HEADER RNA 22-APR-21 7EOJ TITLE CRYSTAL STRUCTURE OF THE PEPPER APTAMER IN COMPLEX WITH HBC, CESIUM TITLE 2 SOAK COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPPER (49-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS FLUORESCENT RNA, APTAMER, HBC, RNA EXPDTA X-RAY DIFFRACTION AUTHOR K.Y.HUANG,A.M.REN REVDAT 3 29-NOV-23 7EOJ 1 REMARK REVDAT 2 16-FEB-22 7EOJ 1 JRNL REVDAT 1 24-NOV-21 7EOJ 0 JRNL AUTH K.HUANG,X.CHEN,C.LI,Q.SONG,H.LI,L.ZHU,Y.YANG,A.REN JRNL TITL STRUCTURE-BASED INVESTIGATION OF FLUOROGENIC PEPPER APTAMER. JRNL REF NAT.CHEM.BIOL. V. 17 1289 2021 JRNL REFN ESSN 1552-4469 JRNL PMID 34725509 JRNL DOI 10.1038/S41589-021-00884-6 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 26858 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.320 REMARK 3 FREE R VALUE TEST SET COUNT : 1430 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 45.8480 - 3.8120 0.98 2566 164 0.2105 0.1992 REMARK 3 2 3.8120 - 3.0259 0.99 2648 119 0.1955 0.2083 REMARK 3 3 3.0259 - 2.6434 0.98 2600 126 0.2159 0.2467 REMARK 3 4 2.6434 - 2.4018 0.99 2600 146 0.2028 0.1939 REMARK 3 5 2.4018 - 2.2296 0.98 2576 158 0.1903 0.2177 REMARK 3 6 2.2296 - 2.0982 0.99 2597 129 0.2047 0.2038 REMARK 3 7 2.0982 - 1.9931 0.98 2588 136 0.2234 0.2387 REMARK 3 8 1.9931 - 1.9063 0.96 2530 162 0.2231 0.2369 REMARK 3 9 1.9063 - 1.8329 0.94 2410 141 0.2113 0.2521 REMARK 3 10 1.8329 - 1.7700 0.87 2313 149 0.2306 0.2416 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.23 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7EOJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300021885. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.240 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26858 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 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 (%) : 97.1 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.28100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 7EOG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM CHLORIDE, 0.005 M REMARK 280 MAGNESIUM CHLORIDE, 0.025 M HEPES, PH 7.0, 1.25 M 1,6-HEXANEDIOL, REMARK 280 40% MPD, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 46.13850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.37450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.13850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.37450 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 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 HOH A 297 LIES ON A SPECIAL POSITION. 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 MG MG A 106 O HOH A 250 1.13 REMARK 500 O2' C A 49 O HOH A 201 1.99 REMARK 500 O HOH A 341 O HOH A 349 2.00 REMARK 500 O3' C A 49 O HOH A 201 2.12 REMARK 500 O HOH A 212 O HOH A 342 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 311 O HOH A 320 4555 2.10 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 GDP A 1 C3' - O3' - P ANGL. DEV. = 15.7 DEGREES REMARK 500 G A 2 O3' - P - O5' ANGL. DEV. = -15.3 DEGREES REMARK 500 G A 2 O3' - P - OP1 ANGL. DEV. = -55.7 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 CS A 112 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 3 O2 REMARK 620 2 C A 29 O3' 56.5 REMARK 620 3 A A 30 OP1 56.7 2.7 REMARK 620 4 C A 48 O2 71.7 110.1 108.1 REMARK 620 5 HOH A 260 O 147.6 92.5 92.8 134.7 REMARK 620 6 HOH A 286 O 74.4 25.2 27.3 135.3 73.