1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Hosur, R.V.
Patel, P.K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
27
2457
2464
10.1093/nar/27.12.2457
10352174
NMR observation of T-tetrads in a parallel stranded DNA quadruplex formed by Saccharomyces cerevisiae telomere repeats.
1999
10.2210/pdb1emq/pdb
pdb_00001emq
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
ONLY TWO REPEATS AND ONE C AT 3' END
2169.433
DNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3')
YEAST TELOMERE REPEATS
4
syn
polymer
no
no
(DT)(DG)(DG)(DT)(DG)(DG)(DC)
TGGTGGC
A,B,C,D
polydeoxyribonucleotide
n
n
n
n
n
n
n
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2000-04-04
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
RCSB
Y
RCSB
2000-03-17
REL
This sequence is two repeats of Saccharomyces cerevisiae telomere sequence
sample
0-70 C Temperature dependent one dimensional spectra. pH dependent spectra.
structures with the lowest energy
8
1
2D NOESY
E-COSY
2D-TOCSY
7.0
1
atm
293
K
A total of 234 NOEs constarint. 20 hydrogen bonds constraints. 8 convergant structure after IRMA refinement. R1 factor = 0.31-0.33. r.m.s.d.s from average structure 0.2-0.4. Nil violation exceeding 0.2 A.
An initial model of quadruplex was generated on a IRIS workastation.Energy minimization by steepest descent followed by conjugate gradients methods was done using AMBER force field. Conformational search for the cquadruplex was performed by simulated annealing-reastarined molecular dynamics using AMBER forcefield. Relaxation matrix refinement was performed.
1
minimized average structure
1-2 mM DNA in 0.6 ml(90%H20/10%D2O) having 10 mM potassium phosphate, 0.2 mM EDTA, pH 7.0 and 100 mM KCl
90% H2O/10% D2O
1-2 mM DNA in 0.6 ml(D2O) having 10 mM potassium phosphate, 0.2 mM EDTA, pH 7.0 and 100 mM KCl
D2O
MSI
processing
Felix
230
Varian
collection
VNMR
6.1
MSI
structure solution
Discover
3.1
MSI
refinement
IRMA
2.3
600
Varian
UNITYPLUS
500
Bruker
AMX
T
101
n
1
DT
101
A
G
102
n
2
DG
102
A
G
103
n
3
DG
103
A
T
104
n
4
DT
104
A
G
105
n
5
DG
105
A
G
106
n
6
DG
106
A
C
107
n
7
DC
107
A
T
201
n
1
DT
201
B
G
202
n
2
DG
202
B
G
203
n
3
DG
203
B
T
204
n
4
DT
204
B
G
205
n
5
DG
205
B
G
206
n
6
DG
206
B
C
207
n
7
DC
207
B
T
401
n
1
DT
401
C
G
402
n
2
DG
402
C
G
403
n
3
DG
403
C
T
404
n
4
DT
404
C
G
405
n
5
DG
405
C
G
406
n
6
DG
406
C
C
407
n
7
DC
407
C
T
301
n
1
DT
301
D
G
302
n
2
DG
302
D
G
303
n
3
DG
303
D
T
304
n
4
DT
304
D
G
305
n
5
DG
305
D
G
306
n
6
DG
306
D
C
307
n
7
DC
307
D
author_defined_assembly
4
tetrameric
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
DG
102
0.089
SIDE CHAIN
1
A
DT
104
0.060
SIDE CHAIN
1
A
DC
107
0.076
SIDE CHAIN
1
B
DG
202
0.090
SIDE CHAIN
1
B
DT
204
0.078
SIDE CHAIN
1
B
DC
