HEADER RNA 24-APR-06 2GRB TITLE CRYSTAL STRUCTURE OF AN RNA QUADRUPLEX CONTAINING INOSINE-TETRAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RNA QUADRUPLEX, RNA EXPDTA X-RAY DIFFRACTION AUTHOR B.PAN,K.SHI,M.SUNDARALINGAM REVDAT 3 14-FEB-24 2GRB 1 REMARK LINK REVDAT 2 24-FEB-09 2GRB 1 VERSN REVDAT 1 21-NOV-06 2GRB 0 JRNL AUTH B.PAN,K.SHI,M.SUNDARALINGAM JRNL TITL CRYSTAL STRUCTURE OF AN RNA QUADRUPLEX CONTAINING INOSINE JRNL TITL 2 TETRAD: IMPLICATIONS FOR THE ROLES OF NH2 GROUP IN PURINE JRNL TITL 3 TETRADS. JRNL REF J.MOL.BIOL. V. 363 451 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16978642 JRNL DOI 10.1016/J.JMB.2006.08.022 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 19509 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1006 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1011 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.3970 REMARK 3 BIN FREE R VALUE SET COUNT : 47 REMARK 3 BIN FREE R VALUE : 0.4190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 970 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 178 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : -2.35000 REMARK 3 B33 (A**2) : 1.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.66000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.136 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1069 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1647 ; 2.780 ; 3.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL 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): 208 ; 0.291 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 497 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 451 ; 0.351 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 636 ; 0.265 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 170 ; 0.254 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 53 ; 0.176 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 33 ; 0.163 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.127 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.283 ; 0.200 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): 1135 ; 2.488 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1647 ; 3.070 ; 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): 1135 ; 1.969 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 217 ; 3.507 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 959 ; 3.436 ; 3.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2GRB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037459. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-03 REMARK 200 TEMPERATURE (KELVIN) : NULL 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 : 14-BM-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9195,0.9200,0.8984 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23152 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 6.870 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) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.5 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 32.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: KCL, CACL2, MPD , PH 7.0, EVAPORATION, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.36900 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 BIOLOGICAL ASSEMBLY IS ONE TETRAMER (E.G. CHAIN A, B, C, REMARK 300 D), HALF OF THE ASYMMETRIC UNIT. 