1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Gochin, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C7 H14 O4
162.184
2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose
D-saccharide, alpha linking
C8 H14 O5
190.194
4-O-acetyl-2,6-dideoxy-beta-D-galactopyranose
D-saccharide, beta linking
Co 2
58.933
COBALT (II) ION
non-polymer
C21 H24 O9
420.410
(1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose
None
non-polymer
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C6 H12 O4
148.157
beta-D-Olivopyranose
2,6-DIDEOXY-BETA-D-MANNOSE
D-saccharide, beta 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
C9 H16 O5
204.220
n
3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose
L-saccharide, alpha linking
UK
Structure Fold.Des.
FODEFH
1263
0969-2126
8
441
452
10.1016/S0969-2126(00)00124-6
10801486
A high-resolution structure of a DNA-chromomycin-Co(II) complex determined from pseudocontact shifts in nuclear magnetic resonance.
2000
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
121
9276
9285
10.1021/ja9904540
Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally determined constraints
1999
DC A 6 HAS WRONG CHIRALITY AT ATOM C4'
DA A 8 HAS WRONG CHIRALITY AT ATOM C3'
DA B 18 HAS WRONG CHIRALITY AT ATOM C4'
DA B 18 HAS WRONG CHIRALITY AT ATOM C3'
2GL D 1 HAS WRONG CHIRALITY AT ATOM C5
DDA E 1 HAS WRONG CHIRALITY AT ATOM C4
DDA F 1 HAS WRONG CHIRALITY AT ATOM C4
CPH A 33 HAS WRONG CHIRALITY AT ATOM C4'
DA A 8 HAS WRONG CHIRALITY AT ATOM C4'
CPH A 33 HAS WRONG CHIRALITY AT ATOM C1'
CPH B 23 HAS WRONG CHIRALITY AT ATOM C1'
DT B 11 HAS WRONG CHIRALITY AT ATOM C1'
DA A 7 HAS WRONG CHIRALITY AT ATOM C3'
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
TWO MOLECULES OF THE DRUG CHROMOMYCIN A3 (1GL-2GL-DXB-DDA-DDA-1AR, CHAINS C, AND D) ARE BOUND IN THE MINOR GROOVE
2426.617
DNA (5'-D(*TP*TP*GP*GP*CP*CP*AP*A)-3')
2
syn
polymer
334.363
2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-4-O-acetyl-2,6-dideoxy-beta-D-galactopyranose
2
man
branched
464.504
3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-beta-D-Olivopyranose-(1-3)-beta-D-Olivopyranose
2
man
branched
58.933
COBALT (II) ION
1
syn
non-polymer
420.410
(1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose
2
syn
non-polymer
no
no
(DT)(DT)(DG)(DG)(DC)(DC)(DA)(DA)
TTGGCCAA
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
37.450
1
20
A
1
B
18
0.780
A_DT1:DA18_B
1
1.800
0.129
0.166
-0.092
5.331
1
20
A
2
B
17
-3.144
A_DT2:DA17_B
2
-12.926
-0.124
-0.528
-0.037
-5.698
1
19
A
3
B
16
0.814
A_DG3:DC16_B
3
-5.686
-0.498
0.043
-0.174
-2.005
1
19
A
4
B
15
-4.783
A_DG4:DC15_B
4
-24.815
0.074
0.454
-0.256
5.560
1
19
A
5
B
14
-3.867
A_DC5:DG14_B
5
-23.428
-0.195
0.374
-0.157
7.791
1
19
A
6
B
13
0.416
A_DC6:DG13_B
6
-5.754
0.303
-0.185
-0.139
4.611
1
20
A
7
B
12
-2.372
A_DA7:DT12_B
7
-13.027
0.252
-0.273
-0.063
-41.202
1
20
A
8
B
11
8.589
A_DA8:DT11_B
8
4.684
-0.156
0.597
-0.178
2.737
44.126
A
A
1
2
38.364
B
B
18
17
4.260
26.401
0.301
-0.937
AA_DT1DT2:DA17DA18_BB
1
