HEADER DNA 09-OCT-97 1AW4 TITLE STRUCTURAL BASIS OF DNA FOLDING AND RECOGNITION IN AMP-DNA APTAMER TITLE 2 COMPLEX, NMR, 7 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-BINDING DNA APTAMER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS ADAPTIVE BINDING, AMP BINDING, DNA APTAMER, DNA BINDING, DNA KEYWDS 2 RECOGNITION, AMP-DNA APTAMER COMPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 7 AUTHOR C.H.LIN,D.J.PATEL REVDAT 4 22-MAY-24 1AW4 1 REMARK REVDAT 3 16-FEB-22 1AW4 1 REMARK REVDAT 2 24-FEB-09 1AW4 1 VERSN REVDAT 1 15-APR-98 1AW4 0 JRNL AUTH C.H.LIN,D.J.PATEL JRNL TITL STRUCTURAL BASIS OF DNA FOLDING AND RECOGNITION IN AN JRNL TITL 2 AMP-DNA APTAMER COMPLEX: DISTINCT ARCHITECTURES BUT COMMON JRNL TITL 3 RECOGNITION MOTIFS FOR DNA AND RNA APTAMERS COMPLEXED TO JRNL TITL 4 AMP. JRNL REF CHEM.BIOL. V. 4 817 1997 JRNL REFN ISSN 1074-5521 JRNL PMID 9384529 JRNL DOI 10.1016/S1074-5521(97)90115-0 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: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1AW4 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_1000171329. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 6.35 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; COSY; 1H-13C HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : VARIAN INOVA 600 REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XVNMR, X-PLOR REMARK 210 METHOD USED : DISTANCE GEOMETRY AND DISTANCE REMARK 210 RESTRAINED MD REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 21 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 7 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST TOTAL ENERGY, NOE REMARK 210 VIOLATION, VDW 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 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 H22 DG A 7 OP1 DG A 9 1.51 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 DG A 5 N7 DG A 5 C8 0.043 REMARK 500 1 DG A 6 C5 DG A 6 N7 -0.040 REMARK 500 1 DG A 6 N7 DG A 6 C8 0.044 REMARK 500 1 DG A 7 N7 DG A 7 C8 0.043 REMARK 500 1 DG A 8 C5 DG A 8 N7 -0.038 REMARK 500 1 DG A 9 N7 DG A 9 C8 0.051 REMARK 500 1 DG A 11 N7 DG A 11 C8 0.044 REMARK 500 1 DA A 13 C5' DA A 13 C4' 0.056 REMARK 500 1 DA A 13 N7 DA A 13 C8 0.044 REMARK 500 1 DA A 13 N9 DA A 13 C4 -0.048 REMARK 500 1 DT A 14 C5 DT A 14 C6 -0.043 REMARK 500 1 DT A 14 C6 DT A 14 N1 -0.048 REMARK 500 1 DT A 15 C6 DT A 15 N1 -0.053 REMARK 500 1 DG A 16 N7 DG A 16 C8 0.045 REMARK 500 1 DG A 18 N7 DG A 18 C8 0.041 REMARK 500 1 DG A 19 C5 DG A 19 N7 -0.044 REMARK 500 1 DG A 19 C8 DG A 19 N9 -0.058 REMARK 500 1 DG A 21 C5 DG A 21 N7 -0.038 REMARK 500 1 DG A 22 N7 DG A 22 C8 0.039 REMARK 500 1 DA A 23 C5 DA A 23 N7 -0.036 REMARK 500 1 DG A 25 N7 DG A 25 C8 0.051 REMARK 500 1 DG A 26 N7 DG A 26 C8 0.038 REMARK 500 2 DG A 5 N7 DG A 5 C8 0.043 REMARK 500 2 DG A 6 C5 DG A 6 N7 -0.037 REMARK 500 2 DG A 6 N7 DG A 6 C8 0.044 REMARK 500 2 DG A 7 N7 DG A 7 C8 0.047 REMARK 500 2 DG A 8 C5 DG A 8 N7 -0.043 REMARK 500 2 DG A 9 N7 DG A 9 C8 0.045 REMARK 500 2 DA A 10 C5 DA A 10 N7 -0.040 REMARK 500 2 DG A 11 N7 DG A 11 C8 0.044 REMARK 500 2 DA A 13 C5' DA A 13 C4' 0.058 REMARK 500 2 DA A 13 N7 DA A 13 C8 0.045 REMARK 500 2 DA A 13 N9 DA A 13 C4 -0.046 REMARK 500 2 DT A 14 C3' DT A 14 C2' -0.059 REMARK 500 2 DT A 14 C6 DT A 14 N1 -0.045 REMARK 500 2 DT A 15 C6 DT A 15 N1 -0.055 REMARK 500 2 DG A 16 N7 DG A 16 C8 0.044 REMARK 500 2 DG A 18 N7 DG A 18 C8 0.039 REMARK 500 2 DG A 19 C5 DG A 19 N7 -0.042 REMARK 500 2 DG A 19 C8 DG A 19 N9 -0.065 REMARK 500 2 DG A 21 C5 DG A 21 N7 -0.037 REMARK 500 2 DG A 22 N7 DG A 22 C8 0.041 REMARK 500 2 DA A 23 C5 DA A 23 N7 -0.037 REMARK 500 2 DG A 25 N7 DG A 25 C8 0.051 REMARK 500 2 DG A 26 N7 DG A 26 C8 0.039 REMARK 500 3 DG A 5 N7 DG A 5 C8 0.043 REMARK 500 3 DG A 6 C5 DG A 6 N7 -0.040 REMARK 500 3 DG A 6 N7 DG A 6 C8 0.044 REMARK 500 3 DG A 7 N7 DG A 7 C8 0.043 REMARK 500 3 DG A 8 C5 DG A 8 N7 -0.038 REMARK 500 REMARK 500 THIS ENTRY HAS 158 BOND DEVIATIONS. 