207
0.091
SIDE CHAIN
1
C
DG
402
0.132
SIDE CHAIN
1
C
DG
406
0.052
SIDE CHAIN
1
C
DC
407
0.138
SIDE CHAIN
1
D
DG
302
0.087
SIDE CHAIN
1
D
DT
304
0.069
SIDE CHAIN
1
3.46
0.30
108.30
111.76
A
A
A
O4'
C1'
N1
DT
DT
DT
101
101
101
N
1
-4.67
0.60
122.90
118.23
A
A
A
C6
C5
C7
DT
DT
DT
101
101
101
N
1
-5.43
0.80
105.90
100.47
A
A
A
O4'
C1'
C2'
DT
DT
DT
104
104
104
N
1
-4.94
0.60
122.90
117.96
A
A
A
C6
C5
C7
DT
DT
DT
104
104
104
N
1
2.29
0.30
108.30
110.59
A
A
A
O4'
C1'
N9
DG
DG
DG
106
106
106
N
1
-4.92
0.70
119.90
114.98
A
A
A
N3
C2
N2
DG
DG
DG
106
106
106
N
1
-5.38
0.70
118.00
112.62
A
A
A
N3
C4
N4
DC
DC
DC
107
107
107
N
1
3.78
0.30
108.30
112.08
B
B
B
O4'
C1'
N1
DT
DT
DT
201
201
201
N
1
-4.62
0.60
122.90
118.28
B
B
B
C6
C5
C7
DT
DT
DT
201
201
201
N
1
-5.29
0.80
105.90
100.61
B
B
B
O4'
C1'
C2'
DT
DT
DT
204
204
204
N
1
-4.63
0.60
122.90
118.27
B
B
B
C6
C5
C7
DT
DT
DT
204
204
204
N
1
1.87
0.30
108.30
110.17
B
B
B
O4'
C1'
N9
DG
DG
DG
206
206
206
N
1
-4.95
0.70
118.00
113.05
B
B
B
N3
C4
N4
DC
DC
DC
207
207
207
N
1
2.95
0.30
108.30
111.25
C
C
C
O4'
C1'
N1
DT
DT
DT
401
401
401
N
1
-3.64
0.60
122.30
118.66
C
C
C
N3
C2
O2
DT
DT
DT
401
401
401
N
1
-4.64
0.60
122.90
118.26
C
C
C
C6
C5
C7
DT
DT
DT
401
401
401
N
1
-5.62
0.80
105.90
100.28
C
C
C
O4'
C1'
C2'
DT
DT
DT
404
404
404
N
1
1.91
0.30
108.30
110.21
C
C
C
O4'
C1'
N1
DT
DT
DT
404
404
404
N
1
3.61
0.60
114.60
118.21
C
C
C
N1
C2
N3
DT
DT
DT
404
404
404
N
1
-5.18
0.60
122.90
117.72
C
C
C
C6
C5
C7
DT
DT
DT
404
404
404
N
1
2.76
0.30
108.30
111.06
C
C
C
O4'
C1'
N9
DG
DG
DG
406
406
406
N
1
-4.49
0.70
118.00
113.51
C
C
C
N3
C4
N4
DC
DC
DC
407
407
407
N
1
3.16
0.30
108.30
111.46
D
D
D
O4'
C1'
N1
DT
DT
DT
301
301
301
N
1
-4.94
0.60
122.90
117.96
D
D
D
C6
C5
C7
DT
DT
DT
301
301
301
N
1
-5.66
0.80
105.90
100.24
D
D
D
O4'
C1'
C2'
DT
DT
DT
304
304
304
N
1
-4.97
0.60
122.90
117.93
D
D
D
C6
C5
C7
DT
DT
DT
304
304
304
N
1
2.59
0.30
108.30
110.89
D
D
D
O4'
C1'
N9
DG
DG
DG
306
306
306
N
minimized average
NMR OBSERVATION OF T-TETRADS IN A PARALLEL STRANDED DNA QUADRUPLEX FORMED BY SACCHAROMYCES CEREVISIAE TELOMERE REPEATS
1
N
N
1
N
N
1
N
N
1
N
N
hydrog
DT-DT MISPAIR
A
DT
101
A
O4
DT
1
1_555
B
DT
201
B
N3
DT
1
1_555
hydrog
DT-DT MISPAIR
A
DT
101
A
N3
DT
1
1_555
C
DT
401
C
O4
DT
1
1_555
hydrog
TYPE_6_PAIR
A
DG
102
A
N7
DG
2
1_555
B
DG
202
B
N2
DG
2
1_555
hydrog
TYPE_6_PAIR
A
DG
102
A
O6
DG
2
1_555
B
DG
202
B
N1
DG
2
1_555
hydrog
TYPE_6_PAIR
A
DG
102
A
N1
DG
2
1_555
C
DG
402
C
O6
DG
2
1_555
hydrog
TYPE_6_PAIR
A
DG
102
A
N2
DG
2
1_555
C
DG
402
C
N7
DG
2
1_555
hydrog
TYPE_6_PAIR
A
DG
103
A
N7
DG
3
1_555
B
DG
203
B
N2
DG
3
1_555
hydrog
TYPE_6_PAIR
A
DG
103
A
O6
DG
3
1_555
B
DG
203
B
N1
DG
3
1_555
hydrog
TYPE_6_PAIR
A
DG
103
A
N1
DG
3
1_555
C
DG
403
C
O6
DG
3
1_555
hydrog
