HEADER RNA 24-JAN-18 6C8D TITLE RNA-DGMP COMPLEX WITH MG ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) COMPND 3 P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RNA, DEOXYGUANOSINE EXPDTA X-RAY DIFFRACTION AUTHOR W.ZHANG,J.W.SZOSTAK REVDAT 5 04-OCT-23 6C8D 1 LINK REVDAT 4 19-FEB-20 6C8D 1 REMARK HET SITE ATOM REVDAT 3 20-NOV-19 6C8D 1 REMARK REVDAT 2 31-OCT-18 6C8D 1 JRNL REVDAT 1 30-MAY-18 6C8D 0 JRNL AUTH W.ZHANG,T.WALTON,L.LI,J.W.SZOSTAK JRNL TITL CRYSTALLOGRAPHIC OBSERVATION OF NONENZYMATIC RNA PRIMER JRNL TITL 2 EXTENSION. JRNL REF ELIFE V. 7 2018 JRNL REFN ESSN 2050-084X JRNL PMID 29851379 JRNL DOI 10.7554/ELIFE.36422 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 8674 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) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 471 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) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 640 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.13 REMARK 3 BIN R VALUE (WORKING SET) : 0.3230 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.4530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 598 REMARK 3 HETEROGEN ATOMS : 101 REMARK 3 SOLVENT ATOMS : 70 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.09000 REMARK 3 B12 (A**2) : 0.01000 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): 0.160 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.165 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.119 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.361 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 764 ; 0.024 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 344 ; 0.064 ; 0.024 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1180 ; 2.987 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 828 ; 4.423 ; 3.261 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): 134 ; 0.161 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 388 ; 0.018 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 144 ; 0.002 ; 0.022 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): 762 ; 3.719 ; 3.574 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 758 ; 3.572 ; 3.551 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1175 ; 4.705 ; 5.309 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1210 ; 5.533 ;35.359 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1123 ; 5.478 ;35.140 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 : NULL 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 REMARK 4 REMARK 4 6C8D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000232276. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 99 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9264 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.72200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.640 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: 5DHC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V/V (+/-)-2-METHYL-2,4 REMARK 280 -PENTANEDIOL, 0.040 M SODIUM CACODYLATE TRIHYDRATE PH 7.0, 0.012 REMARK 280 M SPERMINE TETRAHYDROCHLORIDE, 0.080 M SODIUM CHLORIDE, 0.020 M REMARK 280 MAGNESIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 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 MG MG A 106 LIES ON A SPECIAL POSITION. REMARK 375 MG MG B 106 LIES ON A SPECIAL POSITION. 