0.039562
0.000000
0.000000
0.000000
0.024950
0.000000
0.000000
0.000000
0.015184
0.000000
0.000000
0.000000
Wilds, C.J.
Wawrzak, Z.
Krishnamurthy, R.
Eschenmoser, A.
Egli, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
25.277
40.080
65.860
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
C9 H13 N2 O8 P
308.182
n
(L)-ALPHA-THREOFURANOSYL-THYMINE-3'-MONOPHOSPHATE
DNA linking
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
148
N
P
N
149
N
O
N
150
N
O
N
151
N
O
N
152
N
N
N
153
N
C
N
154
N
C
N
155
N
O
N
156
N
N
N
157
N
C
N
158
N
O
N
159
N
C
N
160
N
C
N
161
R
C
N
162
N
C
N
163
N
O
N
164
R
C
N
165
S
C
N
166
N
O
N
167
N
O
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
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
N
152
N
doub
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
doub
N
162
N
sing
N
163
N
doub
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
doub
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
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
124
13716
13721
10.1021/ja0207807
12431101
Crystal Structure of a B-Form DNA Duplex Containing (L)-alpha-Threofuranosyl (3'-->2') Nucleosides: A
Four-Carbon Sugar Is Easily Accommodated into the Backbone of DNA
2002
10.2210/pdb1n1o/pdb
pdb_00001n1o
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
1
CCD
2001-02-20
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
0.978
1.0
5ID-B
APS
0.978
SYNCHROTRON
APS BEAMLINE 5ID-B
Dickerson-Drew dodecamer duplex
3649.366
5'-D(*CP*GP*CP*GP*AP*AP*(TFT)P*TP*CP*GP*CP*G)-3'
2
syn
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
197
nat
water
no
yes
(DC)(DG)(DC)(DG)(DA)(DA)(TFT)(DT)(DC)(DG)(DC)(DG)
CGCGAATTCGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
1
1.75
29.04
VAPOR DIFFUSION, SITTING DROP
7
oligonucleotide, sodium cacodylate, magnesium acetate, spermine tetrahydrochloride, 2-methyl-2,4-pentanediol (MPD), pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
oligonucleotide
1
sodium cacodylate
1
magnesium acetate
1
spermine tetrahydrochloride
1
MPD
1
MPD
2
4.713
1
19
A
1
B
124
-0.442
A_DC1:DG124_B
1
-13.772
0.218
0.115
-0.106
6.936
1
19
A
2
B
123
-2.598
A_DG2:DC123_B
2
-11.760
-0.178
0.446
-0.176
-4.299
1
19
A
3
B
122
-0.681
A_DC3:DG122_B
3
-4.342
0.147
0.176
-0.175
12.715
1
19
A
4
B
121
0.581
A_DG4:DC121_B
4
-7.773
-0.224
0.039
-0.066
10.520
1
20
A
5
B
120
4.520
A_DA5:DT120_B
5
-12.652
-0.070
0.006
-0.102
5.108
1
20
A
6
B
119
1.042
A_DA6:TFT119_B
6
-15.361
0.200
0.021
-0.040
-0.110
1
20
A
7
B
118
