HEADER RNA 19-JUN-97 1AM0 TITLE AMP RNA APTAMER COMPLEX, NMR, 8 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA APTAMER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS COMPLEX (RIBONUCLEIC ACID-AMP), RNA APTAMER, GNRA MOTIF, G(DOT)G KEYWDS 2 MISMATCH, G(DOT)A MISMATCH, RIBONUCLEIC ACID, RNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR F.JIANG,R.A.KUMAR,R.A.JONES,D.J.PATEL REVDAT 4 22-MAY-24 1AM0 1 REMARK REVDAT 3 16-FEB-22 1AM0 1 REMARK REVDAT 2 24-FEB-09 1AM0 1 VERSN REVDAT 1 23-JUL-97 1AM0 0 SPRSDE 23-JUL-97 1AM0 1ARA JRNL AUTH F.JIANG,R.A.KUMAR,R.A.JONES,D.J.PATEL JRNL TITL STRUCTURAL BASIS OF RNA FOLDING AND RECOGNITION IN AN JRNL TITL 2 AMP-RNA APTAMER COMPLEX JRNL REF NATURE V. 382 183 1996 JRNL REFN ISSN 0028-0836 JRNL PMID 8700212 JRNL DOI 10.1038/382183A0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.R.LORSCH,J.W.SZOSTAK REMARK 1 TITL IN VITRO EVOLUTION OF NEW RIBOZYMES WITH POLYNUCLEOTIDE REMARK 1 TITL 2 KINASE ACTIVITY REMARK 1 REF NATURE V. 371 31 1994 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.SASSANFAR,J.W.SZOSTAK REMARK 1 TITL AN RNA MOTIF THAT BINDS ATP REMARK 1 REF NATURE V. 364 550 1993 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1AM0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170983. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 273 REMARK 210 PH : 6.7; 6.7 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : NULL; NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : IN D2O - NOESY; COSY; TOCSY; 2D REMARK 210 (1)H-(31)P COSY; 2D(1)H-(13)C CT REMARK 210 HSQC; 3D (1)H-(13)C-(1)H NOESY- REMARK 210 HMQC; HCCH-TOCSY; HCCH-COSY. REMARK 210 DISTANCE RESTRAINTS FROM 120 MS REMARK 210 NOESY; 120 MS 3D NOESY-HMQC. REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DISTANCE GEOMETRY AND RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 8 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-8 REMARK 465 RES C SSSEQI REMARK 465 G A 1 REMARK 465 G A 2 REMARK 465 G A 3 REMARK 465 U A 4 REMARK 465 U A 5 REMARK 465 G A 19 REMARK 465 G A 20 REMARK 465 C A 21 REMARK 465 A A 22 REMARK 465 C A 23 REMARK 465 U A 24 REMARK 465 U A 25 REMARK 465 C A 26 REMARK 465 G A 27 REMARK 465 G A 28 REMARK 465 U A 29 REMARK 465 G A 30 REMARK 465 C A 31 REMARK 465 C A 32 REMARK 465 A A 36 REMARK 465 A A 37 REMARK 465 C A 38 REMARK 465 C A 39 REMARK 465 C A 40 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 H1' U A 18 O3' AMP A 41 1.52 REMARK 500 HO2' C A 15 O5' U A 16 1.53 REMARK 500 O2' C A 15 H6 U A 16 1.