HEADER DNA 02-FEB-12 4AH1 TITLE CRYSTAL STRUCTURE OF THE DB 921-D(CGCAAATTTGCG)2 COMPLEX AT 1.42 A TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*GP)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DNA, DNA DOUBLE HELIX, MINOR GROOVE, DODECAMER, A3T3, DNA-DRUG KEYWDS 2 COMPLEX, DNA HYDRATION EXPDTA X-RAY DIFFRACTION AUTHOR D.G.MUNNUR,E.P.MITCHELL,V.T.FORSYTH,S.C.M.TEIXEIRA,S.NEIDLE REVDAT 3 20-DEC-23 4AH1 1 REMARK LINK REVDAT 2 30-JAN-19 4AH1 1 REMARK REVDAT 1 16-JAN-13 4AH1 0 JRNL AUTH D.G.MUNNUR,E.P.MITCHELL,V.T.FORSYTH,S.C.M.TEIXEIRA,S.NEIDLE JRNL TITL A DETAILED STUDY OF WATER NETWORK IN THE MINOR GROOVE OF JRNL TITL 2 D(CGCGAATTCGCG)2 AND D(CGCAAATTTGCG)2 IN PRESENCE OF LINEAR JRNL TITL 3 GROOVE BINDERS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 10451 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 520 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) : 1.42 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 784 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 37 REMARK 3 BIN FREE R VALUE : 0.3590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 109 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 0.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : 0.07000 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): 0.076 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.090 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.641 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 574 ; 0.025 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 238 ; 0.014 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 879 ; 3.408 ; 2.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): 579 ; 1.448 ; 3.030 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): 94 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 287 ; 0.031 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 57 ; 0.001 ; 0.021 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): 574 ; 2.381 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 879 ; 3.283 ; 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 : BABINET MODEL WITH 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4AH1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1290049273. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11003 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 38.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1S2R REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAGNESIUM CHLORIDE, DNA, DB921, MPD, REMARK 280 SPERMINE TETRAHYDROCHLORIDE, VAPOUR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 285 K, PH 6.50, VAPOR DIFFUSION, SITTING DROP 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 11.81100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.33000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.44050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.33000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.81100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.44050 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: 1230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.2 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 OP1 DT A 8 O HOH A 2039 1.58 REMARK 500 OP1 DA A 5 O HOH A 2029 2.16 REMARK 500 OP2 DA A 4 O HOH A 2025 2.18 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 2 O3' DG A 2 C3' -0.036 REMARK 500 DC A 3 N3 DC A 3 C4 -0.047 REMARK 500 DA A 4 N9 DA A 4 C4 0.040 REMARK 500 DT A 7 O3' DT A 7 C3' -0.082 REMARK 500 DT A 7 C2 DT A 7 O2 -0.061 REMARK 500 DT A 8 P DT A 8 OP2 -0.120 REMARK 500 DT A 8 O3' DT A 8 C3' -0.095 REMARK 500 DT A 8 C5 DT A 8 C6 -0.046 REMARK 500 DT A 8 C2 DT A 8 O2 -0.079 REMARK 500 DT A 8 C4 DT A 8 O4 -0.069 REMARK 500 DT A 9 P DT A 9 OP1 -0.112 REMARK 500 DT A 9 P DT A 9 OP2 -0.142 REMARK 500 DT A 9 C6 DT A 9 N1 -0.043 REMARK 500 DT A 9 C2 DT A 9 O2 -0.057 REMARK 500 DT A 9 C4 DT A 9 O4 -0.061 REMARK 500 DC A 11 N3 DC A 11 C4 0.048 REMARK 500 DG A 12 C2 DG A 12 N3 0.062 REMARK 500 DG A 12 C5 DG A 12 N7 -0.037 REMARK 500 DA B 16 P DA B 16 O5' -0.068 REMARK 500 DA B 16 O3' DA B 16 C3' -0.044 REMARK 500 DA B 17 P DA B 17 O5' 0.060 REMARK 500 DA B 17 O3' DA B 17 C3' -0.084 REMARK 500 DT B 21 P DT B 21 OP2 -0.112 REMARK 500 DT B 21 C4 DT B 21 O4 -0.066 REMARK 500 DG B 22 O3' DG B 22 C3' -0.093 REMARK 500 DG B 22 N1 DG B 22 C2 -0.050 REMARK 500 DG B 22 C8 DG B 22 N9 -0.044 REMARK 500 DG B 22 O3' DC B 23 P -0.074 REMARK 500 DC B 23 C2 DC B 23 O2 -0.060 REMARK 500 DC B 23 N1 DC B 23 C6 -0.037 REMARK 500 DC B 23 C2 DC B 23 N3 -0.052 REMARK 500 DC B 23 N3 DC B 23 C4 -0.055 REMARK 500 DC B 23 C5 DC B 23 C6 -0.053 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 N3 - C4 - C5 ANGL. DEV. = -4.5 DEGREES REMARK 500 DC A 1 C4 - C5 - C6 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC A 1 C5 - C4 - N4 ANGL. DEV. = 6.3 DEGREES REMARK 500 