1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Zhao, C.
Xia, C.
Mao, Q.
Forsterling, H.
DeRose, E.
Antholine, W.E.
Subczynski, W.K.
Petering, D.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
Co 3
58.933
COBALT (III) ION
non-polymer
C55 H85 N17 O21 S3
1416.560
BLEOMYCIN A2
N1-[3-(DIMETHYLSULFONIO)-PROPYL]BLEOMYCINAMIDE
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
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
H2 O2
34.015
HYDROGEN PEROXIDE
non-polymer
US
J.Inorg.Biochem.
JIBIDJ
0525
0162-0134
91
259
268
10.1016/S0162-0134(02)00420-8
12121784
Structures of HO(2)-Co(III)bleomycin A(2) Bound to d(GAGCTC)(2) and d(GGAAGCTTCC)(2): Structure-Reactivity Relationships of Co and Fe Bleomycins
2002
10.2210/pdb1mxk/pdb
pdb_00001mxk
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
3045.005
5'-D(*GP*GP*AP*AP*GP*CP*TP*TP*CP*C)-3'
2
syn
polymer
58.933
COBALT (III) ION
1
syn
non-polymer
34.015
HYDROGEN PEROXIDE
1
syn
non-polymer
1416.560
BLEOMYCIN A2
1
syn
non-polymer
no
no
(DG)(DG)(DA)(DA)(DG)(DC)(DT)(DT)(DC)(DC)
GGAAGCTTCC
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
-0.202
1
19
A
1
B
20
1.464
A_DG1:DC20_B
1
-1.191
-0.604
0.039
-0.377
1.945
1
19
A
2
B
19
2.018
A_DG2:DC19_B
2
-2.138
-0.630
-0.063
-0.350
3.656
1
20
A
3
B
18
0.301
A_DA3:DT18_B
3
-5.133
0.005
-0.019
-0.199
2.247
1
20
A
4
B
17
2.320
A_DA4:DT17_B
4
-5.839
-0.158
-0.067
0.159
-4.357
1
19
A
5
B
16
-11.625
A_DG5:DC16_B
5
1.056
0.186
-0.281
-0.088
15.841
1
19
A
6
B
15
-10.751
A_DC6:DG15_B
6
-10.448
-0.629
-0.143
-0.152
-13.072
A
7
B
14
13.680
A_DT7:DA14_B
7
6.348
-0.322
-0.169
0.395
-4.407
1
20
A
8
B
13
-4.803
A_DT8:DA13_B
8
-1.040
-0.041
-0.109
-0.213
2.843
1
19
A
9
B
12
6.420
A_DC9:DG12_B
9
-4.402
0.723
-0.052
-0.189
-2.836
1
19
A
10
B
11
0.980
A_DC10:DG11_B
10
0.335
0.516
0.146
-0.362
3.488
37.140
A
A
1
2
-10.977
B
B
20
19
3.421
-6.952
0.140
-0.670
AA_DG1DG2:DC19DC20_BB
1
1.020
-1.611
36.492
-0.063
-0.075
3.210
34.889
A
A
2
3
-4.092
B
B
19
18
3.159
-2.452
-0.365
-0.888
AA_DG2DA3:DT18DC19_BB
2
0.266
-0.444
34.805
-1.119
0.648
3.359
33.716
A
A
3
4
-4.799
B
B
18
17
3.274
-2.780
-0.030
-1.199
AA_DA3DA4:DT17DT18_BB
3
-0.636
1.098
33.599
-1.609
-0.054
3.204
32.765
A
A
4
5
10.817
B
B
17
16
3.352
6.064
-1.461
-1.008
AA_DA4DG5:DC16DT17_BB
4
-2.208
3.938
32.140
-2.844
2.205
2.452
29.091
A
A
5
6
-0.662
B
B
16
15
2.396
-0.333
-1.186
0.061
AA_DG5DC6:DG15DC16_BB
5
-1.519
3.025
29.050
0.175
2.115
6.168
38.326
A
A
6
7
20.261
B
B
15
14
6.306
13.047
1.938
1.000
AA_DC6DT7:DA14DG15_BB
6
-2.157
3.350
36.052
-1.696
-3.484
2.809
30.038
A
A
7
8
25.286
B
B
14
13
3.151
12.710
-1.168
-0.138
AA_DT7DT8:DA13DA14_BB
7
0.011
-0.021
27.273
-2.765
2.256
3.216
37.327
A
A
8
9
1.503
B
B
13
12
3.192
0.961
0.745
-0.131
AA_DT8DC9:DG12DA13_BB
8
1.606
-2.510
37.281
-0.328
-0.957
3.713
41.524
A
A
9
10
-14.969
B
B
12
11
3.660
-10.462
-0.589
-0.479
AA_DC9DC10:DG11DG12_BB
9
-6.800
9.730
39.684
0.609
-0.004
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_conn_angle
