HEADER RNA 25-FEB-02 1L2X TITLE ATOMIC RESOLUTION CRYSTAL STRUCTURE OF A VIRAL RNA PSEUDOKNOT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA PSEUDOKNOT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: METAL IONS IN A RNA PSEUDOKNOT SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA SEQUENCE TAKEN FROM BEET WESTERN YELLOW VIRUS KEYWDS PSEUDOKNOT, FRAMESHIFTING, ATOMIC RESOLUTION, VIRAL RNA, METAL IONS, KEYWDS 2 FLEXIBILITY, RNA EXPDTA X-RAY DIFFRACTION AUTHOR M.EGLI,G.MINASOV,L.SU,A.RICH REVDAT 4 16-AUG-23 1L2X 1 REMARK LINK REVDAT 3 24-FEB-09 1L2X 1 VERSN REVDAT 2 01-APR-03 1L2X 1 JRNL REVDAT 1 22-MAR-02 1L2X 0 JRNL AUTH M.EGLI,G.MINASOV,L.SU,A.RICH JRNL TITL METAL IONS AND FLEXIBILITY IN A VIRAL RNA PSEUDOKNOT AT JRNL TITL 2 ATOMIC RESOLUTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 99 4302 2002 JRNL REFN ISSN 0027-8424 JRNL PMID 11904368 JRNL DOI 10.1073/PNAS.062055599 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.142 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2131 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 21348 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 614 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 180 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 ANGLE DISTANCES (A) : 1.300 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : G. PARKINSON ET AL., ACTA CRYST. REMARK 3 (1996) D52, 57-64 REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: KONNERT-HENDRICKSON CONJUGATE-GRADIENT REMARK 3 ALGORITHM USED IN REFINEMENT REMARK 4 REMARK 4 1L2X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1000015597. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 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 : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21462 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.42800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 437D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM MOPS, SPERMIDINE, MAGNESIUM REMARK 280 CHLORIDE, SEC-BUTANOL, PH 7.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 93.51867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.75933 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 46.75933 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 93.51867 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 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 66 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 134 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 173 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 G A 12 C3' - O3' - P ANGL. DEV. = 9.