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS A 111 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 5 OP2 REMARK 620 2 A A 6 N7 66.5 REMARK 620 3 G A 41 O6 128.3 68.4 REMARK 620 4 HOH A 225 O 149.2 89.8 49.8 REMARK 620 5 HOH A 268 O 69.7 130.6 160.8 119.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS A 113 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 5 O2 REMARK 620 2 C A 46 O2 74.8 REMARK 620 3 HOH A 207 O 144.5 76.3 REMARK 620 4 HOH A 331 O 84.4 107.5 124.2 REMARK 620 N 1 2 3 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 C A 7 OP2 REMARK 620 2 U A 8 OP2 93.5 REMARK 620 3 HOH A 256 O 177.9 88.4 REMARK 620 4 HOH A 267 O 88.7 174.5 89.3 REMARK 620 5 HOH A 285 O 92.8 88.1 86.4 86.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS A 114 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 8 OP1 REMARK 620 2 G A 9 OP2 78.9 REMARK 620 3 C A 33 OP1 31.7 77.1 REMARK 620 4 C A 33 O5' 35.2 72.0 6.0 REMARK 620 5 HOH A 243 O 89.4 158.7 83.6 88.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 109 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 12 OP1 REMARK 620 2 HOH A 327 O 88.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS A 115 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 13 O2 REMARK 620 2 C A 38 O2 69.0 REMARK 620 3 HOH A 235 O 140.0 73.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS A 116 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 16 O2 REMARK 620 2 C A 28 O2' 123.3 REMARK 620 3 C A 28 O2 64.1 69.3 REMARK 620 N 1 2 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 A A 30 OP2 REMARK 620 2 HOH A 211 O 103.4 REMARK 620 3 HOH A 228 O 166.2 90.3 REMARK 620 4 HOH A 280 O 85.6 170.7 80.7 REMARK 620 5 HOH A 303 O 92.3 89.8 88.3 87.5 REMARK 620 6 HOH A 309 O 94.4 93.8 83.9 87.7 171.5 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 U A 32 OP2 REMARK 620 2 HOH A 216 O 87.3 REMARK 620 3 HOH A 227 O 92.2 179.5 REMARK 620 4 HOH A 273 O 179.4 92.4 88.1 REMARK 620 5 HOH A 312 O 90.2 90.5 89.4 90.3 REMARK 620 6 HOH A 319 O 96.6 90.9 89.3 82.9 173.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS A 117 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 32 O2 REMARK 620 2 G A 34 O6 86.2 REMARK 620 3 U A 35 O4 66.2 63.5 REMARK 620 4 C A 38 OP1 156.4 111.6 107.0 REMARK 620 5 C A 38 OP2 135.3 69.0 69.5 47.7 REMARK 620 6 HOH A 233 O 49.4 51.0 83.2 154.3 120.0 REMARK 620 7 HOH A 259 O 115.5 60.8 123.9 87.4 84.8 67.7 REMARK 620 N 1 2 3 4 5 6 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 G A 37 O6 REMARK 620 2 HOH A 269 O 101.1 REMARK 620 3 HOH A 314 O 102.1 103.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 42 OP2 REMARK 620 2 HOH A 247 O 88.3 REMARK 620 3 HOH A 249 O 177.4 94.0 REMARK 620 4 HOH A 281 O 93.9 89.8 87.5 REMARK 620 5 HOH A 292 O 92.7 176.8 85.1 87.1 REMARK 620 6 HOH A 325 O 99.4 90.2 79.3 166.7 92.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CS A 118 CS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 49 O2' REMARK 620 2 C A 49 O2 67.2 REMARK 620 3 HOH A 274 O 96.6 76.0 REMARK 620 4 HOH A 294 O 113.8 70.5 119.5 REMARK 620 N 1 2 3 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 202 O REMARK 620 2 HOH A 259 O 98.5 REMARK 620 3 HOH A 329 O 124.0 104.