HEADER RNA 12-MAY-20 6WY2 TITLE CRYSTAL STRUCTURE OF RNA-10MER: CCGG(N4-METHYL-C)GCCGG COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-10MER: CCGG(4-METHYL-C)GCCGG; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RNA DUPLEX, RNA EXPDTA X-RAY DIFFRACTION AUTHOR B.SEKULA,M.RUSZKOWSKI,S.MAO,P.HARUEHANROENGRA,J.SHENG REVDAT 3 18-OCT-23 6WY2 1 REMARK REVDAT 2 04-NOV-20 6WY2 1 JRNL REVDAT 1 02-SEP-20 6WY2 0 JRNL AUTH S.MAO,B.SEKULA,M.RUSZKOWSKI,S.V.RANGANATHAN, JRNL AUTH 2 P.HARUEHANROENGRA,Y.WU,F.SHEN,J.SHENG JRNL TITL BASE PAIRING, STRUCTURAL AND FUNCTIONAL INSIGHTS INTO JRNL TITL 2 N4-METHYLCYTIDINE (M4C) AND N4,N4-DIMETHYLCYTIDINE (M42C) JRNL TITL 3 MODIFIED RNA. JRNL REF NUCLEIC ACIDS RES. V. 48 10087 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32941619 JRNL DOI 10.1093/NAR/GKAA737 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.8 REMARK 3 NUMBER OF REFLECTIONS : 10370 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 504 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.0550 - 3.0599 0.93 2828 133 0.1477 0.1713 REMARK 3 2 3.0599 - 2.4292 0.95 2770 146 0.2288 0.2803 REMARK 3 3 2.4292 - 2.1223 0.91 2658 130 0.2606 0.2866 REMARK 3 4 2.1223 - 1.9283 0.56 1610 95 0.2672 0.2871 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 1185 REMARK 3 ANGLE : 0.844 1840 REMARK 3 CHIRALITY : 0.029 240 REMARK 3 PLANARITY : 0.005 50 REMARK 3 DIHEDRAL : 8.974 585 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.1533 15.1926 26.8359 REMARK 3 T TENSOR REMARK 3 T11: 0.2911 T22: 0.2271 REMARK 3 T33: 0.4568 T12: -0.0116 REMARK 3 T13: 0.0579 T23: 0.0236 REMARK 3 L TENSOR REMARK 3 L11: 4.5501 L22: 0.6738 REMARK 3 L33: 3.3326 L12: -1.1898 REMARK 3 L13: 3.5838 L23: -0.4016 REMARK 3 S TENSOR REMARK 3 S11: -0.2154 S12: 0.2293 S13: 0.8454 REMARK 3 S21: -0.0540 S22: 0.0202 S23: -0.1438 REMARK 3 S31: -0.2589 S32: 0.2827 S33: 0.1795 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9180 14.8633 19.1354 REMARK 3 T TENSOR REMARK 3 T11: 0.2701 T22: 0.3748 REMARK 3 T33: 0.2556 T12: -0.0451 REMARK 3 T13: 0.0357 T23: -0.0606 REMARK 3 L TENSOR REMARK 3 L11: 4.1272 L22: 7.2021 REMARK 3 L33: 2.6872 L12: 2.4847 REMARK 3 L13: 1.1362 L23: 0.3882 REMARK 3 S TENSOR REMARK 3 S11: -0.1541 S12: 0.2734 S13: 0.2177 REMARK 3 S21: -0.2546 S22: -0.1930 S23: 0.2086 REMARK 3 S31: -0.0626 S32: -0.2806 S33: 0.2852 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1546 15.1027 16.8932 REMARK 3 T TENSOR REMARK 3 T11: 0.2291 T22: 0.3648 REMARK 3 T33: 0.2863 T12: 0.0457 REMARK 3 T13: 0.0023 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 5.8242 L22: 9.0176 REMARK 3 L33: 2.6650 L12: 6.0688 REMARK 3 L13: 0.2223 L23: 0.2823 REMARK 3 S TENSOR REMARK 3 S11: -0.4011 S12: 0.6244 S13: 0.2119 REMARK 3 S21: -0.6897 S22: 0.2831 S23: 0.0587 REMARK 3 S31: -0.1611 S32: -0.1280 S33: 0.0834 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.5701 18.4939 5.0283 REMARK 3 T TENSOR REMARK 3 T11: 0.5182 T22: 0.6061 REMARK 3 T33: 0.4017 T12: 0.0116 REMARK 3 T13: 0.0791 T23: 0.0395 REMARK 3 L TENSOR REMARK 3 L11: 2.8384 L22: 3.3399 REMARK 3 L33: 7.5729 