HEADER RNA 09-JUN-15 2N3R TITLE NMR STRUCTURE OF THE II-III-VI THREE-WAY JUNCTION FROM THE VS RIBOZYME TITLE 2 AND IDENTIFICATION OF MAGNESIUM-BINDING SITES USING PARAMAGNETIC TITLE 3 RELAXATION ENHANCEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (62-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEUROSPORA CRASSA; SOURCE 3 ORGANISM_TAXID: 5141; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR: PTZ19R-DERIVED PTR-4 KEYWDS RNA, VS RIBOZYME, CATALYSIS, MG2+ IONS EXPDTA SOLUTION NMR NUMMDL 21 MDLTYP MINIMIZED AVERAGE AUTHOR E.BONNEAU,N.GIRARD,S.LEMIEUX,P.LEGAULT REVDAT 3 01-MAY-24 2N3R 1 REMARK LINK REVDAT 2 02-SEP-15 2N3R 1 JRNL REVDAT 1 15-JUL-15 2N3R 0 JRNL AUTH E.BONNEAU,N.GIRARD,S.LEMIEUX,P.LEGAULT JRNL TITL THE NMR STRUCTURE OF THE II-III-VI THREE-WAY JUNCTION FROM JRNL TITL 2 THE NEUROSPORA VS RIBOZYME REVEALS A CRITICAL TERTIARY JRNL TITL 3 INTERACTION AND PROVIDES NEW INSIGHTS INTO THE GLOBAL JRNL TITL 4 RIBOZYME STRUCTURE. JRNL REF RNA V. 21 1621 2015 JRNL REFN ISSN 1355-8382 JRNL PMID 26124200 JRNL DOI 10.1261/RNA.052076.115 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRDRAW, X-PLOR NIH REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRDRAW), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N3R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000104384. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 298 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM [U-15N] RNA (62-MER), 90% REMARK 210 H2O/10% D2O; 2 MM [U-13C; U-15N] REMARK 210 RNA (62-MER), 100% D2O; 2 MM [U- REMARK 210 13C; U-15N]-ADE RNA (62-MER), REMARK 210 100% D2O; 2 MM [U-13C; U-15N]- REMARK 210 CYT RNA (62-MER), 100% D2O; 2.5 REMARK 210 MM [U-13C; U-15N]-GUA RNA (62- REMARK 210 MER), 100% D2O; 2 MM [U-13C; U- REMARK 210 15N] RNA (62-MER), 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1D 1H WATERGATE; 2D 1H-15N HSQC; REMARK 210 2D 1H-15N HSQC NH2 ONLY; 2D HNN REMARK 210 COSY; 2D 1H-1H NOESY; 2D 1H-15N REMARK 210 CPMG-NOESY; 3D 15N-EDITED NOESY- REMARK 210 HSQC; 3D 15N/13C-EDITED NOESY- REMARK 210 HSQC; 2D G-SPECIFIC H(NC)-TOCSY- REMARK 210 (C)H; 2D A-SPECIFIC H(NC)-TOCSY- REMARK 210 (C)H; 2D 1H-15N MQ-(HC)N(C)H; 2D REMARK 210 1H-13C HSQC; 2D 1H-13C HMQC; 3D REMARK 210 HCCH-COSY; 3D HCCH-TOCSY; 3D 13C- REMARK 210 EDITED NOESY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW, NMRPIPE, CCPNMR, X-PLOR REMARK 210 NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 HO2' U A 38 O6 G A 41 1.57 REMARK 500 REMARK 500 REMARK: NULL 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 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 201 O REMARK 620 2 HOH A 202 O 89.9 REMARK 620 3 HOH A 203 O 90.0 180.0 REMARK 620 4 HOH A 204 O 90.0 90.0 90.0 REMARK 620 5 HOH A 205 O 90.0 89.9 90.1 179.9 REMARK 620 