HEADER RNA 16-APR-10 2XC6 TITLE CRYSTAL STRUCTURE OF THE GNA 3'-CTC(BR)UAGAG-2' COMPND MOL_ID: 1; COMPND 2 MOLECULE: GNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: SYNTHETIC GLYCOL NUCLEIC ACID 3'-((ZCY)P(ZTH)P(ZCY) COMPND 6 P(ZBU)P(ZAD)P(ZGU)P(ZAD)P(ZGU))-2' SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_TAXID: 32630 KEYWDS RNA, WATSON-CRICK BASE PAIR, GLYCOL NUCLEIC ACID EXPDTA X-RAY DIFFRACTION AUTHOR M.K.SCHLEGEL,L.-O.ESSEN,E.MEGGERS REVDAT 4 19-JUN-24 2XC6 1 REMARK REVDAT 3 22-JUN-22 2XC6 1 REMARK SEQRES LINK REVDAT 2 12-OCT-11 2XC6 1 JRNL REVDAT 1 04-MAY-11 2XC6 0 JRNL AUTH A.T.JOHNSON,M.K.SCHLEGEL,E.MEGGERS,L.O.ESSEN,O.WIEST JRNL TITL ON THE STRUCTURE AND DYNAMICS OF DUPLEX GNA. JRNL REF J.ORG.CHEM. V. 76 7964 2011 JRNL REFN ISSN 0022-3263 JRNL PMID 21838272 JRNL DOI 10.1021/JO201469B REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.K.SCHLEGEL,L.-O.ESSEN,E.MEGGERS REMARK 1 TITL DUPLEX STRUCTURE OF A MINIMAL NUCLEIC ACID. REMARK 1 REF J.AM.CHEM.SOC. V. 130 8158 2008 REMARK 1 REFN ISSN 0002-7863 REMARK 1 PMID 18529005 REMARK 1 DOI 10.1021/JA802788G REMARK 1 REFERENCE 2 REMARK 1 AUTH M.K.SCHLEGEL,L.-O.ESSEN,E.MEGGERS REMARK 1 TITL ATOMIC RESOLUTION DUPLEX STRUCTURE OF THE SIMPLIFIED NUCLEIC REMARK 1 TITL 2 ACID GNA. REMARK 1 REF CHEM.COMMUN.(CAMB.) V. 46 1094 2010 REMARK 1 REFN ISSN 1359-7345 REMARK 1 PMID 20126724 REMARK 1 DOI 10.1039/B916851F REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 2068 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 155 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) : 1.83 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 138 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 11 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 137 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.03000 REMARK 3 B22 (A**2) : 1.03000 REMARK 3 B33 (A**2) : -2.05000 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): 0.147 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.141 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.066 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.649 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 169 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 68 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 213 ; 1.715 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 154 ; 0.631 ; 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): 8 ; 0.045 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 84 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 28 ; 0.000 ; 0.020 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): 148 ; 2.064 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 206 ; 2.951 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 