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 29 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP A 1 O1B REMARK 620 2 G A 2 OP1 91.5 REMARK 620 3 HOH A 30 O 92.3 93.3 REMARK 620 4 HOH A 31 O 91.5 89.3 175.4 REMARK 620 5 HOH A 32 O 178.0 89.3 89.5 86.7 REMARK 620 6 HOH A 33 O 86.7 175.4 91.1 86.5 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 34 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP A 1 O6 REMARK 620 2 GTP A 1 O6 39.3 REMARK 620 3 GTP A 1 O6 73.6 43.1 REMARK 620 4 G A 19 OP2 142.5 177.5 134.5 REMARK 620 5 HOH A 35 O 70.1 87.3 74.3 92.1 REMARK 620 6 HOH A 35 O 66.9 98.6 99.8 81.9 27.8 REMARK 620 7 HOH A 36 O 60.0 93.8 133.6 88.6 90.6 64.8 REMARK 620 8 HOH A 37 O 113.2 93.6 103.4 86.8 175.6 155.7 93.7 REMARK 620 9 HOH A 37 O 120.7 88.5 47.5 89.0 85.6 111.1 175.5 90.0 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 59 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP A 1 O2B REMARK 620 2 GTP A 1 O3G 96.0 REMARK 620 3 GTP A 1 O6 78.7 172.2 REMARK 620 4 HOH A 35 O 85.9 89.0 85.0 REMARK 620 5 HOH A 35 O 87.6 111.1 63.3 22.5 REMARK 620 6 HOH A 36 O 152.1 111.0 73.6 87.8 76.7 REMARK 620 7 HOH A 60 O 98.4 95.0 91.5 173.8 152.5 86.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 64 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP A 1 O2' REMARK 620 2 GTP A 1 O3' 45.0 REMARK 620 3 G A 2 N7 80.3 74.5 REMARK 620 4 G A 2 OP2 85.3 43.3 94.8 REMARK 620 5 HOH A 56 O 164.0 121.5 87.7 85.2 REMARK 620 6 HOH A 66 O 130.6 148.6 74.3 137.7 54.2 REMARK 620 7 HOH A 102 O 69.0 105.6 63.0 147.9 114.7 61.9 REMARK 620 8 HOH A 102 O 153.2 139.7 125.8 97.1 41.4 61.8 114.6 REMARK 620 9 HOH A 162 O 110.5 93.1 149.9 59.6 75.4 112.7 146.9 51.0 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 62 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 3 O2' REMARK 620 2 C A 3 O2 86.3 REMARK 620 3 HOH A 101 O 109.6 123.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 63 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 5 O2' REMARK 620 2 A A 21 OP1 131.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 61 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 16 O2' REMARK 620 2 G A 16 N3 93.8 REMARK 620 3 A A 21 OP2 172.2 91.8 REMARK 620 4 HOH A 92 O 68.7 98.2 115.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 38 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 39 O REMARK 620 2 HOH A 40 O 88.9 REMARK 620 3 HOH A 41 O 89.7 178.5 REMARK 620 4 HOH A 42 O 96.8 91.5 88.0 REMARK 620 5 HOH A 43 O 168.7 90.6 90.9 94.5 REMARK 620 6 HOH A 44 O 87.8 91.2 89.4 174.8 80.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 45 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 46 O REMARK 620 2 HOH A 47 O 88.1 REMARK 620 3 HOH A 47 O 94.0 40.1 REMARK 620 4 HOH A 48 O 91.9 53.2 92.7 REMARK 620 5 HOH A 49 O 87.2 145.0 174.9 92.3 REMARK 620 6 HOH A 50 O 174.0 97.7 91.5 90.4 87.2 REMARK 620 7 HOH A 51 O 87.7 128.9 89.5 177.8 85.5 89.