HEADER DNA 01-NOV-00 1GJ2 TITLE CO(III)-BLEOMYCIN-OOH BOUND TO AN OLIGONUCLEOTIDE TITLE 2 CONTAINING A PHOSPHOGLYCOLATE LESION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*AP*AP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(P*AP*CP*TP*GP*GP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES KEYWDS DAMAGED DNA, DNA-DRUG COMPLEX, INTERCALATION EXPDTA SOLUTION NMR AUTHOR S.T.HOEHN,H.-D.JUNKER,R.C.BUNT,C.J.TURNER,J.STUBBE REVDAT 3 24-FEB-09 1GJ2 1 VERSN REVDAT 2 01-APR-03 1GJ2 1 JRNL REVDAT 1 06-JUN-01 1GJ2 0 JRNL AUTH S.T.HOEHN,H.D.JUNKER,R.C.BUNT,C.J.TURNER,J.STUBBE JRNL TITL SOLUTION STRUCTURE OF CO(III)-BLEOMYCIN-OOH BOUND JRNL TITL 2 TO A PHOSPHOGLYCOLATE LESION CONTAINING JRNL TITL 3 OLIGONUCLEOTIDE: IMPLICATIONS FOR JRNL TITL 4 BLEOMYCIN-INDUCED DOUBLE-STRAND DNA CLEAVAGE. JRNL REF BIOCHEMISTRY V. 40 5894 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11352724 JRNL DOI 10.1021/BI002635G REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 729 NOE- REMARK 3 DERIVED DISTANCE CONSTRAINTS AND 96 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1GJ2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-NOV-00. REMARK 100 THE RCSB ID CODE IS RCSB001568. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 278 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 40 MM SODIUM PHOSPHATE REMARK 210 BUFFER; 40 MM SODIUM PHOSPHATE REMARK 210 BUFFER REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.25 MM DRUG-DNA COMPLEX; 40 REMARK 210 MM SODIUM PHOSPHATE BUFFER; REMARK 210 1.25 MM DRUG-DNA COMPLEX; 40 REMARK 210 MM SODIUM PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, TOCSY, PE-COSY, REMARK 210 WATERGATE-NOESY, 31P- HCOSY, REMARK 210 13C-HSQC, ROESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : HOME-BUILT REMARK 210 SPECTROMETER MANUFACTURER : HOME-BUILT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 95.0, X-PLOR 3.851 REMARK 210 METHOD USED : 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: DNA WAS SYNTHESIZED AS A DOUBLE HAIRPIN, BUT FOR REMARK 210 MODELING PURPOSED WAS TREATED AS TWO STRANDS OF DNA; THE REMARK 210 HEXAETHYLENE GLYCOL SPACERS WERE NOT INCLUDED IN THE MODELING 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 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 DA C 17 N9 DA C 17 C4 0.036 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DC A 2 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG A 6 N3 - C2 - N2 ANGL. DEV. = 7.0 DEGREES REMARK 500 DA B 8 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA B 8 N1 - C6 - N6 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 9 N3 - C4 - C5 ANGL. DEV. = -2.7 DEGREES REMARK 500 DC B 9 N3 - C4 - N4 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT B 10 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT B 10 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG B 11 N1 - C2 - N3 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG B 11 N3 - C2 - N2 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG B 12 N3 - C2 - N2 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG B 13 N3 - C2 - N2 ANGL. DEV. = 6.0 DEGREES REMARK 500 DC C 14 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC C 15 P - O5' - C5' ANGL. DEV. = 13.0 DEGREES REMARK 500 DC C 15 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC C 15 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC C 16 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC C 16 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA C 17 N1 - C6 - N6 ANGL. DEV. = 6.0 DEGREES REMARK 500 DA C 17 C5 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 DG C 18 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DA C 17 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 DT C 19 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT C 19 C4 - C5 - C7 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT C 19 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES REMARK 500 DA C 20 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA C 20 