0.055617
0.000000
0.000000
0.000000
0.032499
0.000000
0.000000
0.000000
0.022341
0.00000
0.00000
0.00000
Cervi, A.R.
Guy, A.
Leonard, G.A.
Teoule, R.
Hunter, W.N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
17.980
30.770
44.760
C10 H16 N3 O7 P
321.224
n
N4-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
DNA linking
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
H2 O
18.015
WATER
non-polymer
N
1
N
P
N
2
N
O
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
R
C
N
10
N
N
N
11
N
C
N
12
N
C
N
13
N
O
N
14
N
N
N
15
N
C
N
16
N
N
N
17
N
C
N
18
N
C
N
19
N
C
N
20
S
C
N
21
N
O
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
O
N
39
N
P
N
40
N
O
N
41
N
O
N
42
N
O
N
43
N
C
N
44
R
C
N
45
N
O
N
46
S
C
N
47
N
O
N
48
N
C
N
49
R
C
N
50
N
N
N
51
N
C
N
52
N
O
N
53
N
N
N
54
N
C
N
55
N
N
N
56
N
C
N
57
N
C
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
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
O
N
73
N
P
N
74
N
O
N
75
N
O
N
76
N
O
N
77
N
C
N
78
R
C
N
79
N
O
N
80
S
C
N
81
N
O
N
82
N
C
N
83
R
C
Y
84
N
N
Y
85
N
C
Y
86
N
N
Y
87
N
C
N
88
N
C
N
89
N
O
N
90
N
N
N
91
N
C
N
92
N
N
N
93
N
N
Y
94
N
C
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
106
N
H
N
107
N
H
N
108
N
H
N
109
N
O
N
110
N
H
N
111
N
H
N
1
N
doub
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
doub
N
21
N
sing
N
22
N
doub
N
23
N
sing
N
24
N
doub
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
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
doub
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
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
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
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
21
5623
5629
10.1093/nar/21.24.5623
8284207
The crystal structure of N4-methylcytosine.guanosine base-pairs in the synthetic hexanucleotide d(CGCGm4CG).
1993
10.2210/pdb133d/pdb
pdb_0000133d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
295.00
1
DIFFRACTOMETER
RIGAKU AFC-5
x-ray
1
1.0
ROTATING ANODE
RIGAKU RU200
1824.232
DNA (5'-D(*CP*GP*CP*GP*(C34)P*G)-3')
2
syn
polymer
18.015
water
49
nat
water
no
yes
(DC)(DG)(DC)(DG)(C34)(DG)
CGCGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
1.70
27.51
VAPOR DIFFUSION
6.50
pH 6.50, VAPOR DIFFUSION, temperature 277.00K
277.00
WATER
1
MPD
1
NA CACODYLATE
1
MGCL2
1
SPERMINE_HCL
1
WATER
2
MPD
2
3.579
1
19
A
1
B
12
2.750
A_DC1:DG12_B
1
-2.919
-0.567
0.473
-0.438
0.205
1
19
A
2
B
11
6.091
A_DG2:C3411_B
2
0.691
0.513
0.125
-0.393
1.897
1
19
A
3
B
10
-0.082
A_DC3:DG10_B
3
-3.169
-0.048
0.101
-0.242
-7.509
1
19
A
4
B
9
6.510
A_DG4:DC9_B
4
2.953
0.372
0.059
-0.212
1.441
1
19
A
5
B
8
0.065
A_C345:DG8_B
5
-2.156
-0.320
0.108
-0.511
-11.755
1
19
A
6
B
7
0.482
A_DG6:DC7_B
6
6.155
0.525
-0.206
0.039
2.449
-8.594
A
A
1
2
-9.837
B
B
12
11
3.825
1.426
0.349
5.211
AA_DC1DG2:C3411DG12_BB
1
3.429
23.658
-7.752
-38.423
11.097
3.405
-50.684
A
A
2
3
4.038
B
B
11
10
3.484
-3.454
-0.350
-1.181
AA_DG2DC3:DG10C3411_BB
2
0.523
0.611
-50.572
1.637
-0.370
4.624
-8.277
A
A
3
4
9.788
B
B
10
9
3.850
-1.402
0.348
5.336
AA_DC3DG4:DC9DG10_BB
3
1.028
7.174
-8.093
-31.948
6.089
3.275
-55.853
A
A
4
5
5.845
B
B
9
8
3.365
-5.468
-0.292
-0.886