14.507
-21.081
32.625
-4.348
1.303
2.696
32.317
A
A
2
3
25.645
B
B
17
16
3.525
13.770
0.706
-0.824
AA_DT2DG3:DC16DA17_BB
2
-5.323
9.912
28.828
-3.941
-2.219
3.468
31.414
A
A
3
4
2.051
B
B
16
15
3.395
1.106
1.091
-1.536
AA_DG3DG4:DC15DC16_BB
3
4.976
-9.229
31.008
-3.055
-1.030
2.645
29.141
A
A
4
5
4.569
B
B
15
14
2.830
2.297
0.029
-2.291
AA_DG4DC5:DG14DC15_BB
4
-0.093
0.185
29.052
-4.975
-0.074
3.542
31.513
A
A
5
6
-1.827
B
B
14
13
3.395
-0.988
-0.868
-1.791
AA_DC5DC6:DG13DG14_BB
5
-5.089
9.411
31.094
-3.101
0.585
3.190
31.161
A
A
6
7
16.323
B
B
13
12
3.719
8.576
-0.706
-0.448
AA_DC6DA7:DT12DG13_BB
6
7.418
-14.119
29.072
-2.625
2.862
3.395
50.320
A
A
7
8
39.505
B
B
12
11
4.596
30.659
-0.198
-0.092
AA_DA7DA8:DT11DT12_BB
7
-17.452
22.488
36.472
-3.293
-1.581
atom_site
chem_comp
database_PDB_caveat
entity
pdbx_branch_scheme
pdbx_chem_comp_identifier
pdbx_entity_branch
pdbx_entity_branch_descriptor
pdbx_entity_branch_link
pdbx_entity_branch_list
pdbx_entity_nonpoly
pdbx_nmr_software
pdbx_nonpoly_scheme
pdbx_struct_assembly_gen
pdbx_struct_conn_angle
pdbx_unobs_or_zero_occ_atoms
pdbx_validate_chiral
pdbx_validate_close_contact
struct_asym
struct_conn
struct_site
struct_site_gen
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Version format compliance
Advisory
Advisory
Atomic model
Data collection
Derived calculations
Structure summary
1
0
2000-03-20
1
1
2008-04-27
1
2
2011-07-13
1
3
2011-12-28
2
0
2020-07-29
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.label_asym_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_entity_id
_atom_site.type_symbol
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.type
_pdbx_nmr_software.name
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr2_label_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.value
A
2GL
32
n
C
2GL
1
A
1GL
31
n
C
1GL
2
B
2GL
22
n
D
2GL
1
B
1GL
21
n
D
1GL
2
B
DDA
26
n
E
DDA
1
B
DDA
25
n
E
DDA
2
B
ERI
24
n
E
ERI
3
B
DDA
36
n
F
DDA
1
B
DDA
35
n
F
DDA
2
B
ERI
34
n
F
ERI
3
a-D-2-deoxy-Fucp4OMe
DOlib
b-D-Olivopyranose
b-D-2,6-deoxy-Glcp
Oli
2000-03-20
SPRSDE
the average structure
RCSB
Y
RCSB
2000-03-08
REL
REL
oligosaccharide
oligosaccharide
WURCS=2.0/2,2,1/[ad112m-1b_1-5_4*OCC/3=O][ad112m-1a_1-5_4*OC]/1-2/a3-b1
2
PDB2Glycan
1.1.0
WURCS
[][b-D-2-deoxy-Fucp4Ac]{[(3+1)][a-D-2-deoxy-Fucp4Me]{}}
2
PDB-CARE
LINUCS
WURCS=2.0/2,3,2/[ad122m-1b_1-5][ad611m-1a_1-5_3*C_4*OCC/3=O]/1-1-2/a3-b1_b3-c1
3
PDB2Glycan
1.1.0
WURCS
[][b-D-2,6-deoxy-Glcp]{[(3+1)][b-D-2,6-deoxy-Glcp]{[(3+1)][a-L-2,6-deoxy-Glcp4Ac]{}}}
3
PDB-CARE
LINUCS
C1
O3
1GL
2GL
2
1
2
O1
HO3
sing
C1
O3
DDA
DDA
2
1
3
O1
HO3
sing
C1
O3
ERI
DDA
3
2
3
O1
HO3
sing
n
n
n
n
n
CO
COBALT (II) ION
CPH
(1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose
THE STRUCTURE WAS DETERMINED USING PSEUDOCONTACT SHIFTS IN THE NMR SPECTRUM. PSEUDOCONTACT SHIFTS WERE MEASURED AS THE DIFFERENCE IN THE CHEMICAL SHIFT BETWEEN THE CO(II) COMPLEX AND THE ZN(II) COMPLEX. IN MODELS 1-3, ONLY SHIFTS WERE USED; IN MODELS 4-6 SHIFTS + NOE'S WERE USED IN REFINEMENT.