2.172
A_TFT7:DA118_B
7
-15.226
-0.116
0.051
-0.116
-1.918
1
20
A
8
B
117
3.586
A_DT8:DA117_B
8
-12.344
-0.028
-0.088
-0.148
-13.576
1
19
A
9
B
116
-1.593
A_DC9:DG116_B
9
-7.098
0.232
0.124
-0.111
5.561
1
19
A
10
B
115
2.149
A_DG10:DC115_B
10
-6.742
-0.149
0.273
-0.105
0.884
1
19
A
11
B
114
-2.131
A_DC11:DG114_B
11
-15.718
0.126
0.213
-0.177
4.294
1
19
A
12
B
113
-0.990
A_DG12:DC113_B
12
-5.894
-0.280
0.306
-0.132
3.194
34.893
A
A
1
2
8.714
B
B
124
123
3.232
5.203
0.099
0.067
AA_DC1DG2:DC123DG124_BB
1
-2.414
4.042
34.432
-0.668
-0.527
3.526
43.109
A
A
2
3
-9.256
B
B
123
122
3.605
-6.771
0.588
0.453
AA_DG2DC3:DG122DC123_BB
2
2.849
-3.895
42.508
1.348
-0.492
3.004
27.922
A
A
3
4
19.694
B
B
122
121
3.008
9.321
-0.221
0.552
AA_DC3DG4:DC121DG122_BB
3
1.683
-3.556
26.296
-0.958
0.839
3.295
35.117
A
A
4
5
3.983
B
B
121
120
3.317
2.402
-0.102
-0.239
AA_DG4DA5:DT120DC121_BB
4
-0.548
0.909
35.034
-0.759
0.086
3.295
37.448
A
A
5
6
4.860
B
B
120
119
3.356
3.117
0.077
-0.607
AA_DA5DA6:TFT119DT120_BB
5
-0.657
1.025
37.318
-1.362
-0.207
3.350
33.179
A
A
6
7
-8.542
B
B
119
118
3.345
-4.861
0.127
-0.281
AA_DA6TFT7:DA118TFT119_BB
6
-0.235
0.413
32.830
0.348
-0.263
3.228
35.207
A
A
7
8
0.703
B
B
118
117
3.241
0.425
-0.124
-0.419
AA_TFT7DT8:DA117DA118_BB
7
1.444
-2.388
35.176
-0.755
0.417
3.517
42.815
A
A
8
9
-1.284
B
B
117
116
3.507
-0.937
-0.306
-0.363
AA_DT8DC9:DG116DA117_BB
8
-0.595
0.815
42.801
-0.396
0.356
2.923
25.820
A
A
9
10
5.715
B
B
116
115
2.962
2.544
0.615
0.728
AA_DC9DG10:DC115DG116_BB
9
-3.162
7.105
25.505
0.986
-2.174
3.315
43.700
A
A
10
11
-12.624
B
B
115
114
3.423
-9.327
-1.256
0.480
AA_DG10DC11:DG114DC115_BB
10
-2.394
3.241
42.677
1.576
1.448
3.202
33.026
A
A
11
12
8.486
B
B
114
113
3.196
4.807
-0.129
0.253
AA_DC11DG12:DC113DG114_BB
11
-1.110
1.959
32.666
-0.356
0.041
software
software
struct_conn
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Derived calculations
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2002-11-15
1
1
2008-04-28
1
2
2011-07-13
1
3
2017-10-11
1
4
2019-07-24
1
5
2024-02-14
1
6
2024-04-03
_software.classification
_software.name
_struct_conn.pdbx_leaving_atom_flag
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_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.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.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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2002-10-18
REL
REL
MG
MAGNESIUM ION
HOH
water
solid phase oligonucleotide synthesis was used.