L12: 1.8813 REMARK 3 L13: -4.3125 L23: -1.0881 REMARK 3 S TENSOR REMARK 3 S11: -0.5558 S12: 0.5752 S13: -0.0501 REMARK 3 S21: -0.5416 S22: 0.2495 S23: 0.0322 REMARK 3 S31: 0.5157 S32: 0.2385 S33: 0.3726 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.5659 18.2241 7.2896 REMARK 3 T TENSOR REMARK 3 T11: 0.4998 T22: 0.5863 REMARK 3 T33: 0.4986 T12: 0.0143 REMARK 3 T13: 0.0533 T23: -0.0074 REMARK 3 L TENSOR REMARK 3 L11: 7.0823 L22: 7.5357 REMARK 3 L33: 7.4857 L12: 6.1984 REMARK 3 L13: -4.4295 L23: -5.6639 REMARK 3 S TENSOR REMARK 3 S11: -0.4930 S12: 1.1153 S13: 0.1720 REMARK 3 S21: -0.4928 S22: 0.7249 S23: 0.6586 REMARK 3 S31: 0.3169 S32: -0.7499 S33: -0.2494 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6WY2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000240690. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10372 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.928 REMARK 200 RESOLUTION RANGE LOW (A) : 28.052 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.74300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: 4MS9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V/V (+/-)-2-METHYL-2,4-PENTANEDIOL REMARK 280 (MPD), 0.040 M SODIUM CACODYLATE TRIHYDRATE PH 7.0, 0.012 M REMARK 280 SPERMINE TETRAHYDROCHLORIDE, 0.08 M POTASSIUM CHLORIDE, 0.02 M REMARK 280 MAGNESIUM CHLORIDE HEXAHYDRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 47.37000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.21250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.37000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.21250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: 1220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 -1.000000 0.000000 0.000000 -16.60823 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 56.10440 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 1300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 REMARK 350 BIOMOLECULE: 3 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: 1350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E 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 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 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 206 O REMARK 620 2 HOH A 207 O 86.9 REMARK 620 3 HOH A 220 O 90.4 93.9 REMARK 620 4 HOH A 232 O 96.5 170.5 95.0 REMARK 620 5 HOH A 234 O 177.7 93.0 91.9 83.4 REMARK 620 6 HOH A 237 O 90.4 89.1 176.9 81.9 87.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 231 O REMARK 620 2 HOH B 213 O 92.0 REMARK 620 3 HOH B 214 O 78.0 76.8 REMARK 620 4 HOH B 218 O 151.7 77.5 74.0 REMARK 620 5 HOH B 229 O 110.9 81.1 156.5 93.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 7 O2 REMARK 620 2 HOH B 220 O 91.4 REMARK 620 3 B8T C 5 O2 76.3 93.9 REMARK 620 4 HOH C 203 O 148.8 75.0 76.8 REMARK 620 5 HOH C 219 O 96.2 169.9 94.4 101.3 REMARK 620 6 G D 9 O3' 126.1 65.5 58.9 22.8 114.5 REMARK 620 7 G D 10 OP1 126.6 64.7 59.9 22.4 115.1 1.1 REMARK 620 N 1 2 3 4 5 6 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 B 205 O REMARK 620 2 HOH B 207 O 97.6 REMARK 620 3 HOH B 227 O 91.5 97.3 REMARK 620 4 HOH B 230 O 85.0 177.3 82.5 REMARK 620 5 HOH B 232 O 171.6 90.7 86.3 86.7 REMARK 620 6 HOH B 235 O 90.1 91.2 171.0 88.8 90.