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- PDB-1c38: SOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS INTERMEDIATE -

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Entry
Database: PDB / ID: 1c38
TitleSOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS INTERMEDIATE
ComponentsDNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
KeywordsDNA / APTAMER / THROMBIN BINDING / POTASSIUM / METAL ION BINDING SITES / QUADRUPLEX / INTERMEDIATE
Function / homology: / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / THE DNA-POTASSIUM STRUCTURE WAS MINIMIZED IN 500 STEPS OF POWELL'S CONJUGATE GRADIENT MINIMIZATION.
AuthorsBolton, P.H. / Marathias, V.M. / Wang, K.
Citation
Journal: Nucleic Acids Res. / Year: 2000
Title: Structures of the potassium-saturated, 2:1, and intermediate, 1:1, forms of a quadruplex DNA.
Authors: Marathias, V.M. / Bolton, P.H.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Determination of the Number and Location of the Manganese Binding Sites of DNA Quadruplexes in Solution by EPR and NMR in the Presence and Absence of Thrombin
Authors: Bolton, P.H. / Marathias, V.M. / Wang, K.
History
DepositionJul 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / 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_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,52521
Polymers4,7431
Non-polymers78220
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 / -
Representative

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Components

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


Mass: 4743.051 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THROMBIN BINDING APTAMER INTERMEDIATE WITH MULTIPLE POTASSIUM MINIMIZATIONS
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE 10 POTASSIUM POSITIONS IN EACH QUARTET ARE THE LOWEST ENERGY POSITION CALCULATED USING X-PLOR AND BASED ON THE REFINED SOLUTION STRUCTURE OF THE INTERMEDIATE APTAMER QUADRUPLEX. THE ...Text: THE 10 POTASSIUM POSITIONS IN EACH QUARTET ARE THE LOWEST ENERGY POSITION CALCULATED USING X-PLOR AND BASED ON THE REFINED SOLUTION STRUCTURE OF THE INTERMEDIATE APTAMER QUADRUPLEX. THE DISPERSION OF THE POTASSIUM POSITION INDICATE THE BINDING SITE STABILITY.

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
RefinementMethod: THE DNA-POTASSIUM STRUCTURE WAS MINIMIZED IN 500 STEPS OF POWELL'S CONJUGATE GRADIENT MINIMIZATION.
Software ordinal: 1
Details: X-PLOR 3.1 WAS USED TO DETERMINE THE MINIMUM ENERGY POSITIONS OF THE POTASSIUM IONS. A VAN DER WALLS RADIUS OF 1.96 A AND A CHARGE OF PLUS ONE WAS USED FOR EACH POTASSIUM ION. A DISTANCE- ...Details: X-PLOR 3.1 WAS USED TO DETERMINE THE MINIMUM ENERGY POSITIONS OF THE POTASSIUM IONS. A VAN DER WALLS RADIUS OF 1.96 A AND A CHARGE OF PLUS ONE WAS USED FOR EACH POTASSIUM ION. A DISTANCE-DEPENDENT DIELECTRIC FUNCTION WAS INCLUDED IN THE NON-BONDED TERMS. THE OPTIONS FOR THE DISTANCE-DEPENDENT DIELECTRIC FUNCTION USED IN THIS PROTOCOL INVOLVE USING A VAN DER WAALS FUNCTION IN COMBINATION WITH A ELECTROSTATIC FUNCTION AND A 1/R-DEPENDENT DIELECTRIC FUNCTION, WHERE R INDICATES THE DISTANCE BETWEEN ATOMS (COULOMB'S LAW). IN ORDER TO SIMULATE AN AQUEOUS ENVIRONMENT, THE DIELECTRIC CONSTANT OF THE SYSTEM WAS SET TO 64. THE SWITCHING FUNCTION FOR THE NON-BONDED INTERACTIONS WAS ACTIVE BETWEEN 7.5 AND 10.0 A. THE NON-BONDED INTERACTION CUT-OFF WAS SET TO BE A SMOOTH TRANSITION BETWEEN 0.5 AND 10.0 A. THE DNA/POTASSIUM COMPLEXES WERE SUBJECTED TO A 500-STEP MINIMIZATION ALLOWING ONLY THE POTASSIUM TO MOVE WHILE THE DNA WAS HELD RIGID. ENERGY MINIMIZATION'S WERE RUN WITH VARIOUS STARTING POSITIONS FOR THE POTASSIUM IONS IN ORDER TO DETERMINE IF THE INITIAL POSITION HAD AN EFFECT ON THE MINIMIZED POSITION. RANDOM STARTING POSITIONS OF THE K+ FROM 5 TO 10 A AWAY FROM THE DNA WERE USED AND THE FINAL RESULTS WERE FOUND TO BE INDEPENDENT OF THE INITIAL COORDINATES OF THE POTASSIUM. THE MINIMIZATIONS WERE CARRIED OUT FIRST WITH ONE POTASSIUM ION PER QUADRUPLEX AND THEN WITH TWO PER QUADRUPLEX. THE POSITION OF THE FIRST BINDING SITE DID NOT CHANGE, UPON ADDITION OF THE SECOND POTASSIUM, FOR EITHER DNA. ADDITIONAL MINIMIZATIONS DID NOT CHANGE THE POSITIONS OF THE POTASSIUM IONS.
NMR ensembleConformers submitted total number: 1

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