1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Znosko, B.M.
Burkard, M.E.
Krugh, T.R.
Turner, D.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C10 H13 N4 O7 P
332.207
n
PURINE RIBOSIDE-5'-MONOPHOSPHATE
RNA linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
US
Biochemistry
BICHAW
0033
0006-2960
41
14978
14987
10.1021/bi0203278
12475247
Molecular Recognition in Purine-Rich Internal Loops: Thermodynamic, Structural, and Dynamic Consequences of Purine for Adenine Substitutions in 5'(rGGCAAGCCU)2
2002
US
Biochemistry
BICHAW
0033
0006-2960
41
14969
14977
10.1021/bi020326f
Sheared Aanti-Aanti Base Pairs in a Destabilizing 2x2 Internal Loop: The NMR Structure of 5'(rGGCAAGCCU)2
2002
10.2210/pdb1mv6/pdb
pdb_00001mv6
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
2840.755
5'-R(*GP*GP*CP*(P5P)P*(P5P)P*GP*CP*CP*U)-3'
2
syn
polymer
no
yes
GGC(P5P)(P5P)GCCU
GGCAAGCCU
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
n
-8.258
1
19
A
1
B
8
-1.243
A_G1:C8_B
1
-4.544
-0.619
-0.293
-0.173
-4.460
1
19
A
2
B
7
-0.432
A_G2:C7_B
2
-10.259
-0.370
-0.115
-0.075
-2.369
1
19
A
3
B
6
1.559
A_C3:G6_B
3
-15.275
0.717
0.046
-0.181
-5.724
1
19
A
6
B
3
0.836
A_G6:C3_B
4
-16.838
-0.554
-0.324
-0.185
-6.205
1
19
A
7
B
2
-1.054
A_C7:G2_B
5
-5.706
0.445
0.019
-0.086
7.224
1
19
A
8
B
1
-0.765
A_C8:G1_B
6
-2.004
0.573
-0.295
-0.150
2.891
31.134
A
A
1
2
8.600
B
B
8
7
3.195
4.600
-0.021
-1.874
AA_G1G2:C7C8_BB
1
-0.294
0.549
30.799
-4.313
-0.013
3.022
33.639
A
A
2
3
5.888
B
B
7
6
3.209
3.402
0.085
-1.741
AA_G2C3:G6C7_BB
2
-0.310
0.537
33.470
-3.539
-0.195
2.951
33.743
A
A
6
7
8.572
B
B
3
2
3.257
4.957
0.111
-1.857
AA_G6C7:G2C3_BB
3
-1.465
2.534
33.356
-3.966
-0.418
2.878
28.262
A
A
7
8
3.669
B
B
2
1
2.998
1.790
0.074
-1.817
AA_C7C8:G1G2_BB
4
1.640
-3.363
28.159
-4.096
0.190
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-12-18
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
1yfv is the Tandem, sheared GA pairs in the same stem, determined by 2D NMR
1gid is the Tandem, sheared AA pairs in the J4/5 loop of Tetrahymena thermophila, determined by x-ray crystallography
1mUV is The tandem, sheared AA Pairs with same stem
1MV1 IS THE Tandem, Sheared PA Pairs in 5'(rGGCPAGCCU)2
1mv2 is The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2
RCSB
Y
RCSB
2002-09-24
REL
REL
Random Structures to show variety
33
3
2D NOESY
90% H2O, 10% D2O
6.5
ambient
273
K
99.996% D2O
7.7
ambient
303
K
total of 63 interproton distance restraints per strand, 18 hydrogen bond restraints, and 50 dihedral angle restraints per strand.
simulated annealing, energy minimization
3
closest to the average
1mM RNA, 80 mM NaCl, 10mM phosphate buffer, 0.5mM EDTA; 90% H2O, 10% D2O
90% H2O/10% D2O
2mM RNA, 80 mM NaCl, 10mM phosphate buffer, 0.5mM EDTA; 99.996% D2O
99.996% D2O
Varian
collection
VNMR
5.2
MSI
data analysis
Felix
2000
MSI
structure solution
Discover
95.0
MSI
refinement
Discover
95.0
500
Varian
INOVA
G
1
n
1
G
1
A
G
2
n
2
G
2
A
C
3
n
3
C
3
A
P
4
n
4
P5P
4
A
P
5
n
5
P5P
5
A
G
6
n
6
G
6
A
C
7
n
7
C
7
A
C
8
n
8
C
8
A
U
9
n
9
U
9
A
G
1
n
1
G
1
B
G
2
n
2
G
2
B
C
3
n
3
C
3
B
P
4
n
4
P5P
4
B
P
5
n
5
P5P
5
B
G
6
n
6
G
6
B
C
7
n
7
C
7
B
C
8
n
8
C
8
B
U
9
n
9
U
9
B
author_defined_assembly
2
dimeric
A
P5P
4
