0.055081
0.000000
0.000000
0.000000
0.033296
0.000000
0.000000
0.000000
0.023816
0.000000
0.000000
0.000000
Schuerman, G.
Van Hecke, K.
Van Meervelt, L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
18.155
30.034
41.988
C9 H12 I N2 O8 P
434.078
n
5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
DNA linking
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
H2 O
18.015
WATER
non-polymer
Co H18 N6 3
161.116
COBALT HEXAMMINE(III)
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
O
N
8
N
O
N
9
N
I
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
O
N
35
N
P
N
36
N
O
N
37
N
O
N
38
N
O
N
39
N
C
N
40
R
C
N
41
N
O
N
42
S
C
N
43
N
O
N
44
N
C
N
45
R
C
Y
46
N
N
Y
47
N
C
Y
48
N
N
Y
49
N
C
Y
50
N
C
N
51
N
N
Y
52
N
N
Y
53
N
C
Y
54
N
N
Y
55
N
C
N
56
N
H
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
O
N
71
N
P
N
72
N
O
N
73
N
O
N
74
N
O
N
75
N
C
N
76
R
C
N
77
N
O
N
78
S
C
N
79
N
O
N
80
N
C
N
81
R
C
N
82
N
N
N
83
N
C
N
84
N
O
N
85
N
N
N
86
N
C
N
87
N
N
N
88
N
C
N
89
N
C
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
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
O
N
105
N
P
N
106
N
O
N
107
N
O
N
108
N
O
N
109
N
C
N
110
R
C
N
111
N
O
N
112
S
C
N
113
N
O
N
114
N
C
N
115
R
C
Y
116
N
N
Y
117
N
C
Y
118
N
N
Y
119
N
C
N
120
N
C
N
121
N
O
N
122
N
N
N
123
N
C
N
124
N
N
N
125
N
N
Y
126
N
C
N
127
N
H
N
128
N
H
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
O
N
142
N
H
N
143
N
H
N
144
N
CO
N
145
N
N
N
146
N
N
N
147
N
N
N
148
N
N
N
149
N
N
N
150
N
N
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
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
sing
N
7
N
sing
N
8
N
sing
N
9
N
doub
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
doub
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
doub
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
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
Y
58
N
sing
Y
59
N
sing
Y
60
N
doub
N
61
N
sing
Y
62
N
sing
Y
63
N
sing
Y
64
N
doub
N
65
N
sing
Y
66
N
doub
N
67
N
sing
N
68
N
sing
Y
69
N
sing
Y
70
N
doub
N
71
N
sing
Y
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
doub
N
76
N
sing
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
N
97
N
sing
N
98
N
doub
N
99
N
sing
N
100
N
doub
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
doub
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
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
Y
131
N
sing
Y
132
N
sing
Y
133
N
doub
N
134
N
sing
Y
135
N
sing
N
136
N
sing
Y
137
N
doub
N
138
N
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
doub
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
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
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
59
1525
1528
10.1107/S0907444903012381
12876373
Exploration of the influence of 5-iodo-2'-deoxyuridine incorporation on the structure of d[CACG(IDU)G].
2003
10.2210/pdb1omk/pdb
pdb_00001omk
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
120.0
1
IMAGE PLATE
1998-05-05
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.000
1.0
X11
EMBL/DESY, HAMBURG
1.000
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X11
1921.087
5'-D(*CP*AP*CP*GP*(5IU)P*G)-3'
2
syn
polymer
161.116
COBALT HEXAMMINE(III)
2
syn
non-polymer
18.015
water
43
nat
water
no
yes
(DC)(DA)(DC)(DG)(5IU)(DG)
