HEADER DNA 13-FEB-13 2M54 TITLE REFINED NMR SOLUTION STRUCTURE OF METAL-MODIFIED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*TP*AP*AP*TP*TP*TP*(D33)P*(D33)P*(D33) COMPND 3 P*AP*AP*AP*TP*TP*AP*A)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA, ARTIFICIAL NUCLEOBASE, IMIDAZOLE NUCLEOSIDE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.KUMBHAR,S.JOHANNSEN,R.K.SIGEL,M.P.WALLER,J.MUELLER REVDAT 3 14-JUN-23 2M54 1 REMARK LINK REVDAT 2 25-SEP-13 2M54 1 JRNL REVDAT 1 15-MAY-13 2M54 0 JRNL AUTH S.KUMBHAR,S.JOHANNSEN,R.K.SIGEL,M.P.WALLER,J.MULLER JRNL TITL A QM/MM REFINEMENT OF AN EXPERIMENTAL DNA STRUCTURE WITH JRNL TITL 2 METAL-MEDIATED BASE PAIRS. JRNL REF J.INORG.BIOCHEM. V. 127 203 2013 JRNL REFN ISSN 0162-0134 JRNL PMID 23622950 JRNL DOI 10.1016/J.JINORGBIO.2013.03.009 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, 2.0, 2.1, X-PLOR NIH 2.15 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M54 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000103220. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278 REMARK 210 PH : 7.2; 7.2 REMARK 210 IONIC STRENGTH : 0.12; 0.12 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3-0.5 MM DS DNA, 0.9-1.5 MM REMARK 210 SILVER ION, 120 MM SODIUM REMARK 210 PERCHLORATE, 100% D2O; 0.3-0.5 REMARK 210 MM DS DNA, 0.9-1.5 MM SILVER ION, REMARK 210 120 MM SODIUM PERCHLORATE, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-13C HSQC; 2D 1H-15N HSQC; REMARK 210 1D 31P REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.1, DYANA 1.5, X-PLOR REMARK 210 NIH 2.15 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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 AG A 101 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 D33 A 8 N3 REMARK 620 2 D33 B 27 N3 176.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG A 102 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 D33 A 9 N3 REMARK 620 2 D33 B 26 N3 179.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AG A 103 AG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 D33 A 10 N3 REMARK 620 2 D33 B 25 N3 176.6 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 AG A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AG A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AG A 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16138 RELATED DB: BMRB REMARK 900 NMR DATA RELATED TO NMR SOLUTION STRUCTURE OF METAL-MODIFIED DNA REMARK 900 RELATED ID: 2KE8 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF METAL-MODIFIED DNA REMARK 900 RELATED ID: 2K68 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF MODIFIED DNA CONTAINING IMIDAZOLE REMARK 900 NUCLEOSIDES AT NEUTRAL PH DBREF 2M54 A 1 17 PDB 2M54 2M54 1 17 DBREF 2M54 B 18 34 PDB 2M54 2M54 18 34 SEQRES 1 A 17 DT DT DA DA DT DT DT D33 D33 D33 DA DA DA SEQRES 2 A 17 DT DT DA DA SEQRES 1 B 17 DT DT DA DA DT DT DT D33 D33 D33 DA DA DA SEQRES 2 B 17 DT DT DA DA HET D33 A 8 26 HET D33 A 9 26 HET D33 A 10 26 HET D33 B 25 26 HET D33 B 26 26 HET D33 B 27 26 HET AG A 101 1 HET AG A 102 1 HET AG A 103 1 HETNAM D33 1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 D33 PENTOFURANOSYL)-1H-IMIDAZOLE HETNAM AG SILVER ION FORMUL 1 D33 6(C8 H13 N2 O6 P) FORMUL 3 AG 3(AG 1+) LINK O3' DT A 7 P D33 A 8 1555 1555 1.61 LINK O3' D33 A 8 P D33 A 9 1555 1555 1.61 LINK O3' D33 A 9 P D33 A 10 1555 1555 1.61 LINK O3' D33 A 10 P DA A 11 1555 1555 1.61 LINK O3' DT B 24 P D33 B 25 1555 1555 1.61 LINK O3' D33 B 25 P D33 B 26 1555 1555 1.61 LINK O3' D33 B 26 P D33 B 27 1555 1555 1.61 LINK O3' D33 B 27 P DA B 28 1555 1555 1.61 LINK N3 D33 A 8 AG AG A 101 1555 1555 2.14 LINK N3 D33 A 9 AG AG A 102 1555 1555 2.14 LINK N3 D33 A 10 AG AG A 103 1555 1555 2.13 LINK AG AG A 101 N3 D33 B 27 1555 1555 2.13 LINK AG AG A 102 N3 D33 B 26 1555 1555 2.14 LINK AG AG A 103 N3 D33 B 25 1555 1555 2.14 SITE 1 AC1 4 D33 A 8 D33 A 9 AG A 102 D33 B 27 SITE 1 AC2 6 D33 A 9 D33 A 10 AG A 101 AG A 103 SITE 2 AC2 6 D33 B 26 D33 B 27 SITE 1 AC3 4 D33 A 10 AG A 102 D33 B 25 D33 B 26 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