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 LCC A 1 O3' LCC A 2 P 0.096 REMARK 500 LCC A 2 O3' LCC A 3 P 0.078 REMARK 500 LCC B 1 O3' LCC B 2 P 0.094 REMARK 500 LCG B 4 O3' A B 5 P 0.075 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 LCC A 3 C3' - O3' - P ANGL. DEV. = 17.2 DEGREES REMARK 500 A A 5 O3' - P - OP2 ANGL. DEV. = 10.1 DEGREES REMARK 500 LCC B 3 C3' - O3' - P ANGL. DEV. = 25.3 DEGREES REMARK 500 LCG B 4 O3' - P - OP1 ANGL. DEV. = 12.4 DEGREES REMARK 500 A B 5 O3' - P - OP2 ANGL. DEV. = 9.7 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 MG A 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 201 O REMARK 620 2 HOH A 206 O 93.1 REMARK 620 3 HOH A 217 O 85.8 83.6 REMARK 620 4 HOH B 215 O 103.6 90.7 169.3 REMARK 620 5 HOH B 228 O 173.2 87.9 87.7 83.1 REMARK 620 6 HOH B 229 O 91.4 174.8 94.4 90.5 87.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 208 O REMARK 620 2 HOH A 221 O 92.8 REMARK 620 3 HOH A 232 O 92.0 91.9 REMARK 620 4 HOH B 208 O 177.6 88.2 85.8 REMARK 620 5 HOH B 214 O 89.8 89.1 177.9 92.4 REMARK 620 6 HOH B 232 O 88.1 177.0 85.2 90.8 93.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 203 O REMARK 620 2 HOH A 212 O 101.0 REMARK 620 3 HOH A 225 O 84.2 88.9 REMARK 620 4 HOH A 230 O 173.3 83.7 91.1 REMARK 620 5 HOH A 234 O 79.9 175.4 95.8 95.8 REMARK 620 6 HOH A 235 O 87.4 89.2 170.9 97.5 86.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 106 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 202 O REMARK 620 2 HOH B 202 O 88.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 107 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 209 O REMARK 620 2 HOH A 220 O 91.7 REMARK 620 3 HOH A 233 O 66.0 82.1 REMARK 620 4 HOH B 222 O 170.8 80.2 108.0 REMARK 620 5 HOH B 223 O 93.6 172.9 95.8 94.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 106 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 202 O REMARK 620 2 HOH A 202 O 71.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 211 O REMARK 620 2 HOH A 228 O 83.1 REMARK 620 3 HOH A 229 O 90.2 88.7 REMARK 620 4 HOH B 201 O 102.8 174.1 91.2 REMARK 620 5 HOH B 211 O 91.2 89.3 177.5 90.5 REMARK 620 6 HOH B 220 O 168.9 86.3 93.0 87.8 85.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 105 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 224 O REMARK 620 2 HOH A 226 O 88.2 REMARK 620 3 HOH B 205 O 162.4 107.5 REMARK 620 4 HOH B 217 O 84.0 172.0 80.5 REMARK 620 5 HOH B 233 O 116.9 100.4 68.8 81.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 203 O REMARK 620 2 HOH B 207 O 100.1 REMARK 620 3 HOH B 226 O 83.6 86.6 REMARK 620 4 HOH B 230 O 171.4 83.7 89.0 REMARK 620 5 HOH B 234 O 76.0 176.0 92.1 100.0 REMARK 620 6 HOH B 235 O 88.4 91.7 171.4 99.2 89.