sample
B-form DNA (native Dickerson-Drew dodecamer)
Other
experimental model
MG
901
2
MG
MG
901
A
TIP
701
3
HOH
HOH
701
A
TIP
702
3
HOH
HOH
702
A
TIP
703
3
HOH
HOH
703
A
TIP
705
3
HOH
HOH
705
A
TIP
707
3
HOH
HOH
707
A
TIP
709
3
HOH
HOH
709
A
TIP
710
3
HOH
HOH
710
A
TIP
711
3
HOH
HOH
711
A
TIP
716
3
HOH
HOH
716
A
TIP
718
3
HOH
HOH
718
A
TIP
719
3
HOH
HOH
719
A
TIP
721
3
HOH
HOH
721
A
TIP
723
3
HOH
HOH
723
A
TIP
724
3
HOH
HOH
724
A
TIP
725
3
HOH
HOH
725
A
TIP
726
3
HOH
HOH
726
A
TIP
728
3
HOH
HOH
728
A
TIP
731
3
HOH
HOH
731
A
TIP
734
3
HOH
HOH
734
A
TIP
737
3
HOH
HOH
737
A
TIP
740
3
HOH
HOH
740
A
TIP
743
3
HOH
HOH
743
A
TIP
744
3
HOH
HOH
744
A
TIP
745
3
HOH
HOH
745
A
TIP
747
3
HOH
HOH
747
A
TIP
750
3
HOH
HOH
750
A
TIP
751
3
HOH
HOH
751
A
TIP
754
3
HOH
HOH
754
A
TIP
757
3
HOH
HOH
757
A
TIP
764
3
HOH
HOH
764
A
TIP
766
3
HOH
HOH
766
A
TIP
773
3
HOH
HOH
773
A
TIP
775
3
HOH
HOH
775
A
TIP
778
3
HOH
HOH
778
A
TIP
780
3
HOH
HOH
780
A
TIP
783
3
HOH
HOH
783
A
TIP
788
3
HOH
HOH
788
A
TIP
789
3
HOH
HOH
789
A
TIP
790
3
HOH
HOH
790
A
TIP
791
3
HOH
HOH
791
A
TIP
796
3
HOH
HOH
796
A
TIP
800
3
HOH
HOH
800
A
TIP
801
3
HOH
HOH
801
A
TIP
802
3
HOH
HOH
802
A
TIP
805
3
HOH
HOH
805
A
TIP
808
3
HOH
HOH
808
A
TIP
809
3
HOH
HOH
809
A
TIP
814
3
HOH
HOH
814
A
TIP
815
3
HOH
HOH
815
A
TIP
817
3
HOH
HOH
817
A
TIP
820
3
HOH
HOH
820
A
TIP
821
3
HOH
HOH
821
A
TIP
824
3
HOH
HOH
824
A
TIP
830
3
HOH
HOH
830
A
TIP
831
3
HOH
HOH
831
A
TIP
833
3
HOH
HOH
833
A
TIP
834
3
HOH
HOH
834
A
TIP
838
3
HOH
HOH
838
A
TIP
839
3
HOH
HOH
839
A
TIP
840
3
HOH
HOH
840
A
TIP
841
3
HOH
HOH
841
A
TIP
849
3
HOH
HOH
849
A
TIP
851
3
HOH
HOH
851
A
TIP
852
3
HOH
HOH
852
A
TIP
860
3
HOH
HOH
860
A
TIP
861
3
HOH
HOH
861
A
TIP
863
3
HOH
HOH
863
A
TIP
866
3
HOH
HOH
866
A
TIP
867
3
HOH
HOH
867
A
TIP
869
3
HOH
HOH
869
A
TIP
871
3
HOH
HOH
871
A
TIP
872
3
HOH
HOH
872
A
TIP
873
3
HOH
HOH
873
A
TIP
875
3
HOH
HOH
875
A
TIP
876
3
HOH
HOH
876
A
TIP
878
3
HOH
HOH
878
A
TIP
879
3
HOH
HOH
879
A
TIP
882
3
HOH
HOH
882
A
TIP
887
3
HOH
HOH
887
A
TIP
888
3
HOH
HOH
888
A
TIP
890
3
HOH
HOH
890
A
TIP
892
3
HOH
HOH
892
A
TIP
893
3
HOH
HOH
893
A
TIP
898
3
HOH
HOH
898
A
TIP
900
3
HOH
HOH
900
A
TIP
902
3
HOH
HOH
902
A
TIP
903
3
HOH
HOH
903
A
TIP
905
3
HOH
HOH
905
A
TIP
906
3
HOH
HOH
906
A
TIP
911
3
HOH
HOH
911
A
TIP
912
3
HOH
HOH
912
A
TIP
913
3
HOH
HOH
913
A
TIP
914
3
HOH
HOH
914
A
TIP
917
3
HOH
HOH
917
A
TIP
918
3
HOH
HOH
918
A
TIP
920
3
HOH
HOH
920
A
TIP
924
3
HOH
HOH
924
A
TIP
925
3
HOH
HOH
925
A
TIP
927
3
HOH
HOH
927
A
TIP
931
3
HOH
HOH
931
A
TIP
936
3
HOH
HOH
936
A
TIP
937
3
HOH
HOH
937
A
TIP
939
3
HOH
HOH
939
A
TIP
943
3
HOH
HOH
943
A
TIP
949
3
HOH
HOH
949
A
TIP
950
3
HOH
HOH
950
A
TIP
706
3
HOH
HOH
706
B
TIP
708
3
HOH
HOH
708
B
