HEADER RNA 19-AUG-14 2MTK TITLE NMR STRUCTURE OF THE III-IV-V 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 (47-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: NEUROSPORA CRASSA; SOURCE 4 ORGANISM_TAXID: 5141 KEYWDS VS RIBOZYME, THREE-WAY JUNCTION, BASE TRIPLE, U-TURN, RIBOSE ZIPPER, KEYWDS 2 GAAA TETRALOOP, CUUG TETRALOOP, RNA EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR E.BONNEAU,P.LEGAULT REVDAT 2 01-MAY-24 2MTK 1 REMARK LINK REVDAT 1 22-OCT-14 2MTK 0 JRNL AUTH E.BONNEAU,P.LEGAULT JRNL TITL NUCLEAR MAGNETIC RESONANCE STRUCTURE OF THE III-IV-V JRNL TITL 2 THREE-WAY JUNCTION FROM THE VARKUD SATELLITE RIBOZYME AND JRNL TITL 3 IDENTIFICATION OF MAGNESIUM-BINDING SITES USING PARAMAGNETIC JRNL TITL 4 RELAXATION ENHANCEMENT. JRNL REF BIOCHEMISTRY V. 53 6264 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 25238589 JRNL DOI 10.1021/BI500826N 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 2MTK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000104027. 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 : 55; 55 REMARK 210 PRESSURE : NULL; NULL REMARK 210 SAMPLE CONTENTS : 1.5-2.0 MM [U-100% 15N] J345, REMARK 210 90% H2O/10% D2O; 2.0 MM [U-100% REMARK 210 13C; U-100% 15N] J345, 100% D2O; REMARK 210 2.0 MM [U-100% 13C; U-100% 15N] REMARK 210 J345, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1D FLIP-BACK WATERGATE 1H; 2D 1H REMARK 210 -15N HSQC; 2D 1H-15N HSQC NH2 REMARK 210 ONLY; 3D 1H-15N NOESY; 2D 1H-13C REMARK 210 HSQC; 3D 13C-EDITED HMQC-NOESY; REMARK 210 3D CT-HCCH-COSY; 3D HCCH-TOCSY; REMARK 210 3D 15N-EDITED NOESY-HSQC; 2D REMARK 210 H(NC)-TOCSY-(C)H FOR GUANOSINE REMARK 210 RESIDUES; 2D 1H-13C HMQC; 2D 1H- REMARK 210 15N MQ-(HC)N(C)H; 2D 1H-15N CPMG- REMARK 210 NOESY; 2D HNN-COSY 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_SUITE, REMARK 210 X-PLOR NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 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 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 A A 30 OP1 REMARK 620 2 HOH A 201 O 172.0 REMARK 620 3 HOH A 202 O 98.0 89.9 REMARK 620 4 HOH A 203 O 82.0 90.0 180.0 REMARK 620 5 HOH A 204 O 90.0 90.0 90.0 90.0 REMARK 620 6 HOH A 205 O 90.0 90.0 90.0 90.0 180.0 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 206 O REMARK 620 2 HOH A 207 O 90.0 REMARK 620 3 HOH A 208 O 90.0 179.9 REMARK 620 4 HOH A 209 O 90.0 90.0 90.0 REMARK 620 5 HOH A 210 O 90.0 90.0 90.0 180.0 REMARK 620 6 HOH A 211 O 180.0 90.0 90.1 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 212 O REMARK 620 2 HOH A 213 O 89.9 REMARK 620 3 HOH A 214 O 90.0 179.9 REMARK 620 4 HOH A 215 O 90.0 90.0 90.0 REMARK 620 5 HOH A 216 O 90.0 90.0 90.0 179.9 REMARK 620 6 HOH A 217 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 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 218 O REMARK 620 2 HOH A 219 O 89.9 REMARK 620 3 HOH A 220 O 90.0 179.9 REMARK 620 4 HOH A 221 O 90.0 90.0 90.0 REMARK 620 5 HOH A 222 O 90.0 90.0 90.1 179.9 REMARK 620 6 HOH A 223 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 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 224 O REMARK 620 2 HOH A 225 O 90.0 REMARK 620 3 HOH A 226 O 90.0 180.0 REMARK 620 4 HOH A 227 O 90.0 90.0 90.0 REMARK 620 5 HOH A 228 O 90.0 89.9 90.0 179.9 REMARK 620 6 HOH A 229 O 179.9 90.0 90.1 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 230 O REMARK 620 2 HOH A 231 O 90.0 REMARK 620 3 HOH A 232 O 90.0 180.0 REMARK 620 4 HOH A 233 O 90.0 90.0 90.0 REMARK 620 5 HOH A 234 O 90.0 89.9 90.1 179.9 REMARK 620 6 HOH A 235 O 179.9 90.0 90.0 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25164 RELATED DB: BMRB REMARK 900 RELATED ID: 2MTJ RELATED DB: PDB DBREF 2MTK A 1 47 PDB 2MTK 2MTK 1 47 SEQRES 1 A 47 G G A C C U C C C G U C C SEQRES 2 A 47 U U G G A C G G U C G A G SEQRES 3 A 47 C G A A A G C U U G U G A SEQRES 4 A 47 U U G G U C 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 HETNAM MG MAGNESIUM ION FORMUL 2 MG 6(MG 2+) FORMUL 8 HOH *35(H2 O) LINK OP1 A A 30 MG MG A 101 1555 1555 2.34 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 102 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 103 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 104 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 105 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 106 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 SITE 1 AC1 6 A A 30 HOH A 201 HOH A 202 HOH A 203 SITE 2 AC1 6 HOH A 204 HOH A 205 SITE 1 AC2 6 HOH A 206 HOH A 207 HOH A 208 HOH A 209 SITE 2 AC2 6 HOH A 210 HOH A 211 SITE 1 AC3 6 HOH A 212 HOH A 213 HOH A 214 HOH A 215 SITE 2 AC3 6 HOH A 216 HOH A 217 SITE 1 AC4 7 G A 21 HOH A 218 HOH A 219 HOH A 220 SITE 2 AC4 7 HOH A 221 HOH A 222 HOH A 223 SITE 1 AC5 7 A A 39 HOH A 224 HOH A 225 HOH A 226 SITE 2 AC5 7 HOH A 227 HOH A 228 HOH A 229 SITE 1 AC6 7 G A 42 HOH A 230 HOH A 231 HOH A 232 SITE 2 AC6 7 HOH A 233 HOH A 234 HOH A 235 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