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, H 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 U33 A 1 REMARK 465 U33 B 1 REMARK 465 U33 H 1 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 G A 2 P OP1 OP2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 G A 2 O5' C5' REMARK 480 U33 C 1 C4' C5' O5' REMARK 480 U33 G 1 C6 C2' C3' C4' O4' C5' O5' 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 I A 3 O5' - P - OP1 ANGL. DEV. = 10.4 DEGREES REMARK 500 I B 3 O5' - P - OP1 ANGL. DEV. = 11.0 DEGREES REMARK 500 I C 3 O5' - P - OP1 ANGL. DEV. = 10.0 DEGREES REMARK 500 I D 3 O5' - P - OP1 ANGL. DEV. = 11.0 DEGREES REMARK 500 I E 3 O5' - P - OP2 ANGL. DEV. = 11.0 DEGREES REMARK 500 I H 3 O5' - P - OP1 ANGL. DEV. = 14.0 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 K A 304 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 2 O6 REMARK 620 2 I A 3 O6 74.9 REMARK 620 3 G B 2 O6 117.4 156.0 REMARK 620 4 I B 3 O6 150.4 103.4 76.2 REMARK 620 5 G C 2 O6 74.4 134.6 69.2 88.0 REMARK 620 6 I C 3 O6 83.7 67.6 131.3 68.8 76.5 REMARK 620 7 G D 2 O6 79.6 82.1 80.3 129.9 123.4 148.4 REMARK 620 8 I D 3 O6 132.9 65.9 92.8 67.3 152.7 103.3 70.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 303 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 I A 3 O6 REMARK 620 2 G A 4 O6 72.0 REMARK 620 3 K A 304 K 58.4 125.3 REMARK 620 4 I B 3 O6 113.2 159.1 54.9 REMARK 620 5 G B 4 O6 153.3 111.6 123.0 73.3 REMARK 620 6 I C 3 O6 72.1 129.3 55.9 70.1 87.3 REMARK 620 7 G C 4 O6 86.5 70.9 123.2 128.4 70.9 72.3 REMARK 620 8 I D 3 O6 75.8 88.9 59.3 73.6 129.6 115.2 156.6 REMARK 620 9 G D 4 O6 131.3 70.9 127.3 92.7 71.6 156.1 109.5 73.1 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 302 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 4 O6 REMARK 620 2 G A 5 O6 70.3 REMARK 620 3 K A 303 K 56.5 123.2 REMARK 620 4 G B 4 O6 113.3 161.9 56.9 REMARK 620 5 G B 5 O6 159.6 113.4 123.3 69.8 REMARK 620 6 G C 4 O6 73.0 123.8 59.3 73.1 89.5 REMARK 620 7 G C 5 O6 88.2 71.8 120.7 125.1 74.8 65.9 REMARK 620 8 G D 4 O6 73.0 91.0 57.6 74.0 125.7 116.9 158.2 REMARK 620 9 G D 5 O6 126.6 73.7 123.2 91.3 72.2 159.5 116.1 69.5 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 301 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 5 O6 REMARK 620 2 U A 6 O4 65.4 REMARK 620 3 K A 302 K 50.5 114.9 REMARK 620 4 G B 5 O6 101.1 162.2 50.7 REMARK 620 5 U B 6 O4 161.0 130.2 114.9 65.6 REMARK 620 6 G C 5 O6 64.8 113.2 50.4 67.4 96.7 REMARK 620 7 U C 6 O4 95.0 77.1 115.3 117.1 80.4 66.1 REMARK 620 8 G D 5 O6 67.4 97.1 51.6 66.1 115.2 101.9 162.2 REMARK 620 9 U D 6 O4 114.2 79.3 115.0 97.2 82.1 163.2 129.6 64.2 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K D 312 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 315 O REMARK 620 2 U D 6 O2' 158.3 REMARK 620 3 U D 6 O3' 116.8 44.4 REMARK 620 4 HOH D 322 O 119.1 63.5 98.3 REMARK 620 5 HOH D 326 O 135.3 65.8 107.3 58.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR B 401 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 6 O2' REMARK 620 2 U B 6 O3' 53.7 REMARK 620 3 HOH B 63 O 97.8 87.1 REMARK 620 4 HOH B 132 O 73.9 115.7 64.0 REMARK 620 5 HOH B 175 O 77.9 78.8 165.0 126.