MINIMIZED AVERAGED COORDINATES FROM 6 RUNS
100
6
NOESY
COSY
TOCSY
100mM NACL
6.5
1
atm
298
K
Paramagnetic Shifts and NOEs used in refinement. Other REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
simulated annealing
D2O, 90% H2O, 10% D2O
DeLaglio and Bax
processing
NMRPipe
1.7
Kneller and Goddard
data analysis
Sparky
3.0
Brunger (modified by Gochin and Tu)
refinement
X-PLOR
3.0, 3.851
Biosym
data analysis
Felix
2.1
500
GE
OMEGA500
CO
41
4
CO
CO
41
A
CPH
33
5
CPH
CPH
33
A
CPH
23
5
CPH
CPH
23
B
DT
1
n
1
DT
1
A
DT
2
n
2
DT
2
A
DG
3
n
3
DG
3
A
DG
4
n
4
DG
4
A
DC
5
n
5
DC
5
A
DC
6
n
6
DC
6
A
DA
7
n
7
DA
7
A
DA
8
n
8
DA
8
A
DT
11
n
1
DT
11
B
DT
12
n
2
DT
12
B
DG
13
n
3
DG
13
B
DG
14
n
4
DG
14
B
DC
15
n
5
DC
15
B
DC
16
n
6
DC
16
B
DA
17
n
7
DA
17
B
DA
18
n
8
DA
18
B
author_defined_assembly
2
dimeric
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
A
CPH
33
H
O1
CPH
1_555
93.6
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
A
CPH
33
H
C9
CPH
1_555
36.3
A
CPH
33
H
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
A
CPH
33
H
C9
CPH
1_555
78.0
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O9
CPH
1_555
134.2
A
CPH
33
H
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O9
CPH
1_555
123.1
A
CPH
33
H
C9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O9
CPH
1_555
158.6
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O1
CPH
1_555
124.2
A
CPH
33
H
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O1
CPH
1_555
83.5
A
CPH
33
H
C9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O1
CPH
1_555
89.7
B
CPH
23
I
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O1
CPH
1_555
89.2
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C9
CPH
1_555
160.7
A
CPH
33
H
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C9
CPH
1_555
90.1
A
CPH
33
H
C9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C9
CPH
1_555
161.7
B
CPH
23
I
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C9
CPH
1_555
34.3
B
CPH
23
I
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C9
CPH
1_555
75.0
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
O6
CPH
33
H
O6
CPH
1
1
N
1
A
O2
CPH
33
H
O2
CPH
1
1
N
1
B
O6
CPH
23
I
O6
CPH
1
1
N
1
B
O2
CPH
23
I
O2
CPH
1
1
N
2
A
O6
CPH
33
H
O6
CPH
1
1
N
2
A
O2
CPH
33
H
O2
CPH
1
1
N
2
B
O6
CPH
23
I
O6
CPH
1
1
N
2
B
O2
CPH
23
I
O2
CPH
1
1
N
3
A
O6
CPH
33
H
O6
CPH
1
1
N
3
A
O2
CPH
33
H
O2
CPH
1
1
N
3
B
O6
CPH
23
I
O6
CPH
1
1
N
3
B
O2
CPH
23
I
O2
CPH
1
1
N
4
A
O6
CPH
33
H
O6
CPH
1
1
N
4
A
O2
CPH
33
H
O2
CPH
1
1
N
4
B
O6
CPH
23
I
O6
CPH
1
1
N
4
B
O2
CPH
23
I
O2
CPH
1
1
N
5
A
O6
CPH
33
H
O6
CPH
1
1
N
5
A
O2
CPH
33
H
O2
CPH
1
1
N
5
B
O6
CPH
23
I
O6
CPH
1
1
N
5
B
O2
CPH
23
I
O2
CPH
1
1
N
6
A
O6
CPH
33
H
O6
CPH
1
1
N
6
A
O2
CPH
33
H
O2
CPH
1
1
N
6
B
O6
CPH
23
I
O6
CPH
1
1
N
