HEADER DNA 04-OCT-00 1FZS TITLE DNA WITH PYRENE PAIRED AT ABASIC SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*AP*CP*AP*AP*AP*CP*AP*(PYP))-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*TP*GP*CP*(3DR)P*TP*GP*TP*TP*TP*GP*TP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS PYRENE, FURAN, NON-POLAR DNA PAIR, DNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR S.SMIRNOV,T.J.MATRAY,E.T.KOOL,C.DE LOS SANTOS REVDAT 4 23-FEB-22 1FZS 1 REMARK LINK REVDAT 3 24-FEB-09 1FZS 1 VERSN REVDAT 2 07-JAN-03 1FZS 1 JRNL REMARK MASTER REVDAT 1 18-OCT-00 1FZS 0 JRNL AUTH S.SMIRNOV,T.J.MATRAY,E.T.KOOL,C.DE LOS SANTOS JRNL TITL INTEGRITY OF DUPLEX STRUCTURES WITHOUT HYDROGEN BONDING: DNA JRNL TITL 2 WITH PYRENE PAIRED AT ABASIC SITES JRNL REF NUCLEIC ACIDS RES. V. 30 5561 2002 JRNL REFN ISSN 0305-1048 JRNL PMID 12490724 JRNL DOI 10.1093/NAR/GKF688 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 5, X-PLOR 3.8 REMARK 3 AUTHORS : VARIAN CO. (VNMR), A. BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FZS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000012054. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 280; 298 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 50 MM; 50 MM REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 3.9 MM; 3.9 MM REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; COSY, TOCSY, HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 95 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 15 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 DC A 1 C4 DC A 1 N4 0.094 REMARK 500 1 DA A 2 C6 DA A 2 N6 0.093 REMARK 500 1 DC A 3 C2' DC A 3 C1' 0.099 REMARK 500 1 DC A 3 C4 DC A 3 N4 0.095 REMARK 500 1 DC A 3 N1 DC A 3 C6 0.066 REMARK 500 1 DA A 4 C6 DA A 4 N6 0.098 REMARK 500 1 DA A 5 C6 DA A 5 N6 0.093 REMARK 500 1 DA A 6 C6 DA A 6 N6 0.094 REMARK 500 1 DC A 7 C4 DC A 7 N4 0.095 REMARK 500 1 DA A 8 C6 DA A 8 N6 0.093 REMARK 500 1 DG B 14 C2 DG B 14 N2 0.081 REMARK 500 1 DT B 15 C2' DT B 15 C1' 0.062 REMARK 500 1 DT B 15 C5 DT B 15 C7 0.037 REMARK 500 1 DG B 16 C2 DG B 16 N2 0.085 REMARK 500 1 DC B 17 C4 DC B 17 N4 0.095 REMARK 500 1 DG B 20 C2 DG B 20 N2 0.085 REMARK 500 1 DT B 23 C5 DT B 23 C7 0.039 REMARK 500 1 DG B 24 C2 DG B 24 N2 0.084 REMARK 500 1 DG B 26 C2 DG B 26 N2 0.087 REMARK 500 2 DC A 1 C4 DC A 1 N4 0.094 REMARK 500 2 DA A 2 C6 DA A 2 N6 0.092 REMARK 500 2 DC A 3 C2' DC A 3 C1' 0.099 REMARK 500 2 DC A 3 C4 DC A 3 N4 0.094 REMARK 500 2 DC A 3 N1 DC A 3 C6 0.067 REMARK 500 2 DA A 4 C6 DA A 4 N6 0.097 REMARK 500 2 DA A 5 C6 DA A 5 N6 0.092 REMARK 500 2 DA A 6 C6 DA A 6 N6 0.093 REMARK 500 2 DC A 7 C4 DC A 7 N4 0.093 REMARK 500 2 DA A 8 C6 DA A 8 N6 0.093 REMARK 500 2 DG B 14 C2 DG B 14 N2 0.086 REMARK 500 2 DT B 15 C5 DT B 15 C7 0.037 REMARK 500 2 DG B 16 C2 DG B 16 N2 0.085 REMARK 500 2 DC B 17 C4 DC B 17 N4 0.092 REMARK 500 2 DG B 20 C2 DG B 20 N2 0.085 REMARK 500 2 DT B 21 C5 DT B 21 C7 0.039 REMARK 500 2 DT B 23 C5 DT B 23 C7 0.038 REMARK 500 2 DG B 24 C2 DG B 24 N2 0.084 REMARK 500 2 DT B 25 C6 DT B 25 N1 -0.042 REMARK 500 2 DG B 26 C2 DG B 26 N2 0.086 REMARK 500 3 DC A 1 C4 DC A 1 N4 0.094 REMARK 500 3 DA A 2 C6 DA A 2 N6 0.093 REMARK 500 3 DC A 3 C2' DC A 3 C1' 0.098 REMARK 500 3 DC A 3 C4 DC A 3 N4 0.095 REMARK 500 3 DC A 3 N1 DC A 3 C6 0.065 REMARK 500 3 DA A 4 C6 DA A 4 N6 0.096 REMARK 500 3 DA A 5 C6 DA A 5 N6 0.093 REMARK 500 3 DA A 6 C6 DA A 6 N6 0.094 REMARK 500 3 DC A 7 C4 DC A 7 N4 0.094 REMARK 500 3 DA A 8 C6 DA A 8 N6 0.094 REMARK 500 3 DG B 14 C2 DG B 14 N2 0.084 REMARK 500 REMARK 500 THIS ENTRY HAS 166 BOND DEVIATIONS. 