0.040314
0.023276
0.000000
0.000000
0.046551
0.000000
0.000000
0.000000
0.012925
0.000000
0.000000
0.000000
Adamiak, D.A.
Rypniewski, W.R.
Milecki, J.
Adamiak, R.W.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
24.805
24.805
77.372
H2 O
18.015
WATER
non-polymer
Mg 2
24.305
MAGNESIUM ION
non-polymer
C6 H14 O2
118.174
(4S)-2-METHYL-2,4-PENTANEDIOL
non-polymer
C10 H16 N3 O8 P
337.223
n
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
RNA linking
C11 H16 N5 O8 P
377.247
n
O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
RNA linking
N
1
N
O
N
2
N
H
N
3
N
H
N
4
N
MG
N
5
N
C
N
6
N
C
N
7
N
O
N
8
N
C
N
9
N
C
N
10
S
C
N
11
N
O
N
12
N
C
N
13
N
H
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
H
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
N
N
28
N
C
N
29
N
N
N
30
N
C
N
31
N
C
N
32
N
C
N
33
N
O
N
34
N
N
N
35
R
C
N
36
R
C
N
37
N
O
N
38
N
C
N
39
R
C
N
40
R
C
N
41
N
O
N
42
N
O
N
43
N
C
N
44
N
O
N
45
N
P
N
46
N
O
N
47
N
O
N
48
N
O
N
49
N
H
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
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
P
N
66
N
O
N
67
N
O
N
68
N
O
N
69
N
O
N
70
N
C
N
71
R
C
N
72
N
O
N
73
R
C
N
74
N
O
N
75
R
C
N
76
N
O
N
77
N
C
N
78
R
C
Y
79
N
N
Y
80
N
C
Y
81
N
N
Y
82
N
C
N
83
N
C
N
84
N
O
N
85
N
N
N
86
N
C
N
87
N
N
N
88
N
N
Y
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
H
N
105
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
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
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
doub
N
29
N
doub
N
30
N
sing
N
31
N
sing
N
32
N
doub
N
33
N
sing
N
34
N
sing
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
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
N
58
N
doub
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
doub
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
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
Y
90
N
sing
Y
91
N
sing
Y
92
N
doub
N
93
N
sing
Y
94
N
sing
N
95
N
sing
Y
96
N
doub
N
97
N
doub
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
sing
N
105
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
29
4144
4153
10.1093/nar/29.20.4144
11600703
The 1.19 A X-ray structure of 2'-O-Me(CGCGCG)(2) duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove.
2001
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
25
4599
4607
10.1093/nar/25.22.4599
CRYSTAL STRUCTURE OF 2'-O-ME(CGCGCG)2: AN RNA DUPLEX AT 1.3 A RESOLUTION. HYDRATION PATTERN OF 2'-O-METHYLATED RNA
