HEADER DNA 29-MAR-10 2KVY TITLE NMR SOLUTION STRUCTURE OF THE 4:1 COMPLEX BETWEEN AN UNCHARGED TITLE 2 DISTAMYCIN A ANALOGUE AND [D(TGGGGT)]4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*GP*GP*GP*GP*T)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS G-QUADRUPLEX, COULOMBIC INTERACTIONS, NMR TITRATION, DISTAMYCIN A, KEYWDS 2 STRUCTURE CALCULATIONS, ISOTHERMAL TITRATION CALORIMETRY (ITC), DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.COSCONATI,L.MARINELLI,R.TROTTA,A.VIRNO,S.DE TITO,R.ROMAGNOLI, AUTHOR 2 B.PAGANO,V.LIMONGELLI,C.GIANCOLA,P.BARALDI,L.MAYOL,E.NOVELLINO, AUTHOR 3 A.RANDAZZO REVDAT 2 02-JUN-10 2KVY 1 JRNL REVDAT 1 26-MAY-10 2KVY 0 JRNL AUTH S.COSCONATI,L.MARINELLI,R.TROTTA,A.VIRNO,S.DE TITO, JRNL AUTH 2 R.ROMAGNOLI,B.PAGANO,V.LIMONGELLI,C.GIANCOLA,P.G.BARALDI, JRNL AUTH 3 L.MAYOL,E.NOVELLINO,A.RANDAZZO JRNL TITL STRUCTURAL AND CONFORMATIONAL REQUISITES IN DNA QUADRUPLEX JRNL TITL 2 GROOVE BINDING: ANOTHER PIECE TO THE PUZZLE. JRNL REF J.AM.CHEM.SOC. V. 132 6425 2010 JRNL REFN ISSN 0002-7863 JRNL PMID 20394365 JRNL DOI 10.1021/JA1003872 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 10.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KVY COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-10. REMARK 100 THE RCSB ID CODE IS RCSB101640. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 80; 80 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 8 MM KVY-1, 2 MM DNA (5'-D(*DTP* REMARK 210 DGP*DGP*DGP*DGP*DT)-3')-2, 100 % D2O-3, 10 MM POTASSIUM PHOSPHATE REMARK 210 -4, 70 MM POTASSIUM CHLORIDE-5, 90% H2O/10% D2O; 8 MM KVY-6, 2 MM REMARK 210 DNA (5'-D(*DTP*DGP*DGP*DGP*DGP*DT)-3')-7, 10 % D2O-8, 10 MM REMARK 210 POTASSIUM PHOSPHATE-9, 70 MM POTASSIUM CHLORIDE-10, 90 % H2O-11, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H NOESY; 2D 1H-31P COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER 10.0, FELIX REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 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 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 HO5' DT A 1 OP2 DG A 2 1.58 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 9.3 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DT A 6 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT B 7 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DT B 7 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DG B 8 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG B 11 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT B 12 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DT B 12 N3 - C2 - O2 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DT C 13 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG C 15 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG C 17 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DT C 18 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT D 19 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DT D 19 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DG D 20 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG D 21 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG D 23 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DT D 24 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG A 5 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 2 DG A 5 O4' - C1' - N9 ANGL. DEV. = 11.0 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DT A 6 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DT B 7 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT B 7 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DG B 8 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DG B 9 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DG B 11 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DT B 12 O4' - C1' - N1 ANGL. DEV. = 7.8 DEGREES REMARK 500 2 DT B 12 N3 - C2 - O2 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 DT C 13 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG C 15 