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' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DC A 1 C4' - C3' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DC A 1 O4' - C1' - C2' ANGL. DEV. = -7.4 DEGREES REMARK 500 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 15.9 DEGREES REMARK 500 1 DC A 3 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DC A 3 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG B 14 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT B 15 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG B 16 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DC B 17 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT B 19 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DG B 20 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG B 20 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DT B 22 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DT B 22 C4 - C5 - C6 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT B 22 C6 - C5 - C7 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DT B 23 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT B 23 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT B 23 O4' - C1' - C2' ANGL. DEV. = -9.4 DEGREES REMARK 500 1 DT B 23 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT B 23 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG B 24 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG B 24 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DT B 25 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT B 25 C4 - C5 - C6 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DT B 25 C4 - C5 - C7 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT B 25 C6 - C5 - C7 ANGL. DEV. = -8.2 DEGREES REMARK 500 2 DC A 1 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 1 C4' - C3' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 2 DC A 1 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 15.2 DEGREES REMARK 500 2 DC A 3 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DA A 8 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 DG B 14 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DG B 14 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DT B 15 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 2 DG B 16 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG B 16 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 DG B 16 C3' - O3' - P ANGL. DEV. = 11.7 DEGREES REMARK 500 2 DT B 19 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DG B 20 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG B 20 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 272 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FZL RELATED DB: PDB REMARK 900 1FZL CONTAINS A DNA DUPLEX WITH A PYRENE RESIDUE PAIRED AT AN REMARK 900 ABASIC SITE DBREF 1FZS A 1 9 PDB 1FZS 1FZS 1 9 DBREF 1FZS B 14 26 PDB 1FZS 1FZS 14 26 SEQRES 1 A 9 DC DA DC DA DA DA DC DA PYP SEQRES 1 B 13 DG DT DG DC 3DR DT DG DT DT DT DG DT DG HET PYP A 9 44 HET 3DR B 18 19 HETNAM PYP 2'-DEOXYRIBOFURANOSYLPYRENE-5'-MONOPHOSPHATE HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 1 PYP C21 H19 O6 P FORMUL 2 3DR C5 H11 O6 P LINK O3' DA A 8 P PYP A 9 1555 1555 1.61 LINK O3' DC B 17 P 3DR B 18 1555 1555 1.62 LINK O3' 3DR B 18 P DT B 19 1555 1555 1.62 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