PURINE RIBOSIDE-5'-MONOPHOSPHATE
A
P5P
4
A
A
P5P
5
PURINE RIBOSIDE-5'-MONOPHOSPHATE
A
P5P
5
A
B
P5P
4
PURINE RIBOSIDE-5'-MONOPHOSPHATE
B
P5P
4
A
B
P5P
5
PURINE RIBOSIDE-5'-MONOPHOSPHATE
B
P5P
5
A
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
5.75
0.70
108.50
114.25
A
A
A
O4'
C1'
N1
C
C
C
3
3
3
N
1
4.97
0.70
108.50
113.47
A
A
A
O4'
C1'
N1
C
C
C
7
7
7
N
1
5.20
0.70
108.50
113.70
A
A
A
O4'
C1'
N1
C
C
C
8
8
8
N
1
4.68
0.70
108.50
113.18
B
B
B
O4'
C1'
N1
C
C
C
3
3
3
N
1
4.69
0.70
108.50
113.19
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
1
4.88
0.70
108.50
113.38
B
B
B
O4'
C1'
N1
C
C
C
8
8
8
N
1
4.26
0.70
108.50
112.76
B
B
B
O4'
C1'
N1
U
U
U
9
9
9
N
2
5.24
0.70
108.50
113.74
A
A
A
O4'
C1'
N1
C
C
C
3
3
3
N
2
5.19
0.70
108.50
113.69
A
A
A
O4'
C1'
N1
C
C
C
7
7
7
N
2
5.12
0.70
108.50
113.62
A
A
A
O4'
C1'
N1
C
C
C
8
8
8
N
2
5.42
0.70
108.50
113.92
B
B
B
O4'
C1'
N1
C
C
C
3
3
3
N
2
4.28
0.70
108.50
112.78
B
B
B
O4'
C1'
N9
G
G
G
6
6
6
N
2
4.98
0.70
108.50
113.48
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
2
4.93
0.70
108.50
113.43
B
B
B
O4'
C1'
N1
C
C
C
8
8
8
N
3
5.82
0.70
108.50
114.32
A
A
A
O4'
C1'
N1
C
C
C
3
3
3
N
3
5.47
0.70
108.50
113.97
A
A
A
O4'
C1'
N1
C
C
C
7
7
7
N
3
5.18
0.70
108.50
113.68
A
A
A
O4'
C1'
N1
C
C
C
8
8
8
N
3
4.53
0.70
108.50
113.03
B
B
B
O4'
C1'
N1
C
C
C
3
3
3
N
3
4.99
0.70
108.50
113.49
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
3
5.32
0.70
108.50
113.82
B
B
B
O4'
C1'
N1
C
C
C
8
8
8
N
3
4.68
0.70
108.50
113.18
B
B
B
O4'
C1'
N1
U
U
U
9
9
9
N
The tandem, Sheared PP Pairs in 5'(rGGCPPGCCU)2
1
N
N
1
N
N
covale
1.614
both
A
C
3
A
O3'
C
3
1_555
A
P5P
4
A
P
P5P
4
1_555
covale
1.614
both
A
P5P
4
A
O3'
P5P
4
1_555
A
P5P
5
A
P
P5P
5
1_555
covale
1.618
both
A
P5P
5
A
O3'
P5P
5
1_555
A
G
6
A
P
G
6
1_555
covale
1.619
both
B
C
3
B
O3'
C
3
1_555
B
P5P
4
B
P
P5P
4
1_555
covale
1.614
both
B
P5P
4
B
O3'
P5P
4
1_555
B
P5P
5
B
P
P5P
5
1_555
covale
1.618
both
B
P5P
5
B
O3'
P5P
5
1_555
B
G
6
B
P
G
6
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
8
B
N3
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
8
B
O2
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
8
B
N4
C
8
1_555
hydrog
WATSON-CRICK
A
G
2
A
N1
G
2
1_555
B
C
7
B
N3
C
7
1_555
hydrog
WATSON-CRICK
A
G
2
A
N2
G
2
1_555
B
C
7
B
O2
C
7
1_555
hydrog
WATSON-CRICK
A
G
2
A
O6
G
2
1_555
B
C
7
B
N4
C
7
1_555
hydrog
WATSON-CRICK
A
C
3
A
N3
C
3
1_555
B
G
6
B
N1
G
6
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
B
G
6
B
O6
G
6
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
B
G
6
B
N2
G
6
1_555
hydrog
WATSON-CRICK
A
G
6
A
N1
G
6
1_555
B
C
3
B
N3
C
3
1_555
hydrog
WATSON-CRICK
A
G
6
A
N2
G
6
1_555
B
C
3
B
O2
C
3
1_555
hydrog
WATSON-CRICK
A
G
6
A
O6
G
6
1_555
B
C
3
B
N4
C
3
1_555
hydrog
WATSON-CRICK
A
C
7
A
N3
C
7
1_555
B
G
2
B
N1
G
2
1_555
hydrog
WATSON-CRICK
A
C
7
A
N4
C
7
1_555
B
G
2
B
O6
G
2
1_555
hydrog
WATSON-CRICK
A
C
7
A
O2
C
7
1_555
B
G
2
B
N2
G
2
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
B
G
1
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
B
G
1
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
B
G
1
B
N2
G
1
1_555
RNA
ribonucleic acid, duplex, tandem mismatch, purine, RNA
1MV6
PDB
1
1MV6
1
9
1MV6
1
9
1MV6
A
1
1
9
1
9
1MV6
1
9
1MV6
B
1
1
9