3CCO - Header Asymmetric Unit

HEADER DNA 26-FEB-08 3CCO

TITLE STRUCTURAL ADAPTATION AND CONSERVATION IN QUADRUPLEX-DRUG TITLE 2 RECOGNITION

COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3'); COMPND 4 CHAIN: A; COMPND 5 SYNONYM: TELOMERE REPEAT SEQUENCE; COMPND 6 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS

KEYWDS QUADRUPLEX, DNA, PROPELLER, DIMERIC, HUMAN TELOMERE KEYWDS 2 PARALLEL STRANDED, LIGAND, COMPLEX, NAPHTHALENE DIIMIDINE

EXPDTA X-RAY DIFFRACTION

AUTHOR G.N.PARKINSON,S.NEIDLE

REVDAT 2 24-FEB-09 3CCO 1 VERSN REVDAT 1 23-SEP-08 3CCO 0

JRNL AUTH G.N.PARKINSON,F.CUENCA,S.NEIDLE JRNL TITL TOPOLOGY CONSERVATION AND LOOP FLEXIBILITY IN JRNL TITL 2 QUADRUPLEX-DRUG RECOGNITION: CRYSTAL STRUCTURES OF JRNL TITL 3 INTER- AND INTRAMOLECULAR TELOMERIC DNA JRNL TITL 4 QUADRUPLEX-DRUG COMPLEXES JRNL REF J.MOL.BIOL. V. 381 1145 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18619463 JRNL DOI 10.1016/J.JMB.2008.06.022

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 2520 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) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.254 REMARK 3 FREE R VALUE : 0.303 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 123 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 178 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.3240 REMARK 3 BIN FREE R VALUE SET COUNT : 5 REMARK 3 BIN FREE R VALUE : 0.5670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 219 REMARK 3 HETEROGEN ATOMS : 130 REMARK 3 SOLVENT ATOMS : 28 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.39000 REMARK 3 B22 (A**2) : 1.39000 REMARK 3 B33 (A**2) : -2.09000 REMARK 3 B12 (A**2) : 0.70000 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): 0.348 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.263 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.167 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.344 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.894 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 381 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 574 ; 3.306 ; 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): 47 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 190 ; 0.019 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 108 ; 0.394 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 228 ; 0.353 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 15 ; 0.318 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.232 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 66 ; 0.397 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.179 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 3 ; 0.101 ; 0.200 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): 689 ; 1.920 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 574 ; 3.389 ; 4.500 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: NULL

REMARK 4 REMARK 4 3CCO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-FEB-08. REMARK 100 THE RCSB ID CODE IS RCSB046616.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3697 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 22.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 10.000 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.80 REMARK 200 R MERGE FOR SHELL (I) : 0.13400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.800 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 1KF1 REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 300MM SODIUM CHLORIDE, 50MM SODIUM REMARK 280 CACODYLATE PH 6.5, 30% V/V MPD, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 283K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.54333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.08667 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 14.54333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 29.08667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 14.54333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 29.08667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 14.54333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 29.08667 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: 880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 0.500000 0.866025 0.000000 -30.67500 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 53.13066 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -14.54333

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 K K A 30 LIES ON A SPECIAL POSITION. REMARK 375 K K A 32 LIES ON A SPECIAL POSITION.

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 A1001 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DT A1001 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT A1001 C7 C6 REMARK 470 DT A1012 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DT A1012 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT A1012 C7 C6

