PDB Short entry for 2OE5 HEADER RNA 28-DEC-06 2OE5 TITLE 1.5 A X-RAY CRYSTAL STRUCTURE OF APRAMYCIN COMPLEX WITH RNA FRAGMENT TITLE 2 GGCGUCGCUAGUACCG/GGUACUAAAAGUCGCCC CONTAINING THE HUMAN RIBOSOMAL TITLE 3 DECODING A SITE: RNA CONSTRUCT WITH 3'-OVERHANG COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*GP*CP*GP*UP*CP*GP*CP*UP*AP*GP*UP*AP*CP*CP*G)- COMPND 3 3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'- COMPND 8 R(*GP*GP*UP*AP*CP*UP*AP*AP*AP*AP*GP*UP*CP*GP*CP*CP*C)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS AMINOGLYCOSIDE ANTIBIOTICS, APRAMYCIN, RIBOSOMAL DECODING SITE, A KEYWDS 2 SITE, HOMO SAPIENS, RNA DUPLEX, RNA EXPDTA X-RAY DIFFRACTION AUTHOR T.HERMANN,V.TERESHKO,E.SKRIPKIN,D.J.PATEL REVDAT 6 03-APR-24 2OE5 1 REMARK REVDAT 5 27-DEC-23 2OE5 1 REMARK HETSYN LINK REVDAT 4 13-JUL-11 2OE5 1 VERSN REVDAT 3 24-FEB-09 2OE5 1 VERSN REVDAT 2 24-APR-07 2OE5 1 JRNL REVDAT 1 13-FEB-07 2OE5 0 JRNL AUTH T.HERMANN,V.TERESHKO,E.SKRIPKIN,D.J.PATEL JRNL TITL APRAMYCIN RECOGNITION BY THE HUMAN RIBOSOMAL DECODING SITE. JRNL REF BLOOD CELLS MOL.DIS. V. 38 193 2007 JRNL REFN ISSN 1079-9796 JRNL PMID 17258916 JRNL DOI 10.1016/J.BCMD.2006.11.006 REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 13173 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 + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 692 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 888 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3540 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.3500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 698 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 164 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : 0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.097 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.094 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.029 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 827 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 297 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1283 ; 1.793 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 779 ; 1.746 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 149 ; 0.871 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 344 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1 ; 0.000 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 80 ; 0.124 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 391 ; 0.206 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 110 ; 0.216 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 3 ; 0.050 ; 0.500 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.065 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 8 ; 0.112 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 15 ; 0.203 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.247 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 827 ; 1.873 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1283 ; 2.535 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 7 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 3 REMARK 3 RESIDUE RANGE : A 1404 A 1413 REMARK 3 RESIDUE RANGE : A 14 A 17 REMARK 3 RESIDUE RANGE : B 84 B 86 REMARK 3 RESIDUE RANGE : B 1487 B 1497 REMARK 3 RESIDUE RANGE : B 98 B 100 REMARK 3 RESIDUE RANGE : B 101 B 268 REMARK 3 ORIGIN FOR THE GROUP (A): 18.6988 -2.0052 43.4683 REMARK 3 T TENSOR REMARK 3 T11: 0.0382 T22: 0.0006 REMARK 3 T33: 0.0845 T12: 0.0021 REMARK 3 T13: 0.0108 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 1.4523 L22: 0.4043 REMARK 3 L33: 1.3930 L12: 0.2472 REMARK 3 L13: -0.4984 L23: -0.4794 REMARK 3 S TENSOR REMARK 3 S11: 0.1280 S12: 0.0550 S13: 0.1337 REMARK 3 S21: 0.0573 S22: -0.0340 S23: -0.0347 REMARK 3 S31: -0.1493 S32: -0.0226 S33: -0.0939 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE SO4 ION IS PARTIALLY DISORDERED AND REMARK 3 IT WAS REFINED WITH OCCUPANCY 0.5 REMARK 4 REMARK 4 2OE5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041021. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9A 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13865 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL 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) : 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: STANDARD RNA-MODEL BUILT IN TURBO-FRODO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M MES BUFFER, 15-20% MPD, 0.02 REMARK 280 -0.04M MAGNESIUM ACETATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 14.15500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.33950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.34650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.33950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.15500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.34650 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 300 REMARK: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 RNA CHAINS. