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- PDB-5bna: THE PRIMARY MODE OF BINDING OF CISPLATIN TO A B-DNA DODECAMER: C-... -

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Basic information

Entry
Database: PDB / ID: 5bna
TitleTHE PRIMARY MODE OF BINDING OF CISPLATIN TO A B-DNA DODECAMER: C-G-C-G-A-A-T-T-C-G-C-G
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED
Function / homologyPLATINUM TRIAMINE ION / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsWing, R.M. / Pjura, P. / Drew, H.R. / Dickerson, R.E.
Citation
Journal: EMBO J. / Year: 1984
Title: The primary mode of binding of cisplatin to a B-DNA dodecamer: C-G-C-G-A-A-T-T-C-G-C-G
Authors: Wing, R.M. / Pjura, P. / Drew, H.R. / Dickerson, R.E.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983
Title: A Random-Walk Model for Helix Bending in B-DNA
Authors: Dickerson, R.E. / Kopka, M.L. / Pjura, P.
#2: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1983
Title: Helix Geometry and Hydration in A-DNA, B-DNA and Z-DNA
Authors: Dickerson, R.E. / Drew, H.R. / Conner, B.N. / Kopka, M.L. / Pjura, P.E.
#3: Journal: Biological Macromolecules and Assemblies / Year: 1985
Title: Base Sequence, Helix Geometry, Hydration and Helix Stability in B-DNA
Authors: Dickerson, R.E. / Kopka, M.L. / Pjura, P.
#4: Journal: Nature / Year: 1980
Title: Crystal Structure Analysis of a Complete Turn of B-DNA
Authors: Wing, R. / Drew, H.R. / Takano, T. / Broka, C. / Tanaka, S. / Itakura, K. / Dickerson, R.E.
History
DepositionAug 22, 1983Deposition site: BNL / Processing site: BNL
Revision 1.0Nov 2, 1983Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn_type.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: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0655
Polymers7,3272
Non-polymers7393
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.160, 39.930, 66.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THE ANISOTROPIC TEMPERATURE FACTORS FOR THE PLATINUM ATOMS ARE AS FOLLOWS ATOM B11 B22 B33 B12 B13 B23 PT1 PTN 25 0.01510 0.00438 0.00138 0.00214 0.00056 0.00026 PT1 PTN 26 0.01545 0.00544 0.00131- ...1: THE ANISOTROPIC TEMPERATURE FACTORS FOR THE PLATINUM ATOMS ARE AS FOLLOWS ATOM B11 B22 B33 B12 B13 B23 PT1 PTN 25 0.01510 0.00438 0.00138 0.00214 0.00056 0.00026 PT1 PTN 26 0.01545 0.00544 0.00131-0.00462-0.00072 0.00017 PT1 PTN 27 0.00729 0.00382 0.00120-0.00092-0.00060 0.00039
2: TEMPERATURE FACTORS WHICH WERE CALCULATED TO BE NON-POSITIVE-DEFINITE WERE ARBITRARILY SET TO 0.0 IN THE REFINEMENT PROCEDURE.

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-PTN / PLATINUM TRIAMINE ION


Mass: 246.170 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H9N3Pt
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
Crystal grow
*PLUS
Details: Wing, R., (1980) Nature, 287, 755.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
420-30 %MPD1reservoir
1DNA1drop
2magnesium acetate1drop
3spermine hydrochloride molecule1drop

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Data collection

ReflectionHighest resolution: 2.6 Å / Num. obs: 2088

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Processing

SoftwareName: JACK-LEVITT / Classification: refinement
RefinementResolution: 2.6→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.102 725
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL PT ATOMSX-RAY DIFFRACTIONTRanisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 12 128 626
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / Num. reflection all: 2012 / σ(F): 2 / Rfactor all: 0.166 / Rfactor obs: 0.112
Solvent computation
*PLUS
Displacement parameters
*PLUS

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