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- PDB-1g5l: CO(III)-BLEOMYCIN-OOH BOUND TO AN OLIGONUCLEOTIDE CONTAINING A PH... -

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Basic information

Entry
Database: PDB / ID: 1g5l
TitleCO(III)-BLEOMYCIN-OOH BOUND TO AN OLIGONUCLEOTIDE CONTAINING A PHOSPHOGLYCOLATE LESION
Components
  • 5'-D(*CP*CP*AP*AP*AP*G)-3'
  • 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'
  • 5'-D(P*AP*CP*TP*GP*GP*G)-3'
KeywordsDNA / damaged DNA / DNA-drug complex / intercalation
Function / homologyCOBALT (III) ION / BLEOMYCIN B2 / OXYGEN ATOM / HYDROGEN PEROXIDE / 2-PHOSPHOGLYCOLIC ACID / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsHoehn, S.T. / Junker, H.-D. / Bunt, R.C. / Turner, C.J. / Stubbe, J.
CitationJournal: Biochemistry / Year: 2001
Title: Solution structure of Co(III)-bleomycin-OOH bound to a phosphoglycolate lesion containing oligonucleotide: implications for bleomycin-induced double-strand DNA cleavage.
Authors: Hoehn, S.T. / Junker, H.D. / Bunt, R.C. / Turner, C.J. / Stubbe, J.
History
DepositionNov 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,2868
Polymers7,5943
Non-polymers1,6915
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
Representative

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Components

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DNA chain , 3 types, 3 molecules ABC

#1: DNA chain 5'-D(*CP*CP*AP*AP*AP*G)-3'


Mass: 1802.232 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*AP*CP*TP*GP*GP*G)-3'


Mass: 1849.241 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'


Mass: 3942.572 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 5 types, 5 molecules

#4: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#5: Chemical ChemComp-3CO / COBALT (III) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#6: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#7: Chemical ChemComp-BLB / BLEOMYCIN B2


Mass: 1426.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H85N20O21S2
#8: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131PE-COSY
242WATERGATE-NOESY
15131P-HCOSY
16113C-HSQC
171ROESY
NMR detailsText: DNA was synthesized as a double hairpin, but for modeling purposed was treated as two strands of DNA; the hexaethylene glycol spacers were not included in the modeling

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Sample preparation

Details
Solution-IDContentsSolvent system
11.25 mM drug-DNA complex; 40 mM sodium phosphate bufferD2O
21.25 mM drug-DNA complex; 40 mM sodium phosphate buffer90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
140 mM sodium phosphate buffer 6.8ambient 293 K
240 mM sodium phosphate buffer 6.8ambient 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built home builtHome-builthome built7501
Home-built home builtHome-builthome built6002

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Processing

NMR software
NameVersionDeveloperClassification
Felix95MSIprocessing
X-PLOR3.851Brungerstructure solution
Felix95MSIdata analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: The structures are based on 729 NOE-derived distance constraints and 96 dihedral angle restraints.
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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