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2002-10-16
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_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.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr3_label_comp_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
1mtg is HO2-Co(III)bleomycin-A(2) bound to d(GAGCTC)(2)
RCSB
Y
RCSB
2002-10-02
REL
REL
3CO
COBALT (III) ION
PEO
HYDROGEN PEROXIDE
BLM
BLEOMYCIN A2
This structure was determined using standard 2D homonuclear techniques
1
2D NOESY
2D TOCSY
DQF-COSY
31P/1H-COSY
0.1 M NaCl
7.4
ambient
298
K
The structure is based on 424 distance restraints (333 intramolecular DNA, 66 intramolecular bleomycin and 25 intermolecular).
Simulated Annealing, Molecular Dynamics
minimized average structure
2mM Bleomycin/DNA complex;
20 mM phosphate buffer; 0.1 M NaCl
90% H2O/10% D2O
2mM Bleomycin/DNA complex; 20 mM phosphate buffer; 0.1 M NaCl
D2O
Bruker Instr.
collection
XwinNMR
1.3
Biosym
data analysis
Felix
2.3
Axel Brunger
refinement
X-PLOR
3.1
500
Bruker
DRX
3CO
22
2
3CO
3CO
22
A
PEO
23
3
PEO
PEO
23
A
BLM
21
4
BLM
BLM
21
B
GUA
1
n
1
DG
1
A
GUA
2
n
2
DG
2
A
ADE
3
n
3
DA
3
A
ADE
4
n
4
DA
4
A
GUA
5
n
5
DG
5
A
CYT
6
n
6
DC
6
A
THY
7
n
7
DT
7
A
THY
8
n
8
DT
8
A
CYT
9
n
9
DC
9
A
CYT
10
n
10
DC
10
A
GUA
11
n
1
DG
11
B
GUA
12
n
2
DG
12
B
ADE
13
n
3
DA
13
B
ADE
14
n
4
DA
14
B
GUA
15
n
5
DG
15
B
CYT
16
n
6
DC
16
B
THY
17
n
7
DT
17
B
THY
18
n
8
DT
18
B
CYT
19
n
9
DC
19
B
CYT
20
n
10
DC
20
B
author_defined_assembly
2
dimeric
A
PEO
23
D
O1
PEO
1_555
A
3CO
22
C
CO
3CO
1_555
A
PEO
23
D
O2
PEO
1_555
27.3
A
PEO
23
D
O1
PEO
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NG
BLM
1_555
89.7
A
PEO
23
D
O2
PEO
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NG
BLM
1_555
72.8
A
PEO
23
D
O1
PEO
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NC
BLM
1_555
90.7
A
PEO
23
D
O2
PEO
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NC
BLM
1_555
68.1
B
BLM
21
E
NG
BLM
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NC
BLM
1_555
83.8
A
PEO
23
D
O1
PEO
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NB
BLM
1_555
177.3
A
PEO
23
D
O2
PEO
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NB
BLM
1_555
150.7
B
BLM
21
E
NG
BLM
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NB
BLM
1_555
90.5
B
BLM
21
E
NC
BLM
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NB
BLM
1_555
86.6
A
PEO
23
D
O1
PEO
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NH
BLM
1_555
92.2
A
PEO
23
D
O2
PEO
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NH
BLM
1_555
110.9
B
BLM
21
E
NG
BLM
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NH
BLM
1_555
84.3
B
BLM
21
E
NC
BLM
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NH
BLM
1_555
167.7
B
BLM
21
E
NB
BLM
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NH
BLM
1_555
90.5
A
PEO
23
D
O1
PEO
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NJ
BLM
1_555
85.4
A
PEO
23
D
O2
PEO
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NJ
BLM
1_555
104.2
B
BLM
21
E
NG
BLM