8 REMARK 3 ORIGIN FOR THE GROUP (A): 5.0237 6.2082 -12.2048 REMARK 3 T TENSOR REMARK 3 T11: 0.0841 T22: 0.1045 REMARK 3 T33: 0.0904 T12: -0.0770 REMARK 3 T13: 0.0458 T23: -0.0241 REMARK 3 L TENSOR REMARK 3 L11: 2.0610 L22: 1.8936 REMARK 3 L33: 4.7135 L12: 0.4823 REMARK 3 L13: 2.3312 L23: -0.6942 REMARK 3 S TENSOR REMARK 3 S11: 0.0440 S12: -0.3067 S13: 0.0550 REMARK 3 S21: -0.1721 S22: 0.0186 S23: -0.0678 REMARK 3 S31: -0.7083 S32: 0.6294 S33: -0.0626 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 : 1.20 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. GNA DUPLEX OF TYPE N FORMED WITH SYMMETRY-EQUIVALENT REMARK 3 MOLECULE, 3'TERMINAL CYTOSINE NUCLEOTIDE AND 5-BROMO ATOM AT U4 REMARK 3 ONLY PARTIAL OCCUPANCY. REMARK 4 REMARK 4 2XC6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-10. REMARK 100 THE DEPOSITION ID IS D_1290043667. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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) : 0.91985 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2242 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 15.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 17.40 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 17.90 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXE REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 % MPD, 40 MM SODIUM CACODYLATE, PH REMARK 280 5.5, 20 MM COBALT HEXAMINE, 40 MM LICL, 20 MM MGCL2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-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 28.46500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 28.46500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.48500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.46500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 7.24250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.46500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.72750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.46500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.72750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.46500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 7.24250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 28.46500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 28.46500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 14.48500 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 28.46500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 28.46500 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 14.48500 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 28.46500 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 21.72750 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 28.46500 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 