6
B
O2
CPH
23
I
O2
CPH
1
1
N
1
A
C4'
DC
6
WRONG HAND
2
A
C3'
DA
8
WRONG HAND
2
B
C4'
DA
18
WRONG HAND
3
A
C3'
DA
8
WRONG HAND
3
B
C3'
DA
18
WRONG HAND
3
D
C5
2GL
1
WRONG HAND
3
E
C4
DDA
1
WRONG HAND
3
F
C4
DDA
1
WRONG HAND
3
A
C4'
CPH
33
WRONG HAND
4
A
C4'
DA
8
WRONG HAND
4
A
C1'
CPH
33
PLANAR
4
A
C4'
CPH
33
WRONG HAND
4
B
C1'
CPH
23
PLANAR
5
A
C3'
DA
8
WRONG HAND
5
B
C1'
DT
11
WRONG HAND
5
B
C4'
DA
18
WRONG HAND
5
A
C1'
CPH
33
PLANAR
5
B
C1'
CPH
23
PLANAR
6
A
C3'
DA
7
WRONG HAND
6
A
C3'
DA
8
WRONG HAND
6
B
C3'
DA
18
WRONG HAND
6
D
C5
2GL
1
WRONG HAND
6
E
C4
DDA
1
WRONG HAND
6
F
C4
DDA
1
WRONG HAND
6
B
C1'
CPH
23
PLANAR
1
E
B
O1
C2
DDA
CPH
1
23
1.43
1
D
B
O1
C6
2GL
CPH
1
23
1.44
1
C
A
O1
C6
2GL
CPH
1
33
1.45
1
F
A
O1
C2
DDA
CPH
1
33
1.45
2
E
B
O1
C2
DDA
CPH
1
23
1.41
2
F
A
O1
C2
DDA
CPH
1
33
1.44
2
C
A
O1
C6
2GL
CPH
1
33
1.44
2
D
B
O1
C6
2GL
CPH
1
23
1.44
3
E
B
O1
C2
DDA
CPH
1
23
1.42
3
D
B
O1
C6
2GL
CPH
1
23
1.45
3
C
A
O1
C6
2GL
CPH
1
33
1.45
3
F
A
O1
C2
DDA
CPH
1
33
1.48
4
E
B
O1
C2
DDA
CPH
1
23
1.41
4
F
A
O1
C2
DDA
CPH
1
33
1.41
4
D
B
O1
C6
2GL
CPH
1
23
1.44
4
C
A
O1
C6
2GL
CPH
1
33
1.44
5
D
B
O1
C6
2GL
CPH
1
23
1.42
5
E
B
O1
C2
DDA
CPH
1
23
1.42
5
C
A
O1
C6
2GL
CPH
1
33
1.43
5
F
A
O1
C2
DDA
CPH
1
33
1.44
6
D
B
O1
C6
2GL
CPH
1
23
1.43
6
C
A
O1
C6
2GL
CPH
1
33
1.43
6
E
B
O1
C2
DDA
CPH
1
23
1.43
6
F
A
O1
C2
DDA
CPH
1
33
1.44
1
A
DC
6
0.068
SIDE CHAIN
2
B
DT
11
0.066
SIDE CHAIN
2
B
DG
14
0.066
SIDE CHAIN
3
A
DT
1
0.087
SIDE CHAIN
3
A
DC
6
0.129
SIDE CHAIN
3
A
DA
8
0.059
SIDE CHAIN
3
B
DT
11
0.079
SIDE CHAIN
3
B
DG
13
0.064
SIDE CHAIN
4
A
DT
2
0.094
SIDE CHAIN
4
A
DC
6
0.075
SIDE CHAIN
4
B
DT
12
0.089
SIDE CHAIN
4
B
DG
14
0.057
SIDE CHAIN
4
B
DA
18
0.091
SIDE CHAIN
5
A
DT
2
0.073
SIDE CHAIN
5
B
DT
11
0.090
SIDE CHAIN
6
A
DT
2
0.071
SIDE CHAIN
6
A
DG
4
0.070
SIDE CHAIN
6
A
DC
6
0.087
SIDE CHAIN
6
A
DA
8
0.082
SIDE CHAIN
6
B
DT
12
0.088
SIDE CHAIN
6
B
DG
14
0.076
SIDE CHAIN
6
B
DC
16
0.082
SIDE CHAIN
6
B
DA
17
0.069
SIDE CHAIN
1
9.43
1.20
119.70
129.13
A
A
A
C3'
O3'
P
DT
DT
DG
2
2
3
Y
1
11.37
1.60
120.90
132.27
A
A
A
P
O5'
C5'
DG
DG
DG
3
3
3
N
1
7.72
1.20
119.70
127.42
A
A
A
C3'
O3'
P
DG
DG
DG
3
3
4
Y
1
12.39
1.60
120.90
133.29
A
A
A
P
O5'
C5'
DG
DG
DG
4
4
4
N
1
-2.55
0.40
104.50
101.95
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
1
6.28
0.70
119.90
126.18
A
A
A
N3
C2
N2
DG
DG
DG
4
4
4
N
1
7.70
1.20
119.70
127.40
A
A
A
C3'
O3'
P
DG
DG
DC
4
4
5
Y
1
9.90
1.60
120.90
130.80
A
A
A
P
O5'
C5'
DC
DC
DC
5
5
5
N
1
-2.97
0.40
104.50
101.53
A
A
A
O4'
C4'
C3'
DC
DC
DC
5
5
5
N
1
6.22
0.30
108.30
114.52
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
17.88
1.20
119.70
137.58
A
A
A
C3'
O3'
P
DC
DC
DC
5
5
6
Y
1
7.19
0.30
108.30
115.49
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
1
-3.27
0.40
120.30
