HEADER RNA 23-JAN-05 1YN2 TITLE SOLUTION STRUCTURE OF THE NEUROSPORA VS RIBOZYME STEM-LOOP TITLE 2 V IN THE PRESENCE OF MGCL2 WITH MODELING OF BOUND TITLE 3 MANGANESE IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: VS RIBOZYME STEM-LOOP V; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SL5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE IS DERIVED FROM THE SOURCE 4 NEUROSPORA VARKUD SATELLITE RIBOZYME KEYWDS U-TURN; HAIRPIN; MAGNESIUM IONS; MANGANESE IONS; KEYWDS 2 PARAMAGNETIC, RNA EXPDTA SOLUTION NMR NUMMDL 11 MDLTYP MINIMIZED AVERAGE AUTHOR D.O.CAMPBELL,P.LEGAULT REVDAT 3 24-FEB-09 1YN2 1 VERSN REVDAT 2 19-SEP-06 1YN2 1 REVDAT 1 24-JAN-06 1YN2 0 JRNL AUTH D.O.CAMPBELL,P.BOUCHARD,G.DESJARDINS,P.LEGAULT JRNL TITL NMR STRUCTURE OF VARKUD SATELLITE RIBOZYME JRNL TITL 2 STEM-LOOP V IN THE PRESENCE OF MAGNESIUM IONS AND JRNL TITL 3 LOCALIZATION OF METAL-BINDING SITES JRNL REF BIOCHEMISTRY V. 45 10591 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16939211 JRNL DOI 10.1021/BI0607150 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.O.CAMPBELL,P.LEGAULT REMARK 1 TITL NMR STRUCTURE OF THE VS RIBOZYME STEM-LOOP V RNA REMARK 1 TITL 2 AND MAGNESIUM-ION BINDING FROM CHEMICAL-SHIFT REMARK 1 TITL 3 MAPPING REMARK 1 REF TO BE PUBLISHED 2005 REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH-2.0.6 REMARK 3 AUTHORS : BRUNGER, A. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CONFORMER 1 REPRESENTS THE MINIMIZED REMARK 3 AVERAGE STRUCTURE, THE 10 FOLLOWING STRUCTURES REPRESENT THE REMARK 3 ENSEMBLE OF LOW-ENERGY STRUCTURES REMARK 4 REMARK 4 1YN2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-05. REMARK 100 THE RCSB ID CODE IS RCSB031703. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : VARIABLE (SEE SAMPLE DETAILS) REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM TO 2.0 MM OF REMARK 210 UNLABELED, 15N, OR 13C/15N SL5 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N CPMG-NOESY, 3D 13C- REMARK 210 EDITED HMQC-NOESY, 2D HNN- REMARK 210 COSY, 3D HCCH E.COSY, 2D 1H- REMARK 210 13C CT-HSQC, 2D 1H-15N HSQC, REMARK 210 1D 31P REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH-2.0.6, NMRPIPE REMARK 210 MOST CURRENT, NMRVIEW 5.0.3, REMARK 210 MOLMOL 2K.2 REMARK 210 METHOD USED : SIMULATED ANNEALING, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 46 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 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: BOUND MANGANESE IONS WERE MODELED USING DISTANCE REMARK 210 RESTRAINTS DERIVED FROM MN-INDUCED PARAMAGNETIC LINE BROADENING 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 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 690 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 690 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 692 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 692 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 693 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 694 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 694 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 697 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 697 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 698 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 701 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 705 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 705 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 690 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 690 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 692 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 692 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 693 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 694 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 694 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 697 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 697 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 698 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 701 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 705 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 705 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 G A 690 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 690 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 G A 692 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 692 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 A A 693 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 G A 694 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 694 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 