HEADER DNA 03-JUL-15 5CDB TITLE STRUCTURE OF THE COMPLEX OF A BIMOLECULAR HUMAN TELOMERIC DNA WITH A TITLE 2 13-DIPHENYLALKYL BERBERINE DERIVATIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN TELOMERIC DNA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS DRUG-DNA COMPLEX, G-QUADRUPLEX, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.FERRARONI,C.BAZZICALUPI,P.GRATTERI,F.PAPI REVDAT 2 10-JAN-24 5CDB 1 LINK REVDAT 1 20-JUL-16 5CDB 0 JRNL AUTH M.FERRARONI,C.BAZZICALUPI,F.PAPI,G.FIORILLO, JRNL AUTH 2 L.M.GUAMAN-ORTIZ,A.NOCENTINI,A.I.SCOVASSI,P.LOMBARDI, JRNL AUTH 3 P.GRATTERI JRNL TITL SOLUTION AND SOLID-STATE ANALYSIS OF BINDING OF JRNL TITL 2 13-SUBSTITUTED BERBERINE ANALOGUES TO HUMAN TELOMERIC JRNL TITL 3 G-QUADRUPLEXES. JRNL REF CHEM ASIAN J V. 11 1107 2016 JRNL REFN ESSN 1861-471X JRNL PMID 26865223 JRNL DOI 10.1002/ASIA.201600116 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 7120 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) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 355 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 482 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 28 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.50000 REMARK 3 B22 (A**2) : 0.50000 REMARK 3 B33 (A**2) : -1.01000 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): 0.140 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.141 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.681 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 589 ; 0.006 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 905 ; 1.813 ; 1.679 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): 72 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 286 ; 0.009 ; 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 ; 3.291 ; 4.863 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: U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5CDB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-14 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 : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7183 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 35.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 25.50 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.8300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 11.90 REMARK 200 R MERGE FOR SHELL (I) : 2.01200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.840 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 4P1D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, LITHIUM SULPHATE, REMARK 280 SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 35.60200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.56600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.56600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.80100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.56600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.56600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.40300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.56600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.56600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.80100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.56600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.56600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.40300 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 35.60200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 DT A 1 O5' REMARK 470 DT B 13 O5' C5' REMARK 470 DT B 18 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT B 18 C7 C6 REMARK 470 DT B 24 C2 O2 N3 C4 O4 C5 C7 REMARK 470 DT B 24 C6 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 DT A 1 N3 DT A 1 C4 -0.048 REMARK 500 DT A 6 N1 DT A 6 C2 0.049 REMARK 500 DT A 6 C5 DT A 6 C6 0.050 REMARK 500 DT A 7 N1 DT A 7 C2 0.050 REMARK 500 DT A 7 C5 DT A 7 C6 0.046 REMARK 500 DT A 12 N1 DT A 12 C2 0.052 REMARK 500 DT A 12 C5 DT A 12 C6 0.043 REMARK 500 DT B 13 N3 DT B 13 C4 -0.050 REMARK 500 DT B 13 C5 DT B 13 C6 0.045 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 DT A 1 N1 - C2 - N3 ANGL. DEV. = 6.0 DEGREES REMARK 500 DT A 1 C2 - N3 - C4 ANGL. DEV. = -6.5 DEGREES REMARK 500 DT A 1 N3 - C4 - C5 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT A 1 