7.24250 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 28.46500 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 7.24250 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 28.46500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 21.72750 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 28.46500 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 28.46500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 14.48500 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 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 -28.97000 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 999 REMARK 999 SEQUENCE REMARK 999 URACIL U4 IS BROMINATED AT C5 FOR MAD ANALYSIS AT BROMINE REMARK 999 EDGE DBREF 2XC6 A 1 8 PDB 2XC6 2XC6 1 8 SEQRES 1 A 8 ZCY ZTH ZCY ZBU ZAD ZGU ZAD ZGU MODRES 2XC6 ZCY A 1 C (S)-1'-(2',3'-DIHYDROXYPROPYL)-CYTOSINE MODRES 2XC6 ZTH A 2 T (S)-1'-(2',3'-DIHYDROXYPROPYL)-THYMINE MODRES 2XC6 ZCY A 3 C (S)-1'-(2',3'-DIHYDROXYPROPYL)-CYTOSINE MODRES 2XC6 ZBU A 4 U MODRES 2XC6 ZAD A 5 A (S)-1'-(2',3'-DIHYDROXYPROPYL)-ADENINE MODRES 2XC6 ZGU A 6 G (S)-1'-(2',3'-DIHYDROXYPROPYL)-GUANINE MODRES 2XC6 ZAD A 7 A (S)-1'-(2',3'-DIHYDROXYPROPYL)-ADENINE MODRES 2XC6 ZGU A 8 G (S)-1'-(2',3'-DIHYDROXYPROPYL)-GUANINE HET ZCY A 1 13 HET ZTH A 2 17 HET ZCY A 3 16 HET ZBU A 4 17 HET ZAD A 5 18 HET ZGU A 6 19 HET ZAD A 7 18 HET ZGU A 8 19 HET NA A1001 1 HET NA A1002 1 HETNAM ZCY (S)-1'-(2',3'-DIHYDROXYPROPYL)-CYTOSINE HETNAM ZTH (S)-1'-(2',3'-DIHYDROXYPROPYL)-THYMINE HETNAM ZBU (S)-1'-(2',3'-DIHYDROXYPROPYL)-5-BROMO-URACIL HETNAM ZAD (S)-1'-(2',3'-DIHYDROXYPROPYL)-ADENINE HETNAM ZGU (S)-1'-(2',3'-DIHYDROXYPROPYL)-GUANINE HETNAM NA SODIUM ION FORMUL 1 ZCY 2(C7 H12 N3 O6 P) FORMUL 1 ZTH C8 H13 N2 O7 P FORMUL 1 ZBU C7 H10 BR N2 O7 P FORMUL 1 ZAD 2(C8 H12 N5 O5 P) FORMUL 1 ZGU 2(C8 H12 N5 O6 P) FORMUL 2 NA 2(NA 1+) FORMUL 4 HOH *21(H2 O) LINK O2G ZCY A 1 P ZTH A 2 1555 1555 1.60 LINK O2G ZTH A 2 P ZCY A 3 1555 1555 1.58 LINK O2G ZCY A 3 P ZBU A 4 1555 1555 1.59 LINK O2G ZBU A 4 P ZAD A 5 1555 1555 1.60 LINK O2G ZAD A 5 P ZGU A 6 1555 1555 1.60 LINK O2G ZGU A 6 P ZAD A 7 1555 1555 1.58 LINK O2G ZAD A 7 P ZGU A 8 1555 1555 1.60 SITE 1 AC1 1 ZBU A 4 CRYST1 56.930 56.930 28.970 90.00 90.00 90.00 I 41 2 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 0.017565 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017565 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034518 0.00000 HETATM 1 O2 ZCY A 1 7.581 11.893 -23.952 0.70 36.08 O HETATM 2 C2 ZCY A 1 7.970 13.075 -23.822 0.70 36.53 C HETATM 3 N3 ZCY A 1 7.084 14.094 -23.709 0.70 35.72 N HETATM 4 C4 ZCY A 1 7.475 15.357 -23.565 0.70 34.67 C HETATM 5 N4 ZCY A 1 6.520 16.287 -23.462 0.70 33.49 N HETATM 6 C5 ZCY A 1 