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DGP A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DGP A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DGP B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DGP B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 106 DBREF 6C8D A 1 14 PDB 6C8D 6C8D 1 14 DBREF 6C8D B 1 14 PDB 6C8D 6C8D 1 14 SEQRES 1 A 14 LCC LCC LCC LCG A C U U A A G U C SEQRES 2 A 14 G SEQRES 1 B 14 LCC LCC LCC LCG A C U U A A G U C SEQRES 2 B 14 G HET LCC A 1 19 HET LCC A 2 22 HET LCC A 3 22 HET LCG A 4 24 HET LCC B 1 19 HET LCC B 2 22 HET LCC B 3 22 HET LCG B 4 24 HET DGP A 101 23 HET DGP A 102 23 HET MG A 103 1 HET MG A 104 1 HET MG A 105 1 HET MG A 106 1 HET MG A 107 1 HET DGP B 101 23 HET DGP B 102 23 HET MG B 103 1 HET MG B 104 1 HET MG B 105 1 HET MG B 106 1 HETNAM LCC [(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5- HETNAM 2 LCC DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN HETNAM 3 LCC PHOSPHATE HETNAM LCG [(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5- HETNAM 2 LCG DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN HETNAM 3 LCG PHOSPHATE HETNAM DGP 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 1 LCC 6(C11 H16 N3 O8 P) FORMUL 1 LCG 2(C11 H14 N5 O8 P) FORMUL 3 DGP 4(C10 H14 N5 O7 P) FORMUL 5 MG 9(MG 2+) FORMUL 16 HOH *70(H2 O) LINK O3' LCC A 1 P LCC A 2 1555 1555 1.70 LINK O3' LCC A 2 P LCC A 3 1555 1555 1.69 LINK O3' LCC A 3 P LCG A 4 1555 1555 1.66 LINK O3' LCG A 4 P A A 5 1555 1555 1.66 LINK O3' LCC B 1 P LCC B 2 1555 1555 1.70 LINK O3' LCC B 2 P LCC B 3 1555 1555 1.66 LINK O3' LCC B 3 P LCG B 4 1555 1555 1.64 LINK O3' LCG B 4 P A B 5 1555 1555 1.68 LINK MG MG A 103 O HOH A 201 1555 1555 2.09 LINK MG MG A 103 O HOH A 206 1555 1555 2.06 LINK MG MG A 103 O HOH A 217 1555 2665 2.10 LINK MG MG A 103 O HOH B 215 1555 1555 2.11 LINK MG MG A 103 O HOH B 228 1555 1555 2.01 LINK MG MG A 103 O HOH B 229 1555 1555 2.09 LINK MG MG A 104 O HOH A 208 1555 1555 1.98 LINK MG MG A 104 O HOH A 221 1555 1555 2.00 LINK MG MG A 104 O HOH A 232 1555 1555 2.19 LINK MG MG A 104 O HOH B 208 1555 1555 2.04 LINK MG MG A 104 O HOH B 214 1555 1555 2.04 LINK MG MG A 104 O HOH B 232 1555 1555 2.13 LINK MG MG A 105 O HOH A 203 1555 1555 2.18 LINK MG MG A 105 O HOH A 212 1555 1555 2.20 LINK MG MG A 105 O HOH A 225 1555 1555 1.96 LINK MG MG A 105 O HOH A 230 1555 1555 2.00 LINK MG MG A 105 O HOH A 234 1555 1555 2.04 LINK MG MG A 105 O HOH A 235 1555 1555 2.12 LINK MG MG A 106 O HOH B 202 1555 1555 2.19 LINK MG MG A 106 O HOH B 202 1555 2665 2.16 LINK MG MG A 107 O HOH A 209 1555 1555 1.98 LINK MG MG A 107 O HOH A 220 1555 1555 2.09 LINK MG MG A 107 O HOH A 233 1555 1555 2.23 LINK MG MG A 107 O HOH B 222 1555 1555 1.95 LINK MG MG A 107 O HOH B 223 1555 1555 2.28 LINK O HOH A 202 MG MG B 106 1555 1555 2.38 LINK O HOH A 202 MG MG B 106 3565 1555 2.39 LINK O HOH A 211 MG MG B 103 1555 1555 2.10 LINK O HOH A 224 MG MG B 105 1555 1555 1.91 LINK O HOH A 226 MG MG B 105 1555 1555 2.08 LINK O HOH A 228 MG MG B 103 1555 1555 2.01 LINK O HOH A 229 MG MG B 103 1555 1555 2.11 LINK MG MG B 103 O HOH B 201 1555 1555 2.12 LINK MG MG B 103 O HOH B 211 1555 1555 2.08 LINK MG MG B 103 O HOH B 220 1555 1555 2.10 LINK MG MG B 104 O HOH B 203 1555 1555 2.26 LINK MG MG