HEADER DNA 01-FEB-09 3G2R TITLE CRYSTAL STRUCTURE OF D(CACGCG).D(CGCGTG) COCRYSTALLIZED WITH MNCL2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*TP*GP*CP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DUPLEX Z-FORM DNA WITH WATSON-CRICK BASE PAIRING, DNA EXPDTA X-RAY DIFFRACTION AUTHOR S.VENKADESH,P.K.MANDAL,R.KANNAN,N.GAUTHAM REVDAT 2 20-MAR-24 3G2R 1 REMARK REVDAT 1 03-MAR-09 3G2R 0 JRNL AUTH S.VENKADESH,P.K.MANDAL,R.KANNAN,N.GAUTHAM JRNL TITL CRYSTAL STUDIES OF D(CACGCG).D(CGCGTG) GROWN WITH VARIOUS JRNL TITL 2 COUNTER IONS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 693 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) : 0.269 REMARK 3 R VALUE (WORKING SET) : 0.269 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600 REMARK 3 FREE R VALUE TEST SET COUNT : 41 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3580 REMARK 3 BIN FREE R VALUE SET COUNT : 1 REMARK 3 BIN FREE R VALUE : 0.0660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 121 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 6 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.12000 REMARK 3 B22 (A**2) : -0.45000 REMARK 3 B33 (A**2) : 1.57000 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): 0.390 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.258 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.188 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.295 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 138 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 211 ; 4.056 ; 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): 23 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 64 ; 0.017 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 53 ; 0.227 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 74 ; 0.345 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 3 ; 0.451 ; 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): 22 ; 0.459 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.688 ; 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): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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: NULL REMARK 4 REMARK 4 3G2R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.99 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOMAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 742 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.830 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : 0.03830 REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.87 REMARK 200 R MERGE FOR SHELL (I) : 0.23770 REMARK 200 R SYM FOR SHELL (I) : 0.21620 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM SODIUM CACODYLATE, 5MM MNCL2, 1MM REMARK 280 SPERMINE, 50% METHYL PENTANE DIOL, PH 6.99, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.70250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.70250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 8.93900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 15.48500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 8.93900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 15.48500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 21.70250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 8.93900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 15.48500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 21.70250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 