8.862 15.706 -23.524 0.70 36.44 C HETATM 7 C6 ZCY A 1 9.745 14.702 -23.641 0.70 36.70 C HETATM 8 N1 ZCY A 1 9.332 13.398 -23.791 0.70 36.99 N HETATM 9 C1G ZCY A 1 10.364 12.338 -23.897 0.70 38.91 C HETATM 10 C2G ZCY A 1 10.757 11.867 -22.502 0.70 40.75 C HETATM 11 O2G ZCY A 1 11.447 12.941 -21.833 0.70 41.90 O HETATM 12 C3G ZCY A 1 11.621 10.606 -22.577 0.70 41.26 C HETATM 13 O3G ZCY A 1 12.789 10.845 -23.365 0.70 41.52 O HETATM 14 O4 ZTH A 2 1.443 14.835 -20.103 1.00 32.99 O HETATM 15 C4 ZTH A 2 2.673 14.853 -20.127 1.00 33.75 C HETATM 16 N3 ZTH A 2 3.417 13.713 -20.400 1.00 31.96 N HETATM 17 C2 ZTH A 2 4.780 13.595 -20.455 1.00 32.95 C HETATM 18 O2 ZTH A 2 5.327 12.536 -20.697 1.00 32.96 O HETATM 19 C5 ZTH A 2 3.453 16.036 -19.861 1.00 34.65 C HETATM 20 C5M ZTH A 2 2.788 17.347 -19.557 1.00 37.76 C HETATM 21 C6 ZTH A 2 4.792 15.942 -19.913 1.00 35.18 C HETATM 22 N1 ZTH A 2 5.468 14.766 -20.187 1.00 34.85 N HETATM 23 C1G ZTH A 2 6.957 14.771 -20.229 1.00 37.60 C HETATM 24 C2G ZTH A 2 7.643 14.274 -18.969 1.00 39.16 C HETATM 25 O2G ZTH A 2 7.214 15.100 -17.879 1.00 38.66 O HETATM 26 C3G ZTH A 2 9.160 14.381 -19.147 1.00 41.31 C HETATM 27 O3G ZTH A 2 9.642 13.435 -20.119 1.00 43.38 O HETATM 28 P ZTH A 2 11.227 13.236 -20.280 1.00 45.41 P HETATM 29 O1P ZTH A 2 11.956 14.305 -19.518 0.50 41.98 O HETATM 30 O2P ZTH A 2 10.963 11.941 -19.560 0.50 42.17 O HETATM 31 O2 ZCY A 3 2.905 9.435 -17.774 1.00 26.09 O HETATM 32 C2 ZCY A 3 1.887 10.125 -17.690 1.00 26.81 C HETATM 33 N3 ZCY A 3 0.635 9.615 -17.742 1.00 27.03 N HETATM 34 C4 ZCY A 3 -0.442 10.400 -17.624 1.00 29.21 C HETATM 35 N4 ZCY A 3 -1.660 9.843 -17.684 1.00 29.83 N HETATM 36 C5 ZCY A 3 -0.299 11.796 -17.447 1.00 29.41 C HETATM 37 C6 ZCY A 3 0.944 12.303 -17.392 1.00 28.43 C HETATM 38 N1 ZCY A 3 2.046 11.498 -17.509 1.00 26.74 N HETATM 39 C1G ZCY A 3 3.409 12.074 -17.457 1.00 27.57 C HETATM 40 C2G ZCY A 3 3.987 12.050 -16.056 1.00 30.02 C HETATM 41 O2G ZCY A 3 3.216 12.987 -15.304 1.00 29.37 O HETATM 42 C3G ZCY A 3 5.471 12.400 -16.081 1.00 34.51 C HETATM 43 O3G ZCY A 3 5.661 13.689 -16.649 1.00 34.99 O HETATM 44 P ZCY A 3 7.043 14.469 -16.441 1.00 38.28 P HETATM 45 O2P ZCY A 3 6.848 15.592 -15.466 1.00 40.66 O HETATM 46 O1P ZCY A 3 8.115 13.432 -16.225 1.00 39.70 O HETATM 47 O1P ZBU A 4 2.267 13.914 -13.020 1.00 37.66 O HETATM 48 P ZBU A 4 2.993 12.812 -13.745 1.00 37.23 P HETATM 49 O2P ZBU A 4 4.225 12.224 -13.113 1.00 38.02 O HETATM 50 O3G ZBU A 4 2.104 11.498 -13.762 1.00 32.88 O HETATM 51 C3G ZBU A 4 0.937 11.406 -12.976 1.00 32.67 C HETATM 52 C2G ZBU A 4 0.453 9.965 -13.040 1.00 30.32 C HETATM 53 O2G ZBU A 4 -0.660 9.815 -12.169 1.00 32.12 O HETATM 54 C1G ZBU A 4 0.040 9.654 -14.478 1.00 29.77 C HETATM 55 N1 ZBU A 4 -0.478 8.244 -14.685 