HEADER RNA 07-AUG-02 1MDG TITLE AN ALTERNATING ANTIPARALLEL OCTAPLEX IN AN RNA CRYSTAL STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*UP*(BGM)GP*AP*GP*GP*U)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS TETRAPLEX, BASE TETRADS, BASE OCTADS, RNA EXPDTA X-RAY DIFFRACTION AUTHOR B.C.PAN,Y.XIONG,K.SHI,M.SUNDARALINGAM REVDAT 4 14-FEB-24 1MDG 1 REMARK LINK REVDAT 3 28-SEP-11 1MDG 1 HETATM REVDAT 2 24-FEB-09 1MDG 1 VERSN REVDAT 1 12-AUG-03 1MDG 0 JRNL AUTH B.C.PAN,Y.XIONG,K.SHI,M.SUNDARALINGAM JRNL TITL AN EIGHT-STRANDED HELICAL FRAGMENT IN RNA CRYSTAL STRUCTURE: JRNL TITL 2 IMPLICATIONS FOR TETRAPLEX INTERACTION JRNL REF STRUCTURE V. 11 825 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 12842045 JRNL DOI 10.1016/S0969-2126(03)00108-4 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 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) (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 3763 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 381 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 : 128 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 16 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 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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: NULL REMARK 4 REMARK 4 1MDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016835. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-01 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9195, 0.9192, 0.800 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3800 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 41.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30900 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 20.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, MGCL2, COBALT(III)HEXAMMINE, REMARK 280 ETHIDINE BROMIDE, SODIUM CACODYLATE, PH 6.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 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 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 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 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 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 17.97800 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 17.97800 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 19.02250 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 17.97800 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 17.97800 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 19.02250 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 17.97800 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 17.97800 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 19.02250 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 17.97800 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 17.97800 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 19.02250 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 17.97800 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 17.97800 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 