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 52 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 53 O REMARK 620 2 HOH A 54 O 91.1 REMARK 620 3 HOH A 55 O 167.8 90.4 REMARK 620 4 HOH A 56 O 59.9 93.0 107.9 REMARK 620 5 HOH A 56 O 83.0 90.0 84.9 23.2 REMARK 620 6 HOH A 57 O 103.6 161.2 77.7 104.4 103.2 REMARK 620 7 HOH A 58 O 107.5 87.5 84.6 167.4 169.2 77.0 REMARK 620 N 1 2 3 4 5 6 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 29 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 34 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 38 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 45 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 52 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 59 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 61 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 62 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 63 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 64 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 437D RELATED DB: PDB REMARK 900 437D IS THE SAME RNA PSEUDOKNOT STRUCTURE AT 1.6 ANGSTROM RESOLUTION REMARK 900 RELATED ID: 1L3D RELATED DB: PDB REMARK 900 LOW RESOLUTION CRYSTAL STRUCTURE OF A VIRAL RNA PSEUDOKNOT DBREF 1L2X A 1 28 PDB 1L2X 1L2X 1 28 SEQRES 1 A 28 GTP G C G C G G C A C C G U SEQRES 2 A 28 C C G C G G A A C A A A C SEQRES 3 A 28 G G MODRES 1L2X GTP A 1 G GUANOSINE-5'-TRIPHOSPHATE HET GTP A 1 52 HET MG A 29 1 HET MG A 34 1 HET MG A 38 1 HET MG A 45 1 HET MG A 52 1 HET MG A 59 1 HET NA A 61 1 HET NA A 62 1 HET NA A 63 1 HET K A 64 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM K POTASSIUM ION FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 MG 6(MG 2+) FORMUL 8 NA 3(NA 1+) FORMUL 11 K K 1+ FORMUL 12 HOH *180(H2 O) LINK O3'AGTP A 1 P G A 2 1555 1555 1.61 LINK O3'BGTP A 1 P G A 2 1555 1555 1.60 LINK O1B GTP A 1 MG MG A 29 1555 1555 2.00 LINK O6 AGTP A 1 MG MG A 34 1455 1555 2.58 LINK O6 BGTP A 1 MG MG A 34 1455 1555 2.09 LINK O6 BGTP A 1 MG MG A 34 5575 1555 2.63 LINK O2B GTP A 1 MG MG A 59 1555 1555 1.75 LINK O3G GTP A 1 MG MG A 59 1555 1555 2.29 LINK O6 AGTP A 1 MG MG A 59 5675 1555 2.22 LINK O2'AGTP A 1 K A K A 64 1555 1555 2.50 LINK O3'AGTP A 1 K A K A 64 1555 1555 3.69 LINK OP1 G A 2 MG MG A 29 1555 1555 1.96 LINK N7 G A 2 K A K A 64 1555 1555 3.09 LINK OP2 G A 2 K A K A 64 1555 1555 2.71 LINK O2' C A 3 NA NA A 62 1555 1555 2.71 LINK O2 C A 3 NA NA A 62 1555 1555 2.74 LINK O2' C A 5 NA NA A 63 1555 1555 2.59 LINK O2' G A 16 NA NA A 61 1555 1555 2.88 LINK N3 G A 16 NA NA A 61 1555 1555 2.84 LINK OP2 G A 19 MG MG A 34 1555 1555 2.06 LINK OP2 A A 21 NA NA A 61 1555 