1.00 29.17 N HETATM 56 C2 ZBU A 4 0.345 7.186 -14.969 1.00 28.21 C HETATM 57 O2 ZBU A 4 1.531 7.238 -15.018 1.00 26.22 O HETATM 58 N3 ZBU A 4 -0.289 5.968 -15.149 1.00 29.51 N HETATM 59 C6 ZBU A 4 -1.821 8.079 -14.653 1.00 32.68 C HETATM 60 C5 ZBU A 4 -2.404 6.904 -14.838 1.00 34.26 C HETATM 61 BR5 ZBU A 4 -4.253 6.823 -14.723 0.60 40.71 BR HETATM 62 C4 ZBU A 4 -1.628 5.734 -15.106 1.00 31.10 C HETATM 63 O4 ZBU A 4 -2.077 4.609 -15.297 1.00 33.19 O HETATM 64 O2P ZAD A 5 -1.723 9.693 -10.228 1.00 41.85 O HETATM 65 P ZAD A 5 -0.331 9.346 -10.673 1.00 37.53 P HETATM 66 O1P ZAD A 5 0.844 10.096 -10.107 1.00 35.50 O HETATM 67 O3G ZAD A 5 -0.122 7.805 -11.003 1.00 34.88 O HETATM 68 C3G ZAD A 5 1.047 7.179 -10.456 1.00 33.54 C HETATM 69 C2G ZAD A 5 0.936 5.669 -10.630 1.00 29.74 C HETATM 70 O2G ZAD A 5 -0.275 5.225 -9.999 1.00 28.86 O HETATM 71 C1G ZAD A 5 0.857 5.313 -12.106 1.00 28.49 C HETATM 72 N9 ZAD A 5 0.938 3.887 -12.307 1.00 26.60 N HETATM 73 C4 ZAD A 5 2.044 3.165 -12.603 1.00 25.62 C HETATM 74 N3 ZAD A 5 3.306 3.632 -12.742 1.00 24.79 N HETATM 75 C2 ZAD A 5 4.122 2.616 -13.031 1.00 23.38 C HETATM 76 N1 ZAD A 5 3.862 1.305 -13.158 1.00 25.17 N HETATM 77 C6 ZAD A 5 2.564 0.908 -12.981 1.00 25.13 C HETATM 78 N6 ZAD A 5 2.238 -0.364 -13.095 1.00 24.55 N HETATM 79 C5 ZAD A 5 1.601 1.883 -12.694 1.00 24.78 C HETATM 80 N7 ZAD A 5 0.224 1.785 -12.466 1.00 24.65 N HETATM 81 C8 ZAD A 5 -0.109 3.013 -12.262 1.00 26.53 C HETATM 82 P ZGU A 6 -0.288 4.607 -8.525 1.00 29.08 P HETATM 83 O1P ZGU A 6 -1.720 4.239 -8.280 1.00 28.50 O HETATM 84 O2P ZGU A 6 0.314 5.529 -7.525 1.00 28.19 O HETATM 85 O3G ZGU A 6 0.437 3.193 -8.732 1.00 24.67 O HETATM 86 C3G ZGU A 6 0.644 2.304 -7.650 1.00 21.46 C HETATM 87 C2G ZGU A 6 1.903 1.473 -7.924 1.00 22.46 C HETATM 88 O2G ZGU A 6 1.874 0.330 -7.095 1.00 22.54 O HETATM 89 C1G ZGU A 6 1.930 1.018 -9.379 1.00 24.47 C HETATM 90 N9 ZGU A 6 2.991 0.074 -9.671 1.00 25.79 N HETATM 91 C8 ZGU A 6 2.944 -1.299 -9.733 1.00 24.41 C HETATM 92 N7 ZGU A 6 4.087 -1.846 -10.025 1.00 25.59 N HETATM 93 C4 ZGU A 6 4.267 0.432 -9.982 1.00 23.20 C HETATM 94 C5 ZGU A 6 4.923 -0.754 -10.196 1.00 23.46 C HETATM 95 N3 ZGU A 6 4.738 1.691 -10.022 1.00 22.06 N HETATM 96 C2 ZGU A 6 6.004 1.737 -10.388 1.00 24.92 C HETATM 97 N2 ZGU A 6 6.651 2.925 -10.488 1.00 24.04 N HETATM 98 N1 ZGU A 6 6.748 0.599 -10.627 1.00 21.84 N HETATM 99 C6 ZGU A 6 6.275 -0.713 -10.558 1.00 24.73 C HETATM 100 O6 ZGU A 6 7.029 -1.669 -10.777 1.00 25.77 O HETATM 101 O2P ZAD A 7 2.362 -1.019 -5.125 1.00 24.44 O HETATM 102 P ZAD A 7 2.633 0.336 -5.705 1.00 22.85 P HETATM 103 O1P ZAD A 7 2.144 1.521 -4.903 1.00 23.28 O HETATM 104 O3G ZAD A 7 4.130 0.464 -6.232 1.00 23.19 O HETATM 105 C3G ZAD A 7 5.130 1.033 -5.382 1.00 25.38 