1997
10.2210/pdb1i7j/pdb
pdb_00001i7j
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
IMAGE PLATE
1996-10-03
MARRESEARCH
Si
SINGLE WAVELENGTH
M
x-ray
1
0.900
1.0
BW7A
EMBL/DESY, HAMBURG
0.900
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE BW7A
1990.361
5'-R(*(OMC)P*(OMG)P*(OMC)P*(OMG)P*(OMC)P*(OMG))-3'
2
syn
polymer
24.305
MAGNESIUM ION
5
syn
non-polymer
118.174
(4S)-2-METHYL-2,4-PENTANEDIOL
2
syn
non-polymer
18.015
water
65
nat
water
no
yes
(OMC)(OMG)(OMC)(OMG)(OMC)(OMG)
CGCGCG
A,B
polyribonucleotide
n
n
n
n
n
n
1
1.73
38
VAPOR DIFFUSION, HANGING DROP
7.5
15 mM MgCl2, 1 mM spermine tetrahydrochloride and 30-40% 2-methyl-2,4-pentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
MgCl2
1
spermine tetrahydrochloride
1
MPD
1
MPD
2
9.032
1
19
A
1
B
6
-2.306
A_OMC1:OMG6_B
1
-16.361
0.028
-0.065
-0.068
6.930
1
19
A
2
B
5
-0.442
A_OMG2:OMC5_B
2
-13.356
-0.183
0.268
-0.141
3.680
1
19
A
3
B
4
-1.232
A_OMC3:OMG4_B
3
-15.822
0.195
-0.074
-0.148
-3.036
1
19
A
4
B
3
-1.537
A_OMG4:OMC3_B
4
-15.390
-0.155
-0.044
-0.176
-5.489
1
19
A
5
B
2
-1.409
A_OMC5:OMG2_B
5
-14.397
0.151
0.120
-0.145
-8.044
1
19
A
6
B
1
-3.630
A_OMG6:OMC1_B
6
-17.141
-0.041
-0.009
-0.123
2.143
36.279
A
A
1
2
24.985
B
B
6
5
3.133
15.004
-0.374
-1.817
AA_OMC1OMG2:OMC5OMG6_BB
1
-7.429
12.371
32.300
-4.719
-0.292
2.767
36.382
A
A
2
3
16.833
B
B
5
4
3.295
10.373
-0.580
-1.419
AA_OMG2OMC3:OMG4OMC5_BB
2
0.447
-0.725
34.917
-3.641
0.988
1.849
36.510
A
A
3
4
33.469
B
B
4
3
3.233
19.895
-0.015
-1.672
AA_OMC3OMG4:OMC3OMG4_BB
3
-0.411
0.691
30.766
-5.004
-0.024
2.756
35.909
A
A
4
5
17.261
B
B
3
2
3.276
10.495
0.544
-1.412
AA_OMG4OMC5:OMG2OMC3_BB
4
1.107
-1.821
34.372
-3.706
-0.733
2.140
36.173
A
A
5
6
25.724
B
B
2
1
3.162
15.419
0.386
-1.819
AA_OMC5OMG6:OMC1OMG2_BB
5
5.835
-9.735
32.310
-4.798
0.086
chem_comp_atom
chem_comp_bond
database_2
diffrn_source
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2001-09-21
1
1
2008-04-27
1
2
2011-07-13
1
3
2023-08-09
_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_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr2_auth_asym_id
_pdbx_struct_conn_angle.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_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_symmetry
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
310D contains the same 2'-O-methylated RNA, at room temperature
and higher hydration state.
RCSB
Y
RCSB
2001-03-09
REL
REL
MG
MAGNESIUM ION
MPD
(4S)-2-METHYL-2,4-PENTANEDIOL
HOH