117.03
A
A
A
C6
N1
C2
DC
DC
DC
6
6
6
N
1
9.97
1.20
119.70
129.67
A
A
A
C3'
O3'
P
DC
DC
DA
6
6
7
Y
1
10.70
1.60
120.90
131.60
A
A
A
P
O5'
C5'
DA
DA
DA
7
7
7
N
1
17.38
1.20
119.70
137.08
A
A
A
C3'
O3'
P
DA
DA
DA
7
7
8
Y
1
9.83
1.60
120.90
130.73
B
B
B
P
O5'
C5'
DT
DT
DT
12
12
12
N
1
8.57
1.20
119.70
128.27
B
B
B
C3'
O3'
P
DT
DT
DG
12
12
13
Y
1
10.80
1.60
120.90
131.70
B
B
B
P
O5'
C5'
DG
DG
DG
13
13
13
N
1
11.74
1.60
120.90
132.64
B
B
B
P
O5'
C5'
DG
DG
DG
14
14
14
N
1
5.41
0.70
119.90
125.31
B
B
B
N3
C2
N2
DG
DG
DG
14
14
14
N
1
9.08
1.20
119.70
128.78
B
B
B
C3'
O3'
P
DG
DG
DC
14
14
15
Y
1
2.50
0.30
108.30
110.80
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
14.75
1.20
119.70
134.45
B
B
B
C3'
O3'
P
DA
DA
DA
17
17
18
Y
2
7.49
1.20
119.70
127.19
A
A
A
C3'
O3'
P
DT
DT
DG
2
2
3
Y
2
11.26
1.60
120.90
132.16
A
A
A
P
O5'
C5'
DG
DG
DG
3
3
3
N
2
12.29
1.60
120.90
133.19
A
A
A
P
O5'
C5'
DG
DG
DG
4
4
4
N
2
-2.41
0.40
104.50
102.09
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
2
6.51
0.70
119.90
126.41
A
A
A
N3
C2
N2
DG
DG
DG
4
4
4
N
2
9.31
1.20
119.70
129.01
A
A
A
C3'
O3'
P
DG
DG
DC
4
4
5
Y
2
1.95
0.30
108.30
110.25
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
2
14.10
1.20
119.70
133.80
A
A
A
C3'
O3'
P
DC
DC
DC
5
5
6
Y
2
3.51
0.30
108.30
111.81
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
2
16.57
1.20
119.70
136.27
A
A
A
C3'
O3'
P
DA
DA
DA
7
7
8
Y
2
2.19
0.30
108.30
110.49
B
B
B
O4'
C1'
N1
DT
DT
DT
12
12
12
N
2
16.43
1.20
119.70
136.13
B
B
B
C3'
O3'
P
DT
DT
DG
12
12
13
Y
2
11.22
1.60
120.90
132.12
B
B
B
P
O5'
C5'
DG
DG
DG
14
14
14
N
2
6.26
0.70
119.90
126.16
B
B
B
N3
C2
N2
DG
DG
DG
14
14
14
N
2
8.66
1.20
119.70
128.36
B
B
B
C3'
O3'
P
DG
DG
DC
14
14
15
Y
2
2.75
0.30
108.30
111.05
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
2
3.64
0.60
118.90
122.54
B
B
B
N1
C2
O2
DC
DC
DC
15
15
15
N
2
18.54
1.20
119.70
138.24
B
B
B
C3'
O3'
P
DA
DA
DA
17
17
18
Y
3
9.19
1.20
119.70
128.89
A
A
A
C3'
O3'
P
DT
DT
DG
2
2
3
Y
3
10.72
1.60
120.90
131.62
A
A
A
P
O5'
C5'
DG
DG
DG
3
3
3
N
3
4.28
0.70
119.90
124.18
A
A
A
N3
C2
N2
DG
DG
DG
3
3
3
N
3
9.21
1.20
119.70
128.91
A
A
A
C3'
O3'
P
DG
DG
DG
3
3
4
Y
3
12.58
1.60
120.90
133.48
A
A
A
P
O5'
C5'
DG
DG
DG
4
4
4
N
3
-2.70
0.40
104.50
101.80
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
3
2.13
0.30
108.30
110.43
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
3
6.75
0.70
119.90
126.65
A
A
A
N3
C2
N2
DG
DG
DG
4
4
4
N
3
2.38
0.30
108.30
110.68
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
3
-9.49
0.70
102.20
92.71
A
A
A
C4'
C3'
C2'
DC
DC
DC
6
6
6
N
3
2.54
0.30
108.30
110.84
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
3
14.71
1.20
119.70
134.41
A
A
A
C3'
O3'
P
DC
DC
DA
6
6
7
Y
3
12.17
1.20
119.70
131.87
A
A
A
C3'
O3'
P
DA
DA