C HETATM 106 C2G ZAD A 7 6.471 0.417 -5.738 1.00 22.89 C HETATM 107 O2G ZAD A 7 6.501 -0.900 -5.239 1.00 27.49 O HETATM 108 C1G ZAD A 7 6.624 0.325 -7.253 1.00 23.49 C HETATM 109 N9 ZAD A 7 7.987 -0.110 -7.512 1.00 25.41 N HETATM 110 C4 ZAD A 7 9.018 0.738 -7.691 1.00 24.17 C HETATM 111 N3 ZAD A 7 8.993 2.078 -7.695 1.00 24.27 N HETATM 112 C2 ZAD A 7 10.212 2.572 -7.904 1.00 28.14 C HETATM 113 N1 ZAD A 7 11.356 1.905 -8.102 1.00 27.93 N HETATM 114 C6 ZAD A 7 11.318 0.551 -8.104 1.00 27.18 C HETATM 115 N6 ZAD A 7 12.418 -0.170 -8.278 1.00 27.43 N HETATM 116 C5 ZAD A 7 10.106 -0.084 -7.883 1.00 26.88 C HETATM 117 N7 ZAD A 7 9.763 -1.419 -7.812 1.00 28.05 N HETATM 118 C8 ZAD A 7 8.465 -1.374 -7.596 1.00 27.15 C HETATM 119 P ZGU A 8 7.035 -1.246 -3.773 1.00 31.50 P HETATM 120 O1P ZGU A 8 6.961 -2.747 -3.826 1.00 34.39 O HETATM 121 O2P ZGU A 8 6.307 -0.537 -2.690 1.00 29.36 O HETATM 122 O3G ZGU A 8 8.557 -0.846 -3.991 1.00 34.31 O HETATM 123 C3G ZGU A 8 9.414 -1.026 -2.896 1.00 34.94 C HETATM 124 C2G ZGU A 8 10.729 -0.315 -3.177 1.00 33.59 C HETATM 125 O2G ZGU A 8 11.671 -0.916 -2.313 1.00 36.00 O HETATM 126 C1G ZGU A 8 11.154 -0.421 -4.646 1.00 32.49 C HETATM 127 N9 ZGU A 8 12.393 0.290 -4.951 1.00 31.34 N HETATM 128 C8 ZGU A 8 13.633 -0.217 -5.233 1.00 31.87 C HETATM 129 N7 ZGU A 8 14.549 0.701 -5.467 1.00 29.97 N HETATM 130 C4 ZGU A 8 12.549 1.647 -5.000 1.00 31.36 C HETATM 131 C5 ZGU A 8 13.865 1.900 -5.319 1.00 30.56 C HETATM 132 N3 ZGU A 8 11.549 2.508 -4.765 1.00 31.47 N HETATM 133 C2 ZGU A 8 11.942 3.760 -4.878 1.00 31.72 C HETATM 134 N2 ZGU A 8 11.006 4.700 -4.667 1.00 35.30 N HETATM 135 N1 ZGU A 8 13.229 4.146 -5.175 1.00 31.90 N HETATM 136 C6 ZGU A 8 14.291 3.261 -5.422 1.00 31.06 C HETATM 137 O6 ZGU A 8 15.415 3.705 -5.702 1.00 30.56 O TER 138 ZGU A 8 HETATM 139 NA NA A1001 -4.788 6.965 -9.098 1.00 53.04 NA HETATM 140 NA NA A1002 5.158 12.754 -9.857 0.50 58.19 NA HETATM 141 O HOH A2001 4.967 8.731 -9.292 1.00 71.01 O HETATM 142 O HOH A2002 16.082 12.600 -22.517 0.50 58.03 O HETATM 143 O HOH A2003 6.820 10.392 -20.198 1.00 39.64 O HETATM 144 O HOH A2004 0.724 4.095 -1.515 1.00 50.42 O HETATM 145 O HOH A2005 -5.122 10.024 -17.391 1.00 55.93 O HETATM 146 O HOH A2006 4.322 7.666 -14.838 1.00 48.45 O HETATM 147 O HOH A2007 -4.168 3.440 -16.855 1.00 36.87 O HETATM 148 O HOH A2008 -0.919 15.064 -11.368 0.50 35.59 O HETATM 149 O HOH A2009 -4.243 10.410 -13.680 1.00 64.77 O HETATM 150 O HOH A2010 4.598 6.005 -12.695 0.50 26.32 O HETATM 151 O HOH A2011 4.905 6.378 -10.931 0.50 37.51 O HETATM 152 O HOH A2012 6.931 -4.199 -10.204 1.00 46.04 O HETATM 153 O HOH A2013 -0.231 2.011 -3.769 1.00 32.21 O HETATM 154 O HOH A2014 7.156 3.839 -6.970 1.00 30.03 O HETATM 155 O HOH A2015 3.157 -3.253 -6.181 