6612
-32.7067
22.6536
30.3165
107.1232
0.1292
-0.5096
0.0630
-0.4661
-0.2052
-0.4721
0.0036
-0.3136
0.0760
0.1066
-0.0720
0.0047
0.2026
-0.0243
0.2755
refined
-14.2913
1.3489
27.6848
X-RAY DIFFRACTION
59.6155
71.8881
-9.6549
162.2134
1.5461
-42.6892
-1.4804
1.4455
0.7564
2.2728
1.3931
0.4064
-0.9413
0.3748
0.0873
0.3146
-0.1756
-0.0833
0.2856
0.0802
0.1667
refined
-18.0137
3.7555
22.4572
X-RAY DIFFRACTION
8.2776
-19.7388
-2.8114
38.3785
-3.8300
61.2367
-0.2251
-0.2312
0.4469
-0.2035
-0.3202
-0.1867
0.2207
0.3154
0.5453
0.1741
-0.0832
-0.0243
0.2198
0.0199
0.2443
refined
-18.3580
1.1795
26.6899
X-RAY DIFFRACTION
-41.0798
-31.7196
-17.0197
63.5557
23.7012
57.0608
0.2935
1.0608
0.2487
-0.3870
-1.3218
0.5709
0.6020
-0.2607
1.0284
0.1749
-0.1084
0.0053
0.3344
0.0244
0.1953
refined
-20.1023
-0.5850
19.1224
X-RAY DIFFRACTION
4.4227
-14.3141
11.4269
0.9409
-10.5879
26.3161
0.2848
0.1522
-0.0319
-0.1219
-0.5185
-0.1114
-0.4637
0.5255
0.2337
0.2111
-0.0829
0.0173
0.2290
0.0155
0.2570
refined
-21.0493
-1.6655
24.0961
X-RAY DIFFRACTION
3.6290
-36.9332
-21.0067
58.3032
9.8516
10.7368
0.5185
-0.5715
0.4547
-2.2513
-0.8048
1.4123
0.7825
0.6165
0.2863
0.2532
-0.0615
-0.0166
0.2330
-0.0118
0.1486
refined
-21.5352
-6.4913
17.9436
X-RAY DIFFRACTION
10.6415
-10.2606
4.4836
13.8311
4.8193
45.4219
0.2459
0.0988
0.2733
-0.1429
-0.3695
0.1657
0.2110
0.1296
0.1236
0.1695
-0.0821
0.0259
0.2139
0.0025
0.2417
refined
-23.6308
-4.6187
22.2279
X-RAY DIFFRACTION
A
1
A
1
A
1
A
1
X-RAY DIFFRACTION
1
A
1
A
1
A
1
A
1
X-RAY DIFFRACTION
2
A
2
A
2
A
2
A
2
X-RAY DIFFRACTION
3
A
2
A
2
A
2
A
2
X-RAY DIFFRACTION
4
A
3
A
3
A
3
A
3
X-RAY DIFFRACTION
5
A
3
A
3
A
3
A
3
X-RAY DIFFRACTION
6
A
4
A
4
A
4
A
4
X-RAY DIFFRACTION
7
A
4
A
4
A
4
A
4
X-RAY DIFFRACTION
8
A
5
A
5
A
5
A
5
X-RAY DIFFRACTION
9
A
5
A
5
A
5
A
5
X-RAY DIFFRACTION
10
A
6
A
6
A
6
A
6
X-RAY DIFFRACTION
11
A
6
A
6
A
6
A
6
X-RAY DIFFRACTION
12
A
7
A
7
A
7
A
7
X-RAY DIFFRACTION
13
A
7
A
7
A
7
A
7
X-RAY DIFFRACTION
14
A
8
A
8
A
8
A
8
X-RAY DIFFRACTION
15
A
8
A
8
A
8
A
8
X-RAY DIFFRACTION
16
A
9
A
9
A
9
A
9
X-RAY DIFFRACTION
17
A
9
A
9
A
9
A
9
X-RAY DIFFRACTION
18
A
10
A
10
A
10
A
10
X-RAY DIFFRACTION
19
A
10
A
10
A
10
A
10
X-RAY DIFFRACTION
20
B
11
B
1
B
11
B
1
X-RAY DIFFRACTION
21
B
11
B
1
B
11
B
1
X-RAY DIFFRACTION
22
B
12
B
2
B
12
B
2
X-RAY DIFFRACTION
23
B
12
B
2
B
12
B
2
X-RAY DIFFRACTION
24
B
13
B
3
B
13
B
3
X-RAY DIFFRACTION
25
B
13
B
3
B
13
B
3
X-RAY DIFFRACTION
26
B
14
B
4
B