TYPE_6_PAIR
A
DG
103
A
N2
DG
3
1_555
C
DG
403
C
N7
DG
3
1_555
hydrog
DT-DT MISPAIR
A
DT
104
A
O4
DT
4
1_555
B
DT
204
B
N3
DT
4
1_555
hydrog
DT-DT MISPAIR
A
DT
104
A
N3
DT
4
1_555
C
DT
404
C
O4
DT
4
1_555
hydrog
TYPE_6_PAIR
A
DG
105
A
N7
DG
5
1_555
B
DG
205
B
N2
DG
5
1_555
hydrog
TYPE_6_PAIR
A
DG
105
A
O6
DG
5
1_555
B
DG
205
B
N1
DG
5
1_555
hydrog
TYPE_6_PAIR
A
DG
105
A
N1
DG
5
1_555
C
DG
405
C
O6
DG
5
1_555
hydrog
TYPE_6_PAIR
A
DG
105
A
N2
DG
5
1_555
C
DG
405
C
N7
DG
5
1_555
hydrog
TYPE_6_PAIR
A
DG
106
A
N7
DG
6
1_555
B
DG
206
B
N2
DG
6
1_555
hydrog
TYPE_6_PAIR
A
DG
106
A
O6
DG
6
1_555
B
DG
206
B
N1
DG
6
1_555
hydrog
TYPE_6_PAIR
A
DG
106
A
N1
DG
6
1_555
C
DG
406
C
O6
DG
6
1_555
hydrog
TYPE_6_PAIR
A
DG
106
A
N2
DG
6
1_555
C
DG
406
C
N7
DG
6
1_555
hydrog
DC-DC MISPAIR
A
DC
107
A
N4
DC
7
1_555
B
DC
207
B
N3
DC
7
1_555
hydrog
DC-DC MISPAIR
A
DC
107
A
N3
DC
7
1_555
C
DC
407
C
N4
DC
7
1_555
hydrog
DT-DT MISPAIR
B
DT
201
B
O4
DT
1
1_555
D
DT
301
D
N3
DT
1
1_555
hydrog
TYPE_6_PAIR
B
DG
202
B
N7
DG
2
1_555
D
DG
302
D
N2
DG
2
1_555
hydrog
TYPE_6_PAIR
B
DG
202
B
O6
DG
2
1_555
D
DG
302
D
N1
DG
2
1_555
hydrog
TYPE_6_PAIR
B
DG
203
B
N7
DG
3
1_555
D
DG
303
D
N2
DG
3
1_555
hydrog
TYPE_6_PAIR
B
DG
203
B
O6
DG
3
1_555
D
DG
303
D
N1
DG
3
1_555
hydrog
DT-DT MISPAIR
B
DT
204
B
O4
DT
4
1_555
D
DT
304
D
N3
DT
4
1_555
hydrog
TYPE_6_PAIR
B
DG
205
B
N7
DG
5
1_555
D
DG
305
D
N2
DG
5
1_555
hydrog
TYPE_6_PAIR
B
DG
205
B
O6
DG
5
1_555
D
DG
305
D
N1
DG
5
1_555
hydrog
TYPE_6_PAIR
B
DG
206
B
N7
DG
6
1_555
D
DG
306
D
N2
DG
6
1_555
hydrog
TYPE_6_PAIR
B
DG
206
B
O6
DG
6
1_555
D
DG
306
D
N1
DG
6
1_555
hydrog
DC-DC MISPAIR
B
DC
207
B
N4
DC
7
1_555
D
DC
307
D
N3
DC
7
1_555
hydrog
DT-DT MISPAIR
C
DT
401
C
N3
DT
1
1_555
D
DT
301
D
O4
DT
1
1_555
hydrog
TYPE_6_PAIR
C
DG
402
C
N1
DG
2
1_555
D
DG
302
D
O6
DG
2
1_555
hydrog
TYPE_6_PAIR
C
DG
402
C
N2
DG
2
1_555
D
DG
302
D
N7
DG
2
1_555
hydrog
TYPE_6_PAIR
C
DG
403
C
N1
DG
3
1_555
D
DG
303
D
O6
DG
3
1_555
hydrog
TYPE_6_PAIR
C
DG
403
C
N2
DG
3
1_555
D
DG
303
D
N7
DG
3
1_555
hydrog
DT-DT MISPAIR
C
DT
404
C
N3
DT
4
1_555
D
DT
304
D
O4
DT
4
1_555
hydrog
TYPE_6_PAIR
C
DG
405
C
N1
DG
5
1_555
D
DG
305
D
O6
DG
5
1_555
hydrog
TYPE_6_PAIR
C
DG
405
C
N2
DG
5
1_555
D
DG
305
D
N7
DG
5
1_555
hydrog
TYPE_6_PAIR
C
DG
406
C
N1
DG
6
1_555
D
DG
306
D
O6
DG
6
1_555
hydrog
TYPE_6_PAIR
C
DG
406
C
N2
DG
6
1_555
D
DG
306
D
N7
DG
6
1_555
hydrog
DC-DG PAIR
C
DC
407
C
N4
DC
7
1_555
D
DG
306
D
O6
DG
6
1_555
hydrog
DC-DC MISPAIR
C
DC
407
C
N3
DC
7
1_555
D
DC
307
D
N4
DC
7
1_555
DNA
T-tetrad, G-quadruplex, Telomere, Yeast, Saccharomyces cerevisiae, DNA
1EMQ
PDB
1
1EMQ
101
107
1EMQ
101
107
1EMQ
A
1
1
7
201
207
1EMQ
201
207
1EMQ
B
1
1
7
401
407
1EMQ
401
407
1EMQ
C
1
1
7
301
307
1EMQ
301
307
1EMQ
D
1
1
7
1
P 1