1555 2.69 LINK OP1 A A 21 NA NA A 63 1555 1555 2.65 LINK MG MG A 29 O HOH A 30 1555 1555 2.11 LINK MG MG A 29 O HOH A 31 1555 1555 2.14 LINK MG MG A 29 O HOH A 32 1555 1555 2.13 LINK MG MG A 29 O HOH A 33 1555 1555 2.12 LINK MG MG A 34 O AHOH A 35 1555 1555 2.07 LINK MG MG A 34 O BHOH A 35 1555 5575 2.61 LINK MG MG A 34 O HOH A 36 1555 1555 2.04 LINK MG MG A 34 O AHOH A 37 1555 1555 2.06 LINK MG MG A 34 O BHOH A 37 1555 1555 2.13 LINK MG MG A 34 O BHOH A 37 1555 5675 1.73 LINK MG MG A 34 O AHOH A 37 1555 5675 2.39 LINK MG MG A 34 MG MG A 59 1555 5575 3.08 LINK MG MG A 34 MG MG A 59 5775 1555 3.08 LINK O BHOH A 35 MG MG A 59 1555 1555 2.01 LINK O AHOH A 35 MG MG A 59 5775 1555 2.83 LINK O HOH A 36 MG MG A 59 5775 1555 1.63 LINK MG MG A 38 O HOH A 39 1555 1555 2.05 LINK MG MG A 38 O HOH A 40 1555 1555 2.16 LINK MG MG A 38 O HOH A 41 1555 1555 2.15 LINK MG MG A 38 O HOH A 42 1555 1555 2.07 LINK MG MG A 38 O HOH A 43 1555 1555 2.07 LINK MG MG A 38 O HOH A 44 1555 1555 2.13 LINK MG MG A 45 O HOH A 46 1555 1555 2.07 LINK MG MG A 45 O AHOH A 47 1555 1555 1.95 LINK MG MG A 45 O BHOH A 47 1555 1555 2.08 LINK MG MG A 45 O BHOH A 48 1555 1555 2.10 LINK MG MG A 45 O HOH A 49 1555 1555 2.10 LINK MG MG A 45 O HOH A 50 1555 1555 2.11 LINK MG MG A 45 O HOH A 51 1555 1555 2.10 LINK MG MG A 52 O HOH A 53 1555 1555 2.10 LINK MG MG A 52 O HOH A 54 1555 1555 2.21 LINK MG MG A 52 O HOH A 55 1555 1555 2.25 LINK MG MG A 52 O AHOH A 56 1555 1555 2.89 LINK MG MG A 52 O BHOH A 56 1555 1555 1.98 LINK MG MG A 52 O HOH A 57 1555 1555 2.19 LINK MG MG A 52 O HOH A 58 1555 1555 2.07 LINK O AHOH A 56 K A K A 64 1555 1555 3.68 LINK MG MG A 59 O HOH A 60 1555 1555 1.95 LINK NA NA A 61 O HOH A 92 1555 1555 2.67 LINK NA NA A 62 O HOH A 101 1555 1555 2.77 LINK K A K A 64 O HOH A 66 1555 1555 2.80 LINK K A K A 64 O HOH A 102 1555 1555 3.09 LINK K A K A 64 O HOH A 102 1555 5675 3.09 LINK K A K A 64 O HOH A 162 1555 5675 3.48 SITE 1 AC1 6 GTP A 1 G A 2 HOH A 30 HOH A 31 SITE 2 AC1 6 HOH A 32 HOH A 33 SITE 1 AC2 6 GTP A 1 G A 19 HOH A 35 HOH A 36 SITE 2 AC2 6 HOH A 37 MG A 59 SITE 1 AC3 6 HOH A 39 HOH A 40 HOH A 41 HOH A 42 SITE 2 AC3 6 HOH A 43 HOH A 44 SITE 1 AC4 6 HOH A 46 HOH A 47 HOH A 48 HOH A 49 SITE 2 AC4 6 HOH A 50 HOH A 51 SITE 1 AC5 6 HOH A 53 HOH A 54 HOH A 55 HOH A 56 SITE 2 AC5 6 HOH A 57 HOH A 58 SITE 1 AC6 6 GTP A 1 G A 19 MG A 34 HOH A 35 SITE 2 AC6 6 HOH A 36 HOH A 60 SITE 1 AC7 3 G A 16 A A 21 HOH A 92 SITE 1 AC8 4 C A 3 G A 4 G A 18 HOH A 101 SITE 1 AC9 4 C A 5 G A 6 A A 21 HOH A 79 SITE 1 BC1 4 GTP A 1 G A 2 HOH A 66 HOH A 102 CRYST1 30.160 30.160 140.278 90.00 90.00 120.00 P 32 2 1 6 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 0.033156 0.019143 0.000000 0.00000 SCALE2 0.000000 0.038286 