HEADER DNA 27-MAR-09 3GSJ TITLE A BULKY RHODIUM COMPLEX BOUND TO AN ADENOSINE-ADENOSINE DNA MISMATCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*AP*CP*CP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC DNA KEYWDS DNA MISMATCH, METALLOINTERCALATOR, DNA RECOGNITION, DNA EXPDTA X-RAY DIFFRACTION AUTHOR B.M.ZEGLIS,V.C.PIERRE,J.T.KAISER,J.K.BARTON REVDAT 3 14-FEB-18 3GSJ 1 REMARK REVDAT 2 02-JUN-09 3GSJ 1 JRNL REVDAT 1 19-MAY-09 3GSJ 0 JRNL AUTH B.M.ZEGLIS,V.C.PIERRE,J.T.KAISER,J.K.BARTON JRNL TITL A BULKY RHODIUM COMPLEX BOUND TO AN ADENOSINE-ADENOSINE DNA JRNL TITL 2 MISMATCH: GENERAL ARCHITECTURE OF THE METALLOINSERTION JRNL TITL 3 BINDING MODE JRNL REF BIOCHEMISTRY V. 48 4247 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19374348 JRNL DOI 10.1021/BI900194E REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 4190 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 198 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 292 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.3770 REMARK 3 BIN FREE R VALUE SET COUNT : 17 REMARK 3 BIN FREE R VALUE : 0.4250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 244 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : 0.36000 REMARK 3 B33 (A**2) : -0.71000 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): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.092 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.081 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 402 ; 0.032 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 173 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 631 ; 4.281 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 409 ; 1.468 ; 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): 50 ; 0.198 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 234 ; 0.025 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 82 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 45 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 169 ; 0.249 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 165 ; 0.289 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 64 ; 0.112 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 30 ; 0.242 ; 0.200 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): 40 ; 0.168 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 66 ; 0.359 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.222 ; 0.200 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): 678 ; 2.125 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 631 ; 3.210 ; 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 : 1.20 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 3GSJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052255. 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 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4469 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 28.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.78200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM SODIUM CACODYLATE, 6 MM REMARK 280 SPERMINE, 4HCL, 40 MM KCL, 5% MPD, PH 7, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.71000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 19.51000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 19.51000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.06500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 19.51000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 19.51000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.35500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 19.51000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.51000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.06500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 19.51000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.51000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 14.35500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 28.71000 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: 1290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -28.71000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 RH R1C A2002 LIES ON A SPECIAL POSITION. 