TIP
712
3
HOH
HOH
712
B
TIP
713
3
HOH
HOH
713
B
TIP
714
3
HOH
HOH
714
B
TIP
715
3
HOH
HOH
715
B
TIP
717
3
HOH
HOH
717
B
TIP
720
3
HOH
HOH
720
B
TIP
727
3
HOH
HOH
727
B
TIP
729
3
HOH
HOH
729
B
TIP
730
3
HOH
HOH
730
B
TIP
733
3
HOH
HOH
733
B
TIP
735
3
HOH
HOH
735
B
TIP
738
3
HOH
HOH
738
B
TIP
741
3
HOH
HOH
741
B
TIP
742
3
HOH
HOH
742
B
TIP
746
3
HOH
HOH
746
B
TIP
748
3
HOH
HOH
748
B
TIP
749
3
HOH
HOH
749
B
TIP
753
3
HOH
HOH
753
B
TIP
755
3
HOH
HOH
755
B
TIP
758
3
HOH
HOH
758
B
TIP
759
3
HOH
HOH
759
B
TIP
760
3
HOH
HOH
760
B
TIP
761
3
HOH
HOH
761
B
TIP
763
3
HOH
HOH
763
B
TIP
765
3
HOH
HOH
765
B
TIP
769
3
HOH
HOH
769
B
TIP
772
3
HOH
HOH
772
B
TIP
774
3
HOH
HOH
774
B
TIP
776
3
HOH
HOH
776
B
TIP
777
3
HOH
HOH
777
B
TIP
782
3
HOH
HOH
782
B
TIP
784
3
HOH
HOH
784
B
TIP
787
3
HOH
HOH
787
B
TIP
792
3
HOH
HOH
792
B
TIP
797
3
HOH
HOH
797
B
TIP
798
3
HOH
HOH
798
B
TIP
799
3
HOH
HOH
799
B
TIP
803
3
HOH
HOH
803
B
TIP
804
3
HOH
HOH
804
B
TIP
806
3
HOH
HOH
806
B
TIP
807
3
HOH
HOH
807
B
TIP
810
3
HOH
HOH
810
B
TIP
811
3
HOH
HOH
811
B
TIP
812
3
HOH
HOH
812
B
TIP
813
3
HOH
HOH
813
B
TIP
819
3
HOH
HOH
819
B
TIP
822
3
HOH
HOH
822
B
TIP
823
3
HOH
HOH
823
B
TIP
832
3
HOH
HOH
832
B
TIP
835
3
HOH
HOH
835
B
TIP
837
3
HOH
HOH
837
B
TIP
843
3
HOH
HOH
843
B
TIP
846
3
HOH
HOH
846
B
TIP
847
3
HOH
HOH
847
B
TIP
848
3
HOH
HOH
848
B
TIP
850
3
HOH
HOH
850
B
TIP
854
3
HOH
HOH
854
B
TIP
855
3
HOH
HOH
855
B
TIP
858
3
HOH
HOH
858
B
TIP
859
3
HOH
HOH
859
B
TIP
862
3
HOH
HOH
862
B
TIP
865
3
HOH
HOH
865
B
TIP
868
3
HOH
HOH
868
B
TIP
870
3
HOH
HOH
870
B
TIP
874
3
HOH
HOH
874
B
TIP
877
3
HOH
HOH
877
B
TIP
880
3
HOH
HOH
880
B
TIP
884
3
HOH
HOH
884
B
TIP
885
3
HOH
HOH
885
B
TIP
889
3
HOH
HOH
889
B
TIP
891
3
HOH
HOH
891
B
TIP
895
3
HOH
HOH
895
B
TIP
899
3
HOH
HOH
899
B
TIP
907
3
HOH
HOH
907
B
TIP
908
3
HOH
HOH
908
B
TIP
909
3
HOH
HOH
909
B
TIP
910
3
HOH
HOH
910
B
TIP
916
3
HOH
HOH
916
B
TIP
919
3
HOH
HOH
919
B
TIP
921
3
HOH
HOH
921
B
TIP
922
3
HOH
HOH
922
B
TIP
928
3
HOH
HOH
928
B
TIP
933
3
HOH
HOH
933
B
TIP
935
3
HOH
HOH
935
B
TIP
938
3
HOH
HOH
938
B
TIP
941
3
HOH
HOH
941
B
TIP
942
3
HOH
HOH
942
B
TIP
945
3
HOH
HOH
945
B
TIP
952
3
HOH
HOH
952
B
CYT
1
n
1
DC
1
A
GUA
2
n
2
DG
2
A
CYT
3
n
3
DC
3
A
GUA
4
n
4
DG
4
A
ADE
5
n
5
DA
5
A
ADE
6
n
6
DA
6
A
THT
7
n
7
TFT
7
A
THY
8
n
8
DT
8
A
CYT
9
n
9
DC
9
A
GUA
10
n
10
DG
10
A
CYT
11
n
11
DC
11
A
GUA
12
n
12
DG
12
A
CYT
113
n
1
DC
113
B
GUA
114
n
2
DG
114
B
CYT
115
n
3
DC
115
B
GUA
116
n
4
DG
116
B
ADE
117
n
5
DA
117
B
ADE
118
n
6
DA
118
B
THT
119
n
7
TFT
119
B
THY
120
n
8
DT
120
B
CYT
121
n
9
DC
121
B
GUA
122
n
10
DG
122
B
CYT
123
n
11
DC
123
B
GUA
124
n
12
DG
124
B
0.156
0.16
0.156
0.16
0.198
0.2
1866
2130
5.0
5.0
18649
21311
author_defined_assembly
2