AA_DG4C345:DG8DC9_BB
4
0.891
0.952
-55.599
1.266
-0.260
3.402
-7.355
A
A
5
6
-0.889
B
B
8
7
3.732
0.112
0.245
5.581
AA_C345DG6:DC7DG8_BB
5
2.202
17.430
-7.017
-43.939
10.422
chem_comp_atom
chem_comp_bond
database_2
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1994-01-15
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
BNL
Y
NDB
1993-07-29
REL
REL
HOH
water
HOH
14
2
HOH
HOH
14
A
HOH
15
2
HOH
HOH
15
A
HOH
16
2
HOH
HOH
16
A
HOH
19
2
HOH
HOH
19
A
HOH
20
2
HOH
HOH
20
A
HOH
24
2
HOH
HOH
24
A
HOH
26
2
HOH
HOH
26
A
HOH
27
2
HOH
HOH
27
A
HOH
28
2
HOH
HOH
28
A
HOH
29
2
HOH
HOH
29
A
HOH
33
2
HOH
HOH
33
A
HOH
34
2
HOH
HOH
34
A
HOH
35
2
HOH
HOH
35
A
HOH
38
2
HOH
HOH
38
A
HOH
41
2
HOH
HOH
41
A
HOH
42
2
HOH
HOH
42
A
HOH
43
2
HOH
HOH
43
A
HOH
44
2
HOH
HOH
44
A
HOH
49
2
HOH
HOH
49
A
HOH
50
2
HOH
HOH
50
A
HOH
52
2
HOH
HOH
52
A
HOH
53
2
HOH
HOH
53
A
HOH
56
2
HOH
HOH
56
A
HOH
57
2
HOH
HOH
57
A
HOH
58
2
HOH
HOH
58
A
HOH
59
2
HOH
HOH
59
A
HOH
61
2
HOH
HOH
61
A
HOH
13
2
HOH
HOH
13
B
HOH
17
2
HOH
HOH
17
B
HOH
18
2
HOH
HOH
18
B
HOH
21
2
HOH
HOH
21
B
HOH
22
2
HOH
HOH
22
B
HOH
23
2
HOH
HOH
23
B
HOH
25
2
HOH
HOH
25
B
HOH
30
2
HOH
HOH
30
B
HOH
31
2
HOH
HOH
31
B
HOH
32
2
HOH
HOH
32
B
HOH
36
2
HOH
HOH
36
B
HOH
37
2
HOH
HOH
37
B
HOH
39
2
HOH
HOH
39
B
HOH
40
2
HOH
HOH
40
B
HOH
45
2
HOH
HOH
45
B
HOH
46
2
HOH
HOH
46
B
HOH
47
2
HOH
HOH
47
B
HOH
48
2
HOH
HOH
48
B
HOH
51
2
HOH
HOH
51
B
HOH
54
2
HOH
HOH
54
B
HOH
55
2
HOH
HOH
55
B
HOH
60
2
HOH
HOH
60
B
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
+C
5
n
5
C34
5
A
G
6
n
6
DG
6
A
C
7
n
1
DC
7
B
G
8
n
2
DG
8
B
C
9
n
3
DC
9
B
G
10
n
4
DG
10
B
+C
11
n
5
C34
11
B
G
12
n
6
DG
12
B
author_defined_assembly
2
dimeric
A
C34
5
A
C34
5
DC
B
C34
11
B
C34
5
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
1
A
A
O
O
HOH
HOH
34
52
2.10
1
7.54
1.20
115.70
123.24
A
A
A
C5'
C4'
C3'
DC
DC
DC
1
1
1
N
1
5.75
0.30
108.30
114.05
A
A
A
O4'
C1'
N1
DC
DC
DC
1
1
1
N
1
-2.65
0.40
121.90
119.25
A
A
A
N3
C4
C5
DC
DC
DC
1
1
1
N
1
-10.53
0.80
109.40
98.87
A
A
A
O5'
C5'
C4'
DG
DG
DG
2
2
2
N
1
4.93
0.60
106.00
110.93
A
A
A
O4'
C4'
C3'
DG
DG
DG
2
2
2
N
1
-3.93
0.60
125.10
121.17
A
A
A
C6
N1
C2
DG
DG
DG
2
2
2
N
1
3.44
0.50
111.50
114.94
A
A
A
C5
C6
N1
DG
DG
DG
2
2
2
N
1
12.99
1.20
119.70
132.69
A
A
A
C3'
O3'
P
DG
DG
DC
2
2
3
Y
1
-9.75
1.50
119.60
109.85
A
A
A
OP1
P
OP2
DC
DC
DC
3
3
3
N
1
4.43
0.30
108.30
112.73
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
-8.04
0.80
109.40
101.36
A
A
A
O5'
C5'
C4'
DG
DG
DG
4
4
4
N
1
3.16
0.50
111.50
114.66
A
A
A
C5
C6
N1
DG
DG
DG
4
4
4
N
1
10.57
1.20
119.70
130.27
A
A
A
C3'
O3'
P
DG
DG
C34
4
4
5
Y
1
-6.44
0.80
109.40
102.96
A
A
A
O5'
C5'
C4'
DG
DG
DG
6
6
6
N
1
1.97
0.30
108.30
110.27
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
-5.61
0.90
116.20
110.59
A
A
A
N1
C2
N2
DG
DG
DG
6
6
6
N
1
4.72
0.70
119.90
124.62
A
A
A
N3
C2
N2
DG
DG
DG
6
6
6
N
1
-4.57
0.60
119.90
115.33
A
A
A
N1
C6
O6
DG
DG
DG
6
6
6
N
1
-6.44
0.80
109.40
102.96
B
B
B
O5'
C5'
C4'
DG
DG
DG
8
8
8
N
1
-11.30
1.60
120.90
109.60
B
B
B
P
O5'
C5'
DG
DG
DG
8
8
8
N
1
1.95
0.30
108.30
110.25
B
B
B
O4'
C1'
N9
DG
DG
DG
8
8
8
N
1
-4.26
0.60
125.10
120.84
B
B
B
C6
N1
C2
DG
DG
DG
8
8
8
N
1
4.28
0.50
111.50
