HEADER DNA 01-NOV-00 1G5L TITLE CO(III)-BLEOMYCIN-OOH BOUND TO AN OLIGONUCLEOTIDE CONTAINING A TITLE 2 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, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.T.HOEHN,H.-D.JUNKER,R.C.BUNT,C.J.TURNER,J.STUBBE REVDAT 4 23-FEB-22 1G5L 1 REMARK REVDAT 3 24-FEB-09 1G5L 1 VERSN REVDAT 2 01-APR-03 1G5L 1 JRNL REVDAT 1 06-JUN-01 1G5L 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 TO A JRNL TITL 2 PHOSPHOGLYCOLATE LESION CONTAINING OLIGONUCLEOTIDE: JRNL TITL 3 IMPLICATIONS FOR BLEOMYCIN-INDUCED DOUBLE-STRAND DNA JRNL TITL 4 CLEAVAGE. JRNL REF BIOCHEMISTRY V. 40 5894 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11352724 JRNL DOI 10.1021/BI002635G REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 95.0, X-PLOR 3.851 REMARK 3 AUTHORS : MSI (FELIX), BRUNGER (X-PLOR) 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 1G5L COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-00. REMARK 100 THE DEPOSITION ID IS D_1000012261. 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 BUFFER; REMARK 210 40 MM SODIUM PHOSPHATE BUFFER REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.25 MM DRUG-DNA COMPLEX; 40 MM REMARK 210 SODIUM PHOSPHATE BUFFER; 1.25 MM REMARK 210 DRUG-DNA COMPLEX; 40 MM SODIUM REMARK 210 PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; PE-COSY; WATERGATE REMARK 210 -NOESY; 31P-HCOSY; 13C-HSQC; REMARK 210 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 : X-PLOR 3.851, FELIX 95.0 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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 MODELING REMARK 210 PURPOSED WAS TREATED AS TWO STRANDS OF DNA; THE HEXAETHYLENE REMARK 210 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 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 CO 3CO B 14 HB1 BLB C 1 1.43 REMARK 500 P DA B 8 O O B 15 1.45 REMARK 500 OP1 DA C 20 HO2 BLB C 1 1.54 REMARK 500 O3' DG A 6 P PGA A 7 1.59 REMARK 500 CO 3CO B 14 HB2 BLB C 1 1.60 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 7 DA C 17 N9 DA C 17 C4 0.038 REMARK 500 9 DA B 8 N9 DA B 8 C4 0.036 REMARK 500 9 DA C 17 N9 DA C 17 C4 0.040 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. = 4.7 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC A 2 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG A 6 N3 - C2 - N2 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DA B 8 N1 - C6 - N6 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA B 8 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DC B 9 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT B 10 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT B 10 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG B 11 N3 - C2 - N2 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG B 12 C2 - N3 - C4 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG B 12 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG B 12 N3 - C2 - N2 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG B 13 N3 - C2 - N2 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DC C 14 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DC C 15 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DC C 15 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DC C 16 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA C 17 N1 - C6 - N6 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG C 18 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT C 19 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT C 19 C4 - C5 - C7 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DT C 19 C6 - C5 - C7 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DA C 20 C3' - O3' - P ANGL. DEV. = 15.2 DEGREES REMARK 500 1 DC C 21 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DC C 21 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 1 DC C 21 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT C 22 C4 - C5 - C7 ANGL. DEV. = 10.5 DEGREES REMARK 500 1 DT C 22 C6 - C5 - C7 ANGL. DEV. = -12.7 DEGREES REMARK 500 1 DT C 22 C3' - O3' - P ANGL. DEV. = 11.2 DEGREES REMARK 500 1 DT C 23 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT C 23 C4 - C5 - C7 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DT C 23 C6 - C5 - C7 ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DT C 24 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT C 24 C4 - C5 - C7 ANGL. DEV. = 11.1 DEGREES REMARK 500 1 DT C 24 C6 - C5 - C7 ANGL. DEV. = -13.5 DEGREES REMARK 500 1 DT C 24 C3' - O3' - P ANGL. DEV. = 9.9 DEGREES REMARK 500 1 DG C 25 N3 - C2 - N2 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG C 25 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DG C 26 N3 - C2 - N2 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DA A 3 C3' - O3' - P ANGL. DEV. = 10.2 DEGREES REMARK 500 2 DA A 4 N1 - C6 - N6 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA A 5 N1 - C6 - N6 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 DG A 6 N1 - C2 - N3 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG A 6 N3 - C2 - N2 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 DC B 9 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DC B 9 N3 - C4 - C5 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 DT B 10 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 442 ANGLE DEVIATIONS. 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 1 PGA A 7 REMARK 610 2 PGA A 7 REMARK 610 3 PGA A 7 REMARK 610 4 PGA A 7 REMARK 610 5 PGA A 7 REMARK 610 6 PGA A 7 REMARK 610 7 PGA A 7 REMARK 610 8 PGA A 7 REMARK 610 9 PGA A 7 REMARK 610 10 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 84.3 REMARK 620 3 BLB C 1 NG 77.3 93.3 REMARK 620 4 BLB C 1 NH 154.3 85.5 79.8 REMARK 620 5 BLB C 1 NJ 115.1 93.5 166.4 89.0 REMARK 620 6 PEO C 11 O1 94.0 173.7 92.3 98.5 81.7 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 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3CO B 14 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE O B 15 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BLB C 1 REMARK 800 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 SITE REMARK 900 (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 SITE REMARK 900 (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 CONTAINING REMARK 900 THE PHOSPHOGLYCOLATE LESION WITHOUT THE 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 WITHOUT THE REMARK 900 BLEOMYCIN BOUND. REMARK 900 RELATED ID: 1GJ2 RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE: 1GJ2 IS CO(III)-BLEOMYCIN-OOH BOUND TO REMARK 900 AN OLIGONUCLEOTIDE CONTAINING A PHOSPHOGLYCOLATE LESION DBREF 1G5L A 1 6 PDB 1G5L 1G5L 1 6 DBREF 1G5L B 8 13 PDB 1G5L 1G5L 8 13 DBREF 1G5L C 14 26 PDB 1G5L 1G5L 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 1.94 LINK CO 3CO B 14 NG BLB C 1 1555 1555 1.85 LINK CO 3CO B 14 NH BLB C 1 1555 1555 1.92 LINK CO 3CO B 14 NJ BLB C 1 1555 1555 1.91 LINK CO 3CO B 14 O1 PEO C 11 1555 1555 2.04 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 10 PGA A 7 DC B 9 DT B 10 DG B 11 SITE 2 AC4 10 DG B 12 3CO B 14 PEO C 11 DG C 18 SITE 3 AC4 10 DT C 19 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 MODEL 1