19.02250 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 17.97800 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 17.97800 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 19.02250 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 17.97800 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 17.97800 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 19.02250 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 17.97800 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 17.97800 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 19.02250 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 300 REMARK: THE THREE STRANDS OF THE TETRAPLEX IS GENERATED BY THE FOUR REMARK 300 FOLD AXIS 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 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 NA NA A 101 LIES ON A SPECIAL POSITION. REMARK 375 NA NA A 102 LIES ON A SPECIAL POSITION. REMARK 375 NA NA A 103 LIES ON A SPECIAL POSITION. REMARK 375 NA NA A 104 LIES ON A SPECIAL POSITION. REMARK 375 NA NA A 105 LIES ON A SPECIAL POSITION. REMARK 375 CO NCO A 201 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 305 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 315 LIES ON A SPECIAL POSITION. 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 U A 6 C2' - C3' - O3' ANGL. DEV. = 29.1 DEGREES REMARK 500 U A 6 O4' - C1' - C2' ANGL. DEV. = -10.4 DEGREES REMARK 500 U A 6 N1 - C1' - C2' ANGL. DEV. = -31.9 DEGREES REMARK 500 U A 6 C1' - C2' - O2' ANGL. DEV. = 22.7 DEGREES REMARK 500 U A 6 C3' - C2' - O2' ANGL. DEV. = -30.9 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 G A 4 0.06 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 NA A 104 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 4 O6 REMARK 620 2 G A 5 O6 71.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 105 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 5 O6 REMARK 620 2 U A 6 O4 69.7 REMARK 620 N 1 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 201 DBREF 1MDG A 1 6 PDB 1MDG 1MDG 1 6 SEQRES 1 A 6 U BGM A G G U MODRES 1MDG BGM A 2 DG HET BGM A 2 23 HET NA A 101 1 HET NA A 102 1 HET NA A 103 1 HET NA A 104 1 HET NA A 105 1 HET NCO A 201 7 HETNAM BGM 8-BROMO-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE HETNAM NA SODIUM ION HETNAM NCO COBALT HEXAMMINE(III) FORMUL 1 BGM C10 H13 BR N5 O7 P FORMUL 2 NA 5(NA 1+) FORMUL 7 NCO CO H18 N6 3+ FORMUL 8 HOH *16(H2 O) LINK O3' U A 1 P BGM A 2 1555 1555 1.59 LINK O3' BGM A 2 P A A 3 1555 1555 1.63 LINK O6 BGM A 2 NA NA A 101 1555 1555 2.87 LINK O6 BGM A 2 NA NA A 102 1555 1555 2.82 LINK O6 G A 4 NA NA A 103 1555 1555 3.00 LINK O6 G A 4 NA NA A 104 1555 1555 2.75 LINK O6 G A 5 NA NA A 104 1555 1555 2.75 LINK O6 G A 5 NA NA A 105 1555 1555 2.83 LINK O4 U A 6 NA NA A 105 1555 1555 2.70 SITE 1 AC1 2 BGM A 2 NA A 102 SITE 1 AC2 4 BGM A 2 A A 3 NA A 101 NA A 103 SITE 1 AC3 4 A A 3 G A 4 NA A 102 NA A 104 SITE 1 AC4 4 G A 4 G A 5 NA A 103 NA A 105 SITE 1 AC5 3 G A 5 U A 6 NA A 104 SITE 1 AC6 6 BGM A 2 