115.78
B
B
B
C5
C6
N1
DG
DG
DG
8
8
8
N
1
15.81
1.20
119.70
135.51
B
B
B
C3'
O3'
P
DG
DG
DC
8
8
9
Y
1
-10.48
1.50
119.60
109.12
B
B
B
OP1
P
OP2
DC
DC
DC
9
9
9
N
1
-9.63
0.80
109.40
99.77
B
B
B
O5'
C5'
C4'
DC
DC
DC
9
9
9
N
1
-9.48
0.80
105.90
96.42
B
B
B
O4'
C1'
C2'
DC
DC
DC
9
9
9
N
1
3.45
0.30
108.30
111.75
B
B
B
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
-10.11
1.20
119.70
109.59
B
B
B
C3'
O3'
P
DC
DC
DG
9
9
10
Y
1
7.63
1.20
110.70
118.33
B
B
B
O5'
P
OP2
DG
DG
DG
10
10
10
N
1
3.75
0.30
108.30
112.05
B
B
B
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
3.16
0.50
111.50
114.66
B
B
B
C5
C6
N1
DG
DG
DG
10
10
10
N
1
-3.98
0.60
119.90
115.92
B
B
B
N1
C6
O6
DG
DG
DG
10
10
10
N
1
-12.25
0.80
109.40
97.15
B
B
B
O5'
C5'
C4'
DG
DG
DG
12
12
12
N
1
-5.42
0.70
102.20
96.78
B
B
B
C4'
C3'
C2'
DG
DG
DG
12
12
12
N
1
8.41
0.30
108.30
116.71
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
-5.65
0.60
125.10
119.45
B
B
B
C6
N1
C2
DG
DG
DG
12
12
12
N
1
3.86
0.60
123.90
127.76
B
B
B
N1
C2
N3
DG
DG
DG
12
12
12
N
1
4.65
0.50
111.50
116.15
B
B
B
C5
C6
N1
DG
DG
DG
12
12
12
N
1
A
A
O4'
C1'
DG
DG
2
2
0.085
0.011
1.420
1.505
N
1
B
B
P
O5'
DG
DG
8
8
0.070
0.010
1.593
1.663
N
1
A
A
O
O
HOH
HOH
28
61
2.00
1_555
2_664
1
B
A
OP1
O
DG
HOH
8
43
2.19
1_555
3_756
0.189
1.800
8.000
1495
1
1.000
TR
isotropic
TR
isotropic
1.800
8.000
49
291
2
240
0
0.019
0.025
0.028
0.029
fix
fix
1.500
133D
2994
1
refinement
NUCLSQ
refinement
X-PLOR
THE CRYSTAL STRUCTURE OF N4-METHYLCYTOSINE.GUANOSIN BASE-PAIRS IN THE SYNTHETIC HEXANUCLEOTIDE D(CGCGM(4)CG)
1
N
N
1
N
N
2
N
N
2
N
N
covale
1.578
both
A
DG
4
A
O3'
DG
4
1_555
A
C34
5
A
P
C34
5
1_555
covale
1.609
both
A
C34
5
A
O3'
C34
5
1_555
A
DG
6
A
P
DG
6
1_555
covale
1.629
both
B
DG
10
B
O3'
DG
4
1_555
B
C34
11
B
P
C34
5
1_555
covale
1.642
both
B
C34
11
B
O3'
C34
5
1_555
B
DG
12
B
P
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
12
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
12
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
12
B
N2
DG
6
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
C34
11
B
N3
C34
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
C34
11
B
O2
C34
5
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
C34
11
B
N4
C34
5
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
10
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
10
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
10
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
9
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
9
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
9
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
C34
5
A
N3
C34
5
1_555
B
DG
8
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
C34
5
A
N4
C34
5
1_555
B
DG
8
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
C34
5
A
O2
C34
5
1_555
B
DG
8
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
7
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
7
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
7
B
N4
DC
1
1_555
DNA
Z-DNA, DOUBLE HELIX, MODIFIED, DNA
133D
PDB
1
133D
1
6
133D
1
6
133D
A
1
1
6
7
12
133D
7
12
133D
B
1
1
6
19
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