water
310D
PDB 310D
PDB
experimental model
MG
1
2
MG
MG
101
A
MG
3
2
MG
MG
103
A
MG
4
2
MG
MG
104
A
MPD
1
3
MPD
MPD
201
A
MG
2
2
MG
MG
102
B
MG
5
2
MG
MG
105
B
MPD
2
3
MPD
MPD
202
B
HOH
1
4
HOH
HOH
202
A
HOH
4
4
HOH
HOH
203
A
HOH
5
4
HOH
HOH
204
A
HOH
6
4
HOH
HOH
205
A
HOH
12
4
HOH
HOH
206
A
HOH
13
4
HOH
HOH
207
A
HOH
14
4
HOH
HOH
208
A
HOH
15
4
HOH
HOH
209
A
HOH
16
4
HOH
HOH
210
A
HOH
17
4
HOH
HOH
211
A
HOH
18
4
HOH
HOH
212
A
HOH
20
4
HOH
HOH
213
A
HOH
24
4
HOH
HOH
214
A
HOH
26
4
HOH
HOH
215
A
HOH
30
4
HOH
HOH
216
A
HOH
32
4
HOH
HOH
217
A
HOH
37
4
HOH
HOH
218
A
HOH
38
4
HOH
HOH
219
A
HOH
39
4
HOH
HOH
220
A
HOH
40
4
HOH
HOH
221
A
HOH
43
4
HOH
HOH
222
A
HOH
44
4
HOH
HOH
223
A
HOH
45
4
HOH
HOH
224
A
HOH
46
4
HOH
HOH
225
A
HOH
47
4
HOH
HOH
226
A
HOH
48
4
HOH
HOH
227
A
HOH
49
4
HOH
HOH
228
A
HOH
51
4
HOH
HOH
229
A
HOH
52
4
HOH
HOH
230
A
HOH
55
4
HOH
HOH
231
A
HOH
59
4
HOH
HOH
232
A
HOH
61
4
HOH
HOH
233
A
HOH
62
4
HOH
HOH
234
A
HOH
2
4
HOH
HOH
203
B
HOH
3
4
HOH
HOH
204
B
HOH
7
4
HOH
HOH
205
B
HOH
8
4
HOH
HOH
206
B
HOH
9
4
HOH
HOH
207
B
HOH
10
4
HOH
HOH
208
B
HOH
11
4
HOH
HOH
209
B
HOH
19
4
HOH
HOH
210
B
HOH
21
4
HOH
HOH
211
B
HOH
22
4
HOH
HOH
212
B
HOH
23
4
HOH
HOH
213
B
HOH
25
4
HOH
HOH
214
B
HOH
27
4
HOH
HOH
215
B
HOH
28
4
HOH
HOH
216
B
HOH
29
4
HOH
HOH
217
B
HOH
31
4
HOH
HOH
218
B
HOH
33
4
HOH
HOH
219
B
HOH
34
4
HOH
HOH
220
B
HOH
35
4
HOH
HOH
221
B
HOH
36
4
HOH
HOH
222
B
HOH
41
4
HOH
HOH
223
B
HOH
42
4
HOH
HOH
224
B
HOH
50
4
HOH
HOH
225
B
HOH
53
4
HOH
HOH
226
B
HOH
54
4
HOH
HOH
227
B
HOH
56
4
HOH
HOH
228
B
HOH
57
4
HOH
HOH
229
B
HOH
58
4
HOH
HOH
230
B
HOH
60
4
HOH
HOH
231
B
HOH
63
4
HOH
HOH
232
B
HOH
64
4
HOH
HOH
233
B
HOH
65
4
HOH
HOH
234
B
+C
1
n
1
OMC
1
A
+G
2
n
2
OMG
2
A
+C
3
n
3
OMC
3
A
+G
4
n
4
OMG
4
A
+C
5
n
5
OMC
5
A
+G
6
n
6
OMG
6
A
+C
1
n
1
OMC
1
B
+G
2
n
2
OMG
2
B
+C
3
n
3
OMC
3
B
+G
4
n
4
OMG
4
B
+C
5
n
5
OMC
5
B
+G
6
n
6
OMG
6
B
0.1415
8667
author_defined_assembly
2
dimeric
A
OMG
2
A
OP1
OMG
2
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
224
J
O
HOH
1_555
75.4
A
OMG
2
A
OP1
OMG
2
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
226
J
O
HOH
1_555
96.4
A
HOH
224
J
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
226
J
O
HOH
1_555
82.7
A
OMG
2
A
OP1
OMG
2
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
228
J
O
HOH
1_555
172.9
A
HOH
224
J
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
228
J
O
HOH
1_555
107.7
A
HOH
226
J
O
HOH
1_555
A
MG
101
C
MG
MG
1_555
A
HOH
228
J
O
HOH