DA
7
7
8
Y
3
12.81
1.60
120.90
133.71
B
B
B
P
O5'
C5'
DT
DT
DT
12
12
12
N
3
8.43
1.20
119.70
128.13
B
B
B
C3'
O3'
P
DG
DG
DG
13
13
14
Y
3
13.22
1.60
120.90
134.12
B
B
B
P
O5'
C5'
DG
DG
DG
14
14
14
N
3
-4.20
0.70
102.20
98.00
B
B
B
C4'
C3'
C2'
DG
DG
DG
14
14
14
N
3
5.97
0.70
119.90
125.87
B
B
B
N3
C2
N2
DG
DG
DG
14
14
14
N
3
10.24
1.20
119.70
129.94
B
B
B
C3'
O3'
P
DG
DG
DC
14
14
15
Y
3
3.32
0.30
108.30
111.62
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
3
3.61
0.60
118.90
122.51
B
B
B
N1
C2
O2
DC
DC
DC
15
15
15
N
3
11.15
1.20
119.70
130.85
B
B
B
C3'
O3'
P
DC
DC
DC
15
15
16
Y
3
3.10
0.30
108.30
111.40
B
B
B
O4'
C1'
N1
DC
DC
DC
16
16
16
N
3
16.15
1.20
119.70
135.85
B
B
B
C3'
O3'
P
DA
DA
DA
17
17
18
Y
4
2.07
0.30
108.30
110.37
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
4
3.50
0.30
108.30
111.80
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
4
7.67
1.20
119.70
127.37
A
A
A
C3'
O3'
P
DT
DT
DG
2
2
3
Y
4
11.26
1.60
120.90
132.16
A
A
A
P
O5'
C5'
DG
DG
DG
3
3
3
N
4
-7.84
0.70
102.20
94.36
A
A
A
C4'
C3'
C2'
DG
DG
DG
3
3
3
N
4
17.31
1.20
119.70
137.01
A
A
A
C3'
O3'
P
DG
DG
DG
3
3
4
Y
4
19.37
1.60
120.90
140.27
A
A
A
P
O5'
C5'
DG
DG
DG
4
4
4
N
4
-2.68
0.40
104.50
101.82
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
4
-4.52
0.70
102.20
97.68
A
A
A
C4'
C3'
C2'
DG
DG
DG
4
4
4
N
4
5.99
0.70
119.90
125.89
A
A
A
N3
C2
N2
DG
DG
DG
4
4
4
N
4
-4.29
0.70
102.20
97.91
A
A
A
C4'
C3'
C2'
DC
DC
DC
5
5
5
N
4
2.95
0.30
108.30
111.25
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
4
1.84
0.30
108.30
110.14
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
4
7.43
1.20
119.70
127.13
A
A
A
C3'
O3'
P
DC
DC
DA
6
6
7
Y
4
12.60
1.60
120.90
133.50
A
A
A
P
O5'
C5'
DA
DA
DA
7
7
7
N
4
14.07
1.20
119.70
133.77
A
A
A
C3'
O3'
P
DA
DA
DA
7
7
8
Y
4
13.81
1.60
120.90
134.71
A
A
A
P
O5'
C5'
DA
DA
DA
8
8
8
N
4
1.98
0.30
108.30
110.28
B
B
B
O4'
C1'
N1
DT
DT
DT
11
11
11
N
4
2.55
0.30
108.30
110.85
B
B
B
O4'
C1'
N1
DT
DT
DT
12
12
12
N
4
-8.03
0.70
102.20
94.17
B
B
B
C4'
C3'
C2'
DG
DG
DG
13
13
13
N
4
18.02
1.20
119.70
137.72
B
B
B
C3'
O3'
P
DG
DG
DG
13
13
14
Y
4
17.29
1.60
120.90
138.19
B
B
B
P
O5'
C5'
DG
DG
DG
14
14
14
N
4
6.74
0.70
119.90
126.64
B
B
B
N3
C2
N2
DG
DG
DG
14
14
14
N
4
7.58
1.20
119.70
127.28
B
B
B
C3'
O3'
P
DG
DG
DC
14
14
15
Y
4
-6.05
1.00
110.10
104.05
B
B
B
C1'
O4'
C4'
DC
DC
DC
15
15
15
N
4
-5.21
0.70
102.20
96.99
B
B
B
C4'
C3'
C2'
DC
DC
DC
15
15
15
N
4
4.45
0.30
108.30
112.75
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
4
9.12
1.20
119.70
128.82
B
B
B
C3'
O3'
P
DC
DC
DA
16
16
17
Y
4
7.86
1.20
119.70
127.56
B
B
B
C3'
O3'
P
DA
DA
DA
17
17
18
Y
5
2.13
0.30
108.30
110.43
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
5
2.59
0.30
108.30
110.89
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