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 A A 9 C2' A A 9 C1' 0.067 REMARK 500 1 C A 15 C3' C A 15 C2' -0.083 REMARK 500 1 C A 15 N1 C A 15 C6 -0.044 REMARK 500 1 G A 34 C2' G A 34 C1' -0.058 REMARK 500 2 A A 9 C2' A A 9 C1' 0.072 REMARK 500 2 A A 33 C2' A A 33 C1' -0.056 REMARK 500 2 A A 33 C8 A A 33 N9 -0.059 REMARK 500 2 C A 35 N1 C A 35 C6 -0.042 REMARK 500 3 G A 34 C5' G A 34 C4' 0.077 REMARK 500 3 C A 35 N1 C A 35 C6 -0.044 REMARK 500 4 A A 10 C4' A A 10 C3' -0.060 REMARK 500 4 G A 11 C8 G A 11 N9 -0.044 REMARK 500 4 A A 13 C5' A A 13 C4' -0.060 REMARK 500 4 A A 13 N9 A A 13 C4 -0.050 REMARK 500 4 C A 15 C3' C A 15 C2' -0.074 REMARK 500 4 C A 15 N1 C A 15 C6 -0.056 REMARK 500 4 A A 33 C2' A A 33 C1' -0.056 REMARK 500 4 A A 33 C8 A A 33 N9 -0.048 REMARK 500 4 C A 35 N1 C A 35 C6 -0.041 REMARK 500 5 G A 7 C3' G A 7 C2' 0.092 REMARK 500 5 C A 15 N1 C A 15 C6 -0.044 REMARK 500 5 C A 35 N1 C A 35 C6 -0.040 REMARK 500 6 G A 7 C4' G A 7 C3' 0.069 REMARK 500 6 G A 7 C3' G A 7 C2' 0.102 REMARK 500 6 G A 7 C2' G A 7 C1' -0.056 REMARK 500 6 A A 10 C4' A A 10 C3' -0.065 REMARK 500 6 A A 12 N9 A A 12 C4 -0.041 REMARK 500 6 C A 15 C3' C A 15 C2' -0.084 REMARK 500 6 C A 15 N1 C A 15 C6 -0.044 REMARK 500 6 A A 33 C8 A A 33 N9 -0.049 REMARK 500 6 G A 34 C2' G A 34 C1' -0.053 REMARK 500 6 C A 35 N1 C A 35 C6 -0.044 REMARK 500 7 A A 9 C3' A A 9 C2' 0.071 REMARK 500 7 A A 9 C2' A A 9 C1' -0.057 REMARK 500 7 A A 9 O3' A A 9 C3' 0.097 REMARK 500 7 A A 9 O3' A A 10 P 0.100 REMARK 500 7 A A 10 C2' A A 10 C1' -0.049 REMARK 500 7 A A 14 C3' A A 14 C2' -0.073 REMARK 500 7 A A 14 N9 A A 14 C4 -0.037 REMARK 500 7 C A 15 N1 C A 15 C6 -0.039 REMARK 500 7 G A 17 C8 G A 17 N9 -0.044 REMARK 500 7 G A 34 C5' G A 34 C4' 0.088 REMARK 500 7 C A 35 N1 C A 35 C6 -0.042 REMARK 500 8 A A 9 C3' A A 9 C2' 0.115 REMARK 500 8 A A 9 C2' A A 9 C1' -0.132 REMARK 500 8 A A 14 C4 A A 14 C5 -0.044 REMARK 500 8 A A 14 C8 A A 14 N9 -0.068 REMARK 500 8 G A 34 C5' G A 34 C4' 0.085 REMARK 500 8 C A 35 N1 C A 35 C6 -0.045 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 6 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 G A 7 O4' - C4' - C3' ANGL. DEV. = -9.5 DEGREES REMARK 500 1 G A 7 C1' - O4' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 1 G A 8 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 A A 9 C1' - O4' - C4' ANGL. DEV. = 7.0 DEGREES REMARK 500 1 A A 9 O4' - C1' - C2' ANGL. DEV. = -10.7 DEGREES REMARK 500 1 A A 10 N9 - C1' - C2' ANGL. DEV. = 13.9 DEGREES REMARK 500 1 A A 10 O4' - C1' - N9 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 G A 11 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 G A 11 C1' - O4' - C4' ANGL. DEV. = -8.1 DEGREES REMARK 500 1 G A 11 C3' - C2' - C1' ANGL. DEV. = 6.2 DEGREES REMARK 500 1 G A 11 O4' - C1' - C2' ANGL. DEV. = -17.0 DEGREES REMARK 500 1 G A 11 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 A A 12 O4' - C4' - C3' ANGL. DEV. = -13.9 DEGREES REMARK 500 1 A A 12 