List of data items in ./cif_ddfb25.0609
data_DDFB25.
_block.id DDFB25
loop_
_atom_site.id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.cartn_x
_atom_site.cartn_y
_atom_site.cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.footnote_id
_atom_site.entity_id
_atom_site.entity_seq_num
1
O5*
C
A
1
.
9.364
20.016
22.840
1.00
12.10
.
1
1
2
C5*
C
A
1
.
9.682
21.104
23.714
1.00
11.61
.
1
1
3
C4*
C
A
1
.
11.127
21.003
24.143
1.00
11.44
.
1
1
4
O4*
C
A
1
.
11.265
19.844
24.954
1.00
11.13
.
1
1
5
C3*
C
A
1
.
12.176
20.888
23.046
1.00
11.47
.
1
1
80
NH2
+A
A
4
.
15.781
11.315
11.433
1.00
9.99
1
1
4
81
CH2
+A
A
4
.
16.956
10.455
11.332
1.00
10.34
1
1
4
124
C1
MAR
A
4
.
15.258
18.419
5.102
1.00
10.77
.
1
.
125
C2
MAR
A
4
.
16.402
19.206
5.113
1.00
10.96
.
1
.
126
C3
MAR
A
4
.
17.727
18.632
5.102
1.00
11.09
.
1
.
127
C4
MAR
A
4
.
17.859
17.170
5.033
1.00
10.77
.
1
.
171
MG
MG
I
7
.
19.853
14.842
2.776
1.00
22.67
.
2
.
172
O1
HOH
S
8
.
18.180
16.807
1.266
1.00
25.55
.
3
.
173
O2
HOH
S
9
.
22.268
13.613
3.709
1.00
27.72
.
3
.
174
O3
HOH
S
10
.
21.065
16.408
0.800
1.00
30.67
.
3
.
_atom_sites.block_id DDFB25
_atom_sites.frac_tran_matrix[1][1] 0.035562
_atom_sites.frac_tran_matrix[1][2] 0.0
_atom_sites.frac_tran_matrix[1][3] 0.0
_atom_sites.frac_tran_matrix[2][1] 0.0
_atom_sites.frac_tran_matrix[2][2] 0.035562
_atom_sites.frac_tran_matrix[2][3] 0.0
_atom_sites.frac_tran_matrix[3][1] 0.0
_atom_sites.frac_tran_matrix[3][2] 0.0
_atom_sites.frac_tran_matrix[3][3] 0.018875
loop_
_atom_sites_footnote.id
_atom_sites_footnote.text
1
;
THERE IS A METHYLENE BRIDGE BETWEEN N2 OF NH2-ADENINE AND N3* OF MAR7.
;
_cell.block_id DDFB25
_cell.length_a 28.120
_cell.length_b 28.120
_cell.length_c 52.980
_cell.angle_alpha 90.00
_cell.angle_beta 90.00
_cell.angle_gamma 90.00
loop_
_chem_comp.id
_chem_comp.name
_chem_comp.mon_nstd_flag
_chem_comp.mon_nstd_class
_chem_comp.mon_nstd_parent
A
ADE
no
.
.
T
THY
no
.
.
C
CYT
no
.
.
G
GUA
no
.
.
+A
ADE-MAR
yes
'MAR70 covalently bound to NH2-adenine via CH2 bridge'
ADE
MAR
MAR70
.
.
.
MG
MAGNESIUM
.
.
.
HOH
WATER
.
.
.
loop_
_citation.id
_citation.title
_citation.country
_citation.journal_abbrev
_citation.journal_volume
_citation.page_first
_citation.year
_citation.page_last
_citation.journal_coden_ASTM
_citation.journal_coden_ISSN
primary
;
Facile Formation of a Crosslinked Adduct between
DNA and the Daunorubicin Derivative MAR70 Mediated
by Formaldehyde: Molecular Structure of the
MAR70-d(CGTnACG) Covalent Adduct
;
US
'Proc.Natl.Acad.Sci.U.S.A.'
88
4845
1991
4849
PNASA6
0027-8424
2
;
Influence of Aglycone Modifications on the Binding
of Anthracycline Drugs to DNA: The Molecular
Structure of Idarubicin and
4-O-Demethyl-11-Deoxydoxorubicin Complexed to d(CGATCG)
;
UK
'Anti-Cancer Drug Des.'
6
137
1991
.
ACDDEA
0266-9536
loop_
_citation_author.citation_id
_citation_author.name
primary
'Gao, Y. -G.'
primary
'Liaw, Y. -C.'
primary
'Van Der Marel, G. A.'
primary
'Van Boom, J. H.'
primary
'Wang, A. H. -J.'
2
'Gao, Y. -G.'
2
'Wang, A. H. -J.'
_diffrn.block_id DDFB25
_diffrn.ambient_temp 295.0
_diffrn_measurement.block_id DDFB25
_diffrn_measurement.device_type DIFFRACTOMETER
_diffrn_measurement.device_specific 'RIGAKU AFC-5R'
_diffrn_radiation.block_id DDFB25
_diffrn_radiation.source_type 'ROTATING ANODE'
loop_
_entity.id
_entity.type
_entity.src_method
1
polymer
'SYNTHETIC'
2
non-polymer
.