G A 697 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 697 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 A A 698 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 A A 701 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 G A 705 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 705 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 4 G A 690 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 690 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 4 G A 692 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 G A 692 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 4 A A 693 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 G A 694 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 G A 694 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 4 G A 697 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 G A 697 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 4 A A 698 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 A A 701 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 143 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 1 MN A 707 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 711 O REMARK 620 2 HOH A 712 O 178.7 REMARK 620 3 HOH A 713 O 88.8 89.9 REMARK 620 4 HOH A 714 O 87.7 93.6 176.5 REMARK 620 5 HOH A 715 O 90.6 89.7 88.3 91.1 REMARK 620 6 HOH A 716 O 91.8 87.8 84.9 95.9 172.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 MN A 708 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 717 O REMARK 620 2 HOH A 718 O 178.7 REMARK 620 3 HOH A 719 O 88.9 89.8 REMARK 620 4 HOH A 720 O 87.7 93.6 176.5 REMARK 620 5 HOH A 721 O 90.5 89.7 88.2 91.1 REMARK 620 6 HOH A 722 O 91.9 87.8 84.9 96.0 172.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 MN A 709 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 723 O REMARK 620 2 HOH A 724 O 178.7 REMARK 620 3 HOH A 725 O 88.9 89.8 REMARK 620 4 HOH A 726 O 87.7 93.6 176.5 REMARK 620 5 HOH A 727 O 90.6 89.7 88.3 91.0 REMARK 620 6 HOH A 728 O 91.8 87.7 84.9 96.0 172.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 MN A 710 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 729 O REMARK 620 2 HOH A 730 O 178.7 REMARK 620 3 HOH A 731 O 88.9 89.9 REMARK 620 4 HOH A 732 O 87.7 93.6 176.4 REMARK 620 5 HOH A 733 O 90.6 89.6 88.3 91.1 REMARK 620 6 HOH A 734 O 91.8 87.8 84.9 95.9 172.7 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 MN A 707 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 708 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 709 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 710 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TBK RELATED DB: PDB REMARK 900 THE SAME RNA IN THE ABSENCE OF MAGNESIUM IONS REMARK 900 RELATED ID: 1YN1 RELATED DB: PDB REMARK 900 THE SAME RNA ALSO IN THE PRESENCE OF MAGNESIUM IONS BUT REMARK 900 WITHOUT MODELED MANGANESE IONS DBREF 1YN2 A 690 706 PDB 1YN2 1YN2 690 706 SEQRES 1 A 17 G C G A G U U G A C U A C SEQRES 2 A 17 U C G C HET MN A 707 1 HET MN A 708 1 HET MN A 709 1 HET MN A 710 1 HETNAM MN MANGANESE (II) ION FORMUL 2 MN 4(MN 2+) FORMUL 6 HOH *24(H2 O) LINK MN MN A 707 O HOH A 711 1555 1555 2.00 LINK MN MN A 707 O HOH A 712 1555 1555 2.00 LINK MN MN A 707 O HOH A 713 1555 1555 2.00 LINK MN MN A 707 O HOH A 714 1555 1555 2.00 LINK MN MN A 707 O HOH A 715 1555 1555 2.00 LINK MN MN A 707 O HOH A 716 1555 1555 2.00 LINK MN MN A 708 O HOH A 717 1555 1555 2.00 LINK MN MN A 708 O HOH A 718 1555 1555 2.00 LINK MN MN A 708 O HOH A 719 1555 1555 2.00 LINK MN MN A 708 O HOH A 720 1555 1555 2.00 LINK MN MN A 708 O HOH A 721 1555 1555 2.00 LINK MN MN A 708 O HOH A 722 1555 1555 2.00 LINK MN MN A 709 O HOH A 723 1555 1555 2.00 LINK MN MN A 709 O HOH A 724 1555 1555 2.00 LINK MN MN A 709 O HOH A 725 1555 1555 2.00 LINK MN MN A 709 O HOH A 726 1555 1555 2.00 LINK MN MN A 709 O HOH A 727 1555 1555 2.00 LINK MN MN A 709 O HOH A 728 1555 1555 2.00 LINK MN MN A 710 O HOH A 729 1555 1555 2.00 LINK MN MN A 710 O HOH A 730 1555 1555 2.00 LINK MN MN A 710 O HOH A 731 1555 1555 2.00 LINK MN MN A 710 O HOH A 732 1555 1555 2.00 LINK MN MN A 710 O HOH A 733 1555 1555 2.00 LINK MN MN A 710 O HOH A 734 1555 1555 2.00 SITE 1 AC1 6 HOH A 711 HOH A 712 HOH A 713 HOH A 714 SITE 2 AC1 6 HOH A 715 HOH A 716 SITE 1 AC2 6 HOH A 717 HOH A 718 HOH A 719 HOH A 720 SITE 2 AC2 6 HOH A 721 HOH A 722 SITE 1 AC3 6 HOH A 723 HOH A 724 HOH A 725 HOH A 726 SITE 2 AC3 6 HOH A 727 HOH A 728 SITE 1 AC4 6 HOH A 729 HOH A 730 HOH A 731 HOH A 732 SITE 2 AC4 6 HOH A 733 HOH A 734 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 203 0 4 0 0 0 8 6 0 0 0 2 END