B 104 O HOH B 207 1555 1555 2.21 LINK MG MG B 104 O HOH B 226 1555 1555 1.99 LINK MG MG B 104 O HOH B 230 1555 1555 2.04 LINK MG MG B 104 O HOH B 234 1555 1555 1.94 LINK MG MG B 104 O HOH B 235 1555 1555 2.08 LINK MG MG B 105 O HOH B 205 1555 1555 2.12 LINK MG MG B 105 O HOH B 217 1555 1555 2.22 LINK MG MG B 105 O HOH B 233 1555 1555 2.27 SITE 1 AC1 8 LCC A 2 LCC A 3 DGP A 102 HOH A 202 SITE 2 AC1 8 HOH A 224 HOH A 226 G B 14 MG B 105 SITE 1 AC2 4 LCC A 1 LCC A 2 DGP A 101 HOH A 222 SITE 1 AC3 6 HOH A 201 HOH A 206 HOH A 217 HOH B 215 SITE 2 AC3 6 HOH B 228 HOH B 229 SITE 1 AC4 6 HOH A 208 HOH A 221 HOH A 232 HOH B 208 SITE 2 AC4 6 HOH B 214 HOH B 232 SITE 1 AC5 6 HOH A 203 HOH A 212 HOH A 225 HOH A 230 SITE 2 AC5 6 HOH A 234 HOH A 235 SITE 1 AC6 1 HOH B 202 SITE 1 AC7 6 HOH A 209 HOH A 220 HOH A 233 DGP B 101 SITE 2 AC7 6 HOH B 222 HOH B 223 SITE 1 AC8 9 G A 14 MG A 107 HOH A 209 LCC B 2 SITE 2 AC8 9 LCC B 3 DGP B 102 HOH B 202 HOH B 222 SITE 3 AC8 9 HOH B 223 SITE 1 AC9 4 LCC B 1 LCC B 2 DGP B 101 HOH B 225 SITE 1 AD1 6 HOH A 211 HOH A 228 HOH A 229 HOH B 201 SITE 2 AD1 6 HOH B 211 HOH B 220 SITE 1 AD2 6 HOH B 203 HOH B 207 HOH B 226 HOH B 230 SITE 2 AD2 6 HOH B 234 HOH B 235 SITE 1 AD3 6 DGP A 101 HOH A 224 HOH A 226 HOH B 205 SITE 2 AD3 6 HOH B 217 HOH B 233 SITE 1 AD4 1 HOH A 202 CRYST1 49.547 49.547 81.337 90.00 90.00 120.00 P 3 2 1 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 0.020183 0.011653 0.000000 0.00000 SCALE2 0.000000 0.023305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012295 0.00000 HETATM 1 O5' LCC A 1 6.889 48.125 3.573 1.00 46.85 O HETATM 2 C5' LCC A 1 5.474 48.434 3.408 1.00 40.04 C HETATM 3 C4' LCC A 1 4.915 47.026 3.076 1.00 39.60 C HETATM 4 O4' LCC A 1 5.504 46.292 1.980 1.00 34.98 O HETATM 5 C1' LCC A 1 5.008 44.966 2.041 1.00 36.14 C HETATM 6 N1 LCC A 1 6.129 44.068 1.921 1.00 34.04 N HETATM 7 C6 LCC A 1 7.449 44.454 2.042 1.00 32.08 C HETATM 8 C5 LCC A 1 8.433 43.494 1.840 1.00 39.21 C HETATM 9 C5M LCC A 1 9.823 43.804 1.998 1.00 40.34 C HETATM 10 C4 LCC A 1 7.985 42.188 1.539 1.00 35.46 C HETATM 11 N4 LCC A 1 8.877 41.222 1.391 1.00 35.67 N HETATM 12 N3 LCC A 1 6.685 41.865 1.442 1.00 30.46 N HETATM 13 C2 LCC A 1 5.784 42.810 1.652 1.00 34.81 C HETATM 14 O2 LCC A 1 4.594 42.511 1.535 1.00 32.69 O HETATM 15 C3' LCC A 1 5.158 45.974 4.090 1.00 39.25 C HETATM 16 C2' LCC A 1 4.280 44.958 3.360 1.00 39.07 C HETATM 17 O2' LCC A 1 2.999 45.728 3.225 1.00 39.30 O HETATM 18 O3' LCC A 1 4.506 46.370 5.295 1.00 37.39 O HETATM 19 C6' LCC A 1 3.393 47.121 2.945 1.00 39.41 C HETATM 20 O5' LCC A 2 3.626 44.047 6.348 1.00 34.65 O HETATM 21 C5' LCC A 2 2.230 44.183 6.316 1.00 37.14 C HETATM 22 C4' LCC A 2 1.836 42.771 5.848 1.00 33.00 C HETATM 23 O4' LCC A 2 2.416 42.301 4.630 1.00 30.71 O HETATM 24 C1' LCC A 2 2.398 40.847 4.718 1.00 31.15 C HETATM 25 N1 LCC A 2 3.792 40.330 4.594 1.00 28.41 N HETATM 26 C6 LCC A 2 4.920 41.150 4.707 1.00 30.33 C HETATM 27 C5 LCC A 2 6.153 40.570 4.539 1.00 31.20 C HETATM 28 C5M LCC A 2 7.320 41.318 4.693 1.00 36.09 C HETATM 29 C4 LCC A 2 6.196 39.211 4.281 1.00 36.06 C HETATM 30 N4 LCC