A A 3 G A 5 U A 6 SITE 2 AC6 6 HOH A 308 HOH A 314 CRYST1 35.956 35.956 38.045 90.00 90.00 90.00 I 4 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 0.027812 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027812 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026285 0.00000 ATOM 1 O5' U A 1 -13.803 2.639 24.658 1.00 27.14 O ATOM 2 C5' U A 1 -13.007 3.811 24.477 1.00 23.39 C ATOM 3 C4' U A 1 -11.860 3.465 23.558 1.00 19.89 C ATOM 4 O4' U A 1 -11.136 2.347 24.049 1.00 18.63 O ATOM 5 C3' U A 1 -12.222 3.170 22.103 1.00 19.80 C ATOM 6 O3' U A 1 -11.455 4.177 21.446 1.00 18.56 O ATOM 7 C2' U A 1 -11.564 1.819 21.792 1.00 20.15 C ATOM 8 O2' U A 1 -10.924 1.647 20.547 1.00 23.56 O ATOM 9 C1' U A 1 -10.597 1.641 22.964 1.00 19.03 C ATOM 10 N1 U A 1 -10.339 0.271 23.391 1.00 16.96 N ATOM 11 C2 U A 1 -9.007 -0.143 23.445 1.00 15.52 C ATOM 12 O2 U A 1 -8.065 0.602 23.187 1.00 13.87 O ATOM 13 N3 U A 1 -8.826 -1.446 23.820 1.00 13.87 N ATOM 14 C4 U A 1 -9.809 -2.357 24.169 1.00 14.59 C ATOM 15 O4 U A 1 -9.484 -3.465 24.564 1.00 14.68 O ATOM 16 C5 U A 1 -11.146 -1.857 24.091 1.00 16.18 C ATOM 17 C6 U A 1 -11.361 -0.587 23.734 1.00 16.65 C HETATM 18 P BGM A 2 -11.990 4.917 20.142 1.00 16.06 P HETATM 19 OP1 BGM A 2 -12.839 6.056 20.601 1.00 19.02 O HETATM 20 OP2 BGM A 2 -12.531 3.927 19.182 1.00 19.84 O HETATM 21 O5' BGM A 2 -10.662 5.571 19.596 1.00 13.78 O HETATM 22 C5' BGM A 2 -9.590 4.725 19.191 1.00 12.14 C HETATM 23 C4' BGM A 2 -8.471 5.567 18.629 1.00 10.79 C HETATM 24 O4' BGM A 2 -7.252 4.823 18.694 1.00 12.76 O HETATM 25 C1' BGM A 2 -6.544 4.883 17.479 1.00 10.90 C HETATM 26 N9 BGM A 2 -5.706 3.690 17.391 1.00 9.93 N HETATM 27 C8 BGM A 2 -6.079 2.363 17.415 1.00 9.73 C HETATM 28 N7 BGM A 2 -5.063 1.548 17.368 1.00 10.90 N HETATM 29 C5 BGM A 2 -3.955 2.375 17.307 1.00 9.36 C HETATM 30 C4 BGM A 2 -4.325 3.698 17.318 1.00 8.77 C HETATM 31 N3 BGM A 2 -3.546 4.790 17.321 1.00 10.08 N HETATM 32 C2 BGM A 2 -2.272 4.495 17.294 1.00 9.28 C HETATM 33 N2 BGM A 2 -1.386 5.490 17.245 1.00 9.61 N HETATM 34 N1 BGM A 2 -1.781 3.212 17.286 1.00 9.79 N HETATM 35 C6 BGM A 2 -2.584 2.054 17.292 1.00 10.15 C HETATM 36 O6 BGM A 2 -2.079 0.942 17.286 1.00 10.04 O HETATM 37 C2' BGM A 2 -7.643 5.042 16.457 1.00 10.32 C HETATM 38 C3' BGM A 2 -8.590 5.997 17.168 1.00 9.64 C HETATM 39 O3' BGM A 2 -8.150 7.358 17.070 1.00 11.42 O HETATM 40 BR BGM A 2 -7.838 1.766 17.673 1.00 4.99 BR ATOM 41 P A A 3 -8.373 8.194 15.685 1.00 12.90 P ATOM 42 OP1 A A 3 -8.386 9.640 16.013 1.00 15.91 O ATOM 43 OP2 A A 3 -9.501 7.568 14.958 1.00 13.39 O ATOM 44 O5' A A 3 -7.035 7.914 14.848 1.00 13.04 O ATOM 45 C5' A A 3 -5.730 8.391 15.242 1.00 12.88 C ATOM 46 C4' A A 3 -4.710 7.770 14.307 1.00 12.95 C ATOM 47 O4' A A 3 -4.585 6.362 14.576 1.00 12.14 O ATOM 48 C3' A A 3 -5.188 7.901 12.853 1.00 11.96 C ATOM 49 O3' A A 3 -4.040 8.318 12.105 1.00 12.93 O ATOM 50 C2' A A 3 -5.592 6.492 12.457 1.00 10.33 C ATOM 51 O2' A A 3 -5.535 6.104 11.093 1.00 13.94 O ATOM 52 C1' A A 3 -4.661 5.672 13.339 1.00 11.59 C ATOM 53 N9 A A 3 -5.092 4.313 13.573 1.00 9.12 N ATOM 54 C8 A A 3 -6.341 3.792 13.648 1.00 9.33 C ATOM 55 N7 A A 3 -6.353 2.517 13.874 1.00 9.91 N ATOM 56 C5 A A 3 -5.015 2.171 13.917 1.00 9.78 C ATOM 57 C6 A A 3 -4.382 0.946 14.044 1.00 12.03 C ATOM 58 N6 A A 3 -5.049 -0.209 14.192 1.00 11.88 N ATOM 59 N1 A A 3 -3.031 0.935 14.023 1.00 10.48 N ATOM 60 C2 A A 3 -2.378 2.113 13.875 1.00 8.22 C ATOM 61 N3 A A 3 -2.879 3.320 13.753 1.00 11.14 N ATOM 62 C4 A A 3 -4.223 3.273 13.769 1.00 10.21 C ATOM 63 P G A 4 -4.199 9.169 10.755 1.00 14.09 P ATOM 64 OP1 G A 4 -4.870 10.471 11.057 1.00 15.20 O ATOM 65 OP2 G A 4 -4.790 8.276 9.721 1.00 14.17 O ATOM 66 O5' G A 4 -2.695 9.420 10.288 1.00 12.57 O ATOM 67 C5' G A 4 -1.901 10.461 10.848 1.00 12.73 C ATOM 68 C4' G A 4 -0.434 10.097 10.777 1.00 11.24 C ATOM 69 O4' G A 4 -0.142 8.974 11.652 1.00 13.50 O ATOM 70 C3' G A 4 0.028 9.616 9.418 1.00 12.41 C ATOM 71 O3' G A 4 0.229 10.730 8.577 1.00 12.76 O ATOM 72 C2' G A 4 1.296 8.854 9.777 1.00 10.27 C ATOM 73 O2' G A 4 2.388 9.710 10.102 1.00 12.31 O ATOM 74 C1' G A 4 0.835 8.132 11.053 1.00 9.93 C ATOM 75 N9 G A 4 0.227 6.825 10.840 1.00 9.26 N ATOM 76 C8 G A 4 -1.112 6.508 10.824 1.00 11.42 C ATOM 77 N7 G A 4 -1.327 5.225 10.726 1.00 10.86 N ATOM 78 C5 G A 4 -0.058 4.671 10.640 1.00 10.25 C ATOM 79 C6 G A 4 0.342 3.320 10.590 1.00 10.31 C ATOM 80 O6 G A 4 -0.379 2.315 10.605 1.00 9.85 O ATOM 81 N1 G A 4 1.729 3.194 10.531 1.00 11.27 N ATOM 82 C2 G A 4 2.618 4.257 10.505 1.00 8.01 C ATOM 83 N2 G A 4 3.928 3.912 10.401 1.00 10.53 N ATOM 84 N3 G A 4 2.252 5.520 10.568 1.00 11.05 N ATOM 85 C4 G A 4 0.907 5.652 10.662 1.00 8.38 C ATOM 86 P G A 5 -0.032 10.580 6.994 1.00 14.17 P ATOM 87 OP1 G A 5 0.110 11.998 6.602 1.00 16.98 O ATOM 88 OP2 G A 5 -1.274 9.842 6.735 1.00 16.51 O ATOM 89 O5' G A 5 1.180 9.730 6.491 1.00 12.32 O ATOM 90 C5' G A 5 2.458 10.327 6.408 1.00 14.68 C ATOM 91 C4' G A 5 3.479 9.289 6.067 1.00 13.26 C ATOM 92 O4' G A 5 3.531 8.310 7.145 1.00 12.54 O ATOM 93 C3' G A 5 3.174 8.416 4.859 1.00 15.65 C ATOM 94 O3' G A 5 3.481 9.131 3.691 1.00 15.73 O ATOM 95 C2' G A 5 4.105 7.239 5.104 1.00 12.32 C ATOM 96 O2' G A 5 5.467 7.565 4.830 1.00 12.92 O ATOM 97 C1' G A 5 3.908 7.045 6.613 1.00 11.63 C ATOM 98 N9 G A 5 2.836 6.081 6.892 1.00 11.06 N ATOM 99 C8 G A 5 1.479 6.321 7.007 1.00 10.71 C ATOM 100 N7 G A 5 0.777 5.222 7.180 1.00 9.09 N ATOM 101 C5 G A 5 1.731 4.212 7.197 1.00 9.83 C ATOM 102 C6 G A 5 1.597 2.804 7.363 1.00 10.18 C ATOM 103 O6 G A 5 0.570 2.130 7.527 1.00 10.81 O ATOM 104 N1 G A 5 2.838 2.164 7.331 1.00 10.61 N ATOM 105 C2 G A 5 4.038 2.795 7.162 1.00 10.96 C ATOM 106 N2 G A 5 5.121 2.023 7.145 1.00 13.01 N ATOM 107 N3 G A 5 4.182 4.097 7.011 1.00 10.81 N ATOM 108 C4 G A 5 3.005 4.738 7.033 1.00 9.37 C ATOM 109 P U A 6 2.766 8.721 2.312 1.00 18.59 P ATOM 110 OP1 U A 6 3.136 7.289 2.040 1.00 19.98 O ATOM 111 OP2 U A 6 3.164 9.813 1.347 1.00 20.74 O ATOM 112 O5' U A 6 1.219 8.711 2.681 1.00 19.22 O ATOM 113 C5' U A 6 0.233 9.483 2.037 1.00 19.32 C ATOM 114 C4' U A 6 -1.106 8.875 2.343 1.00 