HEADER DNA-RNA HYBRID 15-FEB-00 1EGK TITLE CRYSTAL STRUCTURE OF A NUCLEIC ACID FOUR-WAY JUNCTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*AP*GP*GP*AP*GP*AP*GP*AP*GP*AP*UP*GP*GP*GP*UP*GP*CP*GP*AP*G)-3'); COMPND 4 CHAIN: A, C; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: RNA SUBSTRATE; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 10-23 DNA ENZYME; COMPND 9 CHAIN: B, D; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: 10-23 DNA ENZYME BOUND TO RNA SUBSTRATE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: DNA AND RNA WERE SYNTHESIZED ON SOLID SUPPORT USING SOURCE 4 PHOSPHORAMIDITE CHEMISTRY; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES KEYWDS FOUR-WAY JUNCTION, NUCLEIC ACID, RNA-DNA COMPLEX, 10-23 DNA ENZYME, KEYWDS 2 RIBOZYME, DNA-RNA COMPLEX, DNA-RNA HYBRID EXPDTA X-RAY DIFFRACTION AUTHOR J.NOWAKOWSKI,P.J.SHIM,C.D.STOUT,G.F.JOYCE REVDAT 4 07-FEB-24 1EGK 1 REMARK LINK REVDAT 3 31-JAN-18 1EGK 1 REMARK REVDAT 2 24-FEB-09 1EGK 1 VERSN REVDAT 1 26-JUN-00 1EGK 0 JRNL AUTH J.NOWAKOWSKI,P.J.SHIM,C.D.STOUT,G.F.JOYCE JRNL TITL ALTERNATIVE CONFORMATIONS OF A NUCLEIC ACID FOUR-WAY JRNL TITL 2 JUNCTION. JRNL REF J.MOL.BIOL. V. 300 93 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10864501 JRNL DOI 10.1006/JMBI.2000.3826 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 78.0 REMARK 3 NUMBER OF REFLECTIONS : 10948 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 SET) : 0.226 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1094 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 2240 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 80.00 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.272 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: GROUPED B REFINEMENT OF RIBOSE, BASE REMARK 3 AND PHOSPHATE GROUPS REMARK 4 REMARK 4 1EGK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1000010552. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 4 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10948 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM SODIUM CACODYLATE 6.0, 20MM REMARK 280 MAGNESIUM CHLORIDE, 1MM SPERMINE, 25% MPD, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 24.5K, PH 6.0, TEMPERATURE 297.5K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+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 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 31.40500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.13000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 85.72500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.40500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.13000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 85.72500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.40500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.13000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 85.72500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.40500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 57.13000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 85.72500 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 A A 10 O2' REMARK 470 A C 110 O2' REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OP1 G A 3 O HOH A 46 2.05 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 DG B 24 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DG B 36 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA B 41 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG B 36 0.06 SIDE CHAIN REMARK 500 DT B 51 0.09 SIDE CHAIN REMARK 500 A C 101 0.06 SIDE CHAIN REMARK 500 G C 113 0.06 SIDE CHAIN REMARK 500 G C 116 0.06 SIDE CHAIN REMARK 500 DT D 138 0.07 SIDE CHAIN 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 25 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 3 OP1 REMARK 620 2 HOH A 46 O 44.4 REMARK 620 3 HOH A 47 O 72.4 90.4 REMARK 620 4 HOH A 48 O 54.4 93.0 91.3 REMARK 620 5 HOH B 65 O 107.3 89.8 179.4 88.0 REMARK 620 6 HOH B 66 O 126.3 87.6 88.8 179.4 91.8 REMARK 620 7 HOH D 70 O 136.4 179.2 90.2 87.5 89.7 91.