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 A 48 O HOH A 62 1.66 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 23 O HOH A 58 7554 2.04 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 1 N1 DC A 1 C6 -0.037 REMARK 500 DC A 1 N1 DC A 1 C6 -0.038 REMARK 500 DG A 3 C2 DG A 3 N3 -0.051 REMARK 500 DA A 5 O3' DA A 5 C3' -0.037 REMARK 500 DA A 5 C6 DA A 5 N6 -0.056 REMARK 500 DA A 6 C5 DA A 6 N7 -0.048 REMARK 500 DA A 6 N7 DA A 6 C8 -0.075 REMARK 500 DA A 6 C8 DA A 6 N9 -0.057 REMARK 500 DT A 8 C2 DT A 8 O2 -0.071 REMARK 500 DT A 8 C5 DT A 8 C7 -0.038 REMARK 500 DA A 9 P DA A 9 O5' -0.066 REMARK 500 DC A 11 C2' DC A 11 C1' -0.061 REMARK 500 DG A 12 P DG A 12 OP1 -0.117 REMARK 500 DG A 12 O4' DG A 12 C1' 0.106 REMARK 500 DG A 12 O3' DG A 12 C3' -0.048 REMARK 500 DG A 12 C5 DG A 12 N7 -0.047 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 O5' - C5' - C4' ANGL. DEV. = -5.5 DEGREES REMARK 500 DC A 1 C1' - O4' - C4' ANGL. DEV. = 5.0 DEGREES REMARK 500 DC A 1 N1 - C1' - C2' ANGL. DEV. = 11.3 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = -7.4 DEGREES REMARK 500 DC A 1 N3 - C4 - C5 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC A 1 N3 - C4 - N4 ANGL. DEV. = 5.5 DEGREES REMARK 500 DC A 1 C5 - C4 - N4 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC A 1 C3' - O3' - P ANGL. DEV. = 12.5 DEGREES REMARK 500 DG A 2 O3' - P - O5' ANGL. DEV. = -12.2 DEGREES REMARK 500 DG A 2 O5' - P - OP2 ANGL. DEV. = -7.4 DEGREES REMARK 500 DG A 3 O5' - P - OP2 ANGL. DEV. = -6.2 DEGREES REMARK 500 DG A 3 N1 - C2 - N3 ANGL. DEV. = -4.8 DEGREES REMARK 500 DG A 3 C2 - N3 - C4 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 3 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 DA A 4 O5' - P - OP1 ANGL. DEV. = 14.3 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = -8.9 DEGREES REMARK 500 DA A 4 C6 - N1 - C2 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 5 OP1 - P - OP2 ANGL. DEV. = 12.4 DEGREES REMARK 500 DA A 5 O5' - C5' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 DA A 5 O4' - C4' - C3' ANGL. DEV. = -3.6 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 DA A 5 C6 - N1 - C2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA A 5 N3 - C4 - C5 ANGL. DEV. = 4.2 DEGREES REMARK 500 DA A 5 C8 - N9 - C4 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA A 6 O5' - C5' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA A 6 C2 - N3 - C4 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA A 6 C5 - C6 - N1 ANGL. DEV. = -5.7 DEGREES REMARK 500 DA A 6 C5 - C6 - N6 ANGL. DEV. = 5.6 DEGREES REMARK 500 DT A 7 O5' - P - OP2 ANGL. DEV. = -5.5 DEGREES REMARK 500 DT A 7 N1 - C1' - C2' ANGL. DEV. = 11.0 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = -10.6 DEGREES REMARK 500 DT A 7 N1 - C2 - O2 ANGL. DEV. = 5.8 DEGREES REMARK 500 DT A 8 OP1 - P - OP2 ANGL. DEV. = 10.1 DEGREES REMARK 500 DA A 9 O5' - P - OP1 ANGL. DEV. = 7.5 DEGREES REMARK 500 DA A 9 O4' - C4' - C3' ANGL. DEV. = -3.4 DEGREES REMARK 500 DA A 9 C1' - O4' - C4' ANGL. DEV. = 4.3 DEGREES REMARK 500 DA A 9 C6 - N1 - C2 ANGL. DEV. = 5.1 DEGREES REMARK 500 DA A 9 N1 - C2 - N3 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA A 9 C5 - C6 - N1 ANGL. DEV. = -3.8 DEGREES REMARK 500 DA A 9 N9 - C4 - C5 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA A 9 N1 - C6 - N6 ANGL. DEV. = 5.7 DEGREES REMARK 500 DC A 10 OP1 - P - OP2 ANGL. DEV. = 10.2 DEGREES REMARK 500 DC A 10 O5' - C5' - C4' ANGL. DEV. = -8.4 DEGREES REMARK 500 DC A 10 P - O5' - C5' ANGL. DEV. = 13.1 DEGREES REMARK 500 DC A 10 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES REMARK 500 DC A 11 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DC A 11 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC A 11 C6 - N1 - C2 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 59 ANGLE 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 NA A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R1C A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R1C A 2002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2O1I RELATED DB: PDB REMARK 900 RELATED ID: 3GSK RELATED DB: PDB DBREF 3GSJ A 1 12 PDB 3GSJ 3GSJ 1 12 SEQRES 1 A 12 DC DG DG DA DA DA DT DT DA DC DC DG HET NA A1002 1 HET CL A1003 1 HET R1C A2001 45 HET R1C A2002 45 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM R1C BIS(2,2'-BIPYRIDINE-KAPPA~2~N~1~,N~1'~)[CHRYSENE-5,6- HETNAM 2 R1C DIIMINATO(2-)-KAPPA~2~N,N']RHODIUM(4+) HETSYN R1C DELTA-RHODIUM(III)- BIS-(2,2'-BIPYRIDYL)-5,6- HETSYN 2 R1C CHRYSENEQUINONE DIIMINE FORMUL 2 NA NA 1+ FORMUL 3 CL CL 1- FORMUL 4 R1C 2(C38 H26 N6 RH 4+) FORMUL 6 HOH *63(H2 O) LINK NA NA A1002 O HOH A 54 1555 1555 2.62 SITE 1 AC1 2 HOH A 54 R1C A2001 SITE 1 AC2 2 DA A 4 DG A 12 SITE 1 AC3 10 DG A 3 DA A 4 DA A 5 DT A 8 SITE 2 AC3 10 DA A 9 DC A 10 DC A 11 HOH A 35 SITE 3 AC3 10 HOH A 58 NA A1002 SITE 1 AC4 6 DC A 1 DA A 5 DA A 6 DT A 7 SITE 2 AC4 6 DG A 12 HOH A 34 CRYST1 39.020 39.020 57.420 90.00 90.00 90.00 P 43 21 2 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 0.025628 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025628 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017416 0.00000 MASTER 420 0 4 0 0 0 7 6 0 0 0 1 END