HEADER DNA 26-APR-05 2BQ2 TITLE SOLUTION STRUCTURE OF THE DNA DUPLEX ACGCGU-NA WITH A 2' AMIDO-LINKED TITLE 2 NALIDIXIC ACID RESIDUE AT THE 3' TERMINAL NUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*CP*GP*CP*GP*2AU)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: NALIDIXIC ACID APPENDED TO THE AMINO FUNCTION OF 2'- COMPND 6 AMINOURIDINE VIA AN AMIDE BOND SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS NUCLEIC ACID, DEOXYRIBONUCLEIC ACID, DISRUPTED TERMINAL BASEPAIRS, KEYWDS 2 DNA, QUINOLONE, SYNTHETIC HYBRID, DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 2 AUTHOR K.SIEGMUND,S.MAHESHWARY,S.NARAYANAN,W.CONNORS,M.RICHERT REVDAT 5 09-MAY-18 2BQ2 1 JRNL REMARK ATOM REVDAT 4 01-MAY-13 2BQ2 1 HEADER COMPND REMARK VERSN REVDAT 4 2 1 FORMUL HETATM REVDAT 3 24-FEB-09 2BQ2 1 VERSN REVDAT 2 11-AUG-06 2BQ2 1 ATOM HETATM CONECT REVDAT 1 03-AUG-06 2BQ2 0 JRNL AUTH K.SIEGMUND,S.MAHESHWARY,S.NARAYANAN,W.CONNORS,M.RIEDRICH, JRNL AUTH 2 M.PRINTZ,C.RICHERT JRNL TITL MOLECULAR DETAILS OF QUINOLONE-DNA INTERACTIONS: SOLUTION JRNL TITL 2 STRUCTURE OF AN UNUSUALLY STABLE DNA DUPLEX WITH COVALENTLY JRNL TITL 3 LINKED NALIDIXIC ACID RESIDUES AND NON-COVALENT COMPLEXES JRNL TITL 4 DERIVED FROM IT. JRNL REF NUCLEIC ACIDS RES. V. 33 4838 2005 JRNL REFN ESSN 1362-4962 JRNL PMID 16126848 JRNL DOI 10.1093/NAR/GKI795 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SEE PRIMARY CITATION FOR DETAILS REMARK 4 REMARK 4 2BQ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-APR-05. REMARK 100 THE DEPOSITION ID IS D_1290022848. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283.0 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 160 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : D2O AND 90% WATER/ 10%D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY; HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 2 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST CALCULATED ENERGIES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NONE REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NIX A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NIX B 7 DBREF 2BQ2 A 1 6 PDB 2BQ2 2BQ2 1 6 DBREF 2BQ2 B 1 6 PDB 2BQ2 2BQ2 1 6 SEQRES 1 A 6 DA DC DG DC DG 2AU SEQRES 1 B 6 DA DC DG DC DG 2AU MODRES 2BQ2 2AU A 6 U 2'-AMINOURIDINE MODRES 2BQ2 2AU B 6 U 2'-AMINOURIDINE HET 2AU A 6 31 HET 2AU B 6 31 HET NIX A 7 27 HET NIX B 7 27 HETNAM 2AU 2'-AMINOURIDINE HETNAM NIX NALIDIXIC ACID FORMUL 1 2AU 2(C9 H14 N3 O8 P) FORMUL 3 NIX 2(C12 H12 N2 O3) LINK O3' DG A 5 P 2AU A 6 1555 1555 1.61 LINK N2' 2AU A 6 C1L NIX A 7 1555 1555 1.36 LINK O3' DG B 5 P 2AU B 6 1555 1555 1.61 LINK N2' 2AU B 6 C1L NIX B 7 1555 1555 1.36 SITE 1 AC1 4 DG A 5 2AU A 6 DA B 1 DC B 2 SITE 1 AC2 4 DA A 1 DC A 2 DG B 5 2AU B 6 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1