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 DA A 1 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DC A 2 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DC A 2 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DC A 3 O4' - C4' - C3' ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DC A 3 C3' - C2' - C1' ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DG A 5 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 8 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DG A 9 N9 - C4 - C5 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 10 O4' - C1' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DA A 10 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 1 DG A 11 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 12 C4' - C3' - C2' ANGL. DEV. = -8.1 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 1 DT A 12 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DA A 13 P - O5' - C5' ANGL. DEV. = 10.5 DEGREES REMARK 500 1 DA A 13 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 13 C5' - C4' - O4' ANGL. DEV. = 8.3 DEGREES REMARK 500 1 DA A 13 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA A 13 O4' - C1' - N9 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DA A 13 N9 - C4 - C5 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA A 13 N3 - C4 - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DT A 14 C5' - C4' - O4' ANGL. DEV. = 11.6 DEGREES REMARK 500 1 DT A 14 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DT A 14 C4 - C5 - C7 ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DT A 14 C6 - C5 - C7 ANGL. DEV. = -11.5 DEGREES REMARK 500 1 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 15 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 16 C4' - C3' - C2' ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG A 18 O4' - C1' - C2' ANGL. DEV. = -8.8 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 18 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DG A 19 C1' - O4' - C4' ANGL. DEV. = -9.1 DEGREES REMARK 500 1 DG A 19 O4' - C1' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DA A 23 N1 - C6 - N6 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DA A 23 C5 - C6 - N6 ANGL. DEV. = -9.3 DEGREES REMARK 500 1 DA A 24 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DG A 25 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DG A 26 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 26 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG A 26 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 350 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 28 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 29 DBREF 1AW4 A 1 27 PDB 1AW4 1AW4 1 27 SEQRES 1 A 27 DA DC DC DT DG DG DG DG DG DA DG DT DA SEQRES 2 A 27 DT DT DG DC DG DG DA DG DG DA DA DG DG SEQRES 3 A 27 DT HET AMP A 28 35 HET AMP A 29 35 HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 2 AMP 2(C10 H14 N5 O7 P) SITE 1 AC1 5 DG A 8 DG A 9 DA A 10 DG A 11 SITE 2 AC1 5 DG A 19 SITE 1 AC2 6 DG A 6 DG A 19 DG A 21 DG A 22 SITE 2 AC2 6 DA A 23 DA A 24 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