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NJ
BLM
1_555
173.4
B
BLM
21
E
NC
BLM
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NJ
BLM
1_555
100.7
B
BLM
21
E
NB
BLM
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NJ
BLM
1_555
94.6
B
BLM
21
E
NH
BLM
1_555
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NJ
BLM
1_555
91.5
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
B
O1
HNK
PEO
BLM
23
21
1.39
1
A
B
O2
H21
DC
DG
9
12
1.51
1
A
B
H21
O2
DG
DC
1
20
1.56
1
A
B
O2
H21
DC
DG
10
11
1.57
1
A
B
H21
O2
DG
DC
2
19
1.58
1
A
B
H41
O6
DC
DG
6
15
1.59
1
A
B
O6
H41
DG
DC
5
16
1.60
1
2.89
0.30
108.30
111.19
A
A
A
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
4.48
0.50
113.10
117.58
A
A
A
N7
C8
N9
DG
DG
DG
1
1
1
N
1
-2.63
0.40
106.40
103.77
A
A
A
C8
N9
C4
DG
DG
DG
1
1
1
N
1
3.06
0.30
108.30
111.36
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
4.57
0.50
113.10
117.67
A
A
A
N7
C8
N9
DG
DG
DG
2
2
2
N
1
-2.47
0.40
106.40
103.93
A
A
A
C8
N9
C4
DG
DG
DG
2
2
2
N
1
2.93
0.30
108.30
111.23
A
A
A
O4'
C1'
N9
DA
DA
DA
3
3
3
N
1
3.77
0.50
113.80
117.57
A
A
A
N7
C8
N9
DA
DA
DA
3
3
3
N
1
2.83
0.30
108.30
111.13
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
3.89
0.50
113.80
117.69
A
A
A
N7
C8
N9
DA
DA
DA
4
4
4
N
1
4.18
0.30
108.30
112.48
A
A
A
O4'
C1'
N9
DG
DG
DG
5
5
5
N
1
4.51
0.50
113.10
117.61
A
A
A
N7
C8
N9
DG
DG
DG
5
5
5
N
1
-2.52
0.40
106.40
103.88
A
A
A
C8
N9
C4
DG
DG
DG
5
5
5
N
1
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
1
1.99
0.30
108.30
110.29
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
-3.79
0.60
122.90
119.11
A
A
A
C6
C5
C7
DT
DT
DT
7
7
7
N
1
3.43
0.30
108.30
111.73
A
A
A
O4'
C1'
N1
DT
DT
DT
8
8
8
N
1
2.79
0.30
108.30
111.09
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
2.24
0.30
108.30
110.54
A
A
A
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
2.91
0.30
108.30
111.21
B
B
B
O4'
C1'
N9
DG
DG
DG
11
11
11
N
1
4.46
0.50
113.10
117.56
B
B
B
N7
C8
N9
DG
DG
DG
11
11
11
N
1
-2.57
0.40
106.40
103.83
B
B
B
C8
N9
C4
DG
DG
DG
11
11
11
N
1
2.59
0.30
108.30
110.89
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
4.62
0.50
113.10
117.72
B
B
B
N7
C8
N9
DG
DG
DG
12
12
12
N
1
-2.56
0.40
106.40
103.84
B
B
B
C8
N9
C4
DG
DG
DG
12
12
12
N
1
2.61
0.30
108.30
110.91
B
B
B
O4'
C1'
N9
DA
DA
DA
13
13
13
N
1
3.90
0.50
113.80
117.70
B
B
B
N7
C8
N9
DA
DA
DA
13
13
13
N
1
3.39
0.30
108.30
111.69
B
B
B
O4'
C1'
N9
DA
DA
DA
14
14
14
N
1
3.74
0.50
113.80
117.54
B
B
B
N7
C8
N9
DA
DA
DA
14
14
14
N
1
2.47
0.30
108.30
110.77
B
B
B
O4'
C1'
N9
DG
DG
DG
15
15
15
N
1
4.60
0.50
113.10
117.70
B
B
B
N7
C8
N9
DG
DG
DG
15
15
15
N
1
-2.73
0.40
106.40
103.67
B
B
B
C8
N9
C4
DG
DG
DG
15
15
15
N
1
3.88
0.30
108.30
112.18
B
B
B
O4'
C1'
N1
DC
DC
DC
16
16
16
N
1
3.35
0.30
108.30
111.65
B
B
B
O4'
C1'
N1
DT
DT
DT
17
17
17
N
1
2.48
0.30
108.30
110.78
B
B
B
O4'
C1'
N1
DT
DT
DT
18
18
18
N
1
3.97
0.30
108.30
112.27
B
B
B
O4'
C1'
N1
DC
DC
DC
19
19
19
N
1
2.73
0.30
108.30
111.03
B
B
B
O4'
C1'
N1
DC
DC
DC
20
20
20
N
minimized average