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 21 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 28 O REMARK 620 2 HOH A 29 O 179.2 REMARK 620 3 HOH A 30 O 89.7 89.9 REMARK 620 4 HOH A 31 O 90.7 89.7 179.5 REMARK 620 5 HOH A 32 O 90.5 88.9 90.1 90.3 REMARK 620 6 HOH A 33 O 89.4 91.2 90.1 89.5 179.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 22 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 55 O REMARK 620 2 HOH B 56 O 179.6 REMARK 620 3 HOH B 57 O 91.2 88.9 REMARK 620 4 HOH B 58 O 88.6 91.2 179.5 REMARK 620 5 HOH B 59 O 89.4 90.9 89.4 90.1 REMARK 620 6 HOH B 60 O 91.0 88.6 90.8 89.7 179.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 23 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 34 O REMARK 620 2 HOH A 35 O 179.8 REMARK 620 3 HOH A 36 O 90.8 89.3 REMARK 620 4 HOH A 37 O 89.7 90.2 179.3 REMARK 620 5 HOH A 38 O 90.5 89.6 90.0 89.5 REMARK 620 6 HOH A 39 O 89.2 90.7 89.2 91.3 179.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 24 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 40 O REMARK 620 2 HOH A 41 O 179.9 REMARK 620 3 HOH A 42 O 89.7 90.2 REMARK 620 4 HOH A 43 O 90.2 89.9 179.3 REMARK 620 5 HOH A 44 O 90.0 90.1 90.2 89.2 REMARK 620 6 HOH A 45 O 89.9 90.0 89.8 90.8 179.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 26 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 49 O REMARK 620 2 HOH A 50 O 177.7 REMARK 620 3 HOH A 51 O 88.2 89.7 REMARK 620 4 HOH A 52 O 91.4 90.7 179.3 REMARK 620 5 HOH A 53 O 89.6 91.3 90.3 89.1 REMARK 620 6 HOH A 54 O 91.2 87.9 90.9 89.7 178.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 27 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 55 O REMARK 620 2 HOH A 56 O 179.1 REMARK 620 3 HOH A 57 O 90.9 89.3 REMARK 620 4 HOH A 58 O 88.2 91.6 178.9 REMARK 620 5 HOH A 59 O 90.1 89.0 90.0 89.4 REMARK 620 6 HOH A 60 O 90.1 90.8 90.1 90.6 179.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 3 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 61 O REMARK 620 2 HOH C 28 O 179.1 REMARK 620 3 HOH C 29 O 89.4 90.1 REMARK 620 4 HOH C 30 O 90.3 90.2 179.3 REMARK 620 5 HOH C 31 O 91.1 88.2 91.4 89.3 REMARK 620 6 HOH C 32 O 89.9 90.8 88.3 91.0 178.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 4 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 62 O REMARK 620 2 HOH B 63 O 88.9 REMARK 620 3 HOH C 34 O 179.4 90.9 REMARK 620 4 HOH C 35 O 90.8 90.8 89.7 REMARK 620 5 HOH C 36 O 89.3 89.7 90.1 179.5 REMARK 620 6 HOH C 37 O 91.6 179.3 88.6 89.6 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 9 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 64 O REMARK 620 2 HOH C 64 O 90.3 REMARK 620 3 HOH C 65 O 179.2 90.1 REMARK 620 4 HOH C 67 O 89.0 90.1 91.7 REMARK 620 5 HOH C 68 O 90.8 90.0 88.5 179.8 REMARK 620 6 HOH D 63 O 90.0 179.1 89.6 89.1 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 6 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 45 O REMARK 620 2 HOH C 46 O 179.6 REMARK 620 3 HOH C 47 O 90.9 88.7 REMARK 620 4 HOH C 48 O 88.8 91.6 179.3 REMARK 620 5 HOH C 49 O 88.7 91.2 90.2 89.1 REMARK 620 6 HOH C 50 O 90.9 89.1 89.8 90.8 179.