HEADER DNA 05-JUL-09 3I5L TITLE ALLOSTERIC MODULATION OF DNA BY SMALL MOLECULES COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*GP*GP*(C38)P*CP*TP*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SOLID PHASE SYNTHESIS KEYWDS CYCLIC POLYAMIDE, DNA BINDER, MINOR GROOVE BINDER, PYIM POLYAMIDE, KEYWDS 2 DNA EXPDTA X-RAY DIFFRACTION AUTHOR D.M.CHENOWETH,P.B.DERVAN REVDAT 4 21-FEB-24 3I5L 1 COMPND REMARK HETNAM LINK REVDAT 3 15-SEP-09 3I5L 1 HET HETATM REVDAT 2 25-AUG-09 3I5L 1 JRNL REVDAT 1 28-JUL-09 3I5L 0 JRNL AUTH D.M.CHENOWETH,P.B.DERVAN JRNL TITL ALLOSTERIC MODULATION OF DNA BY SMALL MOLECULES JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 13175 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19666554 JRNL DOI 10.1073/PNAS.0906532106 REMARK 2 REMARK 2 RESOLUTION. 1.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 16139 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.103 REMARK 3 R VALUE (WORKING SET) : 0.099 REMARK 3 FREE R VALUE : 0.138 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1835 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1138 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.0870 REMARK 3 BIN FREE R VALUE SET COUNT : 126 REMARK 3 BIN FREE R VALUE : 0.1490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 406 REMARK 3 HETEROGEN ATOMS : 91 REMARK 3 SOLVENT ATOMS : 258 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 5.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.04000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.037 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.038 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.018 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.816 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 587 ; 0.026 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 232 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 896 ; 2.565 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 576 ; 1.481 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 85 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 364 ; 0.037 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 84 ; 0.020 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 107 ; 0.238 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 362 ; 0.272 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 209 ; 0.238 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 117 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 206 ; 0.376 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 20 ; 0.082 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 8 ; 0.141 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 13 ; 0.150 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 86 ; 0.364 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.082 ; 0.200 REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 5 ; 1.668 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3 ; 1.285 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7 ; 2.020 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 826 ; 2.163 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 889 ; 2.604 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1274 ; 1.725 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 268 ;12.406 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 759 ; 5.225 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PARAMETERS FOR MASK CACLULATION REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3I5L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000053992. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19011 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.175 REMARK 200 RESOLUTION RANGE LOW (A) : 26.472 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.15400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% 2-METHYL-2,4-PENTANEDIOL (MPD), 35 REMARK 280 MM CALCIUM ACETATE, 10 MM TRIS PH 7.5 EQUILIBRATED IN SITTING REMARK 280 DROPS AGAINST A RESERVOIR OF 35% MPD AT 4 C. , VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 IN SAME ASYMMETRIC UNIT 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 O HOH B 200 O HOH B 393 1.22 REMARK 500 O HOH A 227 O HOH A 389 1.38 REMARK 500 O HOH A 251 O HOH A 431 1.57 REMARK 500 O HOH A 162 O HOH A 400 1.68 REMARK 500 O HOH A 351 O HOH B 329 1.69 REMARK 500 O3' DG B 4 O HOH B 346 1.71 REMARK 500 O HOH B 185 O HOH B 434 1.73 REMARK 500 O HOH A 249 O HOH A 373 1.79 REMARK 500 O HOH A 323 O HOH A 405 1.80 REMARK 500 O HOH B 175 O HOH B 397 1.91 REMARK 500 O HOH A 198 O HOH A 351 1.93 REMARK 500 I C38 B 6 O HOH A 405 1.94 REMARK 500 OP1 DG B 5 O HOH B 346 1.99 REMARK 500 O HOH B 277 O HOH B 402 2.03 REMARK 500 O HOH B 275 O HOH B 339 2.04 REMARK 500 O HOH B 136 O HOH B 401 2.04 REMARK 500 O HOH B 177 O HOH B 346 2.05 REMARK 500 O HOH A 292 O HOH B 337 2.06 REMARK 500 O HOH A 143 O HOH A 332 2.08 REMARK 500 O HOH A 193 O HOH B 380 2.09 REMARK 500 O HOH A 244 O HOH B 303 2.14 REMARK 500 O HOH A 193 O HOH A 198 2.16 REMARK 500 O HOH B 265 O HOH B 309 2.18 REMARK 500 O HOH A 257 O HOH A 316 2.18 REMARK 500 O HOH B 171 O HOH B 348 2.18 REMARK 500 O HOH A 182 O HOH A 316 2.18 REMARK 500 O HOH B 330 O HOH B 401 2.19 REMARK 500 P DG B 5 O HOH B 346 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 168 O HOH A 358 1564 1.59 REMARK 500 O HOH A 280 O HOH A 431 1556 1.67 REMARK 500 O HOH A 325 O HOH B 339 1556 1.77 REMARK 500 O HOH A 325 O HOH B 432 1556 1.78 REMARK 500 O HOH B 240 O HOH B 302 1456 1.84 REMARK 500 O HOH B 222 O HOH B 359 1455 1.89 REMARK 500 O HOH A 350 O HOH A 358 1564 2.04 REMARK 500 O HOH A 373 O HOH B 175 1556 2.09 REMARK 500 O HOH A 430 O HOH B 175 1556 2.09 REMARK 500 O HOH A 291 O HOH B 433 1556 2.09 REMARK 500 O HOH B 236 O HOH B 240 1654 2.13 REMARK 500 O HOH B 258 O HOH B 305 1465 2.14 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 DC A 2 N3 DC A 2 C4 0.052 REMARK 500 DA A 3 N7 DA A 3 C8 -0.043 REMARK 500 DG A 5 C4 DG A 5 C5 -0.049 REMARK 500 DC B 1 C2' DC B 1 C1' -0.061 REMARK 500 DC B 7 C4 DC B 7 N4 -0.058 REMARK 500 DT B 8 C5 DT B 8 C7 0.047 REMARK 500 DG B 9 C5 DG B 9 N7 0.041 REMARK 500 DG B 10 O5' DG B 10 C5' 0.124 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 DC A 2 O4' - C4' - C3' ANGL. DEV. = 5.1 DEGREES REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG A 5 N3 - C4 - N9 ANGL. DEV. = -3.6 DEGREES REMARK 500 DC A 7 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC A 7 C5 - C6 - N1 ANGL. DEV. = -3.0 DEGREES REMARK 500 DC B 1 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 1 N3 - C4 - N4 ANGL. DEV. = 4.6 DEGREES REMARK 500 DC B 2 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 DG B 4 C2 - N3 - C4 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 5 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 5 C5 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG B 9 N3 - C4 - C5 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG B 9 C4 - C5 - N7 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG B 9 N9 - C4 - C5 ANGL. DEV. = 2.4 DEGREES 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 DG A 5 0.07 SIDE CHAIN REMARK 500 DC B 1 0.06 SIDE CHAIN REMARK 500 DG B 5 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 601 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 10 O6 REMARK 620 2 HOH A 116 O 123.9 REMARK 620 3 HOH A 117 O 83.7 81.5 REMARK 620 4 HOH A 191 O 154.7 75.2 83.3 REMARK 620 5 HOH A 427 O 77.7 150.8 82.0 79.1 REMARK 620 6 HOH B 137 O 106.3 108.6 156.2 78.9 79.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 603 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA B 3 OP1 REMARK 620 2 HOH B 110 O 77.2 REMARK 620 3 HOH B 115 O 128.0 74.1 REMARK 620 4 HOH B 125 O 75.1 104.5 71.3 REMARK 620 5 HOH B 129 O 77.7 146.7 139.1 89.7 REMARK 620 6 HOH B 135 O 154.8 125.0 74.2 106.4 77.2 REMARK 620 7 HOH B 139 O 93.7 77.3 120.3 167.8 83.0 81.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 602 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT B 8 OP2 REMARK 620 2 HOH B 114 O 88.7 REMARK 620 3 HOH B 120 O 89.7 159.8 REMARK 620 4 HOH B 141 O 85.9 91.1 108.8 REMARK 620 5 HOH B 166 O 93.0 79.0 80.9 170.