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 DG C 16 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DG C 17 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 DT C 18 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT C 18 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT D 19 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DT D 19 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DG D 20 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 DG D 23 O4' - C4' - C3' ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DG D 23 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DT D 24 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 DT A 1 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 3 DT A 1 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 224 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 A 3 0.07 SIDE CHAIN REMARK 500 1 DG A 5 0.08 SIDE CHAIN REMARK 500 1 DT A 6 0.13 SIDE CHAIN REMARK 500 1 DT B 7 0.13 SIDE CHAIN REMARK 500 1 DG B 8 0.05 SIDE CHAIN REMARK 500 1 DG B 10 0.05 SIDE CHAIN REMARK 500 1 DG B 11 0.06 SIDE CHAIN REMARK 500 1 DG D 22 0.07 SIDE CHAIN REMARK 500 1 DG D 23 0.08 SIDE CHAIN REMARK 500 2 DG A 2 0.07 SIDE CHAIN REMARK 500 2 DG A 3 0.08 SIDE CHAIN REMARK 500 2 DT B 7 0.18 SIDE CHAIN REMARK 500 2 DT B 12 0.12 SIDE CHAIN REMARK 500 2 DT C 13 0.07 SIDE CHAIN REMARK 500 2 DG C 14 0.06 SIDE CHAIN REMARK 500 2 DG C 15 0.06 SIDE CHAIN REMARK 500 2 DT D 19 0.13 SIDE CHAIN REMARK 500 2 DG D 23 0.07 SIDE CHAIN REMARK 500 2 DT D 24 0.08 SIDE CHAIN REMARK 500 3 DG A 3 0.07 SIDE CHAIN REMARK 500 3 DT A 6 0.09 SIDE CHAIN REMARK 500 3 DT B 7 0.09 SIDE CHAIN REMARK 500 3 DG C 14 0.07 SIDE CHAIN REMARK 500 3 DG D 23 0.09 SIDE CHAIN REMARK 500 3 DT D 24 0.07 SIDE CHAIN REMARK 500 4 DG A 3 0.08 SIDE CHAIN REMARK 500 4 DG A 5 0.06 SIDE CHAIN REMARK 500 4 DT B 7 0.08 SIDE CHAIN REMARK 500 4 DG B 10 0.06 SIDE CHAIN REMARK 500 4 DG B 11 0.06 SIDE CHAIN REMARK 500 4 DT B 12 0.08 SIDE CHAIN REMARK 500 4 DG C 17 0.12 SIDE CHAIN REMARK 500 4 DG D 21 0.06 SIDE CHAIN REMARK 500 5 DG A 2 0.06 SIDE CHAIN REMARK 500 5 DG A 5 0.09 SIDE CHAIN REMARK 500 5 DG B 11 0.06 SIDE CHAIN REMARK 500 5 DT B 12 0.07 SIDE CHAIN REMARK 500 5 DG C 16 0.07 SIDE CHAIN REMARK 500 5 DT C 18 0.10 SIDE CHAIN REMARK 500 5 DG D 20 0.05 SIDE CHAIN REMARK 500 5 DG D 21 0.08 SIDE CHAIN REMARK 500 5 DG D 23 0.06 SIDE CHAIN REMARK 500 6 DT A 1 0.07 SIDE CHAIN REMARK 500 6 DG A 3 0.06 SIDE CHAIN REMARK 500 6 DG A 5 0.07 SIDE CHAIN REMARK 500 6 DT A 6 0.10 SIDE CHAIN REMARK 500 6 DG B 9 0.07 SIDE CHAIN REMARK 500 6 DG B 11 0.09 SIDE CHAIN REMARK 500 6 DT C 13 0.07 SIDE CHAIN REMARK 500 6 DG C 17 0.13 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 86 PLANE 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 KVY C 25 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KVY D 26 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KVY A 27 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KVY B 28 DBREF 2KVY A 1 6 PDB 2KVY 2KVY 1 6 DBREF 2KVY B 7 12 PDB 2KVY 2KVY 7 12 DBREF 2KVY C 13 18 PDB 2KVY 2KVY 13 18 DBREF 2KVY D 19 24 PDB 2KVY 2KVY 19 24 SEQRES 1 A 6 DT DG DG DG DG DT SEQRES 1 B 6 DT DG DG DG DG DT SEQRES 1 C 6 DT DG DG DG DG DT SEQRES 1 D 6 DT DG DG DG DG DT HET KVY C 25 62 HET KVY D 26 62 HET KVY A 27 62 HET KVY B 28 62 HETNAM KVY 4-AMINO-1-METHYL-N-{1-METHYL-5-[(1-METHYL-5-{[3- HETNAM 2 KVY (METHYLAMINO)-3-OXOPROPYL]CARBAMOYL}-1H-PYRROL-3-YL) HETNAM 3 KVY CARBAMOYL]-1H-PYRROL-3-YL}-1H-PYRROLE-2-CARBOXAMIDE FORMUL 5 KVY 4(C22 H28 N8 O4) SITE 1 AC1 4 KVY A 27 KVY B 28 DG C 17 DT C 18 SITE 1 AC2 6 DT A 6 KVY A 27 KVY B 28 DG D 22 SITE 2 AC2 6 DG D 23 DT D 24 SITE 1 AC3 10 DG A 4 DG A 5 DT A 6 DT B 12 SITE 2 AC3 10 KVY B 28 DG C 16 DG C 17 DT C 18 SITE 3 AC3 10 KVY C 25 KVY D 26 SITE 1 AC4 7 KVY A 27 DG B 10 DG B 11 DT B 12 SITE 2 AC4 7 KVY C 25 DT D 24 KVY D 26 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 217 0 4 0 0 0 8 6 0 0 0 4 END