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007129 0.00000 HETATM 1 PG GTP A 1 24.181 32.064 27.670 0.10 24.73 P HETATM 2 O1G GTP A 1 24.342 33.433 27.064 0.10 37.56 O HETATM 3 O2G GTP A 1 24.519 32.013 29.136 0.10 32.46 O HETATM 4 O3G GTP A 1 25.048 31.062 26.907 1.00 47.91 O HETATM 5 O3B GTP A 1 22.644 31.665 27.526 1.00 33.11 O ANISOU 5 O3B GTP A 1 1768 6703 4110 -927 -793 986 O HETATM 6 PB GTP A 1 21.944 30.914 26.290 1.00 30.44 P ANISOU 6 PB GTP A 1 1846 4847 4872 -1456 -1208 1806 P HETATM 7 O1B GTP A 1 20.481 30.888 26.504 1.00 30.75 O ANISOU 7 O1B GTP A 1 1687 5226 4771 -1786 -517 1160 O HETATM 8 O2B GTP A 1 22.544 29.597 26.037 1.00 31.25 O ANISOU 8 O2B GTP A 1 1522 4653 5697 -1100 -1318 2736 O HETATM 9 O3A GTP A 1 22.230 31.881 25.061 1.00 27.41 O ANISOU 9 O3A GTP A 1 1253 4156 5004 -742 -677 1526 O HETATM 10 PA GTP A 1 21.357 32.886 24.136 1.00 28.14 P ANISOU 10 PA GTP A 1 1645 3573 5474 -752 -631 1140 P HETATM 11 O1A GTP A 1 22.257 33.379 23.051 1.00 29.88 O ANISOU 11 O1A GTP A 1 1860 3708 5786 -793 -172 1961 O HETATM 12 O2A GTP A 1 20.694 33.906 24.985 1.00 28.72 O ANISOU 12 O2A GTP A 1 2408 2857 5647 -1180 -248 1483 O HETATM 13 O5'AGTP A 1 20.284 31.879 23.543 0.50 23.11 O ANISOU 13 O5'AGTP A 1 1167 3488 4127 -570 86 1088 O HETATM 14 O5'BGTP A 1 20.244 31.934 23.525 0.50 23.80 O ANISOU 14 O5'BGTP A 1 1348 3530 4166 -646 -144 1152 O HETATM 15 C5'AGTP A 1 19.131 32.316 22.825 0.50 21.95 C ANISOU 15 C5'AGTP A 1 1574 2998 3770 -631 -65 776 C HETATM 16 C5'BGTP A 1 19.049 32.533 22.993 0.50 20.46 C ANISOU 16 C5'BGTP A 1 1187 3030 3557 -508 360 642 C HETATM 17 C4'AGTP A 1 18.305 31.114 22.431 0.50 18.93 C ANISOU 17 C4'AGTP A 1 1487 2533 3174 -179 174 587 C HETATM 18 C4'BGTP A 1 18.162 31.423 22.482 0.50 19.32 C ANISOU 18 C4'BGTP A 1 1444 2559 3338 -164 100 647 C HETATM 19 O4'AGTP A 1 19.032 30.287 21.495 0.50 16.95 O ANISOU 19 O4'AGTP A 1 749 2658 3035 254 113 710 O HETATM 20 O4'BGTP A 1 18.804 30.735 21.386 0.50 17.14 O ANISOU 20 O4'BGTP A 1 1066 2537 2910 172 -317 958 O HETATM 21 C3'AGTP A 1 17.949 30.186 23.587 0.50 16.54 C ANISOU 21 C3'AGTP A 1 867 2702 2715 0 -361 678 C HETATM 22 C3'BGTP A 1 17.857 30.361 23.529 0.50 18.33 C ANISOU 22 C3'BGTP A 1 1294 2805 2866 -280 -108 559 C HETATM 23 O3'AGTP A 1 16.747 30.614 24.223 0.50 17.14 O ANISOU 23 O3'AGTP A 1 937 2826 2750 -258 -138 307 O HETATM 24 O3'BGTP A 1 16.664 30.669 24.225 0.50 18.17 O ANISOU 24 O3'BGTP A 1 1481 2715 2708 -408 14 261 O HETATM 25 C2'AGTP A 1 17.816 28.834 22.929 0.50 16.16 C ANISOU 25 C2'AGTP A 1 800 2715 2624 -15 112 704 C HETATM 26 C2'BGTP A 1 17.726 29.094 22.716 0.50 16.55 C ANISOU 26 C2'BGTP A 1 917 2763 2609 -69 30 638 C HETATM 27 O2'AGTP A 1 16.465 28.675 22.491 0.50 17.33 