6 HOH A 206 O 179.9 90.0 90.0 90.0 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 207 O REMARK 620 2 HOH A 208 O 90.0 REMARK 620 3 HOH A 209 O 90.0 180.0 REMARK 620 4 HOH A 210 O 90.0 90.0 90.0 REMARK 620 5 HOH A 211 O 90.0 90.0 90.0 179.9 REMARK 620 6 HOH A 212 O 180.0 90.0 90.0 90.0 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 213 O REMARK 620 2 HOH A 214 O 90.0 REMARK 620 3 HOH A 215 O 90.0 179.9 REMARK 620 4 HOH A 216 O 90.0 90.0 90.0 REMARK 620 5 HOH A 217 O 89.9 90.0 90.0 179.9 REMARK 620 6 HOH A 218 O 180.0 90.0 90.0 90.0 90.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 219 O REMARK 620 2 HOH A 220 O 90.0 REMARK 620 3 HOH A 221 O 90.0 179.9 REMARK 620 4 HOH A 222 O 90.0 90.0 90.0 REMARK 620 5 HOH A 223 O 90.0 90.0 90.0 179.9 REMARK 620 6 HOH A 224 O 180.0 90.0 90.0 90.0 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 225 O REMARK 620 2 HOH A 226 O 90.0 REMARK 620 3 HOH A 227 O 90.0 180.0 REMARK 620 4 HOH A 228 O 90.0 90.0 90.0 REMARK 620 5 HOH A 229 O 90.0 90.0 90.1 180.0 REMARK 620 6 HOH A 230 O 180.0 90.0 90.0 90.0 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 106 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 231 O REMARK 620 2 HOH A 232 O 90.0 REMARK 620 3 HOH A 233 O 90.0 179.9 REMARK 620 4 HOH A 234 O 90.0 90.0 90.0 REMARK 620 5 HOH A 235 O 90.0 90.0 90.0 179.9 REMARK 620 6 HOH A 236 O 180.0 90.0 90.0 90.0 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 107 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 237 O REMARK 620 2 HOH A 238 O 90.0 REMARK 620 3 HOH A 239 O 90.0 179.9 REMARK 620 4 HOH A 240 O 90.0 90.0 90.0 REMARK 620 5 HOH A 241 O 90.0 90.0 90.0 179.9 REMARK 620 6 HOH A 242 O 180.0 90.0 90.1 90.1 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 108 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 243 O REMARK 620 2 HOH A 244 O 89.9 REMARK 620 3 HOH A 245 O 90.0 179.9 REMARK 620 4 HOH A 246 O 90.0 90.0 90.0 REMARK 620 5 HOH A 247 O 90.0 90.0 90.1 179.9 REMARK 620 6 HOH A 248 O 179.9 90.0 90.1 90.0 90.0 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 MG A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 108 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25655 RELATED DB: BMRB DBREF 2N3R A 1 62 PDB 2N3R 2N3R 1 62 SEQRES 1 A 62 G C A G C A G G G A A C U SEQRES 2 A 62 C A C G C U U G C G U A G SEQRES 3 A 62 A G G C U A A G U G C U U SEQRES 4 A 62 C G G C A C A G C A C A A SEQRES 5 A 62 G C C C G C U G C G HET MG A 101 1 HET MG A 102 1 HET MG A 103 1 HET MG A 104 1 HET MG A 105 1 HET MG A 106 1 HET MG A 107 1 HET MG A 108 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG 8(MG 2+) FORMUL 10 HOH *48(H2 O) LINK MG MG A 101 O HOH A 201 1555 1555 1.84 LINK MG MG A 101 O HOH A 202 1555 1555 1.84 LINK MG MG A 101 O HOH A 203 