A 2 7.374 38.698 4.090 1.00 32.84 N HETATM 31 N3 LCC A 2 5.115 38.433 4.180 1.00 32.10 N HETATM 32 C2 LCC A 2 3.895 39.012 4.332 1.00 32.18 C HETATM 33 O2 LCC A 2 2.852 38.312 4.261 1.00 31.27 O HETATM 34 C3' LCC A 2 2.340 41.711 6.736 1.00 34.64 C HETATM 35 C2' LCC A 2 1.723 40.592 6.046 1.00 30.73 C HETATM 36 O2' LCC A 2 0.369 40.996 5.919 1.00 34.00 O HETATM 37 O3' LCC A 2 1.801 41.876 7.978 1.00 38.72 O HETATM 38 C6' LCC A 2 0.296 42.570 5.825 1.00 34.79 C HETATM 39 P LCC A 2 4.598 45.380 6.678 1.00 35.31 P HETATM 40 O1P LCC A 2 3.796 46.141 7.732 1.00 37.21 O HETATM 41 O2P LCC A 2 5.969 44.708 6.933 1.00 32.05 O HETATM 42 O5' LCC A 3 1.841 39.430 9.206 1.00 31.50 O HETATM 43 C5' LCC A 3 0.400 39.104 9.056 1.00 25.87 C HETATM 44 C4' LCC A 3 0.372 37.596 8.673 1.00 26.89 C HETATM 45 O4' LCC A 3 1.087 37.254 7.455 1.00 31.23 O HETATM 46 C1' LCC A 3 1.446 35.850 7.543 1.00 29.25 C HETATM 47 N1 LCC A 3 2.922 35.795 7.407 1.00 26.62 N HETATM 48 C6 LCC A 3 3.752 36.928 7.542 1.00 26.06 C HETATM 49 C5 LCC A 3 5.125 36.769 7.391 1.00 25.90 C HETATM 50 C5M LCC A 3 5.937 37.845 7.565 1.00 29.67 C HETATM 51 C4 LCC A 3 5.669 35.515 7.040 1.00 27.68 C HETATM 52 N4 LCC A 3 6.992 35.428 6.887 1.00 30.63 N HETATM 53 N3 LCC A 3 4.845 34.436 6.869 1.00 30.97 N HETATM 54 C2 LCC A 3 3.490 34.612 7.091 1.00 27.27 C HETATM 55 O2 LCC A 3 2.733 33.673 7.033 1.00 29.68 O HETATM 56 C3' LCC A 3 1.149 36.716 9.565 1.00 27.90 C HETATM 57 C2' LCC A 3 0.829 35.476 8.887 1.00 28.30 C HETATM 58 O2' LCC A 3 -0.686 35.546 8.763 1.00 27.69 O HETATM 59 O3' LCC A 3 0.674 36.706 10.943 1.00 28.56 O HETATM 60 C6' LCC A 3 -1.025 37.020 8.580 1.00 26.89 C HETATM 61 P LCC A 3 2.263 41.002 9.342 1.00 35.76 P HETATM 62 O1P LCC A 3 1.408 41.602 10.521 1.00 32.82 O HETATM 63 O2P LCC A 3 3.898 40.925 9.446 1.00 34.45 O HETATM 64 P LCG A 4 1.303 36.354 12.441 1.00 30.04 P HETATM 65 OP1 LCG A 4 0.348 36.601 13.570 1.00 27.18 O HETATM 66 O5' LCG A 4 1.689 34.797 12.253 1.00 29.00 O HETATM 67 C5' LCG A 4 0.680 33.763 12.311 1.00 27.35 C HETATM 68 C3' LCG A 4 2.528 32.175 12.732 1.00 27.40 C HETATM 69 C6' LCG A 4 0.520 31.197 12.060 1.00 27.74 C HETATM 70 N9 LCG A 4 4.290 32.244 10.335 1.00 28.37 N HETATM 71 C8 LCG A 4 4.567 33.571 10.291 1.00 29.73 C HETATM 72 C4 LCG A 4 5.366 31.618 9.949 1.00 27.95 C HETATM 73 N7 LCG A 4 5.841 33.727 9.877 1.00 26.65 N HETATM 74 C5 LCG A 4 6.331 32.539 9.658 1.00 27.87 C HETATM 75 C6 LCG A 4 7.550 32.155 9.236 1.00 27.62 C HETATM 76 C2' LCG A 4 2.894 30.898 11.987 1.00 27.81 C HETATM 77 O6 LCG A 4 8.462 32.950 8.929 1.00 27.62 O HETATM 78 C4' LCG A 4 1.413 32.502 11.891 1.00 26.85 C HETATM 79 C1' LCG A 4 3.069 31.462 10.620 1.00 28.32 C HETATM 80 C2 LCG A 4 6.789 29.885 9.363 1.00 27.32 C HETATM 81 N1 LCG A 4 7.794 30.808 9.124 1.00 26.40 N HETATM 82 O4' LCG A 4 2.076 32.512 10.533 1.00 30.34 O HETATM 83 OP2 LCG A 4 2.556 37.097 12.377 1.00 27.77 O HETATM 84 N2 LCG A 4 7.105 28.597 9.226 1.00 28.53 N HETATM 85 N3 LCG A 4 5.576 30.286 9.820 1.00 25.96 N HETATM 86 O2' LCG A 4 1.700 30.164 12.090 1.00 28.85 O HETATM 87 O3' LCG A 4 1.978 31.939 14.134 1.00 29.97 O