HEADER DNA 20-DEC-12 4IJ0 TITLE STRUCTURES OF DNA DUPLEXES CONTAINING O6-CARBOXYMETHYLGUANINE, A TITLE 2 LESION ASSOCIATED WITH GASTROINTESTINAL CANCER, REVEAL A MECHANISM TITLE 3 FOR INDUCING TRANSITION MUTATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*CP*GP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DAMAGED DNA, O6-CARBOXYMETHYLGUANINE, MUTAGENESIS, DNA EXPDTA X-RAY DIFFRACTION AUTHOR F.ZHANG,K.SUZUKI,M.TSUNODA,O.WILKINSON,C.L.MILLINGTON,D.M.WILLIAMS, AUTHOR 2 E.C.MORISHITA,A.TAKENAKA REVDAT 3 20-MAR-24 4IJ0 1 REMARK LINK REVDAT 2 19-MAR-14 4IJ0 1 JRNL REVDAT 1 08-MAY-13 4IJ0 0 JRNL AUTH F.ZHANG,M.TSUNODA,K.SUZUKI,Y.KIKUCHI,O.WILKINSON, JRNL AUTH 2 C.L.MILLINGTON,G.P.MARGISON,D.M.WILLIAMS, JRNL AUTH 3 E.CZARINA MORISHITA,A.TAKENAKA JRNL TITL STRUCTURES OF DNA DUPLEXES CONTAINING JRNL TITL 2 O6-CARBOXYMETHYLGUANINE, A LESION ASSOCIATED WITH JRNL TITL 3 GASTROINTESTINAL CANCER, REVEAL A MECHANISM FOR INDUCING JRNL TITL 4 PYRIMIDINE TRANSITION MUTATIONS JRNL REF NUCLEIC ACIDS RES. V. 41 5524 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23580550 JRNL DOI 10.1093/NAR/GKT198 REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 9017 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 481 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) : 1.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 647 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 494 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 135 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : 0.14000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.100 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.544 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 587 ; 0.030 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 884 ; 3.705 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL 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): 96 ; 0.331 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 288 ; 0.037 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 587 ; 2.618 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 884 ; 3.391 ; 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4IJ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000076812. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9559 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 24.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08900 REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.28600 REMARK 200 R SYM FOR SHELL (I) : 0.28600 REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10%(V/V)MPD, 12MM SPERMINE 4HCL, 40MM REMARK 280 LICL, 80MM SRCL2, 40MM NA CACODYLATE(PH7.0), 1MM HOECHST 33258, REMARK 280 1MM DNA, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 12.30000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.53500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.61500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.53500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.30000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.61500 REMARK 290 SMTRY3 4 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: 1830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -78.0 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: 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 1 N1 DC A 1 C2 0.066 REMARK 500 DG A 2 N1 DG A 2 C2 0.071 REMARK 500 DG A 2 C6 DG A 2 O6 0.055 REMARK 500 DC A 3 C5 DC A 3 C6 0.051 REMARK 500 DA A 5 N3 DA A 5 C4 0.039 REMARK 500 DA A 5 C6 DA A 5 N6 0.061 REMARK 500 DA A 6 N3 DA A 6 C4 -0.041 REMARK 