1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
SOME OF THE CYTIDINES ARE PROTONATED AT THE N3 POSITION. THESE RESIDUES HAVE BEEN ASSIGNED THE RESIDUE NAME C IN THE ENTRY AND ATOM H3 HAS BEEN FOOTNOTED.
Leroy, J.-L.
Gueron, M.
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 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N3 O4
241.244
n
5-METHYL-2'-DEOXYCYTIDINE
DNA linking
UK
Structure
STRUE6
2005
0969-2126
3
101
120
10.1016/S0969-2126(01)00138-1
7743125
Solution structures of the i-motif tetramers of d(TCC), d(5methylCCT) and d(T5methylCC): novel NOE connections between amino protons and sugar protons.
1995
10.2210/pdb106d/pdb
pdb_0000106d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
771.646
DNA (5'-D(*MCYP*CP*T)-3')
4
syn
polymer
no
yes
(MCY)(DC)(DT)
CCT
A,B,C,D
polydeoxyribonucleotide
n
n
n
-21.458
2
14
A
1
C
7
179.007
A_MCY1:MCY7_C
1
12.891
2.094
-0.173
0.183
11.400
2
15
D
11
B
5
178.287
D_DC11:DC5_B
2
31.811
2.486
0.743
2.477
-6.151
2
15
A
2
C
8
-179.371
A_DC2:DC8_C
3
-26.612
-2.238
-0.070
-2.274
-8.183
2
15
D
10
B
4
179.363
D_MCY10:MCY4_B
4
13.564
2.423
-0.074
2.151
-0.021
-170.870
A
D
1
11
-58.376
C
B
7
5
-0.211
112.622
-2.981
3.287
AD_MCY1DC11:DC5MCY7_BC
1
127.617
66.149
-42.438
-1.596
-1.555
0.757
-174.244
D
A
11
2
73.763
B
C
5
8
0.932
-144.398
-1.812
-0.708
DA_DC11DC2:DC8DC5_CB
2
96.575
49.333
-47.266
0.814
-0.600
-0.019
-179.577
A
D
2
10
72.330
C
B
8
4
-0.022
-144.428
3.440
2.525
AD_DC2MCY10:MCY4DC8_BC
3
106.663
53.417
-43.065
-1.274
1.712
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1995-02-07
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_struct_conn.pdbx_leaving_atom_flag
Y
BNL
1994-12-22
REL
8
5MC STANDS FOR 5-METHYLCYTIDINE. THE STRUCTURE IS FORMED OF FOUR EQUIVALENT 5MCCT STRANDS DESIGNATED A, B, C, D. STRANDS A AND C, CONNECTED BY TWO HEMI-PROTONATED BASE PAIRS (5MC1.5MC1+ AND C2.C2+), FORM A PARALLEL-STRANDED DUPLEX. THE RELATION BETWEEN STRANDS B AND D IS THE SAME AS THAT BETWEEN STRANDS A AND C. THE STRANDS OF EACH DUPLEX ARE RELATED BY A LONGITUDINAL TWO-FOLD SYMMETRY AXIS. THE DUPLEXES HAVE THE SAME LONGITUDINAL AXIS, AND THEY ARE ANTI-PARALLEL. THEIR HEMI-PROTONATED C.C+ BASE PAIRS ARE INTERCALATED FACE-TO-FACE. THE DUPLEXES CAN BE TRANSFORMED INTO ONE ANOTHER BY A 180 DEGREE ROTATION AROUND A TWO-FOLD AXIS PERPENDICULAR TO THE LONGITUDINAL AXIS, AND CONSEQUENTLY AROUND A THIRD AXIS PERPENDICULAR TO THE FIRST TWO. THE H3 IMINO PROTONS OF THE HEMI-PROTONATED 5MC1.5MC1+ PAIRS WERE NOT INCORPORATED IN THE COMPUTATIONS. THOSE OF THE C2.C2+ PAIRS WERE ARBITRARILY LOCATED ON THE C2 RESIDUES OF STRANDS A AND B, RESPECTIVELY.
