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