HEADER DNA 01-MAR-01 1I5V TITLE SOLUTION STRUCTURE OF 2-(PYRIDO[1,2-E]PURIN-4-YL)AMINO-ETHANOL TITLE 2 INTERCALATED IN THE DNA DUPLEX D(CGATCG)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*AP*TP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DRUG-DNA COMPLEX, DOUBLE HELIX, DNA EXPDTA SOLUTION NMR NUMMDL 22 AUTHOR A.FAVIER,M.BLACKLEDGE,J.P.SIMORRE,D.MARION,J.C.DEBOUSY REVDAT 6 22-MAY-24 1I5V 1 REMARK REVDAT 5 23-FEB-22 1I5V 1 REMARK REVDAT 4 24-FEB-09 1I5V 1 VERSN REVDAT 3 01-APR-03 1I5V 1 JRNL REVDAT 2 22-AUG-01 1I5V 1 JRNL REVDAT 1 14-MAR-01 1I5V 0 JRNL AUTH A.FAVIER,M.BLACKLEDGE,J.P.SIMORRE,S.CROUZY,V.DABOUIS, JRNL AUTH 2 A.GUEIFFIER,D.MARION,J.C.DEBOUZY JRNL TITL SOLUTION STRUCTURE OF JRNL TITL 2 2-(PYRIDO[1,2-E]PURIN-4-YL)AMINO-ETHANOL INTERCALATED IN THE JRNL TITL 3 DNA DUPLEX D(CGATCG)2. JRNL REF BIOCHEMISTRY V. 40 8717 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11467931 JRNL DOI 10.1021/BI0024963 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.A, DISCOVER REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CALCULATION FROM RANDOMIZED CARTESIAN REMARK 3 COORDINATES REMARK 4 REMARK 4 1I5V COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-01. REMARK 100 THE DEPOSITION ID IS D_1000012942. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 7 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM 2-(PYRIDO[1,2-E]PURIN-4 REMARK 210 -YL)AMINO-ETHANOL, 2MM D(CGATCG)2 160 MM KCL, 0.15 MM EDTA, 20 REMARK 210 MM SODIUM PHOSPHATE; 2 MM 2-(PYRIDO[1,2-E]PURIN-4-YL)AMINO- REMARK 210 ETHANOL, 2MM D(CGATCG)2 160 MM KCL, 0.15 MM EDTA, 20 MM SODIUM REMARK 210 PHOSPHATE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; TOCSY; 1H-1H REMARK 210 CT COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AMX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, INSIGHT 97, DISCOVER REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 22 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED CONFORMER MODELS REMARK 210 ARE THE 22 STRUCTURES WITH THE REMARK 210 LOWEST EXPERIMENTAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 12 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H3' DC A 1 H5'' DG A 2 1.35 REMARK 500 REMARK 500 REMARK: NULL 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 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG B 2 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG B 6 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DC B 1 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DG B 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT B 4 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 2 DT B 4 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT B 4 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 4 DG A 6 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 4 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 4 DA B 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DT B 4 C1' - O4' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 4 DT B 4 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 5 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 DC B 1 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 5 DG B 2 C1' - O4' - C4' ANGL. DEV. = -8.1 DEGREES REMARK 500 5 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 5 DT B 4 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 5 DT B 4 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 