O ANISOU 27 O2'AGTP A 1 1542 2637 2407 -605 -197 551 O HETATM 28 O2'BGTP A 1 16.444 29.089 22.088 0.50 15.34 O ANISOU 28 O2'BGTP A 1 982 3158 1687 199 160 477 O HETATM 29 C1'AGTP A 1 18.666 28.915 21.677 0.50 16.51 C ANISOU 29 C1'AGTP A 1 1046 2577 2651 342 110 819 C HETATM 30 C1'BGTP A 1 18.744 29.328 21.616 0.50 17.01 C ANISOU 30 C1'BGTP A 1 1265 2585 2614 127 404 903 C HETATM 31 N9 AGTP A 1 19.931 28.176 21.706 0.50 16.18 N ANISOU 31 N9 AGTP A 1 860 2566 2720 182 401 215 N HETATM 32 N9 BGTP A 1 20.108 28.909 21.927 0.50 17.39 N ANISOU 32 N9 BGTP A 1 1363 2522 2724 146 176 527 N HETATM 33 C8 AGTP A 1 21.156 28.696 22.055 0.50 14.29 C ANISOU 33 C8 AGTP A 1 846 2228 2354 385 23 204 C HETATM 34 C8 BGTP A 1 21.205 29.623 22.323 0.50 17.34 C ANISOU 34 C8 BGTP A 1 1333 2390 2866 141 481 416 C HETATM 35 N7 AGTP A 1 22.126 27.830 21.990 0.50 13.32 N ANISOU 35 N7 AGTP A 1 1034 2206 1820 273 91 -43 N HETATM 36 N7 BGTP A 1 22.271 28.881 22.498 0.50 16.43 N ANISOU 36 N7 BGTP A 1 1352 2153 2736 337 811 -80 N HETATM 37 C5 AGTP A 1 21.513 26.659 21.566 0.50 12.49 C ANISOU 37 C5 AGTP A 1 1116 2271 1359 367 219 163 C HETATM 38 C5 BGTP A 1 21.852 27.595 22.193 0.50 13.82 C ANISOU 38 C5 BGTP A 1 1229 2301 1721 253 158 96 C HETATM 39 C6 AGTP A 1 22.065 25.382 21.305 0.50 11.46 C ANISOU 39 C6 AGTP A 1 732 2203 1420 431 4 334 C HETATM 40 C6 BGTP A 1 22.537 26.352 22.193 0.50 12.69 C ANISOU 40 C6 BGTP A 1 949 2226 1648 475 192 0 C HETATM 41 O6 AGTP A 1 23.234 24.994 21.408 0.50 13.95 O ANISOU 41 O6 AGTP A 1 984 2213 2104 560 37 201 O HETATM 42 O6 BGTP A 1 23.724 26.129 22.476 0.50 15.49 O ANISOU 42 O6 BGTP A 1 900 2304 2681 441 660 -414 O HETATM 43 N1 AGTP A 1 21.092 24.477 20.891 0.50 14.16 N ANISOU 43 N1 AGTP A 1 1234 2434 1710 291 -180 214 N HETATM 44 N1 BGTP A 1 21.700 25.309 21.807 0.50 15.46 N ANISOU 44 N1 BGTP A 1 1508 2561 1807 176 -190 158 N HETATM 45 C2 AGTP A 1 19.759 24.784 20.739 0.50 12.48 C ANISOU 45 C2 AGTP A 1 675 2373 1693 258 -41 371 C HETATM 46 C2 BGTP A 1 20.374 25.434 21.474 0.50 14.75 C ANISOU 46 C2 BGTP A 1 1469 2519 1615 153 7 434 C HETATM 47 N2 AGTP A 1 18.987 23.770 20.325 0.50 16.61 N ANISOU 47 N2 AGTP A 1 1282 2504 2527 -288 -398 504 N HETATM 48 N2 BGTP A 1 19.694 24.334 21.129 0.50 14.15 N ANISOU 48 N2 BGTP A 1 1171 2238 1968 621 -403 -146 N HETATM 49 N3 AGTP A 1 19.232 25.972 20.970 0.50 16.26 N ANISOU 49 N3 AGTP A 1 1428 2395 2355 -141 156 423 N HETATM 50 N3 BGTP A 1 19.724 26.583 21.477 0.50 16.44 N ANISOU 50 N3 BGTP A 1 1201 2504 2541 255 337 319 N HETATM 51 C4 AGTP A 1 20.162 26.863 21.385 0.50 14.30 C ANISOU 51 C4 AGTP A 1 809 2394 2232 252 -543 454 C HETATM 52 C4 BGTP A 1 20.523 27.599 21.841 0.50 13.71 C ANISOU 52 C4 BGTP A 1 1036 2453 1721 423 477 203 C