1_555
90.4
A
OMC
5
A
OP1
OMC
5
1_555
A
MG
103
D
MG
MG
1_555
A
HOH
219
J
O
HOH
1_555
85.4
A
OMC
5
A
OP1
OMC
5
1_555
A
MG
103
D
MG
MG
1_555
A
HOH
221
J
O
HOH
1_555
86.8
A
HOH
219
J
O
HOH
1_555
A
MG
103
D
MG
MG
1_555
A
HOH
221
J
O
HOH
1_555
98.2
A
OMC
5
A
OP1
OMC
5
1_555
A
MG
103
D
MG
MG
1_555
B
HOH
217
K
O
HOH
6_665
100.5
A
HOH
219
J
O
HOH
1_555
A
MG
103
D
MG
MG
1_555
B
HOH
217
K
O
HOH
6_665
162.3
A
HOH
221
J
O
HOH
1_555
A
MG
103
D
MG
MG
1_555
B
HOH
217
K
O
HOH
6_665
98.8
A
OMC
5
A
OP1
OMC
5
1_555
A
MG
103
D
MG
MG
1_555
B
HOH
223
K
O
HOH
6_665
97.7
A
HOH
219
J
O
HOH
1_555
A
MG
103
D
MG
MG
1_555
B
HOH
223
K
O
HOH
6_665
59.3
A
HOH
221
J
O
HOH
1_555
A
MG
103
D
MG
MG
1_555
B
HOH
223
K
O
HOH
6_665
41.6
B
HOH
217
K
O
HOH
6_665
A
MG
103
D
MG
MG
1_555
B
HOH
223
K
O
HOH
6_665
135.0
A
OMC
5
A
OP1
OMC
5
1_555
A
MG
103
D
MG
MG
1_555
B
HOH
224
K
O
HOH
6_665
80.2
A
HOH
219
J
O
HOH
1_555
A
MG
103
D
MG
MG
1_555
B
HOH
224
K
O
HOH
6_665
138.5
A
HOH
221
J
O
HOH
1_555
A
MG
103
D
MG
MG
1_555
B
HOH
224
K
O
HOH
6_665
42.6
B
HOH
217
K
O
HOH
6_665
A
MG
103
D
MG
MG
1_555
B
HOH
224
K
O
HOH
6_665
59.2
B
HOH
223
K
O
HOH
6_665
A
MG
103
D
MG
MG
1_555
B
HOH
224
K
O
HOH
6_665
84.2
A
HOH
208
J
O
HOH
1_555
A
MG
104
E
MG
MG
1_555
A
HOH
212
J
O
HOH
1_555
95.6
A
HOH
208
J
O
HOH
1_555
A
MG
104
E
MG
MG
1_555
A
HOH
218
J
O
HOH
1_555
167.7
A
HOH
212
J
O
HOH
1_555
A
MG
104
E
MG
MG
1_555
A
HOH
218
J
O
HOH
1_555
92.7
A
HOH
208
J
O
HOH
1_555
A
MG
104
E
MG
MG
1_555
A
HOH
222
J
O
HOH
1_555
101.2
A
HOH
212
J
O
HOH
1_555
A
MG
104
E
MG
MG
1_555
A
HOH
222
J
O
HOH
1_555
85.2
A
HOH
218
J
O
HOH
1_555
A
MG
104
E
MG
MG
1_555
A
HOH
222
J
O
HOH
1_555
88.6
B
OMG
2
B
OP1
OMG
2
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
219
K
O
HOH
1_555
102.1
B
OMG
2
B
OP1
OMG
2
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
221
K
O
HOH
1_555
98.8
B
HOH
219
K
O
HOH
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
221
K
O
HOH
1_555
87.2
B
OMG
2
B
OP1
OMG
2
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
222
K
O
HOH
1_555
160.4
B
HOH
219
K
O
HOH
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
222
K
O
HOH
1_555
96.3
B
HOH
221
K
O
HOH
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
222
K
O
HOH
1_555
88.6
B
OMG
2
B
OP1
OMG
2
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
227
K
O
HOH
1_555
95.8
B
HOH
219
K
O
HOH
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
227
K
O
HOH
1_555
78.3
B
HOH
221
K
O
HOH
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