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 108 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 306 O REMARK 620 2 HOH A 322 O 117.7 REMARK 620 3 HOH A 341 O 129.9 110.6 REMARK 620 4 HOH A 349 O 125.4 75.8 55.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 110 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 213 O REMARK 620 2 HOH A 242 O 93.5 REMARK 620 3 HOH A 252 O 173.7 83.3 REMARK 620 4 HOH A 254 O 81.3 102.8 94.1 REMARK 620 5 HOH A 345 O 85.8 157.0 99.3 99.8 REMARK 620 6 HOH A 348 O 100.3 85.6 84.9 171.4 72.0 REMARK 620 N 1 2 3 4 5 DBREF 7EOJ A 1 49 PDB 7EOJ 7EOJ 1 49 SEQRES 1 A 49 GDP G C G C A C U G G C G C SEQRES 2 A 49 U G C G C C U U C G G G C SEQRES 3 A 49 G C C A A U C G U A G C G SEQRES 4 A 49 U G U C G G C G C C HET GDP A 1 28 HET J8F A 101 23 HET MG A 102 1 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 MG A 108 1 HET MG A 109 1 HET MG A 110 1 HET CS A 111 1 HET CS A 112 1 HET CS A 113 1 HET CS A 114 1 HET CS A 115 1 HET CS A 116 1 HET CS A 117 1 HET CS A 118 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM J8F 4-[(~{Z})-1-CYANO-2-[4-[2-HYDROXYETHYL(METHYL) HETNAM 2 J8F AMINO]PHENYL]ETHENYL]BENZENECARBONITRILE HETNAM MG MAGNESIUM ION HETNAM CS CESIUM ION FORMUL 1 GDP C10 H15 N5 O11 P2 FORMUL 2 J8F C19 H17 N3 O FORMUL 3 MG 9(MG 2+) FORMUL 12 CS 8(CS 1+) FORMUL 20 HOH *149(H2 O) LINK O3' GDP A 1 P G A 2 1555 1555 1.57 LINK O2 C A 3 CS CS A 112 1555 1555 3.13 LINK OP2 C A 5 CS CS A 111 1555 1555 3.26 LINK O2 C A 5 CS CS A 113 1555 1555 3.09 LINK N7 A A 6 CS CS A 111 1555 1555 3.24 LINK OP2 C A 7 MG MG A 103 1555 1555 2.00 LINK OP2 U A 8 MG MG A 103 1555 1555 1.96 LINK OP1 U A 8 CS CS A 114 1555 1555 3.01 LINK OP2 G A 9 CS CS A 114 1555 1555 2.96 LINK OP1 G A 12 MG MG A 109 1555 1555 2.40 LINK O2 C A 13 CS CS A 115 1555 1555 3.03 LINK O2 C A 16 CS CS A 116 1555 1555 3.37 LINK O2' C A 28 CS CS A 116 1555 1555 3.41 LINK O2 C A 28 CS CS A 116 1555 1555 2.97 LINK O3' C A 29 CS CS A 112 1555 4555 3.08 LINK OP2 A A 30 MG MG A 104 1555 1555 1.98 LINK OP1 A A 30 CS CS A 112 1555 4555 3.01 LINK OP2 U A 32 MG MG A 105 1555 1555 2.08 LINK O2 U A 32 CS CS A 117 1555 1555 3.07 LINK OP1 C A 33 CS CS A 114 1555 4545 2.98 LINK O5' C A 33 CS CS A 114 1555 4545 3.21 LINK O6 G A 34 CS CS A 117 1555 1555 3.06 LINK O4 U A 35 CS CS A 117 1555 1555 3.26 LINK O6 G A 37 MG MG A 106 1555 1555 2.63 LINK O2 C A 38 CS CS A 115 1555 1555 3.15 LINK OP1 C A 38 CS CS A 117 1555 1555 3.24 LINK OP2 C A 38 CS CS A 117 1555 1555 3.08 LINK O6 G A 41 CS CS A 111 1555 1555 3.07 LINK OP2 U A 42 MG MG A 102 1555 1555 1.97 LINK O2 C A 46 CS CS A 113 1555 1555 3.11 LINK O2 C A 48 CS CS A 112 1555 1555 2.74 LINK O2' C A 49 CS CS A 118 1555 1555 3.18 LINK O2 C A 49 CS CS A 118 1555 1555 3.26 LINK MG MG A 102 O HOH A 247 1555 1555 2.05 LINK MG MG A 102 O HOH A 249 1555 1555 2.00 LINK MG MG A 102 O HOH A 281 1555 1555 2.11 LINK MG MG A 102 O HOH A 292 1555 1555 2.04 LINK MG MG A 102 O HOH A 325 1555 1555 2.11 LINK MG MG A 103 O HOH A 256 1555 1555 2.02 LINK MG MG A 103 O HOH A 267 1555 1555 2.09 LINK MG MG A 103 O HOH A 285 1555 1555 2.13 LINK MG MG A 104 O HOH A 211 1555 1555 2.09 LINK MG MG A 104 O HOH A 228 1555 1555 2.19 LINK MG MG A 104 O HOH A 280 1555 1555 2.18 LINK MG MG A 104 O HOH A 303 