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 DT C 22 C4 - C5 - C7 ANGL. DEV. = 10.4 DEGREES REMARK 500 DT C 22 C6 - C5 - C7 ANGL. DEV. = -12.6 DEGREES REMARK 500 DC C 21 C3' - O3' - P ANGL. DEV. = 10.0 DEGREES REMARK 500 DT C 23 C4 - C5 - C7 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT C 23 C6 - C5 - C7 ANGL. DEV. = -7.1 DEGREES REMARK 500 DT C 22 C3' - O3' - P ANGL. DEV. = 12.0 DEGREES REMARK 500 DT C 24 C4 - C5 - C7 ANGL. DEV. = 11.3 DEGREES REMARK 500 DT C 24 C6 - C5 - C7 ANGL. DEV. = -13.6 DEGREES REMARK 500 DG C 25 N3 - C2 - N2 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT C 24 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DG C 26 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PGA A 7 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 3CO B 14 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BLB C 1 NC REMARK 620 2 BLB C 1 NB 84.5 REMARK 620 3 BLB C 1 NG 77.6 93.5 REMARK 620 4 BLB C 1 NH 154.8 86.9 79.3 REMARK 620 5 BLB C 1 NJ 114.6 93.5 166.5 89.6 REMARK 620 6 PEO C 11 O1 93.6 174.2 91.5 97.0 82.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGA A 7 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3CO B 14 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE O B 15 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BLB C 1 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEO C 11 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G5D RELATED DB: PDB REMARK 900 ENSEMBLE: 1G5D HAS THE SAME SEQUENCE AND CONTAINS AN ABASIC REMARK 900 SITE (ALPHA ANOMER) INSTEAD OF THE PHOSPHOGLYCOLATE LESION REMARK 900 RELATED ID: 1GIZ RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE: 1GIZ HAS THE SAME SEQUENCE AND REMARK 900 CONTAINS AN ABASIC SITE (ALPHA ANOMER) INSTEAD OF THE REMARK 900 PHOSPHOGLYCOLATE LESION REMARK 900 RELATED ID: 1G5E RELATED DB: PDB REMARK 900 ENSEMBLE: 1G5E HAS THE SAME SEQUENCE AND CONTAINS AN ABASIC REMARK 900 SITE (BETA ANOMER) INSTEAD OF THE PHOSPHOGLYCOLATE LESION REMARK 900 RELATED ID: 1GJ0 RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE: 1GJ0 HAS THE SAME SEQUENCE AND REMARK 900 CONTAINS AN ABASIC SITE (BETA ANOMER) INSTEAD OF THE REMARK 900 PHOSPHOGLYCOLATE LESION REMARK 900 RELATED ID: 1G5K RELATED DB: PDB REMARK 900 ENSEMBLE: 1G5K IS THE STRUCTURE OF THE OLIGONUCLEOTIDE REMARK 900 CONTAINING THE PHOSPHOGLYCOLATE LESION WITHOUT THE REMARK 900 BLEOMYCIN BOUND. REMARK 900 RELATED ID: 1GJ1 RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE: 1GJ1 IS THE STRUCTURE OF THE REMARK 900 OLIGONUCLEOTIDE CONTAINING THE PHOSPHOGLYCOLATE LESION REMARK 900 WITHOUT THE BLEOMYCIN BOUND. REMARK 900 RELATED ID: 1G5L RELATED DB: PDB REMARK 900 ENSEMBLE: 1G5L IS CO(III)-BLEOMYCIN-OOH BOUND TO AN REMARK 900 OLIGONUCLEOTIDE CONTAINING A PHOSPHOGLYCOLATE LESION DBREF 1GJ2 A 1 6 PDB 1GJ2 1GJ2 1 6 DBREF 1GJ2 B 8 13 PDB 1GJ2 1GJ2 8 13 DBREF 1GJ2 C 14 26 PDB 1GJ2 1GJ2 14 26 SEQRES 1 A 6 DC DC DA DA DA DG SEQRES 1 B 6 DA DC DT DG DG DG SEQRES 1 C 13 DC DC DC DA DG DT DA DC DT DT DT DG DG HET PGA A 7 10 HET 3CO B 14 1 HET O B 15 1 HET BLB C 1 182 HET PEO C 11 3 HETNAM PGA 2-PHOSPHOGLYCOLIC ACID HETNAM 3CO COBALT (III) ION HETNAM O OXYGEN ATOM HETNAM BLB BLEOMYCIN B2 HETNAM PEO HYDROGEN PEROXIDE FORMUL 4 PGA C2 H5 O6 P FORMUL 5 3CO CO 3+ FORMUL 6 O O FORMUL 7 BLB C55 H85 N20 O21 S2 1+ FORMUL 8 PEO H2 O2 LINK CO 3CO B 14 NC BLB C 1 1555 1555 2.00 LINK CO 3CO B 14 NB BLB C 1 1555 1555 1.95 LINK CO 3CO B 14 NG BLB C 1 1555 1555 1.85 LINK CO 3CO B 14 NH BLB C 1 1555 1555 1.93 LINK CO 3CO B 14 NJ BLB C 1 1555 1555 1.92 LINK CO 3CO B 14 O1 PEO C 11 1555 1555 2.03 LINK O3' DG A 6 P PGA A 7 1555 1555 1.60 LINK P DA B 8 O O B 15 1555 1555 1.48 SITE 1 AC1 2 DG A 6 BLB C 1 SITE 1 AC2 2 BLB C 1 PEO C 11 SITE 1 AC3 1 DA B 8 SITE 1 AC4 13 DG A 6 PGA A 7 DA B 8 DC B 9 SITE 2 AC4 13 DT B 10 DG B 11 DG B 12 DG B 13 SITE 3 AC4 13 3CO B 14 PEO C 11 DG C 18 DT C 19 SITE 4 AC4 13 DA C 20 SITE 1 AC5 3 3CO B 14 BLB C 1 DT C 19 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 MASTER 200 0 5 0 0 0 8 6 0 0 0 3 END