5 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 6 DT A 4 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 6 DT A 4 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 6 DC B 1 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 6 DT B 4 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 DT B 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 6 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 7 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 7 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 7 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 DC B 1 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 7 DC B 1 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 7 DG B 2 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 7 DG B 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 7 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 8 DC A 1 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 136 ANGLE DEVIATIONS. 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 1 DC A 1 0.07 SIDE CHAIN REMARK 500 1 DC A 5 0.14 SIDE CHAIN REMARK 500 1 DG A 6 0.15 SIDE CHAIN REMARK 500 1 DG B 2 0.08 SIDE CHAIN REMARK 500 1 DC B 5 0.14 SIDE CHAIN REMARK 500 1 DG B 6 0.14 SIDE CHAIN REMARK 500 2 DC A 1 0.06 SIDE CHAIN REMARK 500 2 DA A 3 0.07 SIDE CHAIN REMARK 500 2 DG A 6 0.13 SIDE CHAIN REMARK 500 2 DC B 1 0.08 SIDE CHAIN REMARK 500 2 DG B 2 0.07 SIDE CHAIN REMARK 500 2 DC B 5 0.13 SIDE CHAIN REMARK 500 2 DG B 6 0.16 SIDE CHAIN REMARK 500 3 DC A 1 0.07 SIDE CHAIN REMARK 500 3 DG A 2 0.09 SIDE CHAIN REMARK 500 3 DC A 5 0.10 SIDE CHAIN REMARK 500 3 DG A 6 0.16 SIDE CHAIN REMARK 500 3 DG B 2 0.07 SIDE CHAIN REMARK 500 3 DG B 6 0.14 SIDE CHAIN REMARK 500 4 DG A 2 0.07 SIDE CHAIN REMARK 500 4 DC A 5 0.07 SIDE CHAIN REMARK 500 4 DG A 6 0.16 SIDE CHAIN REMARK 500 4 DC B 1 0.06 SIDE CHAIN REMARK 500 4 DC B 5 0.09 SIDE CHAIN REMARK 500 4 DG B 6 0.16 SIDE CHAIN REMARK 500 5 DC A 1 0.07 SIDE CHAIN REMARK 500 5 DC A 5 0.07 SIDE CHAIN REMARK 500 5 DG A 6 0.14 SIDE CHAIN REMARK 500 5 DC B 1 0.09 SIDE CHAIN REMARK 500 5 DC B 5 0.12 SIDE CHAIN REMARK 500 5 DG B 6 0.13 SIDE CHAIN REMARK 500 6 DC A 5 0.08 SIDE CHAIN REMARK 500 6 DG A 6 0.17 SIDE CHAIN REMARK 500 6 DC B 1 0.14 SIDE CHAIN REMARK 500 6 DG B 2 0.06 SIDE CHAIN REMARK 500 6 DA B 3 0.08 SIDE CHAIN REMARK 500 6 DC B 5 0.11 SIDE CHAIN REMARK 500 6 DG B 6 0.16 SIDE CHAIN REMARK 500 7 DC A 1 0.09 SIDE CHAIN REMARK 500 7 DC A 5 0.09 SIDE CHAIN REMARK 500 7 DG A 6 0.16 SIDE CHAIN REMARK 500 7 DC B 1 0.07 SIDE CHAIN REMARK 500 7 DG B 2 0.06 SIDE CHAIN REMARK 500 7 DA B 3 0.06 SIDE CHAIN REMARK 500 7 DC B 5 0.07 SIDE CHAIN REMARK 500 7 DG B 6 0.16 SIDE CHAIN REMARK 500 8 DG A 2 0.08 SIDE CHAIN REMARK 500 8 DC A 5 0.10 SIDE CHAIN REMARK 500 8 DG A 6 0.13 SIDE CHAIN REMARK 500 8 DG B 6 0.15 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 117 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PPZ A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PPZ B 7 DBREF 1I5V A 1 6 PDB 1I5V 1I5V 1 6 DBREF 1I5V B 1 6 PDB 1I5V 1I5V 1 6 SEQRES 1 A 6 DC DG DA DT DC DG SEQRES 1 B 6 DC DG DA DT DC DG HET PPZ A 7 28 HET PPZ B 7 28 HETNAM PPZ 2-(PYRIDO[1,2-E]PURIN-4-YL)AMINO-ETHANOL FORMUL 3 PPZ 2(C11 H11 N5 O) SITE 1 AC1 4 DC A 5 DG A 6 DC B 1 DG B 2 SITE 1 AC2 4 DC A 1 DG A 2 DC B 5 DG B 6 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 MODEL 1