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 208 O REMARK 620 2 HOH C 210 O 90.2 REMARK 620 3 HOH C 217 O 93.8 92.2 REMARK 620 4 HOH C 225 O 90.0 177.6 90.1 REMARK 620 5 HOH C 226 O 176.1 88.2 82.8 91.8 REMARK 620 6 HOH C 228 O 84.2 88.1 177.9 89.6 99.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D 207 O REMARK 620 2 HOH D 210 O 91.2 REMARK 620 3 HOH D 211 O 87.6 77.5 REMARK 620 4 HOH D 216 O 95.6 166.6 91.2 REMARK 620 5 HOH D 218 O 162.2 79.9 75.5 90.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG E 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH E 204 O REMARK 620 2 HOH E 207 O 83.1 REMARK 620 3 HOH E 209 O 91.5 95.4 REMARK 620 4 HOH E 216 O 159.1 80.3 102.4 REMARK 620 5 HOH E 218 O 98.4 162.9 101.6 93.9 REMARK 620 6 HOH E 220 O 86.6 82.0 177.0 78.8 81.0 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 MG A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide G B 4 and B8T B 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide B8T B 5 and G B 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide G C 4 and B8T C 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide B8T C 5 and G C 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide G D 4 and B8T D 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide B8T D 5 and G D 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide G E 4 and B8T E 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide B8T E 5 and G E 6 DBREF 6WY2 A 1 10 PDB 6WY2 6WY2 1 10 DBREF 6WY2 B 1 10 PDB 6WY2 6WY2 1 10 DBREF 6WY2 C 1 10 PDB 6WY2 6WY2 1 10 DBREF 6WY2 D 1 10 PDB 6WY2 6WY2 1 10 DBREF 6WY2 E 1 10 PDB 6WY2 6WY2 1 10 SEQRES 1 A 10 C C G G B8T G C C G G SEQRES 1 B 10 C C G G B8T G C C G G SEQRES 1 C 10 C C G G B8T G C C G G SEQRES 1 D 10 C C G G B8T G C C G G SEQRES 1 E 10 C C G G B8T G C C G G HET B8T A 5 21 HET B8T B 5 21 HET B8T C 5 21 HET B8T D 5 21 HET B8T E 5 21 HET MG A 101 1 HET K B 101 1 HET MG B 102 1 HET MG B 103 1 HET MG C 101 1 HET MG D 101 1 HET MG E 101 1 HETNAM B8T 4-METHYL, CYTIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION FORMUL 1 B8T 5(C10 H16 N3 O8 P) FORMUL 6 MG 6(MG 2+) FORMUL 7 K K 1+ FORMUL 13 HOH *139(H2 O) LINK O3' G A 4 P B8T A 5 1555 1555 1.60 LINK O3' B8T A 5 P G A 6 1555 1555 1.60 LINK O3' G B 4 P B8T B 5 1555 1555 1.60 LINK O3' B8T B 5 P G B 6 1555 1555 1.61 LINK O3' G C 4 P B8T C 5 1555 1555 1.61 LINK O3' B8T C 5 P G C 6 1555 1555 1.61 LINK O3' G D 4 P B8T D 5 1555 1555 1.61 LINK O3' B8T D 5 P G D 6 1555 1555 1.61 LINK O3' G E 4 P B8T E 5 1555 1555 1.61 LINK O3' B8T E 5 P G E 6 1555 1555 1.61 LINK MG MG A 101 O HOH A 206 1555 1555 2.11 LINK MG MG A 101 O HOH A 207 1555 1555 2.04 LINK MG MG A 101 O HOH A 220 1555 1555 2.04 LINK MG MG A 101 O HOH A 232 1555 1555 2.08 LINK MG MG A 101 O HOH A 234 1555 1555 2.11 LINK MG MG A 101 O HOH A 237 1555 1555 2.06 LINK O HOH A 231 MG MG B 102 2556 1555 2.08 LINK O2 C B 7 K K B 101 1555 1555 2.82 LINK K K B 101 O HOH B 220 