227
K
O
HOH
1_555
161.2
B
HOH
222
K
O
HOH
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
227
K
O
HOH
1_555
81.4
B
OMG
2
B
OP1
OMG
2
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
232
K
O
HOH
1_555
75.1
B
HOH
219
K
O
HOH
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
232
K
O
HOH
1_555
177.2
B
HOH
221
K
O
HOH
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
232
K
O
HOH
1_555
93.5
B
HOH
222
K
O
HOH
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
232
K
O
HOH
1_555
86.4
B
HOH
227
K
O
HOH
1_555
B
MG
102
G
MG
MG
1_555
B
HOH
232
K
O
HOH
1_555
101.6
B
HOH
206
K
O
HOH
1_555
B
MG
105
H
MG
MG
1_555
B
HOH
207
K
O
HOH
1_555
87.3
B
HOH
206
K
O
HOH
1_555
B
MG
105
H
MG
MG
1_555
B
HOH
226
K
O
HOH
1_555
104.5
B
HOH
207
K
O
HOH
1_555
B
MG
105
H
MG
MG
1_555
B
HOH
226
K
O
HOH
1_555
96.6
B
HOH
206
K
O
HOH
1_555
B
MG
105
H
MG
MG
1_555
B
HOH
231
K
O
HOH
1_555
94.3
B
HOH
207
K
O
HOH
1_555
B
MG
105
H
MG
MG
1_555
B
HOH
231
K
O
HOH
1_555
172.1
B
HOH
226
K
O
HOH
1_555
B
MG
105
H
MG
MG
1_555
B
HOH
231
K
O
HOH
1_555
90.5
A
OMC
1
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
A
OMC
1
C
A
OMG
2
O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
A
OMG
2
G
A
OMC
3
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
A
OMC
3
C
A
OMG
4
O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
A
OMG
4
G
A
OMC
5
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
A
OMC
5
C
A
OMG
6
O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
A
OMG
6
G
B
OMC
1
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
B
OMC
1
C
B
OMG
2
O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
B
OMG
2
G
B
OMC
3
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
B
OMC
3
C
B
OMG
4
O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
B
OMG
4
G
B
OMC
5
O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
B
OMC
5
C
B
OMG
6
O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
B
OMG
6
G
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
A
HOH
211
J
HOH
1
B
HOH
215
K
HOH
0.155
0.155
0.155
1.19
20
8715
8715
95.8
1
0
0
MOLECULAR REPLACEMENT
PDB 310D
CCP4
1.19
20
81
510
53
376
0
0.068
0.014
0.047
0.155
1.21
95.8
13
1.19
20
1I7J
8715
0
0
0.049
1
23
17
95.8
0.46
1.19
1.21
2.1
415
2.8
94
phasing
AMoRE
refinement
SHELXL-97
data reduction
DENZO
data scaling
SCALEPACK
CRYSTAL STRUCTURE OF 2'-O-ME(CGCGCG)2: AN RNA DUPLEX AT 1.19 A RESOLUTION. 2-METHYL-2,4-PENTANEDIOL AND MAGNESIUM BINDING.
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
