HEADER DNA 04-AUG-06 2HY9 TITLE HUMAN TELOMERE DNA QUADRUPLEX STRUCTURE IN K+ SOLUTION HYBRID-1 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (26-MER); COMPND 3 CHAIN: 1; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: TELOMERIC DNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HOMO SAPIENS SOURCE 4 (HUMAN). KEYWDS G-QUADRUPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.DAI,C.PUNCHIHEWA,R.A.JONES,L.HURLEY,D.YANG REVDAT 4 17-SEP-14 2HY9 1 REMARK TITLE VERSN REVDAT 3 24-FEB-09 2HY9 1 VERSN REVDAT 2 22-MAY-07 2HY9 1 JRNL REVDAT 1 10-APR-07 2HY9 0 JRNL AUTH J.DAI,C.PUNCHIHEWA,A.AMBRUS,D.CHEN,R.A.JONES,D.YANG JRNL TITL STRUCTURE OF THE INTRAMOLECULAR HUMAN TELOMERIC G-QUADRUPLEX JRNL TITL 2 IN POTASSIUM SOLUTION: A NOVEL ADENINE TRIPLE FORMATION. JRNL REF NUCLEIC ACIDS RES. V. 35 2440 2007 JRNL REFN ISSN 0305-1048 JRNL PMID 17395643 JRNL DOI 10.1093/NAR/GKM009 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HY9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-06. REMARK 100 THE RCSB ID CODE IS RCSB038903. 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 : 70MM KCL, 25MM K-PHOSPHATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.1-2.5MM OLIGONUCLEOTIDE, 25MM REMARK 210 PHOSPHATE BUFFER K, 70MM KCL, 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.851 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: 1 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 O2 DT 1 7 H2' DT 1 8 1.40 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 6 DT 1 8 C5 DT 1 8 C7 0.037 REMARK 500 7 DT 1 8 C5 DT 1 8 C7 0.036 REMARK 500 8 DT 1 8 C5 DT 1 8 C7 0.037 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 1 1 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA 1 1 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA 1 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA 1 2 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA 1 3 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DA 1 3 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG 1 4 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG 1 4 C5 - N7 - C8 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG 1 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG 1 5 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG 1 5 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG 1 5 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DG 1 6 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG 1 6 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DT 1 7 C4 - C5 - C6 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT 1 7 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT 1 8 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DA 1 9 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DA 1 9 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG 1 10 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG 1 10 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG 1 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG 1 11 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG 1 11 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG 1 11 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG 1 12 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG 1 12 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT 1 13 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT 1 13 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT 1 14 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA 1 15 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA 1 15 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA 1 15 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG 1 16 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG 1 16 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DG 1 16 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG 1 17 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG 1 17 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG 1 17 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DG 1 18 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG 1 18 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG 1 18 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DT 1 19 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT 1 20 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA 1 21 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DA 1 21 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA 1 21 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG 1 22 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG 1 22 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG 1 23 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 593 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DG 1 6 0.05 SIDE CHAIN REMARK 500 1 DT 1 7 0.08 SIDE CHAIN REMARK 500 1 DT 1 8 0.09 SIDE CHAIN REMARK 500 1 DA 1 25 0.06 SIDE CHAIN REMARK 500 2 DG 1 6 0.06 SIDE CHAIN REMARK 500 2 DT 1 7 0.08 SIDE CHAIN REMARK 500 2 DT 1 8 0.10 SIDE CHAIN REMARK 500 2 DA 1 25 0.06 SIDE CHAIN REMARK 500 3 DT 1 7 0.08 SIDE CHAIN REMARK 500 3 DT 1 8 0.09 SIDE CHAIN REMARK 500 4 DG 1 6 0.05 SIDE CHAIN REMARK 500 4 DT 1 7 0.08 SIDE CHAIN REMARK 500 4 DT 1 8 0.09 SIDE CHAIN REMARK 500 5 DT 1 7 0.09 SIDE CHAIN REMARK 500 5 DT 1 8 0.09 SIDE CHAIN REMARK 500 6 DT 1 7 0.08 SIDE CHAIN REMARK 500 6 DT 1 8 0.09 SIDE CHAIN REMARK 500 6 DA 1 25 0.06 SIDE CHAIN REMARK 500 7 DG 1 6 0.05 SIDE CHAIN REMARK 500 7 DT 1 8 0.09 SIDE CHAIN REMARK 500 8 DG 1 6 0.06 SIDE CHAIN REMARK 500 8 DT 1 7 0.08 SIDE CHAIN REMARK 500 8 DT 1 8 0.10 SIDE CHAIN REMARK 500 9 DG 1 6 0.06 SIDE CHAIN REMARK 500 9 DT 1 7 0.09 SIDE CHAIN REMARK 500 9 DT 1 8 0.09 SIDE CHAIN REMARK 500 10 DG 1 6 0.06 SIDE CHAIN REMARK 500 10 DT 1 8 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JPZ RELATED DB: PDB REMARK 900 RELATED ID: 2KKA RELATED DB: PDB DBREF 2HY9 1 1 26 PDB 2HY9 2HY9 1 26 SEQRES 1 1 26 DA DA DA DG DG DG DT DT DA DG DG DG DT SEQRES 2 1 26 DT DA DG DG DG DT DT DA DG DG DG DA DA 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 MASTER 215 0 0 0 0 0 0 6 0 0 0 2 END