NMR Structure of HO2-Co(III)bleomycin A(2) Bound to d(GGAAGCTTCC)(2)
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
metalc
1.839
A
3CO
22
C
CO
3CO
1_555
A
PEO
23
D
O1
PEO
1_555
metalc
2.749
A
3CO
22
C
CO
3CO
1_555
A
PEO
23
D
O2
PEO
1_555
metalc
1.837
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NG
BLM
1_555
metalc
2.062
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NC
BLM
1_555
metalc
2.154
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NB
BLM
1_555
metalc
1.928
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NH
BLM
1_555
metalc
2.004
A
3CO
22
C
CO
3CO
1_555
B
BLM
21
E
NJ
BLM
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N1
DG
1
1_555
B
DC
20
B
N3
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
1
A
N2
DG
1
1_555
B
DC
20
B
O2
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
1
A
O6
DG
1
1_555
B
DC
20
B
N4
DC
10
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
19
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
19
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
19
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
B
DT
18
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
B
DT
18
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
17
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
17
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N1
DG
5
1_555
B
DC
16
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
5
A
N2
DG
5
1_555
B
DC
16
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
5
A
O6
DG
5
1_555
B
DC
16
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
B
DG
15
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
B
DG
15
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
B
DG
15
B
N2
DG
5
1_555
hydrog
DT-DA PAIR
A
DT
7
A
N3
DT
7
1_555
B
DA
14
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
13
B
N1
DA
3
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
13
B
N6
DA
3
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N3
DC
9
1_555
B
DG
12
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
12
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
12
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N3
DC
10
1_555
B
DG
11
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
N4
DC
10
1_555
B
DG
11
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
A
DC
10
A
O2
DC
10
1_555
B
DG
11
B
N2
DG
1
1_555
DNA
DRUG-DNA COMPLEX, COBALT(III), DNA
1MXK
PDB
1
1MXK
1
10
1MXK
1
10
1MXK
A
1
1
10
11
20
1MXK
11
20
1MXK
B
1
1
10
BINDING SITE FOR RESIDUE 3CO A 22
A
3CO
22
Software
2
BINDING SITE FOR RESIDUE BLM B 21
B
BLM
21
Software
12
BINDING SITE FOR RESIDUE PEO A 23
A
PEO
23
Software
2
A
PEO
23
D
PEO
2
1_555
B
BLM
21
E
BLM
2
1_555
A
DG
5
A
DG
5
12
1_555
A
DC
6
A
DC
6
12
1_555
A
DT
7
A
DT
7
12
1_555
A
3CO
22
C
3CO
12
1_555
A
PEO
23
D
PEO
12
1_555
B
DA
13
B
DA
3
12
1_555
B
DA
14
B
DA
4
12
1_555
B
DG
15
B
DG
5
12
1_555
B
DC
16
B
DC
6
12
1_555
B
DT
17
B
DT
7
12
1_555
B
DT
18
B
DT
8
12
1_555
B
DC
19
B
DC
9
12
1_555
A
3CO
22
C
3CO
2
1_555
B
BLM
21
E
BLM
2
1_555