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 7 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 51 O REMARK 620 2 HOH C 53 O 88.5 REMARK 620 3 HOH C 56 O 89.8 89.8 REMARK 620 4 HOH D 52 O 179.2 90.8 90.5 REMARK 620 5 HOH D 54 O 91.6 179.6 89.9 89.1 REMARK 620 6 HOH D 55 O 90.7 90.2 179.5 89.0 90.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 13 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 87 O REMARK 620 2 HOH C 88 O 179.5 REMARK 620 3 HOH C 90 O 89.4 90.7 REMARK 620 4 HOH C 91 O 89.8 90.6 88.7 REMARK 620 5 HOH C 92 O 90.8 88.8 90.5 179.0 REMARK 620 6 HOH D 89 O 90.5 89.4 178.8 90.1 90.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 14 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 93 O REMARK 620 2 HOH C 94 O 178.9 REMARK 620 3 HOH C 95 O 88.3 91.4 REMARK 620 4 HOH C 96 O 90.6 89.7 178.7 REMARK 620 5 HOH C 97 O 89.3 89.7 91.7 89.0 REMARK 620 6 HOH C 98 O 91.5 89.5 88.0 91.3 179.2 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 21 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 22 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 23 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 24 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 25 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 26 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 27 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 14 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BR3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 10-23 RNA-DNA COMPLEX DBREF 1EGK A 1 20 PDB 1EGK 1EGK 1 20 DBREF 1EGK B 21 54 PDB 1EGK 1EGK 21 54 DBREF 1EGK C 101 120 PDB 1EGK 1EGK 101 120 DBREF 1EGK D 121 154 PDB 1EGK 1EGK 121 154 SEQRES 1 A 20 A G G A G A G A G A U G G SEQRES 2 A 20 G U G C G A G SEQRES 1 B 34 DC DT DC DG DC DA DC DC DC DA DG DG DC SEQRES 2 B 34 DT DA DG DC DT DA DC DA DA DC DG DA DC SEQRES 3 B 34 DT DC DT DC DT DC DC DT SEQRES 1 C 20 A G G A G A G A G A U G G SEQRES 2 C 20 G U G C G A G SEQRES 1 D 34 DC DT DC DG DC DA DC DC DC DA DG DG DC SEQRES 2 D 34 DT DA DG DC DT DA DC DA DA DC DG DA DC SEQRES 3 D 34 DT DC DT DC DT DC DC DT HET MG A 21 1 HET MG A 22 1 HET MG A 23 1 HET MG A 24 1 HET MG A 25 1 HET MG A 26 1 HET MG A 27 1 HET MG C 3 1 HET MG C 4 1 HET MG C 6 1 HET MG C 7 1 HET MG C 9 1 HET MG C 13 1 HET MG C 14 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG 14(MG 2+) FORMUL 19 HOH *84(H2 O) LINK OP1 G A 3 MG MG A 25 1555 1555 2.93 LINK MG MG A 21 O HOH A 28 1555 1555 2.04 LINK MG MG A 21 O HOH A 29 1555 1555 2.05 LINK MG MG A 21 O HOH A 30 1555 1555 2.05 LINK MG MG A 21 O HOH A 31 1555 1555 2.04 LINK MG MG A 21 O HOH A 32 1555 1555 2.04 LINK MG MG A 21 O HOH A 33 1555 1555 2.05 LINK MG MG A 22 O HOH B 55 1555 1555 2.05 LINK MG MG A 22 O HOH B 56 1555 1555 2.05 LINK MG MG A 22 O HOH B 57 1555 1555 2.06 LINK MG MG A 22 O HOH B 58 1555 1555 2.06 LINK MG MG A 22 O HOH B 59 1555 1555 2.06 LINK MG MG A 22 O HOH B 60 1555 1555 2.06 LINK MG MG A 23 O HOH A 34 1555 1555 2.04 LINK MG MG A 23 O HOH A 35 1555 1555 2.04 LINK MG MG A 23 O HOH A 36 1555 1555 2.04 LINK MG MG A 23 O HOH A 37 1555 1555 2.05 LINK MG MG A 23 O HOH A 38 1555 1555 2.06 LINK MG MG A 23 O HOH A 39 1555 1555 2.05 LINK MG MG A 24 O HOH A 40 1555 1555 2.06 LINK MG MG A 24 O HOH A 41 1555 1555 2.06 LINK MG MG A 24 O HOH A 42 1555 1555 2.05 LINK MG MG A 24 O HOH A 43 1555 1555 2.05 LINK MG MG A 24 O HOH A 44 1555 1555 2.05 LINK MG MG A 24 O HOH A 45 1555 1555 2.06 LINK MG MG A 25 O HOH A 46 1555 1555 2.07 LINK MG MG A 25 O HOH A 47 1555 1555 2.07 LINK MG MG A 25 O HOH A 48 1555 1555 2.06 LINK MG MG A 25 O HOH B 65 1555 1555 2.06 LINK MG MG A 25 O HOH B 66 1555 1555 2.07 LINK MG MG A 25 O HOH D 70 1555 1555 2.06 LINK MG MG A 26 O