Header list of 1yn2.pdb file
Complete list - 2 20 Bytes
HEADER RNA 23-JAN-05 1YN2
TITLE SOLUTION STRUCTURE OF THE NEUROSPORA VS RIBOZYME STEM-LOOP V IN THE
TITLE 2 PRESENCE OF MGCL2 WITH MODELING OF BOUND 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 NEUROSPORA VARKUD
SOURCE 4 SATELLITE RIBOZYME
KEYWDS U-TURN; HAIRPIN; MAGNESIUM IONS; MANGANESE IONS; PARAMAGNETIC, RNA
EXPDTA SOLUTION NMR
NUMMDL 11
MDLTYP MINIMIZED AVERAGE
AUTHOR D.O.CAMPBELL,P.LEGAULT
REVDAT 4 02-MAR-22 1YN2 1 REMARK
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 STEM-LOOP V IN
JRNL TITL 2 THE PRESENCE OF MAGNESIUM IONS AND LOCALIZATION OF
JRNL TITL 3 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 AND
REMARK 1 TITL 2 MAGNESIUM-ION BINDING FROM CHEMICAL-SHIFT 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, X-PLOR NIH-2.0.6
REMARK 3 AUTHORS : BRUNGER, A. (X-PLOR), BRUNGER, A. (X-PLOR)
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 DEPOSITION ID IS D_1000031703.
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 UNLABELED,
REMARK 210 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-COSY;
REMARK 210 3D HCCH E.COSY; 2D 1H-13C CT-
REMARK 210 HSQC; 2D 1H-15N HSQC; 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 : NMRPIPE MOST CURRENT, NMRVIEW
REMARK 210 5.0.3, MOLMOL 2K.2
REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR
REMARK 210 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 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 690 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 G A 690 C8 - N9 - C4 ANGL. DEV. = -2.6 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. = -2.6 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. = 4.5 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. = 4.5 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 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 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 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 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
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 708
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 709
REMARK 800
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 WITHOUT
REMARK 900 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
MODEL 1
Complete list - 2 20 Bytes