HEADER RNA 19-DEC-13 2MIS TITLE NMR LOCALIZATION OF DIVALENT CATIONS AT THE ACTIVE SITE OF THE TITLE 2 NEUROSPORA VS RIBOZYME PROVIDES INSIGHTS INTO RNA-METAL ION TITLE 3 INTERACTIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: VS RIBOZYME; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: NEUROSPORA; SOURCE 4 ORGANISM_TAXID: 5140 KEYWDS RIBOZYME, VS, VARKUD SATELLITE, MAGNESIUM ION, ACTIVE SITE, RNA EXPDTA SOLUTION NMR NUMMDL 21 MDLTYP MINIMIZED AVERAGE AUTHOR E.BONNEAU,P.LEGAULT REVDAT 3 01-MAY-24 2MIS 1 REMARK LINK REVDAT 2 12-FEB-14 2MIS 1 JRNL REVDAT 1 22-JAN-14 2MIS 0 JRNL AUTH E.BONNEAU,P.LEGAULT JRNL TITL NMR LOCALIZATION OF DIVALENT CATIONS AT THE ACTIVE SITE OF JRNL TITL 2 THE NEUROSPORA VS RIBOZYME PROVIDES INSIGHTS INTO JRNL TITL 3 RNA-METAL-ION INTERACTIONS. JRNL REF BIOCHEMISTRY V. 53 579 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 24364590 JRNL DOI 10.1021/BI401484A REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MIS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000103662. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 298; 298 REMARK 210 PH : 6.5; 6.5; 6.5 REMARK 210 IONIC STRENGTH : 5 MM MG2+, 50 MM POTASSIUM REMARK 210 CHLORIDE; 5 MM MG2+, 50 MM REMARK 210 POTASSIUM CHLORIDE; 5 MM MG2+/ REMARK 210 CD2+, 50 MM POTASSIUM CHLORIDE REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] RNA, 90% REMARK 210 H2O/10% D2O; 0.9 MM [U-100% 13C; REMARK 210 U-100% 15N] RNA, 100% D2O; 0.2- REMARK 210 0.4 MM PHOSPHOROTHIOATE RNA, 90% REMARK 210 H2O/10% D2O; 0.9 MM [U-100% 13C; REMARK 210 U-100% 15N] RNA, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-15N HSQC REMARK 210 NH2 ONLY; 2D 1H-13C HSQC; 2D 1H- REMARK 210 15N HSQC LONG-RANGE; 1D 31P REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, NMRPIPE 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 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 G A 1 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 G A 6 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 G A 9 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 G A 13 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 G A 19 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 G A 22 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 G A 23 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 A A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 6 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 G A 9 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 G A 13 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 G A 17 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 G A 19 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 G A 22 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 G A 23 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 A A 2 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 G A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 G A 6 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 G A 9 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 G A 13 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 G A 17 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 G A 19 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 G A 22 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 G A 23 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 G A 1 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 A A 2 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 G A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 G A 6 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 4 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 319 ANGLE DEVIATIONS. 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 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 9 OP2 REMARK 620 2 HOH A 212 O 163.0 REMARK 620 3 HOH A 213 O 104.6 90.1 REMARK 620 4 HOH A 214 O 75.4 90.0 179.9 REMARK 620 5 HOH A 215 O 98.2 90.1 90.0 90.0 REMARK 620 6 HOH A 216 O 81.9 89.9 90.0 90.1 180.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 15 OP1 REMARK 620 2 HOH A 201 O 162.2 REMARK 620 3 HOH A 202 O 107.8 89.9 REMARK 620 4 HOH A 203 O 72.3 90.0 179.9 REMARK 620 5 HOH A 204 O 88.5 90.0 90.0 90.0 REMARK 620 6 HOH A 205 O 91.6 89.9 90.0 90.0 179.9 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 89.9 REMARK 620 3 HOH A 208 O 90.1 180.0 REMARK 620 4 HOH A 209 O 90.0 89.9 90.1 REMARK 620 5 HOH A 210 O 90.1 90.1 89.9 179.9 REMARK 620 6 HOH A 211 O 179.9 90.0 89.9 90.0 89.9 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 217 O REMARK 620 2 HOH A 218 O 89.9 REMARK 620 3 HOH A 219 O 90.1 180.0 REMARK 620 4 HOH A 220 O 90.0 90.0 90.0 REMARK 620 5 HOH A 221 O 90.0 89.9 90.1 179.9 REMARK 620 6 HOH A 222 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 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 223 O REMARK 620 2 HOH A 224 O 90.0 REMARK 620 3 HOH A 225 O 90.0 179.9 REMARK 620 4 HOH A 226 O 90.1 90.0 90.0 REMARK 620 5 HOH A 227 O 89.9 90.0 90.0 180.0 REMARK 620 6 HOH A 228 O 180.0 90.0 90.1 89.9 90.1 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2L5Z RELATED DB: PDB REMARK 900 RELATED ID: 17292 RELATED DB: BMRB REMARK 900 RELATED ID: 19692 RELATED DB: BMRB DBREF 2MIS A 1 26 PDB 2MIS 2MIS 1 26 SEQRES 1 A 26 G A G C U G C A G C A C G SEQRES 2 A 26 A A A G U G A C G G C U C 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 HETNAM MG MAGNESIUM ION FORMUL 2 MG 5(MG 2+) FORMUL 7 HOH *28(H2 O) LINK OP2 G A 9 MG MG A 103 1555 1555 2.33 LINK OP1 A A 15 MG MG A 101 1555 1555 2.35 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 104 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 105 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 SITE 1 AC1 7 G A 13 A A 15 HOH A 201 HOH A 202 SITE 2 AC1 7 HOH A 203 HOH A 204 HOH A 205 SITE 1 AC2 8 C A 10 U A 18 HOH A 206 HOH A 207 SITE 2 AC2 8 HOH A 208 HOH A 209 HOH A 210 HOH A 211 SITE 1 AC3 6 G A 9 HOH A 212 HOH A 213 HOH A 214 SITE 2 AC3 6 HOH A 215 HOH A 216 SITE 1 AC4 6 HOH A 217 HOH A 218 HOH A 219 HOH A 220 SITE 2 AC4 6 HOH A 221 HOH A 222 SITE 1 AC5 6 HOH A 223 HOH A 224 HOH A 225 HOH A 226 SITE 2 AC5 6 HOH A 227 HOH A 228 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