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 1006 O HOH A 1026 1.99 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 A1003 C5 DG A1003 C6 -0.063 REMARK 500 DG A1004 P DG A1004 O5' -0.060 REMARK 500 DG A1004 C4 DG A1004 C5 -0.043 REMARK 500 DG A1005 C4 DG A1005 C5 -0.047 REMARK 500 DG A1005 C6 DG A1005 N1 -0.059 REMARK 500 DG A1009 C4 DG A1009 C5 -0.060 REMARK 500 DG A1009 N7 DG A1009 C8 -0.038 REMARK 500 DG A1011 O3' DG A1011 C3' -0.048 REMARK 500 DG A1011 C6 DG A1011 O6 0.057 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 DA A1002 O4' - C4' - C3' ANGL. DEV. = -3.6 DEGREES REMARK 500 DG A1003 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 DG A1003 O4' - C1' - N9 ANGL. DEV. = 8.3 DEGREES REMARK 500 DG A1003 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A1003 C4 - C5 - C6 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG A1003 C5 - C6 - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 DG A1003 C4 - C5 - N7 ANGL. DEV. = 3.5 DEGREES REMARK 500 DG A1003 C5 - N7 - C8 ANGL. DEV. = -3.0 DEGREES REMARK 500 DG A1003 N1 - C6 - O6 ANGL. DEV. = -6.8 DEGREES REMARK 500 DG A1004 N9 - C1' - C2' ANGL. DEV. = 13.3 DEGREES REMARK 500 DG A1004 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG A1004 C5 - C6 - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DG A1004 C4 - C5 - N7 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG A1004 C5 - N7 - C8 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG A1004 C5 - C6 - O6 ANGL. DEV. = -6.0 DEGREES REMARK 500 DG A1005 O4' - C1' - N9 ANGL. DEV. = 11.6 DEGREES REMARK 500 DG A1005 C6 - N1 - C2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DG A1005 N3 - C4 - C5 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG A1005 C5 - C6 - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A1005 N3 - C4 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG A1005 C5 - C6 - O6 ANGL. DEV. = -7.4 DEGREES REMARK 500 DT A1006 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 DT A1006 C4 - C5 - C7 ANGL. DEV. = 5.6 DEGREES REMARK 500 DT A1006 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT A1007 O5' - C5' - C4' ANGL. DEV. = -5.3 DEGREES REMARK 500 DT A1007 C3' - C2' - C1' ANGL. DEV. = -5.2 DEGREES REMARK 500 DT A1007 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT A1007 C2 - N3 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT A1007 O3' - P - OP1 ANGL. DEV. = 9.6 DEGREES REMARK 500 DG A1009 C2 - N3 - C4 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG A1009 C4 - C5 - C6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG A1009 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG A1009 N1 - C6 - O6 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG A1010 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DG A1010 O4' - C1' - N9 ANGL. DEV. = -6.5 DEGREES REMARK 500 DG A1010 N9 - C4 - C5 ANGL. DEV. = -2.8 DEGREES REMARK 500 DG A1010 N1 - C6 - O6 ANGL. DEV. = -5.1 DEGREES REMARK 500 DG A1010 C5 - C6 - O6 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG A1011 O5' - P - OP2 ANGL. DEV. = -6.0 DEGREES REMARK 500 DG A1011 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 DG A1011 C5 - C6 - N1 ANGL. DEV. = -3.4 DEGREES REMARK 500 DG A1011 C5 - C6 - O6 ANGL. DEV. = 4.9 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 A 31 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A1003 O6 REMARK 620 2 DG A1009 O6 66.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 32 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A1003 O6 REMARK 620 2 DG A1009 O6 67.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 30 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A1004 O6 REMARK 620 2 DG A1005 O6 66.1 REMARK 620 3 DG A1011 O6 118.6 75.0 REMARK 620 N 1 2

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 4 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 30 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 31 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 32 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NII A 1 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NII A 2 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NII A 3

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CDM RELATED DB: PDB REMARK 900 HUMAN TELOMERIC SEQUENCE BOUND TO SAME LIGAND

DBREF 3CCO A 1001 1012 PDB 3CCO 3CCO 1 12

SEQRES 1 A 12 DT DA DG DG DG DT DT DA DG DG DG DT

HET NA A 4 1 HET K A 30 1 HET K A 31 1 HET K A 32 1 HET NII A 1 42 HET NII A 2 42 HET NII A 3 42

HETNAM NA SODIUM ION HETNAM K POTASSIUM ION HETNAM NII 2,7-BIS[3-(DIMETHYLAMINO)PROPYL]-4,9-BIS[(3- HETNAM 2 NII HYDROXYPROPYL)AMINO]BENZO[LMN][3,8]PHENANTHROLINE-1,3, HETNAM 3 NII 6,8(2H,7H)-TETRONE

FORMUL 2 NA NA 1+ FORMUL 3 K 3(K 1+) FORMUL 6 NII 3(C30 H42 N6 O6) FORMUL 9 HOH *28(H2 O)

LINK O6 DG A1003 K K A 31 1555 1555 2.86 LINK O6 DG A1003 K K A 32 1555 1555 2.87 LINK O6 DG A1004 K K A 30 1555 1555 2.94 LINK O6 DG A1005 K K A 30 1555 1555 2.77 LINK O6 DG A1009 K K A 31 1555 1555 2.96 LINK O6 DG A1009 K K A 32 1555 1555 2.90 LINK O4' DG A1011 NA NA A 4 1555 1555 2.82 LINK O6 DG A1011 K K A 30 1555 1555 2.66

SITE 1 AC1 4 DG A1011 HOH A1013 HOH A1015 HOH A1020 SITE 1 AC2 5 K A 31 DG A1004 DG A1005 DG A1010 SITE 2 AC2 5 DG A1011 SITE 1 AC3 6 K A 30 K A 32 DG A1003 DG A1004 SITE 2 AC3 6 DG A1009 DG A1010 SITE 1 AC4 3 K A 31 DG A1003 DG A1009 SITE 1 AC5 3 DG A1005 DT A1006 DG A1011 SITE 1 AC6 4 NII A 3 DT A1007 DG A1009 HOH A1016 SITE 1 AC7 1 NII A 2

CRYST1 61.350 61.350 43.630 90.00 90.00 120.00 P 64 2 2 12

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 0.016300 0.009411 0.000000 0.00000

SCALE2 0.000000 0.018822 0.000000 0.00000

SCALE3 0.000000 0.000000 0.022920 0.00000