14
B
4
X-RAY DIFFRACTION
27
B
14
B
4
B
14
B
4
X-RAY DIFFRACTION
28
B
15
B
5
B
15
B
5
X-RAY DIFFRACTION
29
B
15
B
5
B
15
B
5
X-RAY DIFFRACTION
30
B
16
B
6
B
16
B
6
X-RAY DIFFRACTION
31
B
16
B
6
B
16
B
6
X-RAY DIFFRACTION
32
B
17
B
7
B
17
B
7
X-RAY DIFFRACTION
33
B
17
B
7
B
17
B
7
X-RAY DIFFRACTION
34
B
18
B
8
B
18
B
8
X-RAY DIFFRACTION
35
B
18
B
8
B
18
B
8
X-RAY DIFFRACTION
36
B
19
B
9
B
19
B
9
X-RAY DIFFRACTION
37
B
19
B
9
B
19
B
9
X-RAY DIFFRACTION
38
B
20
B
10
B
20
B
10
X-RAY DIFFRACTION
39
B
20
B
10
B
20
B
10
X-RAY DIFFRACTION
40
author_defined_assembly
4
tetrameric
B
HOH
43
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
44
E
O
HOH
1_555
80.4
B
HOH
43
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
45
E
O
HOH
1_555
114.2
B
HOH
44
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
45
E
O
HOH
1_555
76.0
B
HOH
43
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
46
E
O
HOH
1_555
144.1
B
HOH
44
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
46
E
O
HOH
1_555
74.3
B
HOH
45
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
46
E
O
HOH
1_555
84.0
B
HOH
43
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
81
E
O
HOH
1_555
59.1
B
HOH
44
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
81
E
O
HOH
1_555
138.4
B
HOH
45
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
81
E
O
HOH
1_555
127.0
B
HOH
46
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
81
E
O
HOH
1_555
134.7
B
HOH
43
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
98
E
O
HOH
1_555
76.3
B
HOH
44
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
98
E
O
HOH
1_555
132.3
B
HOH
45
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
98
E
O
HOH
1_555
76.6
B
HOH
46
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
98
E
O
HOH
1_555
139.5
B
HOH
81
E
O
HOH
1_555
B
CA
21
C
CA
CA
1_555
B
HOH
98
E
O
HOH
1_555
50.4
A
5CM
8
A
5CM
8
DC
B
5CM
18
B
5CM
8
DC
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_556
-x,y,-z+1
crystal symmetry operation
-12.6522587768
0.0000000000
34.7429269470
1
A
HOH
108
D
HOH
1
B
HOH
76
E
HOH
1
A
B
O
O
HOH
HOH
70
104
1.76
1
B
B
O
O
HOH
HOH
81
98
1.89
1
A
B
O
O
HOH
HOH
96
50
2.01
1
B
B
OP2
O
DG
HOH
20
82
2.01
1
-8.10
0.80
105.90
97.80
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
1
-4.74
0.70
108.00
103.26
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
-4.96
0.70
108.00
103.04
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
-5.23
0.80
105.90
100.67
B