MCY
1
n
1
MCY
1
A
DC
2
n
2
DC
2
A
DT
3
n
3
DT
3
A
MCY
4
n
1
MCY
4
B
DC
5
n
2
DC
5
B
DT
6
n
3
DT
6
B
MCY
7
n
1
MCY
7
C
DC
8
n
2
DC
8
C
DT
9
n
3
DT
9
C
MCY
10
n
1
MCY
10
D
DC
11
n
2
DC
11
D
DT
12
n
3
DT
12
D
author_defined_assembly
4
tetrameric
A
MCY
1
5-METHYL-2'-DEOXYCYTIDINE
A
MCY
1
DC
B
MCY
4
5-METHYL-2'-DEOXYCYTIDINE
B
MCY
1
DC
C
MCY
7
5-METHYL-2'-DEOXYCYTIDINE
C
MCY
1
DC
D
MCY
10
5-METHYL-2'-DEOXYCYTIDINE
D
MCY
1
DC
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
2
B
C
HO3'
HO5'
DT
MCY
6
7
1.26
8
B
C
HO5'
HO3'
MCY
DT
4
9
1.24
8
B
C
HO3'
HO5'
DT
MCY
6
7
1.34
1
2.91
0.30
108.30
111.21
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
3.25
0.50
119.90
123.15
A
A
A
C2
N3
C4
DC
DC
DC
2
2
2
N
1
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
1
2.01
0.30
108.30
110.31
B
B
B
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
3.24
0.50
119.90
123.14
B
B
B
C2
N3
C4
DC
DC
DC
5
5
5
N
1
2.68
0.30
108.30
110.98
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
2.17
0.30
108.30
110.47
C
C
C
O4'
C1'
N1
DC
DC
DC
8
8
8
N
1
2.73
0.30
108.30
111.03
C
C
C
O4'
C1'
N1
DT
DT
DT
9
9
9
N
1
2.74
0.30
108.30
111.04
D
D
D
O4'
C1'
N1
DC
DC
DC
11
11
11
N
1
2.87
0.30
108.30
111.17
D
D
D
O4'
C1'
N1
DT
DT
DT
12
12
12
N
2
2.28
0.30
108.30
110.58
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
2
3.18
0.50
119.90
123.08
A
A
A
C2
N3
C4
DC
DC
DC
2
2
2
N
2
2.44
0.30
108.30
110.74
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
2
1.82
0.30
108.30
110.12
B
B
B
O4'
C1'
N1
DC
DC
DC
5
5
5
N
2
3.37
0.50
119.90
123.27
B
B
B
C2
N3
C4
DC
DC
DC
5
5
5
N
2
3.83
0.60
118.90
122.73
B
B
B
N1
C2
O2
DC
DC
DC
5
5
5
N
2
2.73
0.30
108.30
111.03
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
2
2.28
0.30
108.30
110.58
C
C
C
O4'
C1'
N1
DC
DC
DC
8
8
8
N
2
2.51
0.30
108.30
110.81
C
C
C
O4'
C1'
N1
DT
DT
DT
9
9
9
N
2
2.63
0.30
108.30
110.93
D
D
D
O4'
C1'
N1
DC
DC
DC
11
11
11
N
2
2.53
0.30
108.30
110.83
D
D
D
O4'
C1'
N1
DT
DT
DT
12
12
12
N
3
2.27
0.30
108.30
110.57
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
3
3.22
0.50
119.90
123.12
A
A
A
C2
N3
C4
DC
DC
DC
2
2
2
N
3
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
3
2.23
0.30
108.30
110.53
B
B
B
O4'
C1'
N1
DC
DC
DC
5
5
5
N
3
3.29
0.50
119.90
123.19
B
B
B
C2
N3
C4
DC
DC
DC
5
5
5
N
3
2.61
0.30
108.30
110.91
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
3
