HEADER DNA 25-NOV-15 2N9H TITLE GLUCOSE AS A NUCLEASE MIMIC IN DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*AP*TP*GP*AP*CP*TP*GP*CP*TP*AP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*TP*AP*GP*CP*(GL6)P*GP*TP*CP*AP*TP*C)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS CARBOHYDRATE-DNA INTERACTION, GLUCOSE-NUCLEOBASE, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR I.GOMEZ-PINTO,E.VENGUT-CLIMENT,R.LUCAS,A.AVINO,R.ERITJA,C.GONZALEZ- AUTHOR 2 IBANEZ,J.MORALES,A.MURO,P.PENALVER,C.FONSECA-GUERRA,M.BICKELHAUPT REVDAT 4 15-MAY-24 2N9H 1 REMARK REVDAT 3 14-JUN-23 2N9H 1 HETSYN REVDAT 2 29-JUL-20 2N9H 1 SOURCE REMARK LINK REVDAT 1 31-AUG-16 2N9H 0 JRNL AUTH E.VENGUT-CLIMENT,I.GOMEZ-PINTO,R.LUCAS,P.PENALVER,A.AVINO, JRNL AUTH 2 C.FONSECA GUERRA,F.M.BICKELHAUPT,R.ERITJA,C.GONZALEZ, JRNL AUTH 3 J.C.MORALES JRNL TITL GLUCOSE-NUCLEOBASE PSEUDO BASE PAIRS: BIOMOLECULAR JRNL TITL 2 INTERACTIONS WITHIN DNA. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 55 8643 2016 JRNL REFN ISSN 1433-7851 JRNL PMID 27328804 JRNL DOI 10.1002/ANIE.201603510 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, SPARKY, AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN (AMBER), GODDARD (SPARKY), REMARK 3 BRUKER BIOSPIN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000104590. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 279.6 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : POTASSIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM DNA (5' REMARK 210 -D(*GP*AP*TP*GP*AP*CP*TP*GP*CP*TP*AP*G)-3'), 1 MM DNA (5'-D(*CP* REMARK 210 TP*AP*GP*CP*(GL6)P*GP*TP*CP*AP*TP*C)-3'), 1 MM SUGAR, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER, SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: THE STRUCTURE WAS DETERMINED USING NOE DATA 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 DA A 2 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA A 2 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -6.4 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DC A 6 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 DC A 6 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 6 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DC A 9 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 10 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA A 11 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT B 14 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DA B 15 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC B 17 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DC B 17 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DT B 20 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DA B 22 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DA B 22 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DT B 23 C6 - C5 - C7 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC B 24 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA A 2 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA A 2 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 3 C6 - C5 - C7 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DA A 5 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC A 9 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DT A 10 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DA A 11 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 DA A 11 N1 - C6 - N6 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DT B 14 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DA B 15 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DC B 17 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT B 20 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DA B 22 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA B 22 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT B 23 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 DC B 24 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 DA A 2 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 3 DT A 3 C4 - C5 - C7 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DT A 3 C6 - C5 - C7 ANGL. DEV. = -6.5 DEGREES REMARK 500 3 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 233 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 DA A 5 0.06 SIDE CHAIN REMARK 500 1 DC A 6 0.07 SIDE CHAIN REMARK 500 1 DG A 12 0.08 SIDE CHAIN REMARK 500 2 DA A 5 0.08 SIDE CHAIN REMARK 500 2 DC A 6 0.07 SIDE CHAIN REMARK 500 2 DG A 12 0.06 SIDE CHAIN REMARK 500 2 DC B 13 0.07 SIDE CHAIN REMARK 500 3 DA A 5 0.07 SIDE CHAIN REMARK 500 3 DC A 6 0.08 SIDE CHAIN REMARK 500 3 DG A 12 0.06 SIDE CHAIN REMARK 500 3 DC B 13 0.07 SIDE CHAIN REMARK 500 3 DC B 21 0.06 SIDE CHAIN REMARK 500 4 DA A 5 0.09 SIDE CHAIN REMARK 500 4 DC A 6 0.09 SIDE CHAIN REMARK 500 4 DG A 12 0.06 SIDE CHAIN REMARK 500 4 DC B 13 0.06 SIDE CHAIN REMARK 500 4 DC B 21 0.06 SIDE CHAIN REMARK 500 5 DA A 5 0.09 SIDE CHAIN REMARK 500 5 DC A 6 0.08 SIDE CHAIN REMARK 500 5 DG A 12 0.06 SIDE CHAIN REMARK 500 5 DC B 21 0.07 SIDE CHAIN REMARK 500 6 DA A 5 0.09 SIDE CHAIN REMARK 500 6 DC A 6 0.07 SIDE CHAIN REMARK 500 6 DG A 12 0.05 SIDE CHAIN REMARK 500 6 DC B 13 0.06 SIDE CHAIN REMARK 500 6 DC B 21 0.06 SIDE CHAIN REMARK 500 7 DA A 5 0.07 SIDE CHAIN REMARK 500 7 DC A 6 0.08 SIDE CHAIN REMARK 500 7 DG A 12 0.07 SIDE CHAIN REMARK 500 7 DC B 13 0.06 SIDE CHAIN REMARK 500 7 DC B 21 0.06 SIDE CHAIN REMARK 500 8 DA A 5 0.08 SIDE CHAIN REMARK 500 8 DC A 6 0.07 SIDE CHAIN REMARK 500 8 DG A 12 0.07 SIDE CHAIN REMARK 500 8 DC B 13 0.07 SIDE CHAIN REMARK 500 8 DC B 21 0.06 SIDE CHAIN REMARK 500 9 DA A 5 0.08 SIDE CHAIN REMARK 500 9 DC A 6 0.07 SIDE CHAIN REMARK 500 9 DG A 12 0.06 SIDE CHAIN REMARK 500 9 DG B 19 0.07 SIDE CHAIN REMARK 500 10 DA A 5 0.08 SIDE CHAIN REMARK 500 10 DC A 6 0.06 SIDE CHAIN REMARK 500 10 DG B 19 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25906 RELATED DB: BMRB REMARK 900 RELATED ID: 2N9F RELATED DB: PDB DBREF 2N9H A 1 12 PDB 2N9H 2N9H 1 12 DBREF 2N9H B 13 24 PDB 2N9H 2N9H 13 24 SEQRES 1 A 12 DG DA DT DG DA DC DT DG DC DT DA DG SEQRES 1 B 12 DC DT DA DG DC 4JA DG DT DC DA DT DC HET 4JA B 18 35 HETNAM 4JA (2S)-3-[(6-DEOXY-BETA-D-GLUCOPYRANOSYL)OXY]-2- HETNAM 2 4JA HYDROXYPROPYL DIHYDROGEN PHOSPHATE HETSYN 4JA (2S)-3-[(6-DEOXY-BETA-D-GLUCOSYL)OXY]-2-HYDROXYPROPYL HETSYN 2 4JA DIHYDROGEN PHOSPHATE; (2S)-3-[(6-DEOXY-D-GLUCOSYL) HETSYN 3 4JA OXY]-2-HYDROXYPROPYL DIHYDROGEN PHOSPHATE; (2S)-3-[(6- HETSYN 4 4JA DEOXY-GLUCOSYL)OXY]-2-HYDROXYPROPYL DIHYDROGEN HETSYN 5 4JA PHOSPHATE FORMUL 2 4JA C9 H19 O10 P LINK O3' DC B 17 P 4JA B 18 1555 1555 1.62 LINK O3' 4JA B 18 P DG B 19 1555 1555 1.62 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