5
-8.36
0.70
102.20
93.84
A
A
A
C4'
C3'
C2'
DG
DG
DG
3
3
3
N
5
17.69
1.20
119.70
137.39
A
A
A
C3'
O3'
P
DG
DG
DG
3
3
4
Y
5
16.91
1.60
120.90
137.81
A
A
A
P
O5'
C5'
DG
DG
DG
4
4
4
N
5
6.87
0.70
119.90
126.77
A
A
A
N3
C2
N2
DG
DG
DG
4
4
4
N
5
12.14
1.60
120.90
133.04
A
A
A
P
O5'
C5'
DC
DC
DC
6
6
6
N
5
22.02
1.20
119.70
141.72
A
A
A
C3'
O3'
P
DC
DC
DA
6
6
7
Y
5
14.79
1.20
119.70
134.49
A
A
A
C3'
O3'
P
DA
DA
DA
7
7
8
Y
5
4.80
0.30
108.30
113.10
B
B
B
O4'
C1'
N1
DT
DT
DT
11
11
11
N
5
-3.62
0.60
122.30
118.68
B
B
B
N3
C2
O2
DT
DT
DT
11
11
11
N
5
2.89
0.30
108.30
111.19
B
B
B
O4'
C1'
N1
DT
DT
DT
12
12
12
N
5
-8.07
0.70
102.20
94.13
B
B
B
C4'
C3'
C2'
DG
DG
DG
13
13
13
N
5
17.71
1.20
119.70
137.41
B
B
B
C3'
O3'
P
DG
DG
DG
13
13
14
Y
5
16.13
1.60
120.90
137.03
B
B
B
P
O5'
C5'
DG
DG
DG
14
14
14
N
5
5.62
0.70
119.90
125.52
B
B
B
N3
C2
N2
DG
DG
DG
14
14
14
N
5
13.50
1.20
119.70
133.20
B
B
B
C3'
O3'
P
DC
DC
DC
15
15
16
Y
5
3.09
0.30
108.30
111.39
B
B
B
O4'
C1'
N1
DC
DC
DC
16
16
16
N
5
12.20
1.20
119.70
131.90
B
B
B
C3'
O3'
P
DC
DC
DA
16
16
17
Y
5
14.47
1.20
119.70
134.17
B
B
B
C3'
O3'
P
DA
DA
DA
17
17
18
Y
5
14.67
1.60
120.90
135.57
B
B
B
P
O5'
C5'
DA
DA
DA
18
18
18
N
6
2.20
0.30
108.30
110.50
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
6
2.74
0.30
108.30
111.04
A
A
A
O4'
C1'
N1
DT
DT
DT
2
2
2
N
6
12.32
1.60
120.90
133.22
A
A
A
P
O5'
C5'
DG
DG
DG
3
3
3
N
6
-7.79
0.70
102.20
94.41
A
A
A
C4'
C3'
C2'
DG
DG
DG
3
3
3
N
6
10.83
1.20
119.70
130.53
A
A
A
C3'
O3'
P
DG
DG
DG
3
3
4
Y
6
18.23
1.60
120.90
139.13
A
A
A
P
O5'
C5'
DG
DG
DG
4
4
4
N
6
-2.79
0.40
104.50
101.71
A
A
A
O4'
C4'
C3'
DG
DG
DG
4
4
4
N
6
6.53
0.70
119.90
126.43
A
A
A
N3
C2
N2
DG
DG
DG
4
4
4
N
6
7.68
1.20
119.70
127.38
A
A
A
C3'
O3'
P
DG
DG
DC
4
4
5
Y
6
4.13
0.30
108.30
112.43
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
6
6.09
0.30
108.30
114.39
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
6
-2.47
0.40
120.30
117.83
A
A
A
C6
N1
C2
DC
DC
DC
6
6
6
N
6
-6.10
0.80
102.40
96.30
A
A
A
C3'
C2'
C1'
DA
DA
DA
7
7
7
N
6
1.80
0.30
108.30
110.10
B
B
B
O4'
C1'
N1
DT
DT
DT
11
11
11
N
6
2.67
0.30
108.30
110.97
B
B
B
O4'
C1'
N1
DT
DT
DT
12
12
12
N
6
10.66
1.60
120.90
131.56
B
B
B
P
O5'
C5'
DG
DG
DG
13
13
13
N
6
-8.20
0.70
102.20
94.00
B
B
B
C4'
C3'
C2'
DG
DG
DG
13
13
13
N
6
16.07
1.20
119.70
135.77
B
B
B
C3'
O3'
P
DG
DG
DG
13
13
14
Y
6
17.65
1.60
120.90
138.55
B
B
B
P
O5'
C5'
DG
DG
DG
14
14
14
N
6
7.17
0.70
119.90
127.07
B
B
B
N3
C2
N2
DG
DG
DG
14
14
14
N
6
8.56
1.20
119.70
128.26
B
B
B
C3'
O3'
P
DG
DG
DC
14
14
15
Y
6
-5.30
0.70
102.20
96.90
B
B
B
C4'
C3'
C2'
DC
DC
DC
15
15
15
N
6
4.31
0.30
108.30
112.61
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
6
16.58
1.20
119.70
136.28
B
B
B
C3'
O3'
P
DC
DC
DC
15
15
16
Y
6
4.72
0.30