21.40 C ATOM 115 O4' U A 6 -1.029 7.479 1.935 1.00 20.02 O ATOM 116 C3' U A 6 -1.416 8.777 3.835 1.00 21.77 C ATOM 117 O3' U A 6 -2.073 9.954 4.321 1.00 25.29 O ATOM 118 C2' U A 6 -1.248 7.283 4.098 1.00 23.48 C ATOM 119 O2' U A 6 -1.826 7.630 5.352 1.00 28.13 O ATOM 120 C1' U A 6 -1.816 6.685 2.811 1.00 18.43 C ATOM 121 N1 U A 6 -1.026 5.537 3.298 1.00 16.07 N ATOM 122 C2 U A 6 -1.755 4.409 3.668 1.00 14.21 C ATOM 123 O2 U A 6 -2.962 4.382 3.653 1.00 14.60 O ATOM 124 N3 U A 6 -1.006 3.318 4.040 1.00 12.18 N ATOM 125 C4 U A 6 0.365 3.239 4.110 1.00 14.43 C ATOM 126 O4 U A 6 0.877 2.156 4.379 1.00 12.82 O ATOM 127 C5 U A 6 1.069 4.446 3.734 1.00 13.69 C ATOM 128 C6 U A 6 0.362 5.535 3.351 1.00 15.24 C TER 129 U A 6 HETATM 130 NA NA A 101 0.001 0.000 19.017 0.25 15.69 NA HETATM 131 NA NA A 102 -0.013 -0.001 15.610 0.25 17.84 NA HETATM 132 NA NA A 103 0.018 0.005 12.469 0.25 21.01 NA HETATM 133 NA NA A 104 0.004 -0.001 9.168 0.25 8.23 NA HETATM 134 NA NA A 105 -0.004 0.001 5.753 0.25 8.46 NA HETATM 135 CO NCO A 201 -10.723 10.726 19.019 0.25 20.28 CO HETATM 136 N1 NCO A 201 -10.311 11.179 21.083 0.50 18.90 N HETATM 137 N2 NCO A 201 -11.179 10.293 16.958 0.50 18.95 N HETATM 138 N3 NCO A 201 -10.661 12.810 18.528 0.50 21.20 N HETATM 139 N4 NCO A 201 -12.810 10.659 19.517 0.50 21.20 N HETATM 140 N5 NCO A 201 -10.420 8.590 19.177 0.50 20.87 N HETATM 141 N6 NCO A 201 -8.581 10.417 18.877 0.50 20.89 N HETATM 142 O HOH A 301 -7.645 4.226 10.213 1.00 20.11 O HETATM 143 O HOH A 302 -3.100 7.913 7.414 1.00 20.16 O HETATM 144 O HOH A 303 -8.954 6.023 12.727 1.00 25.80 O HETATM 145 O HOH A 304 -8.271 8.350 8.034 1.00 32.76 O HETATM 146 O HOH A 305 -5.207 12.773 9.515 0.25 29.23 O HETATM 147 O HOH A 306 -11.723 7.739 23.225 1.00 33.44 O HETATM 148 O HOH A 307 -13.454 9.372 24.035 1.00 25.12 O HETATM 149 O HOH A 308 -13.210 12.780 16.839 1.00 24.99 O HETATM 150 O HOH A 309 -10.810 1.127 17.967 1.00 27.12 O HETATM 151 O HOH A 310 -8.988 6.300 8.532 1.00 27.66 O HETATM 152 O HOH A 312 1.767 13.748 7.726 1.00 30.24 O HETATM 153 O HOH A 313 -5.502 6.618 5.790 1.00 38.69 O HETATM 154 O HOH A 314 5.983 10.149 2.526 1.00 42.83 O HETATM 155 O HOH A 315 1.493 16.489 9.503 0.25 41.84 O HETATM 156 O HOH A 316 -11.800 3.386 16.692 1.00 35.75 O HETATM 157 O HOH A 411 2.672 12.387 10.252 1.00 30.07 O CONECT 6 18 CONECT 18 6 19 20 21 CONECT 19 18 CONECT 20 18 CONECT 21 18 22 CONECT 22 21 23 CONECT 23 22 24 38 CONECT 24 23 25 CONECT 25 24 26 37 CONECT 26 25 27 30 CONECT 27 26 28 40 CONECT 28 27 29 CONECT 29 28 30 35 CONECT 30 26 29 31 CONECT 31 30 32 CONECT 32 31 33 34 CONECT 33 32 CONECT 34 32 35 CONECT 35 29 34 36 CONECT 36 35 130 131 CONECT 37 25 38 CONECT 38 23 37 39 CONECT 39 38 41 CONECT 40 27 CONECT 41 39 CONECT 80 132 133 CONECT 103 133 134 CONECT 126 134 CONECT 130 36 CONECT 131 36 CONECT 132 80 CONECT 133 80 103 CONECT 134 103 126 CONECT 135 136 137 138 139 CONECT 135 140 141 CONECT 136 135 CONECT 137 135 CONECT 138 135 CONECT 139 135 CONECT 140 135 CONECT 141 135 MASTER 365 0 7 0 0 0 7 6 156 1 41 1 END