2
N
N
2
N
N
3
N
N
4
N
N
4
N
N
covale
1.611
both
A
OMC
1
A
O3'
OMC
1
1_555
A
OMG
2
A
P
OMG
2
1_555
covale
1.607
both
A
OMG
2
A
O3'
OMG
2
1_555
A
OMC
3
A
P
OMC
3
1_555
covale
1.603
both
A
OMC
3
A
O3'
OMC
3
1_555
A
OMG
4
A
P
OMG
4
1_555
covale
1.624
both
A
OMG
4
A
O3'
OMG
4
1_555
A
OMC
5
A
P
OMC
5
1_555
covale
1.595
both
A
OMC
5
A
O3'
OMC
5
1_555
A
OMG
6
A
P
OMG
6
1_555
covale
1.592
both
B
OMC
1
B
O3'
OMC
1
1_555
B
OMG
2
B
P
OMG
2
1_555
covale
1.588
both
B
OMG
2
B
O3'
OMG
2
1_555
B
OMC
3
B
P
OMC
3
1_555
covale
1.608
both
B
OMC
3
B
O3'
OMC
3
1_555
B
OMG
4
B
P
OMG
4
1_555
covale
1.616
both
B
OMG
4
B
O3'
OMG
4
1_555
B
OMC
5
B
P
OMC
5
1_555
covale
1.611
both
B
OMC
5
B
O3'
OMC
5
1_555
B
OMG
6
B
P
OMG
6
1_555
metalc
2.065
A
OMG
2
A
OP1
OMG
2
1_555
A
MG
101
C
MG
MG
1_555
metalc
1.947
A
OMC
5
A
OP1
OMC
5
1_555
A
MG
103
D
MG
MG
1_555
metalc
1.915
A
MG
101
C
MG
MG
1_555
A
HOH
224
J
O
HOH
1_555
metalc
2.190
A
MG
101
C
MG
MG
1_555
A
HOH
226
J
O
HOH
1_555
metalc
1.895
A
MG
101
C
MG
MG
1_555
A
HOH
228
J
O
HOH
1_555
metalc
2.080
A
MG
103
D
MG
MG
1_555
A
HOH
219
J
O
HOH
1_555
metalc
2.448
A
MG
103
D
MG
MG
1_555
A
HOH
221
J
O
HOH
1_555
metalc
2.159
A
MG
103
D
MG
MG
1_555
B
HOH
217
K
O
HOH
6_665
metalc
1.982
A
MG
103
D
MG
MG
1_555
B
HOH
223
K
O
HOH
6_665
metalc
1.909
A
MG
103
D
MG
MG
1_555
B
HOH
224
K
O
HOH
6_665
metalc
2.110
A
MG
104
E
MG
MG
1_555
A
HOH
208
J
O
HOH
1_555
metalc
1.893
A
MG
104
E
MG
MG
1_555
A
HOH
212
J
O
HOH
1_555
metalc
2.367
A
MG
104
E
MG
MG
1_555
A
HOH
218
J
O
HOH
1_555
metalc
1.906
A
MG
104
E
MG
MG
1_555
A
HOH
222
J
O
HOH
1_555
metalc
2.022
B
OMG
2
B
OP1
OMG
2
1_555
B
MG
102
G
MG
MG
1_555
metalc
2.248
B
MG
102
G
MG
MG
1_555
B
HOH
219
K
O
HOH
1_555
metalc
2.004
B
MG
102
G
MG
MG
1_555
B
HOH
221
K
O
HOH
1_555
metalc
2.206
B
MG
102
G
MG
MG
1_555
B
HOH
222
K
O
HOH
1_555
metalc
2.019
B
MG
102
G
MG
MG
1_555
B
HOH
227
K
O
HOH
1_555
metalc
2.052
B
MG
102
G
MG
MG
1_555
B
HOH
232
K
O
HOH
1_555
metalc
2.089
B
MG
105
H
MG
MG
1_555
B
HOH
206
K
O
HOH
1_555
metalc
2.014
B
MG
105
H
MG
MG
1_555
B
HOH
207
K
O
HOH
1_555
metalc
1.752
B
MG
105
H
MG
MG
1_555
B
HOH
226
K
O
HOH
1_555
metalc
1.976
B
MG
105
H
MG
MG
1_555
B
HOH
231
K
O
HOH
1_555
hydrog
WATSON-CRICK
A
OMC
1
A
N3
OMC
1
1_555
B
OMG
6
B
N1
OMG
6
1_555
hydrog
WATSON-CRICK
A
OMC
1
A
N4
OMC
1
1_555
B
OMG
6
B
O6
OMG
6
1_555
hydrog
WATSON-CRICK
A
OMC
1
A
O2
OMC
1
1_555
B
OMG
6
B
N2
OMG
6
1_555
hydrog
WATSON-CRICK
A
OMG
2
A
N1
OMG
2
1_555
B
OMC
5
B
N3
OMC
5