1.00 40.20 O HETATM 156 O HOH A2016 13.267 -3.233 -7.661 1.00 49.30 O HETATM 157 O HOH A2017 3.056 3.951 -4.227 1.00 41.82 O HETATM 158 O HOH A2018 8.054 3.847 -4.362 1.00 53.20 O HETATM 159 O HOH A2019 18.248 3.674 -5.876 1.00 37.57 O HETATM 160 O HOH A2020 13.646 -3.393 -3.219 0.50 38.50 O HETATM 161 O HOH A2021 5.506 -7.093 -3.369 1.00 66.33 O CONECT 1 2 CONECT 2 1 3 8 CONECT 3 2 4 CONECT 4 3 5 6 CONECT 5 4 CONECT 6 4 7 CONECT 7 6 8 CONECT 8 2 7 9 CONECT 9 8 10 CONECT 10 9 11 12 CONECT 11 10 28 CONECT 12 10 13 CONECT 13 12 CONECT 14 15 CONECT 15 14 16 19 CONECT 16 15 17 CONECT 17 16 18 22 CONECT 18 17 CONECT 19 15 20 21 CONECT 20 19 CONECT 21 19 22 CONECT 22 17 21 23 CONECT 23 22 24 CONECT 24 23 25 26 CONECT 25 24 44 CONECT 26 24 27 CONECT 27 26 28 CONECT 28 11 27 29 30 CONECT 29 28 CONECT 30 28 CONECT 31 32 CONECT 32 31 33 38 CONECT 33 32 34 CONECT 34 33 35 36 CONECT 35 34 CONECT 36 34 37 CONECT 37 36 38 CONECT 38 32 37 39 CONECT 39 38 40 CONECT 40 39 41 42 CONECT 41 40 48 CONECT 42 40 43 CONECT 43 42 44 CONECT 44 25 43 45 46 CONECT 45 44 CONECT 46 44 CONECT 47 48 CONECT 48 41 47 49 50 CONECT 49 48 CONECT 50 48 51 CONECT 51 50 52 CONECT 52 51 53 54 CONECT 53 52 65 CONECT 54 52 55 CONECT 55 54 56 59 CONECT 56 55 57 58 CONECT 57 56 CONECT 58 56 62 CONECT 59 55 60 CONECT 60 59 61 62 CONECT 61 60 CONECT 62 58 60 63 CONECT 63 62 CONECT 64 65 CONECT 65 53 64 66 67 CONECT 66 65 CONECT 67 65 68 CONECT 68 67 69 CONECT 69 68 70 71 CONECT 70 69 82 CONECT 71 69 72 CONECT 72 71 73 81 CONECT 73 72 74 79 CONECT 74 73 75 CONECT 75 74 76 CONECT 76 75 77 CONECT 77 76 78 79 CONECT 78 77 CONECT 79 73 77 80 CONECT 80 79 81 CONECT 81 72 80 CONECT 82 70 83 84 85 CONECT 83 82 CONECT 84 82 CONECT 85 82 86 CONECT 86 85 87 CONECT 87 86 88 89 CONECT 88 87 102 CONECT 89 87 90 CONECT 90 89 91 93 CONECT 91 90 92 CONECT 92 91 94 CONECT 93 90 94 95 CONECT 94 92 93 99 CONECT 95 93 96 CONECT 96 95 97 98 CONECT 97 96 CONECT 98 96 99 CONECT 99 94 98 100 CONECT 100 99 CONECT 101 102 CONECT 102 88 101 103 104 CONECT 103 102 CONECT 104 102 105 CONECT 105 104 106 CONECT 106 105 107 108 CONECT 107 106 119 CONECT 108 106 109 CONECT 109 108 110 118 CONECT 110 109 111 116 CONECT 111 110 112 CONECT 112 111 113 CONECT 113 112 114 CONECT 114 113 115 116 CONECT 115 114 CONECT 116 110 114 117 CONECT 117 116 118 CONECT 118 109 117 CONECT 119 107 120 121 122 CONECT 120 119 CONECT 121 119 CONECT 122 119 123 CONECT 123 122 124 CONECT 124 123 125 126 CONECT 125 124 CONECT 126 124 127 CONECT 127 126 128 130 CONECT 128 127 129 CONECT 129 128 131 CONECT 130 127 131 132 CONECT 131 129 130 136 CONECT 132 130 133 CONECT 133 132 134 135 CONECT 134 133 CONECT 135 133 136 CONECT 136 131 135 137 CONECT 137 136 MASTER 330 0 10 0 0 0 1 6 160 1 137 1 END