3
water
3
.
loop_
_entity_keywords.entity_id
_entity_keywords.text
1
'NUCLEIC ACID'
1
'NUCLEIC ACID DRUG COMPLEX'
2
ION
2
MAGNESIUM
loop_
_entity_poly.entity_id
_entity_poly.nstd_monomer
_entity_poly.number_of_monomers
_entity_poly.type
1
yes
6
'polydeoxyribonucleotide'
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.mon_id
_entity_poly_seq.num
1
C
1
1
G
2
1
T
3
1
+A
4
1
C
5
1
G
6
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.method 'VAPOR DIFFUSION'
_exptl_crystal_grow.pH 6.0
_exptl_crystal_grow.temp 295.0
loop_
_exptl_crystal_grow_comp.id
_exptl_crystal_grow_comp.sol_id
_exptl_crystal_grow_comp.name
1
1
'MPD'
2
1
'HCHO'
3
1
'BaCl2'
4
1
'Na Cacodylate'
5
1
'Spermine'
6
2
'MPD'
_struct.block_id DDFB25
_struct.title
;
5'-D(*CP*GP*TP*(NH2)AP*CP*G)-3', MAR70 AND HCHO
;
_struct.keywords 'DEOXYRIBONUCLEIC ACID'
loop_
_struct_asym.id
_struct_asym.entity_id
_struct_asym.details
A
1
'NUCLEIC ACID DRUG COMPLEX'
I
2
'MAGNESIUM ION'
S
3
'H2O'
_struct_biol.id 1
_struct_biol.details
;
Full duplex DNA covalently bound to MAR70 via methylene bridge
;
loop_
_struct_biol_gen.biol_id
_struct_biol_gen.asym_id
_struct_biol_gen.symmetry
1
A
1_555
1
I
1_555
1
S
1_555
1
A
8_665
1
I
8_665
1
S
8_665
loop_
_struct_biol_keywords.biol_id
_struct_biol_keywords.text
1
'DNA'
1
'DNA DUPLEX'
1
'DNA DRUG COMPLEX'
loop_
_struct_conf.id
_struct_conf.conf_type_id
_struct_conf.beg_label_comp_id
_struct_conf.beg_label_asym_id
_struct_conf.beg_label_seq_id
_struct_conf.end_label_comp_id
_struct_conf.end_label_asym_id
_struct_conf.end_label_seq_id
CHAIN-A
HELX-RHO
C
A
1
G
A
6
loop_
_struct_conf_type.id
_struct_conf_type.criteria
HELX-RHO
'AUTHOR JUDGEMENT'
loop_
_struct_conn_type.id
_struct_conn_type.criteria
hydrog
;
N - O distance > 2.5 Angstroms and < 3.5 Angstroms
N - O - C angle < 120 degrees
;
covale
'AUTHOR JUDGEMENT'
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_symmetry
_struct_conn.details
1
hydrog
C
A
1
O2
1_555
G
A
6
N2
8_665
WATSON-CRICK
2
hydrog
C
A
1
N3
1_555
G
A
6
N1
8_665
WATSON-CRICK
3
hydrog
C
A
1
N4
1_555
G
A
6
O6
8_665
WATSON-CRICK
4
hydrog
G
A
2
N2
1_555
C
A
5
O2
8_665
WATSON-CRICK
5
hydrog
G
A
2
N1
1_555
C
A
5
N3
8_665
WATSON-CRICK
6
hydrog
G
A
2
O6
1_555
C
A
5
N4
8_665
WATSON-CRICK
7
hydrog
T
A
3
N3
1_555
+A
A
4
N1
8_665
WATSON-CRICK
8
hydrog
T
A
3
O4
1_555
+A
A
4
N6
8_665
WATSON-CRICK
9
hydrog
+A
A
4
N1
1_555
T
A
3
N3
8_665
WATSON-CRICK
10
hydrog
+A
A
4
N6
1_555
T
A
3
O4
8_665
WATSON-CRICK
11
hydrog
C
A
5
O2
1_555
G
A
2
N2
8_665
WATSON-CRICK
12
hydrog
C
A
5
N3
1_555
G
A
2
N1
8_665
WATSON-CRICK
13
hydrog
C
A
5
N4
1_555
G
A
2
O6
8_665
WATSON-CRICK
14
hydrog
G
A
6
N2
1_555
C
A
1
O2
8_665
WATSON-CRICK
15
hydrog
G
A
6
N1
1_555
C
A
1
N3
8_665
WATSON-CRICK
16
hydrog
G
A
6
O6
1_555
C
B
1
N4
8_665
WATSON-CRICK
17
covale
+A
A
4
C2
1_555
+A
A
4
N2
1_555
'MODIFIER LINK'
18
covale
+A
A
4
N2
1_555
+A
A
4
CH2
1_555
'MODIFIER LINK'
19
covale
+A
A
4
CH2
1_555
MAR
A
.
N3*
1_555
'MODIFIER LINK'
_symmetry.block_id DDFB25
_symmetry.space_group_name_H-M 'P 41 21 2'