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K E 305 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G E 2 O6 REMARK 620 2 I E 3 O6 75.2 REMARK 620 3 K E 306 K 118.0 50.4 REMARK 620 4 G F 2 O6 119.8 152.5 122.2 REMARK 620 5 I F 3 O6 149.6 100.3 50.0 77.9 REMARK 620 6 G G 2 O6 73.0 132.0 120.7 75.5 90.0 REMARK 620 7 I G 3 O6 82.0 63.9 51.2 136.7 69.5 76.8 REMARK 620 8 G H 2 O6 78.6 85.1 117.5 76.5 131.6 121.7 146.7 REMARK 620 9 I H 3 O6 134.0 66.9 51.5 88.1 65.3 153.0 102.6 73.4 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K E 306 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 I E 3 O6 REMARK 620 2 G E 4 O6 71.9 REMARK 620 3 K E 307 K 120.1 54.8 REMARK 620 4 I F 3 O6 113.1 154.1 126.8 REMARK 620 5 G F 4 O6 155.2 110.5 55.8 76.0 REMARK 620 6 I G 3 O6 70.1 128.2 122.7 75.1 91.5 REMARK 620 7 G G 4 O6 85.4 71.2 55.0 133.3 72.9 71.9 REMARK 620 8 I H 3 O6 73.6 87.6 123.8 70.6 130.5 113.3 154.0 REMARK 620 9 G H 4 O6 129.9 70.4 56.6 89.4 70.9 159.2 111.6 73.2 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K E 307 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G E 4 O6 REMARK 620 2 G E 5 O6 65.7 REMARK 620 3 K E 308 K 119.0 56.6 REMARK 620 4 G F 4 O6 116.6 157.5 124.2 REMARK 620 5 G F 5 O6 163.7 116.4 59.9 68.2 REMARK 620 6 G G 4 O6 75.9 124.7 122.1 75.7 91.0 REMARK 620 7 G G 5 O6 89.1 72.8 57.5 128.4 76.8 68.2 REMARK 620 8 G H 4 O6 72.5 89.6 122.2 71.0 122.8 115.6 158.8 REMARK 620 9 G H 5 O6 120.1 70.3 56.9 91.3 74.0 163.1 114.4 68.5 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K E 308 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G E 5 O6 REMARK 620 2 U E 6 O4 68.6 REMARK 620 3 G F 5 O6 104.7 166.8 REMARK 620 4 U F 6 O4 166.3 123.7 64.5 REMARK 620 5 G G 5 O6 68.5 116.8 68.8 98.9 REMARK 620 6 U G 6 O4 101.1 77.3 115.6 77.8 68.0 REMARK 620 7 G H 5 O6 66.8 99.8 67.0 113.2 103.4 167.6 REMARK 620 8 U H 6 O4 117.1 78.0 96.0 73.8 164.8 121.8 68.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K H 309 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH E 46 O REMARK 620 2 U H 6 O2' 75.3 REMARK 620 3 U H 6 O3' 126.9 51.7 REMARK 620 4 HOH H 27 O 65.0 76.2 95.7 REMARK 620 5 HOH H 40 O 147.0 121.4 74.2 90.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K F 313 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U F 6 O2' REMARK 620 2 U F 6 O3' 52.6 REMARK 620 3 HOH F 18 O 77.3 99.8 REMARK 620 4 HOH F 186 O 85.6 99.0 138.7 REMARK 620 5 HOH H 81 O 70.0 121.9 73.4 65.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K E 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K E 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K E 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K E 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K H 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K D 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K F 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR B 401 DBREF 2GRB A 1 6 PDB 2GRB 2GRB 1 6 DBREF 2GRB B 1 6 PDB 2GRB 2GRB 1 6 DBREF 2GRB C 1 6 PDB 2GRB 2GRB 1 6 DBREF 2GRB D 1 6 PDB 2GRB 2GRB 1 6 DBREF 2GRB E 1 6 PDB 2GRB 2GRB 1 6 DBREF 2GRB F 1 6 PDB 2GRB 2GRB 1 6 DBREF 2GRB G 1 6 PDB 2GRB 2GRB 1 6 DBREF 2GRB H 1 6 PDB 2GRB 2GRB 1 6 SEQRES 1 A 6 U33 G I G G U SEQRES 1 B 6 U33 G I G G U SEQRES 1 C 6 U33 G I G G U SEQRES 1 D 6 U33 G I G G U SEQRES 1 E 6 U33 G I G G U SEQRES 1 F 6 U33 G I G G U SEQRES 1 G 6 U33 G I G G U SEQRES 1 H 6 U33 G I G G U MODRES 2GRB U33 C 1 DU 5-BROMO-2'-DEOXY URIDINE MODRES 2GRB U33 D 1 DU 5-BROMO-2'-DEOXY URIDINE MODRES 2GRB U33 E 1 DU 5-BROMO-2'-DEOXY URIDINE MODRES 2GRB U33 F 1 DU 5-BROMO-2'-DEOXY URIDINE MODRES 2GRB U33 G 1 DU 5-BROMO-2'-DEOXY URIDINE HET U33 C 1 17 HET U33 D 1 17 HET U33 E 1 17 HET U33 F 1 17 HET U33 G 1 17 HET K A 301 1 HET K A 302 1 HET K A 303 1 HET K