2.36
0.30
108.30
110.66
C
C
C
O4'
C1'
N1
DC
DC
DC
8
8
8
N
3
2.39
0.30
108.30
110.69
C
C
C
O4'
C1'
N1
DT
DT
DT
9
9
9
N
3
2.99
0.30
108.30
111.29
D
D
D
O4'
C1'
N1
DC
DC
DC
11
11
11
N
3
2.55
0.30
108.30
110.85
D
D
D
O4'
C1'
N1
DT
DT
DT
12
12
12
N
4
3.00
0.30
108.30
111.30
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
4
3.18
0.50
119.90
123.08
A
A
A
C2
N3
C4
DC
DC
DC
2
2
2
N
4
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
4
3.19
0.50
119.90
123.09
B
B
B
C2
N3
C4
DC
DC
DC
5
5
5
N
4
3.72
0.60
118.90
122.62
B
B
B
N1
C2
O2
DC
DC
DC
5
5
5
N
4
2.81
0.30
108.30
111.11
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
4
3.06
0.30
108.30
111.36
C
C
C
O4'
C1'
N1
DC
DC
DC
8
8
8
N
4
2.73
0.30
108.30
111.03
C
C
C
O4'
C1'
N1
DT
DT
DT
9
9
9
N
4
2.53
0.30
108.30
110.83
D
D
D
O4'
C1'
N1
DC
DC
DC
11
11
11
N
4
2.73
0.30
108.30
111.03
D
D
D
O4'
C1'
N1
DT
DT
DT
12
12
12
N
5
2.46
0.30
108.30
110.76
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
5
3.31
0.50
119.90
123.21
A
A
A
C2
N3
C4
DC
DC
DC
2
2
2
N
5
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
5
2.51
0.30
108.30
110.81
B
B
B
O4'
C1'
N1
DC
DC
DC
5
5
5
N
5
3.34
0.50
119.90
123.24
B
B
B
C2
N3
C4
DC
DC
DC
5
5
5
N
5
2.88
0.30
108.30
111.18
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
5
2.26
0.30
108.30
110.56
C
C
C
O4'
C1'
N1
DC
DC
DC
8
8
8
N
5
2.40
0.30
108.30
110.70
C
C
C
O4'
C1'
N1
DT
DT
DT
9
9
9
N
5
2.46
0.30
108.30
110.76
D
D
D
O4'
C1'
N1
DC
DC
DC
11
11
11
N
5
2.55
0.30
108.30
110.85
D
D
D
O4'
C1'
N1
DT
DT
DT
12
12
12
N
6
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
6
3.27
0.50
119.90
123.17
A
A
A
C2
N3
C4
DC
DC
DC
2
2
2
N
6
2.67
0.30
108.30
110.97
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
6
2.05
0.30
108.30
110.35
B
B
B
O4'
C1'
N1
DC
DC
DC
5
5
5
N
6
3.31
0.50
119.90
123.21
B
B
B
C2
N3
C4
DC
DC
DC
5
5
5
N
6
2.70
0.30
108.30
111.00
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
6
2.42
0.30
108.30
110.72
C
C
C
O4'
C1'
N1
DC
DC
DC
8
8
8
N
6
2.51
0.30
108.30
110.81
C
C
C
O4'
C1'
N1
DT
DT
DT
9
9
9
N
6
2.33
0.30
108.30
110.63
D
D
D
O4'
C1'
N1
DC
DC
DC
11
11
11
N
6
2.60
0.30
108.30
110.90
D
D
D
O4'
C1'
N1
DT
DT
DT
12
12
12
N
7
2.40
0.30
108.30
110.70
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
7
3.29
0.50
119.90
123.19
A
A
A
C2
N3
C4
DC
DC
DC
2
2
2
N
7
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