CACGUG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
1
1.49
17.43
VAPOR DIFFUSION, HANGING DROP
5.5
potassium cacodylate, MPD, magnesium chloride, potassium chloride, cobalt hexamine , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K
290.0
potassium cacodylate
1
MPD
1
magnesium chloride
1
potassium chloride
1
cobalt hexamine
1
MPD
2
potassium cacodylate
2
magnesium chloride
2
potassium chloride
2
7.594
1
19
A
1
B
12
0.421
A_DC1:DG12_B
1
8.691
-0.241
0.334
-0.135
-8.547
1
20
A
2
B
11
-1.784
A_DA2:5IU11_B
2
2.578
0.342
0.147
-0.289
1.492
1
19
A
3
B
10
1.479
A_DC3:DG10_B
3
2.474
-0.290
0.214
-0.191
-4.181
1
19
A
4
B
9
0.383
A_DG4:DC9_B
4
1.754
0.305
0.068
-0.167
-3.893
1
20
A
5
B
8
-0.413
A_5IU5:DA8_B
5
1.599
-0.094
-0.209
-0.134
2.572
1
19
A
6
B
7
0.707
A_DG6:DC7_B
6
-2.664
0.283
0.086
-0.162
2.301
-14.951
A
A
1
2
-16.486
B
B
12
11
4.055
4.218
-0.290
5.670
AA_DC1DA2:5IU11DG12_BB
1
2.058
8.044
-14.200
-25.305
0.600
3.211
-49.259
A
A
2
3
1.097
B
B
11
10
3.213
-0.914
0.344
-0.686
AA_DA2DC3:DG105IU11_BB
2
-2.123
-2.547
-49.208
0.891
0.257
4.012
-9.851
A
A
3
4
4.527
B
B
10
9
3.615
-0.776
-0.037
5.215
AA_DC3DG4:DC9DG10_BB
3
0.431
2.514
-9.811
-28.620
0.755
3.241
-42.976
A
A
4
5
3.545
B
B
9
8
3.395
-2.591
0.282
-1.796
AA_DG45IU5:DA8DC9_BB
4
4.515
6.177
-42.674
2.712
0.840
3.494
-12.366
A
A
5
6
5.291
B
B
8
7
3.176
-1.123
-0.106
5.326
AA_5IU5DG6:DC7DA8_BB
5
-3.406
-16.042
-11.836
-23.293
-4.833
software
chem_comp_atom
chem_comp_bond
database_2
diffrn_source
struct_conn
struct_site
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2003-11-04
1
1
2008-04-29
1
2
2011-07-13
1
3
2017-10-11
1
4
2024-02-14
1
5
2024-04-03
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_diffrn_source.pdbx_synchrotron_site
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2003-02-25
REL
REL
NCO
COBALT HEXAMMINE(III)
HOH
water
THE OLIGONUCLEOTIDE WAS SYNTHESIZED BY THE REGA-INSTITUTE KULEUVEN
sample
242D
NDB ENTRY ZDFB51
PDB
experimental model
NCO
30
2
NCO
NCO
30
A
NCO
31
2
NCO
NCO
31
A
HOH
101
3
HOH
HOH
101
A
HOH
102
3
HOH
HOH
102
A
HOH
103
3
HOH
HOH
103
A
HOH
105
3
HOH
HOH
105
A
HOH
106
3
HOH
HOH
106
A
HOH
109
3
HOH
HOH
109
A
HOH
111
3
HOH
HOH
111
A
HOH
112
3
HOH
HOH
112
A
HOH
114
3
HOH
HOH
114
A
HOH
115
3
HOH
HOH
115
A
HOH
120
3
HOH
HOH
120
A
HOH
121
3
HOH
HOH
121
A
HOH
123
3
HOH
HOH
123
A
HOH
124
3
HOH
HOH
124
A
HOH
125
3
HOH
HOH
125
A
HOH
129
3
HOH
HOH
129
A
HOH
130
3
HOH
HOH
130
A
HOH
132
3
HOH
HOH
132
A
HOH
133
3
HOH
HOH
133
A
HOH
134
3
HOH
HOH
134
A
HOH
137
3
HOH
HOH
137
A
HOH
140
3
HOH
HOH
140
A
HOH
143
3
HOH
HOH
143
A
HOH
104
3
HOH
HOH
104
B
HOH
107
3
HOH
HOH
107
B
HOH
108
3
HOH
HOH
108
B
HOH
110
3
HOH
HOH
110
B
HOH
113
3
HOH
HOH
113
B
HOH
116
3
HOH
HOH
116
B
HOH
117
3
HOH
HOH
117
B
HOH
118
3
HOH
HOH
118
B
HOH
119
3
HOH
HOH
119
B
HOH
122
3
HOH
HOH
122
B
HOH
126
3
HOH
HOH
126
B
HOH
127
3
HOH
HOH
127
B
HOH
128
3
HOH
HOH
128
B
HOH
131
3
HOH
HOH
131
B
HOH
135
3
HOH
HOH
135
B
HOH
136
3
HOH
HOH
136
B
HOH
138
3
HOH
HOH
138
B
HOH
139
3
HOH
HOH
139
B
HOH
141
3
HOH
HOH
141
B
HOH
142
3
HOH
HOH
142
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
+U
5
n
5
5IU
5
A
G
6
n
6
DG
6
A
C
7
n
1
DC
7
B
A
8
n
2
DA
8
B
C
9
n
3
DC
9
B
G
10
n
4
DG
10
B
+U
11
n
5
5IU
11
B
G
12
n
6
DG
12
B
0.159
0.167
5036
author_defined_assembly
2
dimeric
A