8.93900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 15.48500 REMARK 290 SMTRY3 8 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 300 REMARK: THE AUTHOR STATES THAT THERE IS NO POSSIBLE QUATERNARY REMARK 300 STRUCTURE 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 30.97000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 MN MN A 8 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 O3' DG A 6 P DCM A 7 1.89 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 DG A 6 C6 DG A 6 O6 0.063 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 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = -10.2 DEGREES REMARK 500 DG A 2 P - O5' - C5' ANGL. DEV. = -18.7 DEGREES REMARK 500 DG A 2 O4' - C4' - C3' ANGL. DEV. = 4.9 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = -9.7 DEGREES REMARK 500 DG A 2 C2 - N3 - C4 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A 2 N3 - C4 - C5 ANGL. DEV. = -3.3 DEGREES REMARK 500 DG A 2 C4 - C5 - N7 ANGL. DEV. = -4.2 DEGREES REMARK 500 DG A 2 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG A 2 C6 - C5 - N7 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG A 2 N1 - C6 - O6 ANGL. DEV. = -6.2 DEGREES REMARK 500 DG A 2 C5 - C6 - O6 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG A 4 O4' - C4' - C3' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG A 4 C3' - O3' - P ANGL. DEV. = 8.1 DEGREES REMARK 500 DC A 5 O4' - C4' - C3' ANGL. DEV. = -3.2 DEGREES REMARK 500 DC A 5 N1 - C1' - C2' ANGL. DEV. = 8.6 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = -14.1 DEGREES REMARK 500 DC A 5 C2 - N3 - C4 ANGL. DEV. = 3.5 DEGREES REMARK 500 DC A 5 N1 - C2 - O2 ANGL. DEV. = 6.5 DEGREES REMARK 500 DG A 6 O3' - P - O5' ANGL. DEV. = -12.7 DEGREES REMARK 500 DG A 6 O5' - P - OP1 ANGL. DEV. = 9.0 DEGREES REMARK 500 DG A 6 P - O5' - C5' ANGL. DEV. = -11.8 DEGREES REMARK 500 DG A 6 O4' - C4' - C3' ANGL. DEV. = -5.4 DEGREES REMARK 500 DG A 6 N3 - C4 - C5 ANGL. DEV. = -3.5 DEGREES REMARK 500 DG A 6 C5 - C6 - N1 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG A 6 C4 - C5 - N7 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG A 6 C5 - N7 - C8 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG A 6 N9 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG A 6 C5 - C6 - O6 ANGL. DEV. = 6.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 DCM A 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCM A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 8 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3G2A RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D(CACGCG)D(CGCGTG) GROWN IN PRESENCE OF MNCL2 DBREF 3G2R A 1 6 PDB 3G2R 3G2R 1 6 SEQRES 1 A 6 DC DG DT DG DC DG HET DCM A 7 3 HET MN A 8 1 HETNAM DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM MN MANGANESE (II) ION FORMUL 2 DCM C9 H14 N3 O7 P FORMUL 3 MN MN 2+ FORMUL 4 HOH *6(H2 O) LINK O6 DG A 2 MN MN A 8 1555 1555 2.44 SITE 1 AC1 3 DC A 1 DG A 4 DG A 6 SITE 1 AC2 3 DG A 2 DT A 3 HOH A 10 CRYST1 17.878 30.970 43.405 90.00 90.00 90.00 C 2 2 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 0.055935 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032289 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023039 0.00000 ATOM 1 O5' DC A 1 5.920 11.919 -6.283 1.00 42.09 O ATOM 2 C5' DC A 1 5.254 11.669 -5.085 1.00 39.95 C ATOM 3 C4' DC A 1 3.783 