1_555
hydrog
WATSON-CRICK
A
OMG
2
A
N2
OMG
2
1_555
B
OMC
5
B
O2
OMC
5
1_555
hydrog
WATSON-CRICK
A
OMG
2
A
O6
OMG
2
1_555
B
OMC
5
B
N4
OMC
5
1_555
hydrog
WATSON-CRICK
A
OMC
3
A
N3
OMC
3
1_555
B
OMG
4
B
N1
OMG
4
1_555
hydrog
WATSON-CRICK
A
OMC
3
A
N4
OMC
3
1_555
B
OMG
4
B
O6
OMG
4
1_555
hydrog
WATSON-CRICK
A
OMC
3
A
O2
OMC
3
1_555
B
OMG
4
B
N2
OMG
4
1_555
hydrog
WATSON-CRICK
A
OMG
4
A
N1
OMG
4
1_555
B
OMC
3
B
N3
OMC
3
1_555
hydrog
WATSON-CRICK
A
OMG
4
A
N2
OMG
4
1_555
B
OMC
3
B
O2
OMC
3
1_555
hydrog
WATSON-CRICK
A
OMG
4
A
O6
OMG
4
1_555
B
OMC
3
B
N4
OMC
3
1_555
hydrog
WATSON-CRICK
A
OMC
5
A
N3
OMC
5
1_555
B
OMG
2
B
N1
OMG
2
1_555
hydrog
WATSON-CRICK
A
OMC
5
A
N4
OMC
5
1_555
B
OMG
2
B
O6
OMG
2
1_555
hydrog
WATSON-CRICK
A
OMC
5
A
O2
OMC
5
1_555
B
OMG
2
B
N2
OMG
2
1_555
hydrog
WATSON-CRICK
A
OMG
6
A
N1
OMG
6
1_555
B
OMC
1
B
N3
OMC
1
1_555
hydrog
WATSON-CRICK
A
OMG
6
A
N2
OMG
6
1_555
B
OMC
1
B
O2
OMC
1
1_555
hydrog
WATSON-CRICK
A
OMG
6
A
O6
OMG
6
1_555
B
OMC
1
B
N4
OMC
1
1_555
RNA
2'-O-MeRNA duplex, 2-methyl-2, 4-pentanediol, magnesium, groove hydration and binding, RNA
1I7J
PDB
1
1I7J
1
6
1I7J
1
6
1I7J
A
1
1
6
1
6
1I7J
1
6
1I7J
B
1
1
6
BINDING SITE FOR RESIDUE MG A 101
A
MG
101
Software
6
BINDING SITE FOR RESIDUE MG B 102
B
MG
102
Software
6
BINDING SITE FOR RESIDUE MG A 103
A
MG
103
Software
7
BINDING SITE FOR RESIDUE MG A 104
A
MG
104
Software
4
BINDING SITE FOR RESIDUE MG B 105
B
MG
105
Software
4
BINDING SITE FOR RESIDUE MPD A 201
A
MPD
201
Software
5
BINDING SITE FOR RESIDUE MPD B 202
B
MPD
202
Software
6
A
OMG
2
A
OMG
2
6
1_555
A
HOH
224
J
HOH
6
1_555
A
HOH
225
J
HOH
6
1_555
A
HOH
226
J
HOH
6
1_555
A
HOH
228
J
HOH
6
1_555
A
HOH
229
J
HOH
6
1_555
B
OMG
2
B
OMG
2
6
1_555
B
HOH
219
K
HOH
6
1_555
B
HOH
221
K
HOH
6
1_555
B
HOH
222
K
HOH
6
1_555
B
HOH
227
K
HOH
6
1_555
B
HOH
232
K
HOH
6
1_555
A
OMC
5
A
OMC
5
7
1_555
A
HOH
219
J
HOH
7
1_555
A
HOH
221
J
HOH
7
1_555
B
OMC
5
B
OMC
5
7
6_665
B
HOH
217
K
HOH
7
6_665
B
HOH
223
K
HOH
7
6_665
B
HOH
224
K
HOH
7
6_665
A
HOH
208
J
HOH
4
1_555
A
HOH
212
J
HOH
4
1_555
A
HOH
218
J
HOH
4
1_555
A
HOH
222
J
HOH
4
1_555
B
HOH
206
K
HOH
4
1_555
B
HOH
207
K
HOH
4
1_555
B
HOH
226
K
HOH
4
1_555
B
HOH
231
K
HOH
4
1_555
A
OMG
2
A
OMG
2
5
1_555
A
OMC
3
A
OMC
3
5
1_555
A
OMG
4
A
OMG
4
5
6_555
A
OMG
6
A
OMG
6
5
1_545
A
HOH
213
J
HOH
5
1_555
A
OMC
5
A
OMC
5
6
1_555
A
OMG
6
A
OMG
6
6
1_555
B
OMG
2
B
OMG
2
6
1_555
B
OMC
3
B
OMC
3
6
1_555
B
OMG
6
B
OMG
6
6
1_565
B
HOH
216
K
HOH
6
1_555
153
P 32 1 2