HOH A 49 1555 1555 2.05 LINK MG MG A 26 O HOH A 50 1555 1555 2.05 LINK MG MG A 26 O HOH A 51 1555 1555 2.05 LINK MG MG A 26 O HOH A 52 1555 1555 2.07 LINK MG MG A 26 O HOH A 53 1555 1555 2.07 LINK MG MG A 26 O HOH A 54 1555 1555 2.05 LINK MG MG A 27 O HOH A 55 1555 1555 2.05 LINK MG MG A 27 O HOH A 56 1555 1555 2.06 LINK MG MG A 27 O HOH A 57 1555 1555 2.07 LINK MG MG A 27 O HOH A 58 1555 1555 2.07 LINK MG MG A 27 O HOH A 59 1555 1555 2.04 LINK MG MG A 27 O HOH A 60 1555 1555 2.06 LINK O HOH B 61 MG MG C 3 1555 1555 2.06 LINK O HOH B 62 MG MG C 4 1555 1555 2.05 LINK O HOH B 63 MG MG C 4 1555 1555 2.05 LINK O HOH B 64 MG MG C 9 1555 1555 2.06 LINK MG MG C 3 O HOH C 28 1555 1555 2.05 LINK MG MG C 3 O HOH C 29 1555 1555 2.06 LINK MG MG C 3 O HOH C 30 1555 1555 2.07 LINK MG MG C 3 O HOH C 31 1555 1555 2.07 LINK MG MG C 3 O HOH C 32 1555 1555 2.06 LINK MG MG C 4 O HOH C 34 1555 1555 2.04 LINK MG MG C 4 O HOH C 35 1555 1555 2.06 LINK MG MG C 4 O HOH C 36 1555 1555 2.05 LINK MG MG C 4 O HOH C 37 1555 1555 2.04 LINK MG MG C 6 O HOH C 45 1555 1555 2.06 LINK MG MG C 6 O HOH C 46 1555 1555 2.06 LINK MG MG C 6 O HOH C 47 1555 1555 2.06 LINK MG MG C 6 O HOH C 48 1555 1555 2.06 LINK MG MG C 6 O HOH C 49 1555 1555 2.06 LINK MG MG C 6 O HOH C 50 1555 1555 2.05 LINK MG MG C 7 O HOH C 51 1555 1555 2.07 LINK MG MG C 7 O HOH C 53 1555 1555 2.05 LINK MG MG C 7 O HOH C 56 1555 1555 2.06 LINK MG MG C 7 O HOH D 52 1555 1555 2.06 LINK MG MG C 7 O HOH D 54 1555 1555 2.06 LINK MG MG C 7 O HOH D 55 1555 1555 2.06 LINK MG MG C 9 O HOH C 64 1555 1555 2.06 LINK MG MG C 9 O HOH C 65 1555 1555 2.05 LINK MG MG C 9 O HOH C 67 1555 1555 2.06 LINK MG MG C 9 O HOH C 68 1555 1555 2.06 LINK MG MG C 9 O HOH D 63 1555 1555 2.06 LINK MG MG C 13 O HOH C 87 1555 1555 2.07 LINK MG MG C 13 O HOH C 88 1555 1555 2.06 LINK MG MG C 13 O HOH C 90 1555 1555 2.05 LINK MG MG C 13 O HOH C 91 1555 1555 2.05 LINK MG MG C 13 O HOH C 92 1555 1555 2.07 LINK MG MG C 13 O HOH D 89 1555 1555 2.07 LINK MG MG C 14 O HOH C 93 1555 1555 2.07 LINK MG MG C 14 O HOH C 94 1555 1555 2.08 LINK MG MG C 14 O HOH C 95 1555 1555 2.06 LINK MG MG C 14 O HOH C 96 1555 1555 2.08 LINK MG MG C 14 O HOH C 97 1555 1555 2.06 LINK MG MG C 14 O HOH C 98 1555 1555 2.07 SITE 1 AC1 6 HOH A 28 HOH A 29 HOH A 30 HOH A 31 SITE 2 AC1 6 HOH A 32 HOH A 33 SITE 1 AC2 6 HOH B 55 HOH B 56 HOH B 57 HOH B 58 SITE 2 AC2 6 HOH B 59 HOH B 60 SITE 1 AC3 6 HOH B 61 HOH C 28 HOH C 29 HOH C 30 SITE 2 AC3 6 HOH C 31 HOH C 32 SITE 1 AC4 6 HOH B 62 HOH B 63 HOH C 34 HOH C 35 SITE 2 AC4 6 HOH C 36 HOH C 37 SITE 1 AC5 6 HOH A 34 HOH A 35 HOH A 36 HOH A 37 SITE 2 AC5 6 HOH A 38 HOH A 39 SITE 1 AC6 7 HOH C 45 HOH C 46 HOH C 47 HOH C 48 SITE 2 AC6 7 HOH C 49 HOH C 50 G C 113 SITE 1 AC7 6 HOH C 51 HOH C 53 HOH C 56 HOH D 52 SITE 2 AC7 6 HOH D 54 HOH D 55 SITE 1 AC8 6 HOH A 40 HOH A 41 HOH A 42 HOH A 43 SITE 2 AC8 6 HOH A 44 HOH A 45 SITE 1 AC9 7 HOH B 64 HOH C 64 HOH C 65 HOH C 67 SITE 2 AC9 7 HOH C 68 G C 103 HOH D 63 SITE 1 BC1 7 G A 3 HOH A 46 HOH A 47 HOH A 48 SITE 2 BC1 7 HOH B 65 HOH B 66 HOH D 70 SITE 1 BC2 7 G A 16 HOH A 49 HOH A 50 HOH A 51 SITE 2 BC2 7 HOH A 52 HOH A 53 HOH A 54 SITE 1 BC3 6 HOH A 55 HOH A 56 HOH A 57 HOH A 58 SITE 2 BC3 6 HOH A 59 HOH A 60 SITE 1 BC4 7 HOH C 87 HOH C 88 HOH C 90 HOH C 91 SITE 2 BC4 7 HOH C 92 U C 115 HOH D 89 SITE 1 BC5 6 HOH C 93 HOH C 94 HOH C 95 HOH C 96 SITE 2 BC5 6 HOH C 97 HOH C 98 CRYST1 62.810 114.260 171.450 90.00 90.00 90.00 I 2 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 0.015921 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008752 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005833 0.00000