7
2.39
0.30
108.30
110.69
B
B
B
O4'
C1'
N1
DC
DC
DC
5
5
5
N
7
3.24
0.50
119.90
123.14
B
B
B
C2
N3
C4
DC
DC
DC
5
5
5
N
7
2.58
0.30
108.30
110.88
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
7
2.58
0.30
108.30
110.88
C
C
C
O4'
C1'
N1
DC
DC
DC
8
8
8
N
7
2.44
0.30
108.30
110.74
C
C
C
O4'
C1'
N1
DT
DT
DT
9
9
9
N
7
2.09
0.30
108.30
110.39
D
D
D
O4'
C1'
N1
DC
DC
DC
11
11
11
N
7
2.67
0.30
108.30
110.97
D
D
D
O4'
C1'
N1
DT
DT
DT
12
12
12
N
8
2.15
0.30
108.30
110.45
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
8
3.33
0.50
119.90
123.23
A
A
A
C2
N3
C4
DC
DC
DC
2
2
2
N
8
2.61
0.30
108.30
110.91
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
8
2.18
0.30
108.30
110.48
B
B
B
O4'
C1'
N1
DC
DC
DC
5
5
5
N
8
3.32
0.50
119.90
123.22
B
B
B
C2
N3
C4
DC
DC
DC
5
5
5
N
8
2.48
0.30
108.30
110.78
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
8
2.40
0.30
108.30
110.70
C
C
C
O4'
C1'
N1
DC
DC
DC
8
8
8
N
8
3.08
0.30
108.30
111.38
C
C
C
O4'
C1'
N1
DT
DT
DT
9
9
9
N
8
2.28
0.30
108.30
110.58
D
D
D
O4'
C1'
N1
DC
DC
DC
11
11
11
N
8
2.58
0.30
108.30
110.88
D
D
D
O4'
C1'
N1
DT
DT
DT
12
12
12
N
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
Solution structures of the i-motif tetramers of D(TCC), D(5MCCT) and D(T5MCC). Novel NOE connections between amino protons and sugar protons
1
N
N
1
N
N
1
N
N
1
N
N
covale
1.614
both
A
MCY
1
A
O3'
MCY
1
1_555
A
DC
2
A
P
DC
2
1_555
covale
1.611
both
B
MCY
4
B
O3'
MCY
1
1_555
B
DC
5
B
P
DC
2
1_555
covale
1.612
both
C
MCY
7
C
O3'
MCY
1
1_555
C
DC
8
C
P
DC
2
1_555
covale
1.613
both
D
MCY
10
D
O3'
MCY
1
1_555
D
DC
11
D
P
DC
2
1_555
hydrog
TYPE_14_PAIR
A
MCY
1
A
N3
MCY
1
1_555
C
MCY
7
C
N4
MCY
1
1_555
hydrog
TYPE_14_PAIR
A
MCY
1
A
N4
MCY
1
1_555
C
MCY
7
C
N3
MCY
1
1_555
hydrog
DC-DC MISPAIR
A
DC
2
A
N4
DC
2
1_555
B
DC
5
B
N3
DC
2
1_555
hydrog
TYPE_15_PAIR
A
DC
2
A
N4
DC
2
1_555
C
DC
8
C
O2
DC
2
1_555
hydrog
TYPE_15_PAIR
A
DC
2
A
O2
DC
2
1_555
C
DC
8
C
N4
DC
2
1_555
hydrog
TYPE_15_PAIR
B
MCY
4
B
N4
MCY
1
1_555
D
MCY
10
D
O2
MCY
1
1_555
hydrog
TYPE_15_PAIR
B
MCY
4
B
O2
MCY
1
1_555
D
MCY
10
D
N4
MCY
1
1_555
hydrog
TYPE_15_PAIR
B
DC
5
B
N4
DC
2
1_555
D
DC
11
D
O2
DC
2
1_555
hydrog
TYPE_15_PAIR
B
DC
5
B
O2
DC
2
1_555
D
DC
11
D
N4
DC
2
1_555
DNA
DNA
106D
PDB
1
106D
1
3
106D
1
3
106D
A
1
1
3
4
6
106D
4
6
106D
B
1
1
3
7
9
106D
7
9
106D
C
1
1
3
10
12
106D
10
12
106D
D
1
1
3
1
P 1