B
B
O4'
C1'
C2'
DC
DC
DC
12
12
12
N
1
-4.28
0.70
108.00
103.72
B
B
B
O4'
C1'
N1
DC
DC
DC
12
12
12
N
1
-4.43
0.70
108.00
103.57
B
B
B
O4'
C1'
N9
DG
DG
DG
13
13
13
N
1
-5.81
0.70
108.00
102.19
B
B
B
O4'
C1'
N9
DG
DG
DG
14
14
14
N
1
-4.98
0.80
102.40
97.42
B
B
B
C3'
C2'
C1'
DT
DT
DT
15
15
15
N
1
-6.73
0.70
108.00
101.27
B
B
B
O4'
C1'
N9
DA
DA
DA
16
16
16
N
1
-7.28
0.70
108.00
100.72
B
B
B
O4'
C1'
N1
DC
DC
DC
17
17
17
N
0.264
0.218
0.223
0.223
1.5
16.28
852
7986
7986
Random
UNVERIFIED
1
0.0
MOLECULAR REPLACEMENT
G.PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY, A.T. BRUNGER, H.M. BERMAN
1.5
16.28
95
502
3
404
0
0.012
2.08
1.5
16.28
1L6B
7988
7988
0.0
0.0
0.043
1
87.3
0.325
1.5
1.55
39.3
model building
X-PLOR
Custom Script - Real Space translation/rotation/rigid body/rigid part search
refinement
REFMAC
5.0
data reduction
DENZO
data scaling
SCALEPACK
phasing
X-PLOR
CUSTOM SCRIPT - REAL SPACE TRANSLATION/ROTATION/RIGID BODY/RIGID PART SEARCH
CRYSTAL STRUCTURE ANALYSIS OF THE ALL DNA HOLLIDAY JUNCTION STRUCTURE OF CCGGTACM5CGG
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
The second part of the biological assembly is generated by a crystallographic two-fold to give one fully watson-crick basepaired Holliday junction
covale
1.591
both
A
DC
7
A
O3'
DC
7
1_555
A
5CM
8
A
P
5CM
8
1_555
covale
1.598
both
A
5CM
8
A
O3'
5CM
8
1_555
A
DG
9
A
P
DG
9
1_555
covale
1.572
both
B
DC
17
B
O3'
DC
7
1_555
B
5CM
18
B
P
5CM
8
1_555
covale
1.606
both
B
5CM
18
B
O3'
5CM
8
1_555
B
DG
19
B
P
DG
9
1_555
metalc
2.514
B
CA
21
C
CA
CA
1_555
B
HOH
43
E
O
HOH
1_555
metalc
2.427
B
CA
21
C
CA
CA
1_555
B
HOH
44
E
O
HOH
1_555
metalc
2.527
B
CA
21
C
CA
CA
1_555
B
HOH
45
E
O
HOH
1_555
metalc
2.261
B
CA
21
C
CA
CA
1_555
B
HOH
46
E
O
HOH
1_555
metalc
2.121
B
CA
21
C
CA
CA
1_555
B
HOH
81
E
O
HOH
1_555
metalc
2.298
B
CA
21
C
CA
CA
1_555
B
HOH
98
E
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
5CM
18
B
N3
5CM
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
5CM
18
B
O2
5CM
8
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
5CM
18
B
N4
5CM
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, DNA four-way junction, cytosine methylation, DNA
1L6B
PDB
1
1L6B
1
10
1L6B
1
10
1L6B
A
1
1
10
11
20
1L6B
11
20
1L6B
B
1
1
10
BINDING SITE FOR RESIDUE CA B 21
B
CA
21
Software
6
B
HOH
43
E
HOH
6
1_555
B
HOH
44
E
HOH
6
1_555
B
HOH
45
E
HOH
6
1_555
B
HOH
46
E
HOH
6
1_555
B
HOH
81
E
HOH
6
1_555
B
HOH
98
E
HOH
6
1_555
5
C 1 2 1