108.30
113.02
B
B
B
O4'
C1'
N1
DC
DC
DC
16
16
16
N
6
13.06
1.60
120.90
133.96
B
B
B
P
O5'
C5'
DA
DA
DA
17
17
17
N
6
20.19
1.20
119.70
139.89
B
B
B
C3'
O3'
P
DA
DA
DA
17
17
18
Y
5
B
B
N1
C2
DT
DT
11
11
0.052
0.008
1.376
1.428
N
NMR STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND COBALT
NMR STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND COBALT
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
4
N
N
5
N
N
5
N
N
covale
1.457
both
sing
C
2GL
1
C
O3
2GL
1_555
C
1GL
2
C
C1
1GL
1_555
covale
1.454
both
sing
D
2GL
1
D
O3
2GL
1_555
D
1GL
2
D
C1
1GL
1_555
covale
1.423
both
sing
E
DDA
1
E
O3
DDA
1_555
E
DDA
2
E
C1
DDA
1_555
covale
1.443
both
sing
E
DDA
2
E
O3
DDA
1_555
E
ERI
3
E
C1
ERI
1_555
covale
1.424
both
sing
F
DDA
1
F
O3
DDA
1_555
F
DDA
2
F
C1
DDA
1_555
covale
1.433
both
sing
F
DDA
2
F
O3
DDA
1_555
F
ERI
3
F
C1
ERI
1_555
metalc
1.911
A
CPH
33
H
O9
CPH
1_555
A
CO
41
G
CO
CO
1_555
metalc
1.965
A
CPH
33
H
O1
CPH
1_555
A
CO
41
G
CO
CO
1_555
metalc
2.387
A
CPH
33
H
C9
CPH
1_555
A
CO
41
G
CO
CO
1_555
metalc
1.919
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O9
CPH
1_555
metalc
2.023
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
O1
CPH
1_555
metalc
2.486
A
CO
41
G
CO
CO
1_555
B
CPH
23
I
C9
CPH
1_555
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
B
DA
18
B
N1
DA
8
1_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
B
DA
18
B
N6
DA
8
1_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
B
DA
17
B
N1
DA
7
1_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
B
DA
17
B
N6
DA
7
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
DC
16
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
16
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
16
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N1
DG
4
1_555
B
DC
15
B
N3
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
15
B
O2
DC
5
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
15
B
N4
DC
5
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
B
DG
14
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
B
DG
14
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
B
DG
14
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
B
DG
13
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
B
DG
13
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
B
DG
13
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N1
DA
7
1_555
B
DT
12
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
7
A
N6
DA
7
1_555
B
DT
12
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N1
DA
8
1_555
B
DT
11
B
N3
DT
1
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N6
DA
8
1_555
B
DT
11
B
O4
DT
1
1_555
DNA
drug bound in the minor groove of DNA, DNA
1EKH
PDB
1
1EKH
1
8
1EKH
1
8
1EKH
A
1
1
8
11
18
1EKH
11
18
1EKH
B
1
1
8
1
P 1