1555 1555 2.90 LINK K K B 101 O2 B8T C 5 1555 1555 2.84 LINK K K B 101 O HOH C 203 1555 1555 2.90 LINK K K B 101 O HOH C 219 1555 1555 2.86 LINK K K B 101 O3' G D 9 4555 1555 3.09 LINK K K B 101 OP1 G D 10 4555 1555 2.67 LINK MG MG B 102 O HOH B 213 1555 1555 2.10 LINK MG MG B 102 O HOH B 214 1555 1555 2.09 LINK MG MG B 102 O HOH B 218 1555 1555 2.12 LINK MG MG B 102 O HOH B 229 1555 1555 2.07 LINK MG MG B 103 O HOH B 205 1555 1555 2.03 LINK MG MG B 103 O HOH B 207 1555 1555 2.07 LINK MG MG B 103 O HOH B 227 1555 1555 2.06 LINK MG MG B 103 O HOH B 230 1555 1555 2.11 LINK MG MG B 103 O HOH B 232 1555 1555 2.06 LINK MG MG B 103 O HOH B 235 1555 1555 2.09 LINK MG MG C 101 O HOH C 208 1555 1555 2.05 LINK MG MG C 101 O HOH C 210 1555 1555 2.06 LINK MG MG C 101 O HOH C 217 1555 1555 2.12 LINK MG MG C 101 O HOH C 225 1555 1555 2.05 LINK MG MG C 101 O HOH C 226 1555 1555 2.08 LINK MG MG C 101 O HOH C 228 1555 1555 2.07 LINK MG MG D 101 O HOH D 207 1555 1555 2.10 LINK MG MG D 101 O HOH D 210 1555 1555 2.08 LINK MG MG D 101 O HOH D 211 1555 1555 2.10 LINK MG MG D 101 O HOH D 216 1555 1555 2.07 LINK MG MG D 101 O HOH D 218 1555 1555 2.10 LINK MG MG E 101 O HOH E 204 1555 1555 2.06 LINK MG MG E 101 O HOH E 207 1555 1555 2.11 LINK MG MG E 101 O HOH E 209 1555 1555 2.07 LINK MG MG E 101 O HOH E 216 1555 1555 2.07 LINK MG MG E 101 O HOH E 218 1555 1555 2.10 LINK MG MG E 101 O HOH E 220 1555 1555 2.08 SITE 1 AC1 6 HOH A 206 HOH A 207 HOH A 220 HOH A 232 SITE 2 AC1 6 HOH A 234 HOH A 237 SITE 1 AC2 9 G B 6 C B 7 HOH B 220 G C 4 SITE 2 AC2 9 B8T C 5 HOH C 203 HOH C 219 G D 9 SITE 3 AC2 9 G D 10 SITE 1 AC3 5 HOH A 231 HOH B 213 HOH B 214 HOH B 218 SITE 2 AC3 5 HOH B 229 SITE 1 AC4 6 HOH B 205 HOH B 207 HOH B 227 HOH B 230 SITE 2 AC4 6 HOH B 232 HOH B 235 SITE 1 AC5 6 HOH C 208 HOH C 210 HOH C 217 HOH C 225 SITE 2 AC5 6 HOH C 226 HOH C 228 SITE 1 AC6 5 HOH D 207 HOH D 210 HOH D 211 HOH D 216 SITE 2 AC6 5 HOH D 218 SITE 1 AC7 6 HOH E 204 HOH E 207 HOH E 209 HOH E 216 SITE 2 AC7 6 HOH E 218 HOH E 220 SITE 1 AC8 7 G B 3 G B 6 HOH B 201 HOH B 207 SITE 2 AC8 7 G C 6 C C 7 C C 8 SITE 1 AC9 11 G B 4 C B 7 K B 101 HOH B 201 SITE 2 AC9 11 HOH B 219 HOH B 220 HOH B 221 HOH B 224 SITE 3 AC9 11 G C 4 B8T C 5 G C 6 SITE 1 AD1 14 G B 6 C B 7 C B 8 K B 101 SITE 2 AD1 14 G C 3 G C 6 HOH C 201 HOH C 203 SITE 3 AD1 14 HOH C 204 HOH C 206 HOH C 208 HOH C 217 SITE 4 AD1 14 HOH C 218 HOH C 219 SITE 1 AD2 10 G B 4 B8T B 5 G B 6 C B 7 SITE 2 AD2 10 K B 101 G C 4 C C 7 HOH C 203 SITE 3 AD2 10 HOH C 209 HOH C 213 SITE 1 AD3 8 G D 3 G D 6 HOH D 205 HOH D 207 SITE 2 AD3 8 HOH D 211 G E 6 C E 7 C E 8 SITE 1 AD4 7 G D 4 C D 7 HOH D 209 G E 4 SITE 2 AD4 7 B8T E 5 G E 6 C E 7 SITE 1 AD5 8 G D 6 C D 7 C D 8 G E 3 SITE 2 AD5 8 G E 6 HOH E 206 HOH E 207 HOH E 209 SITE 1 AD6 8 G D 4 B8T D 5 G D 6 C D 7 SITE 2 AD6 8 G E 4 C E 7 HOH E 202 HOH E 213 CRYST1 94.740 30.425 58.511 90.00 106.49 90.00 C 1 2 1 20 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 0.010555 0.000000 0.003125 0.00000 SCALE2 0.000000 0.032868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017824 0.00000