12.046 -5.086 1.00 40.58 C ATOM 4 O4' DC A 1 3.794 13.460 -4.780 1.00 38.21 O ATOM 5 C3' DC A 1 2.977 11.869 -6.374 1.00 33.09 C ATOM 6 O3' DC A 1 1.638 11.472 -6.121 1.00 42.52 O ATOM 7 C2' DC A 1 3.035 13.274 -6.980 1.00 31.03 C ATOM 8 C1' DC A 1 2.860 14.041 -5.677 1.00 33.94 C ATOM 9 N1 DC A 1 3.360 15.355 -5.647 1.00 35.87 N ATOM 10 C2 DC A 1 2.496 16.433 -5.531 1.00 30.04 C ATOM 11 O2 DC A 1 1.288 16.201 -5.581 1.00 26.33 O ATOM 12 N3 DC A 1 3.064 17.670 -5.510 1.00 40.02 N ATOM 13 C4 DC A 1 4.391 17.809 -5.524 1.00 29.85 C ATOM 14 N4 DC A 1 4.910 19.036 -5.455 1.00 45.88 N ATOM 15 C5 DC A 1 5.271 16.715 -5.595 1.00 47.96 C ATOM 16 C6 DC A 1 4.714 15.505 -5.667 1.00 30.54 C ATOM 17 P DG A 2 1.288 9.927 -6.107 1.00 50.79 P ATOM 18 OP1 DG A 2 1.657 9.287 -7.401 1.00 59.68 O ATOM 19 OP2 DG A 2 -0.032 9.745 -5.412 1.00 36.50 O ATOM 20 O5' DG A 2 2.315 9.369 -5.070 1.00 37.39 O ATOM 21 C5' DG A 2 1.507 9.079 -3.984 1.00 21.62 C ATOM 22 C4' DG A 2 2.357 8.445 -2.946 1.00 23.93 C ATOM 23 O4' DG A 2 3.734 8.843 -3.075 1.00 21.80 O ATOM 24 C3' DG A 2 1.867 8.686 -1.580 1.00 22.10 C ATOM 25 O3' DG A 2 0.813 7.637 -1.567 1.00 36.46 O ATOM 26 C2' DG A 2 3.158 8.473 -0.826 1.00 23.89 C ATOM 27 C1' DG A 2 4.339 8.779 -1.804 1.00 25.19 C ATOM 28 N9 DG A 2 4.980 10.073 -1.813 1.00 27.79 N ATOM 29 C8 DG A 2 6.310 10.298 -1.899 1.00 29.08 C ATOM 30 N7 DG A 2 6.591 11.572 -1.897 1.00 33.66 N ATOM 31 C5 DG A 2 5.377 12.286 -1.865 1.00 30.92 C ATOM 32 C6 DG A 2 5.025 13.703 -1.882 1.00 38.66 C ATOM 33 O6 DG A 2 5.700 14.760 -1.931 1.00 28.74 O ATOM 34 N1 DG A 2 3.645 13.920 -1.781 1.00 22.35 N ATOM 35 C2 DG A 2 2.733 12.930 -1.730 1.00 24.22 C ATOM 36 N2 DG A 2 1.472 13.389 -1.680 0.50 17.55 N ATOM 37 N3 DG A 2 3.058 11.617 -1.756 1.00 21.50 N ATOM 38 C4 DG A 2 4.368 11.345 -1.825 1.00 25.87 C ATOM 39 P DT A 3 -0.606 7.985 -0.875 0.50 53.42 P ATOM 40 OP1 DT A 3 -1.192 6.646 -0.575 0.50 45.04 O ATOM 41 OP2 DT A 3 -1.325 9.029 -1.650 0.50 38.66 O ATOM 42 O5' DT A 3 -0.311 8.724 0.523 1.00 41.80 O ATOM 43 C5' DT A 3 -1.408 9.019 1.373 1.00 42.88 C ATOM 44 C4' DT A 3 -1.513 10.461 1.830 1.00 36.03 C ATOM 45 O4' DT A 3 -0.251 10.938 2.377 1.00 37.82 O ATOM 46 C3' DT A 3 -1.886 11.379 0.686 1.00 39.08 C ATOM 47 O3' DT A 3 -2.833 12.331 1.170 1.00 49.55 O ATOM 48 C2' DT A 3 -0.512 11.907 0.271 1.00 31.75 C ATOM 49 C1' DT A 3 0.082 12.101 1.657 1.00 31.53 C ATOM 50 N1 DT A 3 1.541 12.415 1.760 1.00 27.26 N ATOM 51 C2 DT A 3 1.864 13.705 2.075 1.00 27.62 C ATOM 52 O2 DT A 3 1.061 14.581 2.228 1.00 26.34 O ATOM 53 N3 DT A 3 3.201 13.936 2.182 1.00 40.90 N ATOM 54 C4 DT A 3 4.204 13.010 2.009 1.00 20.19 C ATOM 55 O4 DT A 3 5.354 13.372 2.159 1.00 42.48 O ATOM 56 C5 DT A 3 3.810 11.647 1.722 1.00 26.93 C ATOM 57 C7 DT A 3 4.837 10.540 1.535 0.50 20.39 C ATOM 58 C6 DT A 3 2.499 11.434 1.604 1.00 29.28 C ATOM 59 P DG A 4 -4.439 12.026 1.271 1.00 50.87 P ATOM 60 OP1 DG A 4 -4.834 11.568 -0.052 1.00 51.10 O ATOM 61 OP2 DG A 4 -5.092 13.247 1.800 1.00 55.89 O ATOM 62 O5' DG A 4 -4.648 10.882 2.349 1.00 46.66 O ATOM 63 C5' DG A 4 -5.586 11.010 3.446 1.00 38.27 C ATOM 64 C4' DG A 4 -5.338 9.914 4.492 1.00 26.69 C ATOM 65 O4' DG A 4 -4.054 9.311 4.233 1.00 23.44 O ATOM 66 C3' DG A 4 -5.114 10.367 5.910 1.00 31.29 C ATOM 67 O3' DG A 4 -6.397 10.544 6.497 1.00 34.46 O ATOM 68 C2' DG A 4 -4.290 9.200 6.528 1.00 17.87 C ATOM 69 C1' DG A 4 -3.678 8.501 5.306 1.00 23.06 