DG A 2 N9 - C1' - C2' ANGL. DEV. = 9.1 DEGREES REMARK 500 DG A 2 C6 - N1 - C2 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A 2 N1 - C2 - N3 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG A 2 C4 - C5 - N7 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG A 2 C5 - N7 - C8 ANGL. DEV. = -3.3 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A 2 N1 - C6 - O6 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG A 2 C5 - C6 - O6 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = -3.2 DEGREES REMARK 500 DA A 4 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 4 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = 5.5 DEGREES REMARK 500 DA A 5 OP1 - P - OP2 ANGL. DEV. = 17.4 DEGREES REMARK 500 DA A 5 O5' - P - OP2 ANGL. DEV. = -8.1 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = -7.7 DEGREES REMARK 500 DA A 5 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 DA A 6 C4 - C5 - C6 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 6 N9 - C4 - C5 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT A 7 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DT A 8 OP1 - P - OP2 ANGL. DEV. = 14.1 DEGREES REMARK 500 DT A 9 N3 - C4 - O4 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG A 10 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A 10 N1 - C2 - N2 ANGL. DEV. = 6.4 DEGREES REMARK 500 DG A 10 N3 - C2 - N2 ANGL. DEV. = -6.6 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -8.3 DEGREES REMARK 500 DC A 11 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 DG A 12 P - O5' - C5' ANGL. DEV. = -9.7 DEGREES REMARK 500 DG A 12 O4' - C4' - C3' ANGL. DEV. = -6.0 DEGREES REMARK 500 DG A 12 C4' - C3' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 DG A 12 N1 - C2 - N3 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG A 12 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 DG A 12 N1 - C2 - N2 ANGL. DEV. = 6.4 DEGREES REMARK 500 DC B 13 O4' - C1' - N1 ANGL. DEV. = -5.3 DEGREES REMARK 500 DC B 13 C2 - N3 - C4 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC B 13 N3 - C4 - C5 ANGL. DEV. = -3.7 DEGREES REMARK 500 DC B 13 N1 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC B 15 N3 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC B 15 C5 - C4 - N4 ANGL. DEV. = 4.8 DEGREES REMARK 500 DA B 16 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA B 16 C6 - N1 - C2 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA B 16 C5 - N7 - C8 ANGL. DEV. = -4.0 DEGREES REMARK 500 DA B 16 N7 - C8 - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 DA B 16 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA B 17 OP1 - P - OP2 ANGL. DEV. = 12.5 DEGREES REMARK 500 DA B 17 O4' - C4' - C3' ANGL. DEV. = -3.7 DEGREES REMARK 500 DA B 17 C1' - O4' - C4' ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 69 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 A 2 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2001 DISTANCE = 6.28 ANGSTROMS 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 MG B2000 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2054 O REMARK 620 2 HOH A2055 O 89.3 REMARK 620 3 HOH B2014 O 95.4 91.7 REMARK 620 4 HOH B2047 O 84.8 85.7 177.4 REMARK 620 5 HOH B2048 O 88.2 177.2 89.8 92.8 REMARK 620 6 HOH B2049 O 172.2 92.1 92.3 87.6 90.2 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 D2A A 1013 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 2000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4AH0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DB 985-D(CGCAAATTTGCG)2 COMPLEX AT 1.20 A REMARK 900 RESOLUTION REMARK 900 RELATED ID: 4AGZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DB 985-D(CGCGAATTCGCG)2 COMPLEX AT 1.25 A REMARK 900 RESOLUTION. DBREF 4AH1 A 1 12 PDB 4AH1 4AH1 1 12 DBREF 4AH1 B 13 24 PDB 4AH1 4AH1 13 24 SEQRES 1 A 12 DC DG DC DA DA DA DT DT DT DG DC DG SEQRES 1 B 12 DC DG DC DA DA DA DT DT DT DG DC DG HET D2A A1013 27 HET MG B2000 1 HETNAM D2A 2-(4'-AMIDINOBIPHENYL-4-YL)-1H-BENZIMIDAZOLE-5-AMIDINE HETNAM MG MAGNESIUM ION HETSYN D2A DB921 FORMUL 3 D2A C21 H18 N6 FORMUL 4 MG MG 2+ FORMUL 5 HOH *109(H2 O) LINK O HOH A2054 MG MG B2000 1555 1555 2.08 LINK O HOH A2055 MG MG B2000 1555 1555 2.07 LINK MG MG B2000 O HOH B2014 1555 1555 2.00 LINK MG MG B2000 O HOH B2047 1555 1555 2.17 LINK MG MG B2000 O HOH B2048 1555 1555 2.12 LINK MG MG B2000 O HOH B2049 1555 1555 2.08 SITE 1 AC1 13 DA A 6 DT A 7 DT A 8 DT A 9 SITE 2 AC1 13 HOH A2035 HOH A2046 HOH A2062 HOH A2063 SITE 3 AC1 13 DA B 18 DT B 19 DT B 20 DT B 21 SITE 4 AC1 13 DG B 22 SITE 1 AC2 6 HOH A2054 HOH A2055 HOH B2014 HOH B2047 SITE 2 AC2 6 HOH B2048 HOH B2049 CRYST1 23.622 38.881 62.660 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 0.042333 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025720 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015959 0.00000