dimeric
A
HOH
702
D
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
A
HOH
705
D
O
HOH
1_555
92.4
A
HOH
702
D
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
706
E
O
HOH
1_555
174.8
A
HOH
705
D
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
706
E
O
HOH
1_555
88.6
A
HOH
702
D
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
708
E
O
HOH
1_555
94.0
A
HOH
705
D
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
708
E
O
HOH
1_555
86.2
B
HOH
706
E
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
708
E
O
HOH
1_555
91.1
A
HOH
702
D
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
715
E
O
HOH
1_555
89.9
A
HOH
705
D
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
715
E
O
HOH
1_555
91.5
B
HOH
706
E
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
715
E
O
HOH
1_555
85.1
B
HOH
708
E
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
715
E
O
HOH
1_555
175.5
A
HOH
702
D
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
720
E
O
HOH
1_555
88.6
A
HOH
705
D
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
720
E
O
HOH
1_555
174.9
B
HOH
706
E
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
720
E
O
HOH
1_555
90.8
B
HOH
708
E
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
720
E
O
HOH
1_555
88.8
B
HOH
715
E
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
B
HOH
720
E
O
HOH
1_555
93.5
A
TFT
7
A
TFT
7
DT
B
TFT
119
B
TFT
7
DT
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
4.01
0.60
106.00
110.01
A
A
A
O4'
C4'
C3'
DC
DC
DC
1
1
1
N
1
8.96
1.40
114.30
123.26
A
A
A
N1
C1'
C2'
DC
DC
DC
1
1
1
N
1
9.15
1.50
119.60
128.75
A
A
A
OP1
P
OP2
DG
DG
DG
2
2
2
N
1
-5.55
0.70
108.00
102.45
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
1.82
0.30
108.30
110.12
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
-4.26
0.70
108.00
103.74
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
11.93
1.40
114.30
126.23
A
A
A
N1
C1'
C2'
DC
DC
DC
9
9
9
N
1
-10.85
0.70
108.00
97.15
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
10.88
1.40
114.30
125.18
A
A
A
N1
C1'
C2'
DC
DC
DC
11
11
11
N
1
-9.08
0.70
108.00
98.92
A
A
A
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
-8.07
0.70
108.00
99.93
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
-4.46
0.70
108.00
103.54
B
B
B
O4'
C1'
N1
DC
DC
DC
113
113
113
N
1
-4.21
0.70
108.00
103.79
B
B
B
O4'
C1'
N9
DG
DG
DG
114
114
114
N
1
-7.27
0.70
108.00
100.73
B
B
B
O4'
C1'
N1
DC
DC
DC
115
115
115
N
1
4.73
0.30
108.30
113.03
B
B
B
O4'
C1'
N9
DG
DG
DG
116
116
116
N
1
9.23
1.20
119.70
128.93
B
B
B
C3'
O3'
P
DG
DG
DA
116
116
117
Y
1
-7.23
0.70
108.00
100.77
B
B
B
O4'
C1'
N9
DA
DA
DA
117
117
117
N
1
8.45
1.20
119.70
128.15
B
B
B
C3'
O3'
P
DA
DA
TFT
118
118