C ATOM 70 N9 DG A 4 -2.226 8.507 5.360 1.00 41.98 N ATOM 71 C8 DG A 4 -1.308 7.484 5.548 1.00 41.12 C ATOM 72 N7 DG A 4 -0.046 7.911 5.600 1.00 36.81 N ATOM 73 C5 DG A 4 -0.133 9.293 5.439 1.00 39.20 C ATOM 74 C6 DG A 4 0.878 10.309 5.361 1.00 45.00 C ATOM 75 O6 DG A 4 2.122 10.187 5.469 1.00 40.56 O ATOM 76 N1 DG A 4 0.310 11.590 5.193 1.00 36.31 N ATOM 77 C2 DG A 4 -1.023 11.847 5.112 1.00 36.95 C ATOM 78 N2 DG A 4 -1.321 13.110 4.949 1.00 28.64 N ATOM 79 N3 DG A 4 -1.985 10.916 5.126 1.00 33.21 N ATOM 80 C4 DG A 4 -1.469 9.669 5.288 1.00 41.61 C ATOM 81 P DC A 5 -7.223 11.923 6.680 0.50 41.01 P ATOM 82 OP1 DC A 5 -8.658 11.647 6.479 0.50 31.86 O ATOM 83 OP2 DC A 5 -6.627 13.092 5.984 0.50 28.69 O ATOM 84 O5' DC A 5 -7.019 12.193 8.217 1.00 40.92 O ATOM 85 C5' DC A 5 -5.861 11.919 8.986 1.00 26.66 C ATOM 86 C4' DC A 5 -5.316 13.262 9.450 1.00 27.52 C ATOM 87 O4' DC A 5 -3.918 13.080 9.775 1.00 33.31 O ATOM 88 C3' DC A 5 -5.246 14.436 8.483 1.00 33.55 C ATOM 89 O3' DC A 5 -5.151 15.674 9.210 1.00 37.32 O ATOM 90 C2' DC A 5 -3.930 14.167 7.750 1.00 27.16 C ATOM 91 C1' DC A 5 -3.083 13.833 8.938 1.00 18.51 C ATOM 92 N1 DC A 5 -2.041 12.822 8.904 1.00 28.23 N ATOM 93 C2 DC A 5 -0.706 13.064 9.229 1.00 24.80 C ATOM 94 O2 DC A 5 -0.204 14.184 9.419 1.00 24.15 O ATOM 95 N3 DC A 5 0.084 11.968 9.262 1.00 29.94 N ATOM 96 C4 DC A 5 -0.354 10.745 8.997 1.00 22.74 C ATOM 97 N4 DC A 5 0.529 9.755 9.053 1.00 27.48 N ATOM 98 C5 DC A 5 -1.707 10.479 8.756 1.00 33.09 C ATOM 99 C6 DC A 5 -2.501 11.544 8.727 1.00 30.03 C ATOM 100 P DG A 6 -5.211 17.072 8.443 1.00 46.96 P ATOM 101 OP1 DG A 6 -4.992 16.831 6.994 1.00 50.56 O ATOM 102 OP2 DG A 6 -4.459 18.197 9.101 1.00 39.19 O ATOM 103 O5' DG A 6 -6.693 17.348 8.988 1.00 35.69 O ATOM 104 C5' DG A 6 -6.609 17.966 10.301 1.00 35.33 C ATOM 105 C4' DG A 6 -7.357 17.177 11.372 1.00 33.37 C ATOM 106 O4' DG A 6 -7.167 15.748 11.242 1.00 32.52 O ATOM 107 C3' DG A 6 -7.027 17.329 12.826 1.00 31.83 C ATOM 108 O3' DG A 6 -7.554 18.577 13.180 1.00 40.65 O ATOM 109 C2' DG A 6 -7.838 16.149 13.405 1.00 29.64 C ATOM 110 C1' DG A 6 -7.859 15.112 12.284 1.00 26.60 C ATOM 111 N9 DG A 6 -7.123 13.865 12.545 1.00 30.86 N ATOM 112 C8 DG A 6 -7.692 12.654 12.727 1.00 27.55 C ATOM 113 N7 DG A 6 -6.829 11.699 12.954 1.00 28.32 N ATOM 114 C5 DG A 6 -5.565 12.251 12.949 1.00 42.46 C ATOM 115 C6 DG A 6 -4.239 11.648 13.123 1.00 43.38 C ATOM 116 O6 DG A 6 -3.805 10.443 13.344 1.00 26.55 O ATOM 117 N1 DG A 6 -3.285 12.663 13.035 1.00 42.70 N ATOM 118 C2 DG A 6 -3.500 13.996 12.792 1.00 43.45 C ATOM 119 N2 DG A 6 -2.367 14.736 12.769 1.00 23.76 N ATOM 120 N3 DG A 6 -4.719 14.539 12.566 1.00 37.14 N ATOM 121 C4 DG A 6 -5.737 13.620 12.675 1.00 42.32 C TER 122 DG A 6 HETATM 123 P DCM A 7 -8.177 19.240 14.839 0.50 35.91 P HETATM 124 O1P DCM A 7 -8.184 18.246 15.940 0.50 28.82 O HETATM 125 O2P DCM A 7 -7.670 20.623 14.946 0.50 30.82 O HETATM 126 MN MN A 8 7.004 15.520 -0.015 0.25 35.16 MN HETATM 127 O HOH A 9 -4.887 8.230 14.659 1.00 28.55 O HETATM 128 O HOH A 10 9.301 16.979 0.341 1.00 30.29 O HETATM 129 O HOH A 11 -6.678 14.940 4.665 1.00 28.65 O HETATM 130 O HOH A 12 -0.887 4.615 -2.683 1.00 50.88 O HETATM 131 O HOH A 13 -3.297 14.427 3.703 1.00 24.07 O HETATM 132 O HOH A 14 -2.460 18.052 10.915 1.00 30.05 O CONECT 33 126 CONECT 123 124 125 CONECT 124 123 CONECT 125 123 CONECT 126 33 MASTER 364 0 2 0 0 0 2 6 131 1 5 1 END