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
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
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/pdb1mv2/pdb
pdb_00001mv2
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
2855.769
5'-R(*GP*GP*CP*AP*(P5P)P*GP*CP*CP*U)-3'
2
syn
polymer
no
yes
GGCA(P5P)GCCU
GGCAAGCCU
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
n
-6.723
1
19
A
1
B
8
-0.667
A_G1:C8_B
1
-8.508
-0.652
-0.333
-0.192
-13.081
1
19
A
2
B
7
0.191
A_G2:C7_B
2
-13.856
-0.435
-0.151
-0.081
-12.957
1
19
A
3
B
6
-2.853
A_C3:G6_B
3
-8.064
0.333
0.259
-0.051
9.956
1
19
A
6
B
3
-2.591
A_G6:C3_B
4
-7.073
-0.400
0.297
-0.075
14.477
1
19
A
7
B
2
0.323
A_C7:G2_B
5
-12.610
0.438
-0.103
-0.072
10.203
1
19
A
8
B
1
-0.560
A_C8:G1_B
6
-9.322
0.636
-0.396
-0.181
3.012
33.421
A
A
1
2
10.734
B
B
8
7
3.413
6.140
-0.003
-1.939
AA_G1G2:C7C8_BB
1
-0.333
0.583
32.867
-4.378
-0.050
3.036
36.958
A
A
2
3
6.081
B
B
7
6
3.232
3.848
-0.289
-1.799
AA_G2C3:G6C7_BB
2
-0.138
0.219
36.764
-3.337
0.438
3.024
36.425
A
A
6
7
4.550
B
B
3
2
3.162
2.841
0.202
-1.702
AA_G6C7:G2C3_BB
3
-0.112
0.179
36.317
-3.096
-0.337
2.923
32.968
A
A
7
8
11.379
B
B
2
1
3.351
6.418
-0.037
-1.935
AA_C7C8:G1G2_BB
4
0.459
-0.814
32.351
-4.467
0.141
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 Tandem, sheared GA pairs in the same stem, determined by 2D NMR
1GID IS Tandem, sheared AA pairs in the J4/5 loop of Tetrahymena thermophila, determined by x-ray crystallography
1MUV IS the Tandem, sheared AA pairs, in 5'(rGGCAAGCCU)2
1mv1 is The tandem, sheared PA Pairs in 5'(rGGCPAGCCU)2
1mv6 is The tandem, Sheared PP Pairs in 5'(rGGCPPGCCU)2
RCSB
Y
RCSB
2002-09-24
REL
REL
1
2D NOESY
90% H2O, 10% D2O
6.5
ambient
273
K
99.996% D2O
7.7
ambient
303
K
The structure is based on a total of 71 interproton distance restraints per strand, 18 hydrogen bond restraints, and 59 dihedral angle restraints per strand.
simulated annealing, energy minimization
1
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
A
4
n
4
A
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
A
4
n
4
A
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
5
PURINE RIBOSIDE-5'-MONOPHOSPHATE
A
P5P
5
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
A
G
6
0.062
SIDE CHAIN
1
B
G
6
0.068
SIDE CHAIN
1
4.39
0.70
108.50
112.89
A
A
A
O4'
C1'
N9
A
A
A
4
4
4
N
1
4.22
0.70
108.50
112.72
A
A
A
O4'
C1'
N1
C
C
C
7
7
7
N
1
4.72
0.70
108.50
113.22
A
A
A
O4'
C1'
N1
C
C
C
8
8
8
N
1
4.47
0.70
108.50
112.97
B
B
B
O4'
C1'
N1
C
C
C
7
7
7
N
1
4.67
0.70
108.50
113.17
B
B
B
O4'
C1'
N1
C
C
C
8
8
8
N
The tandem, Face-to-Face AP Pairs in 5'(rGGCAPGCCU)2
1
N
N
1
N
N
covale
1.617
both
A
A
4
A
O3'
A
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
1.616
both
B
A
4
B
O3'
A
4
1_555
B
P5P
5
B
P
P5P
5
1_555
covale
1.619
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
1MV2
PDB
1
1MV2
1
9
1MV2
1
9
1MV2
A
1
1
9
1
9
1MV2
1
9
1MV2
B
1
1
9