1555 1555 1.84 LINK MG MG A 101 O HOH A 204 1555 1555 1.84 LINK MG MG A 101 O HOH A 205 1555 1555 1.84 LINK MG MG A 101 O HOH A 206 1555 1555 1.84 LINK MG MG A 102 O HOH A 207 1555 1555 1.84 LINK MG MG A 102 O HOH A 208 1555 1555 1.84 LINK MG MG A 102 O HOH A 209 1555 1555 1.84 LINK MG MG A 102 O HOH A 210 1555 1555 1.84 LINK MG MG A 102 O HOH A 211 1555 1555 1.84 LINK MG MG A 102 O HOH A 212 1555 1555 1.84 LINK MG MG A 103 O HOH A 213 1555 1555 1.84 LINK MG MG A 103 O HOH A 214 1555 1555 1.84 LINK MG MG A 103 O HOH A 215 1555 1555 1.84 LINK MG MG A 103 O HOH A 216 1555 1555 1.84 LINK MG MG A 103 O HOH A 217 1555 1555 1.84 LINK MG MG A 103 O HOH A 218 1555 1555 1.84 LINK MG MG A 104 O HOH A 219 1555 1555 1.84 LINK MG MG A 104 O HOH A 220 1555 1555 1.84 LINK MG MG A 104 O HOH A 221 1555 1555 1.84 LINK MG MG A 104 O HOH A 222 1555 1555 1.84 LINK MG MG A 104 O HOH A 223 1555 1555 1.84 LINK MG MG A 104 O HOH A 224 1555 1555 1.84 LINK MG MG A 105 O HOH A 225 1555 1555 1.84 LINK MG MG A 105 O HOH A 226 1555 1555 1.84 LINK MG MG A 105 O HOH A 227 1555 1555 1.84 LINK MG MG A 105 O HOH A 228 1555 1555 1.84 LINK MG MG A 105 O HOH A 229 1555 1555 1.84 LINK MG MG A 105 O HOH A 230 1555 1555 1.84 LINK MG MG A 106 O HOH A 231 1555 1555 1.84 LINK MG MG A 106 O HOH A 232 1555 1555 1.84 LINK MG MG A 106 O HOH A 233 1555 1555 1.84 LINK MG MG A 106 O HOH A 234 1555 1555 1.84 LINK MG MG A 106 O HOH A 235 1555 1555 1.84 LINK MG MG A 106 O HOH A 236 1555 1555 1.84 LINK MG MG A 107 O HOH A 237 1555 1555 1.84 LINK MG MG A 107 O HOH A 238 1555 1555 1.84 LINK MG MG A 107 O HOH A 239 1555 1555 1.84 LINK MG MG A 107 O HOH A 240 1555 1555 1.84 LINK MG MG A 107 O HOH A 241 1555 1555 1.84 LINK MG MG A 107 O HOH A 242 1555 1555 1.84 LINK MG MG A 108 O HOH A 243 1555 1555 1.84 LINK MG MG A 108 O HOH A 244 1555 1555 1.84 LINK MG MG A 108 O HOH A 245 1555 1555 1.84 LINK MG MG A 108 O HOH A 246 1555 1555 1.84 LINK MG MG A 108 O HOH A 247 1555 1555 1.84 LINK MG MG A 108 O HOH A 248 1555 1555 1.84 SITE 1 AC1 6 HOH A 201 HOH A 202 HOH A 203 HOH A 204 SITE 2 AC1 6 HOH A 205 HOH A 206 SITE 1 AC2 6 HOH A 207 HOH A 208 HOH A 209 HOH A 210 SITE 2 AC2 6 HOH A 211 HOH A 212 SITE 1 AC3 6 HOH A 213 HOH A 214 HOH A 215 HOH A 216 SITE 2 AC3 6 HOH A 217 HOH A 218 SITE 1 AC4 6 HOH A 219 HOH A 220 HOH A 221 HOH A 222 SITE 2 AC4 6 HOH A 223 HOH A 224 SITE 1 AC5 6 HOH A 225 HOH A 226 HOH A 227 HOH A 228 SITE 2 AC5 6 HOH A 229 HOH A 230 SITE 1 AC6 6 HOH A 231 HOH A 232 HOH A 233 HOH A 234 SITE 2 AC6 6 HOH A 235 HOH A 236 SITE 1 AC7 9 C A 5 G A 7 C A 56 HOH A 237 SITE 2 AC7 9 HOH A 238 HOH A 239 HOH A 240 HOH A 241 SITE 3 AC7 9 HOH A 242 SITE 1 AC8 7 G A 9 HOH A 243 HOH A 244 HOH A 245 SITE 2 AC8 7 HOH A 246 HOH A 247 HOH A 248 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