500 DA A 6 C8 DA A 6 N9 -0.049 REMARK 500 DA A 6 N9 DA A 6 C4 0.040 REMARK 500 DT A 7 C5 DT A 7 C7 -0.041 REMARK 500 DT A 8 O4' DT A 8 C4' -0.083 REMARK 500 DT A 8 C4 DT A 8 O4 -0.062 REMARK 500 DC A 9 C2 DC A 9 O2 -0.068 REMARK 500 DG A 10 P DG A 10 O5' 0.075 REMARK 500 DG A 12 O3' DG A 12 C3' -0.043 REMARK 500 DG A 12 C2 DG A 12 N3 -0.064 REMARK 500 DG A 12 N7 DG A 12 C8 -0.047 REMARK 500 DC B 13 C5' DC B 13 C4' 0.042 REMARK 500 DG B 14 C2' DG B 14 C1' -0.064 REMARK 500 DA B 17 C5 DA B 17 N7 -0.051 REMARK 500 DA B 17 N9 DA B 17 C4 0.051 REMARK 500 DT B 19 C5 DT B 19 C7 0.038 REMARK 500 DT B 20 P DT B 20 O5' 0.066 REMARK 500 DT B 20 C5 DT B 20 C7 -0.047 REMARK 500 DG B 22 C3' DG B 22 C2' -0.052 REMARK 500 DG B 22 C2 DG B 22 N3 0.057 REMARK 500 DG B 22 C6 DG B 22 N1 0.048 REMARK 500 DG B 22 C5 DG B 22 N7 0.048 REMARK 500 DG B 22 N7 DG B 22 C8 -0.039 REMARK 500 DC B 23 P DC B 23 O5' 0.060 REMARK 500 DC B 23 C2 DC B 23 O2 0.070 REMARK 500 DG B 24 C2 DG B 24 N2 -0.086 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 1 C4' - C3' - C2' ANGL. DEV. = -6.8 DEGREES REMARK 500 DC A 1 O4' - C1' - C2' ANGL. DEV. = -8.3 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = -8.1 DEGREES REMARK 500 DC A 1 C6 - N1 - C2 ANGL. DEV. = -9.8 DEGREES REMARK 500 DC A 1 N1 - C2 - N3 ANGL. DEV. = 8.0 DEGREES REMARK 500 DC A 1 N3 - C4 - C5 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC A 1 C4 - C5 - C6 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC A 1 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC A 1 N1 - C2 - O2 ANGL. DEV. = -10.3 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = -8.5 DEGREES REMARK 500 DG A 2 N1 - C2 - N3 ANGL. DEV. = -5.8 DEGREES REMARK 500 DG A 2 C2 - N3 - C4 ANGL. DEV. = 8.2 DEGREES REMARK 500 DG A 2 C5 - C6 - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 DG A 2 C5 - N7 - C8 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG A 2 C6 - C5 - N7 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 2 N3 - C2 - N2 ANGL. DEV. = 7.5 DEGREES REMARK 500 DG A 2 N1 - C6 - O6 ANGL. DEV. = -6.1 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 DC A 3 C6 - N1 - C2 ANGL. DEV. = 4.6 DEGREES REMARK 500 DC A 3 N3 - C4 - C5 ANGL. DEV. = 5.5 DEGREES REMARK 500 DC A 3 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 DC A 3 C5 - C4 - N4 ANGL. DEV. = -4.3 DEGREES REMARK 500 C6G A 4 C3' - O3' - P ANGL. DEV. = 11.6 DEGREES REMARK 500 DA A 6 O5' - P - OP2 ANGL. DEV. = -8.1 DEGREES REMARK 500 DA A 6 N1 - C2 - N3 ANGL. DEV. = -6.7 DEGREES REMARK 500 DA A 6 C2 - N3 - C4 ANGL. DEV. = 5.1 DEGREES REMARK 500 DA A 6 C5 - N7 - C8 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA A 6 N7 - C8 - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 DA A 6 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 DT A 7 C1' - O4' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 DT A 7 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 DT A 7 C2 - N3 - C4 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT A 7 C6 - C5 - C7 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT A 8 C6 - N1 - C2 ANGL. DEV. = -3.1 DEGREES REMARK 500 DT A 8 C4 - C5 - C6 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT A 8 C5 - C6 - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DC A 9 C4' - C3' - C2' ANGL. DEV. = 5.6 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 DG A 10 OP1 - P - OP2 ANGL. DEV. = 12.7 DEGREES REMARK 500 DG A 10 O5' - P - OP2 ANGL. DEV. = -6.9 DEGREES REMARK 500 DG A 10 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG A 10 C5 - N7 - C8 ANGL. DEV. = -3.9 DEGREES REMARK 500 DC A 11 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -8.2 DEGREES REMARK 500 DG A 12 O4' - C4' - C3' ANGL. DEV. = -4.0 DEGREES REMARK 500 DG A 12 C4' - C3' - C2' ANGL. DEV. = 8.4 DEGREES REMARK 500 DG B 14 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 109 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 DG B 14 0.08 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 SR A 101 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 505 O REMARK 620 2 HOH A 509 O 78.7 REMARK 620 3 HOH A 511 O 148.0 76.9 REMARK 620 4 HOH A 520 O 72.7 73.4 80.8 REMARK 620 5 HOH A 570 O 102.9 138.2 82.6 67.6 REMARK 620 6 HOH B 206 O 75.3 140.4 136.0 124.5 77.2 REMARK 620 7 HOH B 209 O 139.4 106.3 68.3 147.9 99.0 76.9 REMARK 620 8 HOH B 223 O 68.7 72.9 121.9 132.5 147.3 70.1 74.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR A 102 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 502 O REMARK 620 2 HOH A 556 O 68.7 REMARK 620 3 HOH A 569 O 69.4 112.8 REMARK 620 4 HOH B 251 O 140.5 149.5 80.4 REMARK 620 5 HOH B 255 O 138.1 77.4 149.7 78.7 REMARK 620 6 HOH B 257 O 121.4 79.6 80.4 75.6 73.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HT B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ITD RELATED DB: PDB DBREF 4IJ0 A 1 12 PDB 4IJ0 4IJ0 1 12 DBREF 4IJ0 B 13 24 PDB 4IJ0 4IJ0 13 24 SEQRES 1 A 12 DC DG DC C6G DA DA DT DT DC DG DC DG SEQRES 1 B 12 DC DG DC C6G DA DA DT DT DC DG DC DG MODRES 4IJ0 C6G A 4 DG MODRES 4IJ0 C6G B 16 DG HET C6G A 4 26 HET C6G B 16 26 HET SR A 101 1 HET SR A 102 1 HET SR A 103 1 HET HT B 101 32 HETNAM C6G 6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D- HETNAM 2 C6G ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE HETNAM SR STRONTIUM ION HETNAM HT 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'- HETNAM 2 HT BI-BENZIMIDAZOLE HETSYN HT HOECHST 33258 FORMUL 1 C6G 2(C12 H16 N5 O9 P) FORMUL 3 SR 3(SR 2+) FORMUL 6 HT C25 H24 N6 O FORMUL 7 HOH *135(H2 O) LINK O3' DC A 3 P C6G A 4 1555 1555 1.62 LINK O3' C6G A 4 P DA A 5 1555 1555 1.63 LINK O3' DC B 15 P C6G B 16 1555 1555 1.66 LINK O3' C6G B 16 P DA B 17 1555 1555 1.59 LINK SR SR A 101 O HOH A 505 1555 1555 2.50 LINK SR SR A 101 O HOH A 509 1555 1555 2.63 LINK SR SR A 101 O HOH A 511 1555 1555 2.64 LINK SR SR A 101 O HOH A 520 1555 1555 2.59 LINK SR SR A 101 O HOH A 570 1555 1555 2.74 LINK SR SR A 101 O HOH B 206 1555 1555 2.57 LINK SR SR A 101 O HOH B 209 1555 1555 2.43 LINK SR SR A 101 O HOH B 223 1555 1555 2.81 LINK SR SR A 102 O HOH A 502 1555 1555 2.55 LINK SR SR A 102 O HOH A 556 1555 1555 2.67 LINK SR SR A 102 O HOH A 569 1555 1555 2.48 LINK SR SR A 102 O HOH B 251 1555 1555 2.43 LINK SR SR A 102 O HOH B 255 1555 1555 2.46 LINK SR SR A 102 O HOH B 257 1555 1555 2.41 LINK SR SR A 103 O HOH A 514 1555 1555 2.34 SITE 1 AC1 8 HOH A 505 HOH A 509 HOH A 511 HOH A 520 SITE 2 AC1 8 HOH A 570 HOH B 206 HOH B 209 HOH B 223 SITE 1 AC2 8 HOH A 502 HOH A 512 HOH A 523 HOH A 556 SITE 2 AC2 8 HOH A 569 HOH B 251 HOH B 255 HOH B 257 SITE 1 AC3 6 HOH A 514 HOH A 524 HOH B 211 HOH B 213 SITE 2 AC3 6 HOH B 221 HOH B 230 SITE 1 AC4 15 DA A 5 DA A 6 DT A 7 DT A 8 SITE 2 AC4 15 DC A 9 DG A 12 DT B 19 DT B 20 SITE 3 AC4 15 DC B 21 DG B 22 DC B 23 HOH B 202 SITE 4 AC4 15 HOH B 208 HOH B 219 HOH B 238 CRYST1 24.600 41.230 63.070 90.00 90.00 90.00 P 21 21 21 8 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 0.040650 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024254 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015855 0.00000