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- PDB-1mtg: NMR Structure of HO2-Co(III)bleomycin A(2) bound to d(GAGCTC)(2) -

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Basic information

Entry
Database: PDB / ID: 1mtg
TitleNMR Structure of HO2-Co(III)bleomycin A(2) bound to d(GAGCTC)(2)
Components5'-D(*GP*AP*GP*CP*TP*C)-3'
KeywordsDNA / Drug-DNA complex / cobalt(III)
Function / homologyCOBALT (III) ION / BLEOMYCIN A2 / HYDROGEN PEROXIDE / DNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics, simulated annealing, molecular dynamics
Model type detailsminimized average
AuthorsZhao, C. / Xia, C. / Mao, Q. / Forsterling, H. / DeRose, E. / Antholine, W.E. / Subczynski, W.K. / Petering, D.H.
CitationJournal: J.Inorg.Biochem. / Year: 2002
Title: 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
Authors: Zhao, C. / Xia, C. / Mao, Q. / Forsterling, H. / DeRose, E. / Antholine, W.E. / Subczynski, W.K. / Petering, D.H.
History
DepositionSep 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2012Group: Derived calculations
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*AP*GP*CP*TP*C)-3'
B: 5'-D(*GP*AP*GP*CP*TP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1285
Polymers3,6182
Non-polymers1,5103
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain 5'-D(*GP*AP*GP*CP*TP*C)-3'


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-3CO / COBALT (III) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#4: Chemical ChemComp-BLM / BLEOMYCIN A2 / N1-[3-(DIMETHYLSULFONIO)-PROPYL]BLEOMYCINAMIDE


Mass: 1416.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H85N17O21S3 / Comment: medication*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY
1522D 13C-HSQC
1622D 31P/1H-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM Bleomycin/DNA complex; 20 mM Phosphate Buffer; 0.1 M NaCl90% H2O/10% D2O
22mM Bleomycin/DNA complex; 20 mM Phosphate Buffer; 0.1 M NaClD2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 M NaCl 7.4ambient 298 K
20.1 M NaCl 7.4ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Bruker Instrumentscollection
XwinNMR1.3Bruker Instrumentsprocessing
Felix2.3Biosymdata analysis
X-PLOR3.1Axel Brungerrefinement
RefinementMethod: molecular dynamics, simulated annealing, molecular dynamics
Software ordinal: 1
Details: The structure is based on a total of 348 NOE distance restraints (196 DNA, 112 Bleomycin, 34 intermolecular).
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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