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 C A1404 O3' C A1404 C3' 0.075 REMARK 500 G B1494 O5' G B1494 C5' -0.062 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 A B1491 C3' - C2' - C1' ANGL. DEV. = -4.4 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 104 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 111 O REMARK 620 2 HOH A 112 O 93.2 REMARK 620 3 HOH A 113 O 83.1 89.7 REMARK 620 4 HOH A 114 O 172.4 94.5 96.9 REMARK 620 5 HOH A 115 O 85.9 173.5 83.8 86.5 REMARK 620 6 HOH A 116 O 82.2 92.4 165.2 97.6 93.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 109 O REMARK 620 2 HOH B 105 O 176.7 REMARK 620 3 HOH B 106 O 93.3 89.6 REMARK 620 4 HOH B 107 O 91.2 85.7 171.4 REMARK 620 5 HOH B 108 O 89.3 89.2 90.1 82.6 REMARK 620 6 HOH B 110 O 87.5 94.0 89.5 98.0 176.8 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 AM2 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OE6 RELATED DB: PDB REMARK 900 2.4 A X-RAY CRYSTAL STRUCTURE OF UNLIGANDED RNA FRAGMENT REMARK 900 GGGCGUCGCUAGUACC/CGGUACUAAAAGUCGCC CONTAINING THE HUMAN RIBOSOMAL REMARK 900 DECODING A SITE: RNA CONSTRUCT WITH 5'-OVERHANG REMARK 900 RELATED ID: 2OE8 RELATED DB: PDB REMARK 900 1.8 A X-RAY CRYSTAL STRUCTURE OF APRAMYCIN COMPLEX WITH RNA REMARK 900 FRAGMENT GGGCGUCGCUAGUACC/CGGUACUAAAAGUCGCC CONTAINING THE HUMAN REMARK 900 RIBOSOMAL DECODING A SITE: RNA CONSTRUCT WITH 5'-OVERHANG REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE RESIDUES THAT ARE NATURALLY OCCURING IN THE HUMAN REMARK 999 RIBOSOMAL DECODING A SITE ARE NUMBERED 1404-1413 (CHAIN A) REMARK 999 AND 1487-1497 (CHAIN B). THIS NUMBERING IS ADAPTED FROM REMARK 999 THE BACTERIAL ESCHERICHIA COLI SEQUENCE. IN BOTH STRANDS REMARK 999 TERMINAL RESIDUES ARE DISTINCT FROM HUMAN AND REMARK 999 WERE INCORPORATED FOR CRYSTALLIZATION PURPOSES. THE REMARK 999 INCORPORATED RESIDUES ARE NUMBERED 2-3, 14-17 (CHAIN A) REMARK 999 AND 84-86,98-100 (CHAIN B). DBREF 2OE5 A 2 17 PDB 2OE5 2OE5 2 17 DBREF 2OE5 B 84 100 PDB 2OE5 2OE5 84 100 SEQRES 1 A 16 G G C G U C G C U A G U A SEQRES 2 A 16 C C G SEQRES 1 B 17 G G U A C U A A A A G U C SEQRES 2 B 17 G C C C HET SO4 A 102 5 HET MG A 104 1 HET AM2 B 101 37 HET MG B 103 1 HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETNAM AM2 APRAMYCIN HETSYN AM2 NEBRAMYCIN II; 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4- HETSYN 2 AM2 DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8, HETSYN 3 AM2 8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO) HETSYN 4 AM2 PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE FORMUL 3 SO4 O4 S 2- FORMUL 4 MG 2(MG 2+) FORMUL 5 AM2 C21 H41 N5 O11 FORMUL 7 HOH *164(H2 O) LINK MG MG A 104 O HOH A 111 1555 1555 2.16 LINK MG MG A 104 O HOH A 112 1555 1555 2.21 LINK MG MG A 104 O HOH A 113 1555 1555 1.92 LINK MG MG A 104 O HOH A 114 1555 1555 2.18 LINK MG MG A 104 O HOH A 115 1555 1555 2.16 LINK MG MG A 104 O HOH A 116 1555 1555 1.93 LINK O HOH A 109 MG MG B 103 1555 1555 2.00 LINK MG MG B 103 O HOH B 105 1555 1555 2.25 LINK MG MG B 103 O HOH B 106 1555 1555 2.02 LINK MG MG B 103 O HOH B 107 1555 1555 2.12 LINK MG MG B 103 O HOH B 108 1555 1555 2.00 LINK MG MG B 103 O HOH B 110 1555 1555 2.17 SITE 1 AC1 24 SO4 A 102 HOH A 130 HOH A 143 HOH A 200 SITE 2 AC1 24 G A1408 C A1409 U A1410 A A1411 SITE 3 AC1 24 G A1412 U A1413 G B 84 G B 85 SITE 4 AC1 24 U B 86 C B 100 HOH B 118 HOH B 119 SITE 5 AC1 24 HOH B 131 HOH B 134 HOH B 157 HOH B 170 SITE 6 AC1 24 HOH B 194 A B1487 C B1488 U B1489 SITE 1 AC2 8 C A 16 G A 17 HOH A 111 HOH A 149 SITE 2 AC2 8 G B 84 C B 99 C B 100 AM2 B 101 SITE 1 AC3 6 HOH A 109 HOH B 105 HOH B 106 HOH B 107 SITE 2 AC3 6 HOH B 108 HOH B 110 SITE 1 AC4 6 HOH A 111 HOH A 112 HOH A 113 HOH A 114 SITE 2 AC4 6 HOH A 115 HOH A 116 CRYST1 28.310 36.693 86.679 90.00 90.00 90.00 P 21 21 21 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 0.035323 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027253 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011537 0.00000