119
Y
1
-6.84
0.80
109.40
102.56
B
B
B
O5'
C5'
C4'
DT
DT
DT
120
120
120
N
1
-7.75
0.70
108.00
100.25
B
B
B
O4'
C1'
N1
DT
DT
DT
120
120
120
N
1
-8.65
1.00
110.10
101.45
B
B
B
C1'
O4'
C4'
DC
DC
DC
121
121
121
N
1
9.44
1.40
114.30
123.74
B
B
B
N1
C1'
C2'
DC
DC
DC
121
121
121
N
1
-8.03
0.70
108.00
99.97
B
B
B
O4'
C1'
N1
DC
DC
DC
121
121
121
N
1
9.29
1.40
114.30
123.59
B
B
B
N1
C1'
C2'
DC
DC
DC
123
123
123
N
1
-9.13
0.70
108.00
98.87
B
B
B
O4'
C1'
N1
DC
DC
DC
123
123
123
N
1
9.14
1.40
114.30
123.44
B
B
B
N9
C1'
C2'
DG
DG
DG
124
124
124
N
1
-8.23
0.70
108.00
99.77
B
B
B
O4'
C1'
N9
DG
DG
DG
124
124
124
N
1
A
A
O4'
C1'
DC
DC
1
1
0.076
0.011
1.420
1.496
N
1
A
A
C2'
C1'
DC
DC
3
3
-0.063
0.010
1.518
1.455
N
1
A
A
O4'
C1'
DC
DC
3
3
0.109
0.011
1.420
1.529
N
1
A
A
O4'
C1'
DA
DA
5
5
0.098
0.011
1.420
1.518
N
1
A
A
O4'
C1'
DT
DT
8
8
0.077
0.011
1.420
1.497
N
1
A
A
C2'
C1'
DC
DC
9
9
-0.088
0.010
1.518
1.430
N
1
A
A
O4'
C1'
DC
DC
9
9
0.149
0.011
1.420
1.569
N
1
A
A
C2'
C1'
DC
DC
11
11
-0.069
0.010
1.518
1.449
N
1
A
A
O4'
C1'
DC
DC
11
11
0.126
0.011
1.420
1.546
N
1
A
A
C2'
C1'
DG
DG
12
12
-0.073
0.010
1.518
1.445
N
1
A
A
O4'
C1'
DG
DG
12
12
0.092
0.011
1.420
1.512
N
1
B
B
O4'
C1'
DC
DC
113
113
0.079
0.011
1.420
1.499
N
1
B
B
O4'
C1'
DC
DC
115
115
0.104
0.011
1.420
1.524
N
1
B
B
C2'
C1'
DA
DA
117
117
-0.060
0.010
1.518
1.458
N
1
B
B
O4'
C1'
DA
DA
117
117
0.123
0.011
1.420
1.543
N
1
B
B
O4'
C1'
DA
DA
118
118
0.079
0.011
1.420
1.499
N
1
B
B
C2'
C1'
DT
DT
120
120
-0.066
0.010
1.518
1.452
N
1
B
B
O4'
C1'
DT
DT
120
120
0.099
0.011
1.420
1.519
N
1
B
B
C2'
C1'
DC
DC
121
121
-0.079
0.010
1.518
1.439
N
1
B
B
O4'
C1'
DC
DC
121
121
0.129
0.011
1.420
1.549
N
1
B
B
C2'
C1'
DC
DC
123
123
-0.103
0.010
1.518
1.415
N
1
B
B
O4'
C1'
DC
DC
123
123
0.137
0.011
1.420
1.557
N
1
B
B
C2'
C1'
DG
DG
124
124
-0.094
0.010
1.518
1.424
N
1
B
B
O4'
C1'
DG
DG
124
124
0.132
0.011
1.420
1.552
N
0.16
1.20
20
21311
21311
random
1
MOLECULAR REPLACEMENT
B-form DNA (native Dickerson-Drew dodecamer)
1.20
20
197
682
1
484
0
0.007
0.014
1.20
20.0
1N1O
21360
21311
2
1
0.037
1
99.2
0.327
1.20
1.24
98.2
refinement
SHELXL-97
data scaling
SCALEPACK
refinement
CNS
data collection
MAR345
phasing
CNS
Crystal Structure of a B-form DNA Duplex Containing (L)-alpha-threofuranosyl (3'-2') Nucleosides: A Four-Carbon Sugar is Easily Accommodated into the Backbone of DNA
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
covale
1.610
both
A
DA
6
A
O3'
DA
6
1_555
A
TFT
7
A
P
TFT
7
1_555
covale
1.611
one
A
TFT
7
A
O2T
TFT
7
1_555
A
DT
8
A
P
DT
8
1_555
covale
1.583
both
B
DA
118
B
O3'
DA
6
1_555
B
TFT
119
B
P
TFT
7
1_555
covale
1.548
one
B
TFT
119
B
O2T
TFT
7
1_555
B
DT
120
B
P
DT
8
1_555
metalc
2.068
A
HOH
702
D