1555 1555 2.11 LINK MG MG A 104 O HOH A 309 1555 1555 2.09 LINK MG MG A 105 O HOH A 216 1555 1555 2.14 LINK MG MG A 105 O HOH A 227 1555 1555 2.18 LINK MG MG A 105 O HOH A 273 1555 1555 2.08 LINK MG MG A 105 O HOH A 312 1555 1555 2.14 LINK MG MG A 105 O HOH A 319 1555 1555 1.99 LINK MG MG A 106 O HOH A 269 1555 1555 2.63 LINK MG MG A 106 O HOH A 314 1555 1555 2.62 LINK MG MG A 107 O HOH A 202 1555 1555 2.04 LINK MG MG A 107 O HOH A 259 1555 4555 2.68 LINK MG MG A 107 O HOH A 329 1555 1555 1.97 LINK MG MG A 108 O HOH A 306 1555 1555 2.23 LINK MG MG A 108 O HOH A 322 1555 1555 1.87 LINK MG MG A 108 O HOH A 341 1555 1555 2.18 LINK MG MG A 108 O HOH A 349 1555 1555 2.15 LINK MG MG A 109 O HOH A 327 1555 1555 2.06 LINK MG MG A 110 O HOH A 213 1555 2656 1.98 LINK MG MG A 110 O HOH A 242 1555 1555 2.22 LINK MG MG A 110 O HOH A 252 1555 1555 1.97 LINK MG MG A 110 O HOH A 254 1555 2656 2.12 LINK MG MG A 110 O HOH A 345 1555 2656 2.08 LINK MG MG A 110 O HOH A 348 1555 1555 2.13 LINK CS CS A 111 O HOH A 225 1555 1555 3.17 LINK CS CS A 111 O HOH A 268 1555 1555 3.26 LINK CS CS A 112 O HOH A 260 1555 4545 3.03 LINK CS CS A 112 O HOH A 286 1555 1555 2.96 LINK CS CS A 113 O HOH A 207 1555 1555 3.37 LINK CS CS A 113 O HOH A 331 1555 1555 3.42 LINK CS CS A 114 O HOH A 243 1555 4555 2.97 LINK CS CS A 115 O HOH A 235 1555 1555 3.05 LINK CS CS A 117 O HOH A 233 1555 1555 3.32 LINK CS CS A 117 O HOH A 259 1555 1555 3.28 LINK CS CS A 118 O HOH A 274 1555 2656 2.99 LINK CS CS A 118 O HOH A 294 1555 4545 3.31 CRYST1 92.277 34.749 58.124 90.00 127.93 90.00 C 1 2 1 4 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 0.010837 0.000000 0.008445 0.00000 SCALE2 0.000000 0.028778 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021811 0.00000 HETATM 1 PB GDP A 1 33.692 13.794 22.373 1.00 40.83 P HETATM 2 O1B GDP A 1 34.484 14.951 21.801 1.00 36.29 O HETATM 3 O2B GDP A 1 32.344 14.280 22.853 1.00 38.63 O HETATM 4 O3B GDP A 1 34.389 13.144 23.556 1.00 27.42 O HETATM 5 O3A GDP A 1 33.427 12.675 21.244 1.00 34.89 O HETATM 6 PA GDP A 1 34.229 12.377 19.870 1.00 27.16 P HETATM 7 O1A GDP A 1 33.496 13.064 18.762 1.00 24.81 O HETATM 8 O2A GDP A 1 35.716 12.592 19.855 1.00 28.80 O HETATM 9 O5' GDP A 1 33.924 10.797 19.853 1.00 20.99 O HETATM 10 C5' GDP A 1 34.940 9.850 20.148 1.00 20.90 C HETATM 11 C4' GDP A 1 34.236 8.522 20.373 1.00 22.36 C HETATM 12 O4' GDP A 1 33.370 8.635 21.497 1.00 20.17 O HETATM 13 C3' GDP A 1 33.279 8.179 19.235 1.00 19.59 C HETATM 14 O3' GDP A 1 33.929 7.604 18.105 1.00 19.80 O HETATM 15 C2' GDP A 1 32.290 7.257 19.919 1.00 18.90 C HETATM 16 O2' GDP A 1 32.886 5.992 20.186 1.00 20.91 O HETATM 17 C1' GDP A 1 32.153 7.914 21.265 1.00 19.68 C HETATM 18 N9 GDP A 1 31.025 8.867 21.251 1.00 17.83 N HETATM 19 C8 GDP A 1 31.125 10.210 21.243 1.00 20.42 C HETATM 20 N7 GDP A 1 29.900 10.780 21.244 1.00 18.68 N HETATM 21 C5 GDP A 1 28.990 9.786 21.246 1.00 16.95 C HETATM 22 C6 GDP A 1 27.515 9.692 21.250 1.00 18.83 C HETATM 23 O6 GDP A 1 26.809 10.722 21.240 1.00 19.34 O HETATM 24 N1 GDP A 1 26.965 8.467 21.256 1.00 18.66 N HETATM 25 C2 GDP A 1 27.704 7.344 21.262 1.00 18.61 C HETATM 26 N2 GDP A 1 27.074 6.144 21.270 1.00 17.88 N HETATM 27 N3 GDP A 1 29.064 7.358 21.260 1.00 19.00 N HETATM 28 C4 GDP A 1 29.740 8.530 21.251 1.00 15.80 C