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 DT A 1 C5 - C4 - O4 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT A 6 N1 - C2 - N3 ANGL. DEV. = 6.8 DEGREES REMARK 500 DT A 6 C2 - N3 - C4 ANGL. DEV. = -7.1 DEGREES REMARK 500 DT A 6 N3 - C4 - C5 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT A 6 C5 - C6 - N1 ANGL. DEV. = -4.1 DEGREES REMARK 500 DT A 6 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT A 6 C5 - C4 - O4 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT A 7 N1 - C2 - N3 ANGL. DEV. = 5.7 DEGREES REMARK 500 DT A 7 C2 - N3 - C4 ANGL. DEV. = -5.8 DEGREES REMARK 500 DT A 7 N3 - C4 - C5 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT A 7 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 DT A 12 O4' - C1' - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT A 12 N1 - C2 - N3 ANGL. DEV. = 6.0 DEGREES REMARK 500 DT A 12 C2 - N3 - C4 ANGL. DEV. = -6.3 DEGREES REMARK 500 DT A 12 N3 - C4 - C5 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT A 12 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT A 12 C5 - C4 - O4 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT B 13 N1 - C2 - N3 ANGL. DEV. = 5.5 DEGREES REMARK 500 DT B 13 C2 - N3 - C4 ANGL. DEV. = -5.4 DEGREES REMARK 500 DT B 13 N3 - C4 - C5 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT B 13 C5 - C6 - N1 ANGL. DEV. = -3.7 DEGREES REMARK 500 DT B 13 N3 - C2 - O2 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT B 19 N1 - C2 - N3 ANGL. DEV. = 6.2 DEGREES REMARK 500 DT B 19 C2 - N3 - C4 ANGL. DEV. = -6.1 DEGREES REMARK 500 DT B 19 N3 - C4 - C5 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT B 19 C4 - C5 - C7 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT B 24 O5' - C5' - C4' ANGL. DEV. = -5.9 DEGREES 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 K B 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 3 O6 REMARK 620 2 DG A 4 O6 74.1 REMARK 620 3 DG A 9 O6 72.9 89.2 REMARK 620 4 DG A 10 O6 131.4 66.9 78.6 REMARK 620 5 DG B 15 O6 120.9 152.1 75.0 87.3 REMARK 620 6 DG B 16 O6 151.8 104.2 135.1 68.5 73.8 REMARK 620 7 DG B 21 O6 74.8 133.7 113.1 153.8 74.2 88.3 REMARK 620 8 DG B 22 O6 87.5 68.6 153.9 103.4 130.8 66.5 76.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 4 O6 REMARK 620 2 DG A 5 O6 70.7 REMARK 620 3 DG A 10 O6 65.7 90.2 REMARK 620 4 DG A 11 O6 126.1 75.6 73.8 REMARK 620 5 DG B 16 O6 102.3 157.0 67.3 92.8 REMARK 620 6 DG B 17 O6 159.7 121.4 126.3 74.2 72.5 REMARK 620 7 DG B 22 O6 68.4 126.5 102.8 157.9 66.3 91.9 REMARK 620 8 DG B 23 O6 92.5 74.9 157.0 117.7 127.9 76.7 73.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 50B A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 101 DBREF 5CDB A 1 12 PDB 5CDB 5CDB 1 12 DBREF 5CDB B 13 24 PDB 5CDB 5CDB 13 24 SEQRES 1 A 12 DT DA DG DG DG DT DT DA DG DG DG DT SEQRES 1 B 12 DT DA DG DG DG DT DT DA DG DG DG DT HET K A 101 1 HET 50B A 102 41 HET K B 101 1 HETNAM K POTASSIUM ION HETNAM 50B 13-DIPHENYLALKYL BERBERINE FORMUL 3 K 2(K 1+) FORMUL 4 50B C36 H34 N O4 1+ FORMUL 6 HOH *28(H2 O) LINK O6 DG A 3 K K B 101 1555 1555 2.66 LINK O6 DG A 4 K K A 101 1555 1555 2.89 LINK O6 DG A 4 K K B 101 1555 1555 2.86 LINK O6 DG A 5 K K A 101 1555 1555 2.73 LINK O6 DG A 9 K K B 101 1555 1555 2.76 LINK O6 DG A 10 K K A 101 1555 1555 2.89 LINK O6 DG A 10 K K B 101 1555 1555 2.84 LINK O6 DG A 11 K K A 101 1555 1555 2.75 LINK K K A 101 O6 DG B 16 1555 1555 2.89 LINK K K A 101 O6 DG B 17 1555 1555 2.66 LINK K K A 101 O6 DG B 22 1555 1555 2.86 LINK K K A 101 O6 DG B 23 1555 1555 2.69 LINK O6 DG B 15 K K B 101 1555 1555 2.60 LINK O6 DG B 16 K K B 101 1555 1555 2.85 LINK O6 DG B 21 K K B 101 1555 1555 2.81 LINK O6 DG B 22 K K B 101 1555 1555 2.89 SITE 1 AC1 9 DG A 4 DG A 5 DG A 10 DG A 11 SITE 2 AC1 9 DG B 16 DG B 17 DG B 22 DG B 23 SITE 3 AC1 9 K B 101 SITE 1 AC2 8 DT A 1 DA A 2 DG A 5 DG A 11 SITE 2 AC2 8 DT B 13 DA B 14 DG B 17 DG B 23 SITE 1 AC3 9 DG A 3 DG A 4 DG A 9 DG A 10 SITE 2 AC3 9 K A 101 DG B 15 DG B 16 DG B 21 SITE 3 AC3 9 DG B 22 CRYST1 41.132 41.132 71.204 90.00 90.00 90.00 P 41 21 2 16 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 0.024312 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024312 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014044 0.00000