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
metalc
2.050
A
HOH
705
D
O
HOH
1_555
A
MG
901
C
MG
MG
1_555
metalc
2.119
A
MG
901
C
MG
MG
1_555
B
HOH
706
E
O
HOH
1_555
metalc
2.056
A
MG
901
C
MG
MG
1_555
B
HOH
708
E
O
HOH
1_555
metalc
2.066
A
MG
901
C
MG
MG
1_555
B
HOH
715
E
O
HOH
1_555
metalc
2.031
A
MG
901
C
MG
MG
1_555
B
HOH
720
E
O
HOH
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
124
B
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
124
B
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
124
B
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
123
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
123
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
123
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
122
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
122
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
122
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
121
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
121
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
121
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
120
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
120
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
TFT
119
B
N3
TFT
7
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
TFT
119
B
O4
TFT
7
1_555
hydrog
WATSON-CRICK
A
TFT
7
A
N3
TFT
7
1_555
B
DA
118
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
TFT
7
A
O4
TFT
7
1_555
B
DA
118
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
117
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
117
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
116
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
116
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
116
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
115
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
115
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
115
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
114
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
114
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
114
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
B
DC
113
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
B
DC
113
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
B
DC
113
B
N4
DC
1
1_555
DNA
B-DNA, hydrogen bonding, nucleic acid etiology, tetrose, four-carbon sugar, nucleic acid analogue, DNA
1N1O
PDB
1
1N1O
1
12
1N1O
1
12
1N1O
A
1
1
12
113
124
1N1O
113
124
1N1O
B
1
1
12
BINDING SITE FOR RESIDUE MG A 901
A
MG
901
Software
6
A
HOH
702
D
HOH
6
1_555
A
HOH
705
D
HOH
6
1_555
B
HOH
706
E
HOH
6
1_555
B
HOH
708
E
HOH
6
1_555
B
HOH
715
E
HOH
6
1_555
B
HOH
720
E
HOH
6
1_555
19
P 21 21 21