HEADER DNA 12-FEB-02 1L0R TITLE NMR SOLUTION STRUCTURE OF NOGALAMYCIN INTERCALATION BETWEEN CO-AXIALLY TITLE 2 STACKED HAIRPINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*CP*GP*AP*AP*GP*TP*GP*CP*GP*AP*AP*GP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CO-AXIALLY STACKED DNA HAIRPIN SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY SOLID PHASE USING SOURCE 4 PHOSPHORAMIDITE CHEMISTRY. KEYWDS GAA LOOP, SINGLE STRAND BREAK, DRUG-DNA RECOGNITION, NOGALAMYCIN KEYWDS 2 INTERCALATION, DNA EXPDTA SOLUTION NMR AUTHOR H.E.L.WILLIAMS,M.L.COLGRAVE,M.S.SEARLE REVDAT 5 23-FEB-22 1L0R 1 REMARK LINK REVDAT 4 24-FEB-09 1L0R 1 VERSN REVDAT 3 21-SEP-04 1L0R 1 ATOM REVDAT 2 01-APR-03 1L0R 1 JRNL REVDAT 1 19-JUN-02 1L0R 0 JRNL AUTH H.E.L.WILLIAMS,M.L.COLGRAVE,M.S.SEARLE JRNL TITL DRUG RECOGNITION OF A DNA SINGLE STRAND BREAK: NOGALAMYCIN JRNL TITL 2 INTERCALATION BETWEEN COAXIALLY STACKED HAIRPINS. JRNL REF EUR.J.BIOCHEM. V. 269 1726 2002 JRNL REFN ISSN 0014-2956 JRNL PMID 11895443 JRNL DOI 10.1046/J.1432-1327.2002.02819.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6-3.1, AMBER 6 REMARK 3 AUTHORS : REMARK 3 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH, REMARK 3 WEINER,KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1L0R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1000015539. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 100MM NA+ 10MM PO4- REMARK 210 PRESSURE : ATMOSPHERIC ATM REMARK 210 SAMPLE CONTENTS : 3MM HAIRPIN; 10MM PHOSPHATE, REMARK 210 100MM NACL; 0.6MM NAN3; 0.6MM REMARK 210 NA4 EDTA; 2MM REMARK 210 TRIMETHYLISILYLPROPANOATE D2O; REMARK 210 3MM HAIRPIN; 10MM PHOSPHATE, REMARK 210 100MM NACL; 0.6MM NAN3; 0.6MM REMARK 210 NA4 EDTA; 2MM REMARK 210 TRIMETHYLISILYLPROPANOATE 10% REMARK 210 D2O, 90% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D NOESY WITH REMARK 210 WATERGATE SUPPRESION; DQF-COSY; REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ANSIG 3.3, AMBER 6 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA A 1 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 1 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG A 8 C1' - O4' - C4' ANGL. DEV. = -7.6 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA A 11 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA A 11 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 11 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA A 12 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DA A 12 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA A 12 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC A 14 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 DC A 14 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG A 3 0.06 SIDE CHAIN REMARK 500 DT A 7 0.08 SIDE CHAIN REMARK 500 DG A 8 0.05 SIDE CHAIN REMARK 500 DC A 9 0.19 SIDE CHAIN REMARK 500 DG A 10 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 16 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA A 5 O4' REMARK 620 2 DA A 5 N3 70.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 16 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 18 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 19 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 22 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NGP A 15 DBREF 1L0R A 1 14 PDB 1L0R 1L0R 1 14 SEQRES 1 A 14 DA DC DG DA DA DG DT DG DC DG DA DA DG SEQRES 2 A 14 DC HET NA A 16 1 HET NA A 17 1 HET NA A 18 1 HET NA A 19 1 HET NA A 20 1 HET NA A 21 1 HET NA A 22 1 HET NA A 23 1 HET NA A 24 1 HET NA A 25 1 HET NA A 26 1 HET NA A 27 1 HET NGP A 15 106 HETNAM NA SODIUM ION HETNAM NGP NOGALAMYCIN (PROTONATED FORM) FORMUL 2 NA 12(NA 1+) FORMUL 14 NGP C39 H52 N O16 1+ FORMUL 15 HOH *2194(H2 O) LINK O4' DA A 5 NA NA A 16 1555 1555 2.44 LINK N3 DA A 5 NA NA A 16 1555 1555 2.53 LINK NA NA A 18 O HOH A 825 1555 1555 2.48 LINK NA NA A 19 O HOH A1100 1555 1555 2.46 LINK NA NA A 22 O HOH A1917 1555 1555 2.49 SITE 1 AC1 2 DA A 5 DG A 6 SITE 1 AC2 1 HOH A 825 SITE 1 AC3 1 HOH A1100 SITE 1 AC4 1 HOH A1917 SITE 1 AC5 8 DA A 1 DC A 2 DT A 7 DG A 8 SITE 2 AC5 8 DC A 9 DG A 13 DC A 14 HOH A1360 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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