5IU
5
5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
A
5IU
5
DU
B
5IU
11
5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
B
5IU
5
DU
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
-4.82
0.80
109.40
104.58
A
A
A
O5'
C5'
C4'
DC
DC
DC
1
1
1
N
1
-8.14
0.80
109.40
101.26
A
A
A
O5'
C5'
C4'
DA
DA
DA
2
2
2
N
1
-5.07
0.70
108.00
102.93
A
A
A
O4'
C1'
N9
DA
DA
DA
2
2
2
N
1
-4.06
0.60
118.90
114.84
A
A
A
N1
C2
O2
DC
DC
DC
3
3
3
N
1
4.58
0.70
121.90
126.48
A
A
A
N3
C2
O2
DC
DC
DC
3
3
3
N
1
3.02
0.50
111.90
114.92
A
A
A
C2
N3
C4
DG
DG
DG
4
4
4
N
1
3.06
0.50
113.10
116.16
A
A
A
N7
C8
N9
DG
DG
DG
4
4
4
N
1
-5.69
0.70
108.00
102.31
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
-5.40
0.80
105.90
100.50
B
B
B
O4'
C1'
C2'
DC
DC
DC
7
7
7
N
1
3.57
0.50
121.00
124.57
B
B
B
C5
C6
N1
DC
DC
DC
7
7
7
N
1
-4.16
0.40
104.50
100.34
B
B
B
O4'
C4'
C3'
DA
DA
DA
8
8
8
N
1
-6.30
0.70
108.00
101.70
B
B
B
O4'
C1'
N9
DA
DA
DA
8
8
8
N
1
4.23
0.60
118.60
122.83
B
B
B
N1
C6
N6
DA
DA
DA
8
8
8
N
1
10.97
1.60
120.90
131.87
B
B
B
P
O5'
C5'
DC
DC
DC
9
9
9
N
1
-5.05
0.70
108.00
102.95
B
B
B
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
3.39
0.50
111.90
115.29
B
B
B
C2
N3
C4
DG
DG
DG
10
10
10
N
1
4.41
0.70
119.90
124.31
B
B
B
N3
C2
N2
DG
DG
DG
10
10
10
N
1
8.25
1.20
119.70
127.95
B
B
B
C3'
O3'
P
DG
DG
5IU
10
10
11
Y
1
7.53
1.10
110.50
118.03
B
B
B
O3'
P
OP2
DG
5IU
5IU
10
11
11
Y
1
-4.84
0.70
108.00
103.16
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
-5.63
0.60
125.10
119.47
B
B
B
C6
N1
C2
DG
DG
DG
12
12
12
N
1
-3.36
0.50
128.60
125.24
B
B
B
N3
C4
C5
DG
DG
DG
12
12
12
N
1
3.65
0.50
111.50
115.15
B
B
B
C5
C6
N1
DG
DG
DG
12
12
12
N
1
B
B
P
O5'
DG
DG
10
10
0.073
0.010
1.593
1.666
N
The iodo atoms are refined anisotropically
1.30
20.0
5988
5036
98.2
1
Isotropic
4.0
MOLECULAR REPLACEMENT
NDB ENTRY ZDFB51
1.30
20.0
43
297
14
240
0
22.5
1.30
20.0
1OMK
6103
5988
0.062
1
22.9
98.2
0.165
1.30
1.35
903
98.8
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
refinement
SHELXL
The Crystal Structure of d(CACG(5IU)G)
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
covale
1.591
both
A
DG
4
A
O3'
DG
4
1_555
A
5IU
5
A
P
5IU
5
1_555
covale
1.628
both
A
5IU
5
A
O3'
5IU
5
1_555
A
DG
6
A
P
DG
6
1_555
covale
1.577
both
B
DG
10
B
O3'
DG
4
1_555
B
5IU
11
B
P
5IU
5
1_555
covale
1.629
both
B
5IU
11
B
O3'
5IU
5
1_555
B
DG
12
B
P
DG
6
1_555
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
5IU
11
B
N3
5IU
5
1_555
hydrog
WATSON-CRICK
A
DA
2
A
N6
DA
2
1_555
B
5IU
11
B
O4
5IU
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
5IU
5
A
N3
5IU
5
1_555
B
DA
8
B
N1
DA
2
1_555
hydrog
WATSON-CRICK
A
5IU
5
A
O4
5IU
5
1_555
B
DA
8
B
N6
DA
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, 5-IODO-2'-DEOXYURIDINE, DNA
1OMK
PDB
1
1OMK
1
6
1OMK
1
6
1OMK
A
1
1
6
7
12
1OMK
7
12
1OMK
B
1
1
6
BINDING SITE FOR RESIDUE NCO A 30
A
NCO
30
Software
8
BINDING SITE FOR RESIDUE NCO A 31
A
NCO
31
Software
7
A
DC
3
A
DC
3
8
1_455
A
DG
4
A
DG
4
8
1_455
A
DG
4
A
DG
4
8
4_465
A
5IU
5
A
5IU
5
8
4_465
A
DG
6
A
DG
6
8
1_555
A
HOH
102
E
HOH
8
1_455
A
HOH
134
E
HOH
8
1_555
B
DG
10
B
DG
4
8
1_555
A
DG
4
A
DG
4
7
4_565
A
DG
6
A
DG
6
7
1_555
A
HOH
106
E
HOH
7
4_565
A
HOH
109
E
HOH
7
4_565
A
HOH
130
E
HOH
7
4_565
B
DG
12
B
DG
6
7
4_565
B
DG
12
B
DG
6
7
2_564
19
P 21 21 21