C5' - C4' - C3' ANGL. DEV. = 11.2 DEGREES REMARK 500 1 A A 12 C5' - C4' - O4' ANGL. DEV. = -9.9 DEGREES REMARK 500 1 A A 12 C1' - O4' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 1 A A 12 O4' - C1' - C2' ANGL. DEV. = -19.5 DEGREES REMARK 500 1 A A 12 O4' - C1' - N9 ANGL. DEV. = -13.0 DEGREES REMARK 500 1 A A 13 N9 - C1' - C2' ANGL. DEV. = -8.2 DEGREES REMARK 500 1 A A 14 O4' - C4' - C3' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 A A 14 C5' - C4' - O4' ANGL. DEV. = -7.6 DEGREES REMARK 500 1 C A 15 O4' - C1' - C2' ANGL. DEV. = -14.4 DEGREES REMARK 500 1 C A 15 N1 - C1' - C2' ANGL. DEV. = -7.6 DEGREES REMARK 500 1 C A 15 O4' - C1' - N1 ANGL. DEV. = 10.2 DEGREES REMARK 500 1 C A 15 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 1 U A 16 C1' - O4' - C4' ANGL. DEV. = 5.1 DEGREES REMARK 500 1 U A 16 O4' - C1' - C2' ANGL. DEV. = -7.5 DEGREES REMARK 500 1 U A 16 O4' - C1' - N1 ANGL. DEV. = 10.1 DEGREES REMARK 500 1 G A 17 O4' - C1' - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 1 U A 18 C5' - C4' - O4' ANGL. DEV. = 7.2 DEGREES REMARK 500 1 U A 18 C4' - C3' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 1 A A 33 C5' - C4' - C3' ANGL. DEV. = -11.4 DEGREES REMARK 500 1 A A 33 C5' - C4' - O4' ANGL. DEV. = 6.7 DEGREES REMARK 500 1 A A 33 C2' - C3' - O3' ANGL. DEV. = 11.0 DEGREES REMARK 500 1 G A 34 O4' - C4' - C3' ANGL. DEV. = -7.0 DEGREES REMARK 500 1 G A 34 C5' - C4' - O4' ANGL. DEV. = 17.9 DEGREES REMARK 500 1 G A 34 C2' - C3' - O3' ANGL. DEV. = 9.9 DEGREES REMARK 500 1 G A 34 O4' - C1' - C2' ANGL. DEV. = -15.0 DEGREES REMARK 500 1 C A 35 C4' - C3' - C2' ANGL. DEV. = -9.1 DEGREES REMARK 500 1 C A 35 O4' - C1' - C2' ANGL. DEV. = -7.9 DEGREES REMARK 500 1 C A 35 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 C A 35 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 6 C1' - O4' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 2 G A 6 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 2 G A 6 N9 - C1' - C2' ANGL. DEV. = 9.7 DEGREES REMARK 500 2 G A 7 C1' - O4' - C4' ANGL. DEV. = -9.8 DEGREES REMARK 500 2 G A 7 O4' - C1' - C2' ANGL. DEV. = -8.7 DEGREES REMARK 500 2 G A 8 O4' - C1' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 2 G A 8 O4' - C1' - N9 ANGL. DEV. = 6.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 409 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 41 DBREF 1AM0 A 1 40 PDB 1AM0 1AM0 1 40 SEQRES 1 A 40 G G G U U G G G A A G A A SEQRES 2 A 40 A C U G U G G C A C U U C SEQRES 3 A 40 G G U G C C A G C A A C C SEQRES 4 A 40 C HET AMP A 41 36 HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 2 AMP C10 H14 N5 O7 P SITE 1 AC1 7 G A 8 A A 10 G A 11 A A 12 SITE 2 AC1 7 G A 17 U A 18 G A 34 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