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 605 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT B 8 OP1 REMARK 620 2 HOH B 126 O 85.5 REMARK 620 3 HOH B 173 O 78.9 104.7 REMARK 620 4 HOH B 206 O 143.7 80.6 137.1 REMARK 620 5 HOH B 212 O 106.8 165.8 85.0 85.3 REMARK 620 6 HOH B 221 O 71.5 105.5 135.3 80.2 72.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 604 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 160 O REMARK 620 2 HOH B 231 O 111.8 REMARK 620 3 HOH B 334 O 149.1 93.3 REMARK 620 4 1P1 B 500 O2 129.2 95.4 62.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 604 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 160 O REMARK 620 2 HOH B 334 O 131.7 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1P1 B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 605 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I5E RELATED DB: PDB REMARK 900 DUPLEX DNA WITHOUT POLYAMIDE BOUND DBREF 3I5L A 1 10 PDB 3I5L 3I5L 1 10 DBREF 3I5L B 1 10 PDB 3I5L 3I5L 1 10 SEQRES 1 A 10 DC DC DA DG DG C38 DC DT DG DG SEQRES 1 B 10 DC DC DA DG DG C38 DC DT DG DG MODRES 3I5L C38 A 6 DC MODRES 3I5L C38 B 6 DC HET C38 A 6 20 HET C38 B 6 20 HET CA A 601 1 HET 1P1 B 500 86 HET CA B 602 1 HET CA B 603 1 HET CA B 604 2 HET CA B 605 1 HETNAM C38 5-IODO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM CA CALCIUM ION HETNAM 1P1 (22R,51R)-22,51-DIAMINO-5,11,17,28,34,40,46,57- HETNAM 2 1P1 OCTAMETHYL-2,5,8,11,14,17,20,25,28,31,34,37,40,43,46, HETNAM 3 1P1 49,54,57,60,61,64,6 5-DOCOSAAZANONACYCLO[54.2.1.1~4, HETNAM 4 1P1 7~.1~10,13~.1~16,19~.1~27,30~.1~33,36~.1~39,42~.1~45, HETNAM 5 1P1 48~]HEXAHEXACONTA-1(58),4(66),6,10( 65),12,16(64),18, HETNAM 6 1P1 27(63),29,33(62),35,39(61),41,45(60),47,56(59)- HETNAM 7 1P1 HEXADECAENE-3,9,15,21,26,32,38,44,50,55-DECONE HETSYN 1P1 CYCLIC POLYAMIDE FORMUL 1 C38 2(C9 H13 I N3 O7 P) FORMUL 3 CA 5(CA 2+) FORMUL 4 1P1 C52 H60 N24 O10 FORMUL 9 HOH *258(H2 O) LINK O3' DG A 5 P C38 A 6 1555 1555 1.58 LINK O3' C38 A 6 P DC A 7 1555 1555 1.61 LINK O3' DG B 5 P C38 B 6 1555 1555 1.57 LINK O3' C38 B 6 P DC B 7 1555 1555 1.60 LINK O6 DG A 10 CA CA A 601 1555 1555 2.48 LINK O HOH A 116 CA CA A 601 1555 1555 2.36 LINK O HOH A 117 CA CA A 601 1555 1555 2.39 LINK O HOH A 191 CA CA A 601 1555 1555 2.42 LINK O HOH A 427 CA CA A 601 1555 1555 2.40 LINK CA CA A 601 O HOH B 137 1555 1555 2.38 LINK OP1 DA B 3 CA CA B 603 1555 1555 2.32 LINK OP2 DT B 8 CA CA B 602 1555 1555 2.30 LINK OP1 DT B 8 CA CA B 605 1555 1555 2.30 LINK O HOH B 110 CA CA B 603 1555 1555 2.41 LINK O HOH B 114 CA CA B 602 1555 1555 2.38 LINK O HOH B 115 CA CA B 603 1555 1555 2.48 LINK O HOH B 120 CA CA B 602 1555 1555 2.34 LINK O HOH B 125 CA CA B 603 1555 1555 2.38 LINK O HOH B 126 CA CA B 605 1555 1555 2.41 LINK O HOH B 129 CA CA B 603 1555 1555 2.41 LINK O HOH B 135 CA CA B 603 1555 1555 2.38 LINK O HOH B 139 CA CA B 603 1555 1555 2.38 LINK O HOH B 141 CA CA B 602 1555 1555 2.25 LINK O HOH B 160 CA A CA B 604 1555 1555 2.76 LINK O HOH B 160 CA B CA B 604 1555 1555 2.68 LINK O HOH B 166 CA CA B 602 1555 1555 2.44 LINK O HOH B 173 CA CA B 605 1555 1555 2.34 LINK O HOH B 206 CA CA B 605 1555 1555 2.30 LINK O HOH B 212 CA CA B 605 1555 1555 2.31 LINK O HOH B 221 CA CA B 605 1555 1555 2.48 LINK O HOH B 231 CA A CA B 604 1555 1555 2.98 LINK O HOH B 334 CA A CA B 604 1555 1555 2.31 LINK O HOH B 334 CA B CA B 604 1555 1555 2.69 LINK O2 1P1 B 500 CA A CA B 604 1555 1555 2.83 SITE 1 AC1 18 DA A 3 DG A 4 DG A 5 C38 A 6 SITE 2 AC1 18 DC A 7 DT A 8 DG A 9 DG A 10 SITE 3 AC1 18 DC B 1 DA B 3 DG B 4 DG B 5 SITE 4 AC1 18 C38 B 6 DC B 7 DT B 8 DG B 9 SITE 5 AC1 18 DG B 10 CA B 604 SITE 1 AC2 2 DG A 10 DG B 10 SITE 1 AC3 2 DA B 3 DT B 8 SITE 1 AC4 1 DA B 3 SITE 1 AC5 3 DC B 2 DC B 7 1P1 B 500 SITE 1 AC6 1 DT B 8 CRYST1 22.500 25.140 29.090 66.53 79.28 79.57 P 1 2 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 0.044444 -0.008181 -0.005752 0.00000 SCALE2 0.000000 0.040446 -0.016478 0.00000 SCALE3 0.000000 0.000000 0.037779 0.00000