A 304 1 HET SR B 401 1 HET K D 312 1 HET K E 305 1 HET K E 306 1 HET K E 307 1 HET K E 308 1 HET K F 313 1 HET K H 309 1 HETNAM U33 5-BROMO-2'-DEOXY URIDINE HETNAM K POTASSIUM ION HETNAM SR STRONTIUM ION FORMUL 3 U33 5(C9 H11 BR N2 O5) FORMUL 9 K 11(K 1+) FORMUL 13 SR SR 2+ FORMUL 21 HOH *178(H2 O) LINK O3' U33 C 1 P G C 2 1555 1555 1.60 LINK O3' U33 D 1 P G D 2 1555 1555 1.60 LINK O3' U33 E 1 P G E 2 1555 1555 1.60 LINK O3' U33 F 1 P G F 2 1555 1555 1.60 LINK O3' U33 G 1 P G G 2 1555 1555 1.60 LINK O6 G A 2 K K A 304 1555 1555 2.73 LINK O6 I A 3 K K A 303 1555 1555 2.77 LINK O6 I A 3 K K A 304 1555 1555 3.07 LINK O6 G A 4 K K A 302 1555 1555 2.82 LINK O6 G A 4 K K A 303 1555 1555 2.85 LINK O6 G A 5 K K A 301 1555 1555 2.97 LINK O6 G A 5 K K A 302 1555 1555 2.74 LINK O4 U A 6 K K A 301 1555 1555 2.78 LINK K K A 301 K K A 302 1555 1555 3.40 LINK K K A 301 O6 G B 5 1555 1555 2.99 LINK K K A 301 O4 U B 6 1555 1555 2.86 LINK K K A 301 O6 G C 5 1555 1555 3.06 LINK K K A 301 O4 U C 6 1555 1555 2.74 LINK K K A 301 O6 G D 5 1555 1555 3.05 LINK K K A 301 O4 U D 6 1555 1555 2.92 LINK K K A 302 K K A 303 1555 1555 3.16 LINK K K A 302 O6 G B 4 1555 1555 2.84 LINK K K A 302 O6 G B 5 1555 1555 2.76 LINK K K A 302 O6 G C 4 1555 1555 2.88 LINK K K A 302 O6 G C 5 1555 1555 2.77 LINK K K A 302 O6 G D 4 1555 1555 2.74 LINK K K A 302 O6 G D 5 1555 1555 2.83 LINK K K A 303 K K A 304 1555 1555 3.42 LINK K K A 303 O6 I B 3 1555 1555 2.88 LINK K K A 303 O6 G B 4 1555 1555 2.87 LINK K K A 303 O6 I C 3 1555 1555 2.99 LINK K K A 303 O6 G C 4 1555 1555 2.99 LINK K K A 303 O6 I D 3 1555 1555 2.68 LINK K K A 303 O6 G D 4 1555 1555 2.87 LINK K K A 304 O6 G B 2 1555 1555 2.67 LINK K K A 304 O6 I B 3 1555 1555 2.94 LINK K K A 304 O6 G C 2 1555 1555 2.90 LINK K K A 304 O6 I C 3 1555 1555 3.03 LINK K K A 304 O6 G D 2 1555 1555 2.70 LINK K K A 304 O6 I D 3 1555 1555 3.09 LINK O HOH A 315 K K D 312 1555 1555 2.62 LINK O2' U B 6 SR SR B 401 1555 1555 3.15 LINK O3' U B 6 SR SR B 401 1555 1555 2.78 LINK O HOH B 63 SR SR B 401 1555 1555 2.83 LINK O HOH B 132 SR SR B 401 1555 1555 2.49 LINK O HOH B 175 SR SR B 401 1555 1555 2.56 LINK O2' U D 6 K K D 312 1555 1555 3.42 LINK O3' U D 6 K K D 312 1555 1555 3.66 LINK K K D 312 O HOH D 322 1555 1555 2.39 LINK K K D 312 O HOH D 326 1555 1555 3.14 LINK O6 G E 2 K K E 305 1555 1555 2.79 LINK O6 I E 3 K K E 305 1555 1555 3.12 LINK O6 I E 3 K K E 306 1555 1555 2.84 LINK O6 G E 4 K K E 306 1555 1555 2.96 LINK O6 G E 4 K K E 307 1555 1555 2.80 LINK O6 G E 5 K K E 307 1555 1555 2.91 LINK O6 G E 5 K K E 308 1555 1555 3.00 LINK O4 U E 6 K K E 308 1555 1555 2.82 LINK O HOH E 46 K K H 309 1555 1555 2.64 LINK K K E 305 K K E 306 1555 1555 3.49 LINK K K E 305 O6 G F 2 1555 1555 2.68 LINK K K E 305 O6 I F 3 1555 1555 2.97 LINK K K E 305 O6 G G 2 1555 1555 2.82 LINK K K E 305 O6 I G 3 1555 1555 3.05 LINK K K E 305 O6 G H 2 1555 1555 2.78 LINK K K E 305 O6 I H 3 1555 1555 3.09 LINK K K E 306 K K E 307 1555 1555 3.11 LINK K K E 306 O6 I F 3 1555 1555 2.77 LINK K K E 306 O6 G F 4 1555 1555 2.81 LINK K K E 306 O6 I G 3 1555 1555 2.86 LINK K K E 306 O6 G G 4 1555 1555 2.95 LINK K K E 306 O6 I H 3 1555 1555 2.88 LINK K K E 306 O6 G H 4 1555 1555 2.79 LINK K K E 307 K K E 308 1555 1555 3.36 LINK K K E 307 O6 G F 4 1555 1555 2.78 LINK K K E 307 O6 G F 5 1555 1555 2.78 LINK K K E 307 O6 G G 4 1555 1555 2.80 LINK K K E 307 O6 G G 5 1555 1555 2.77 LINK K K E 307 O6 G H 4 1555 1555 2.81 LINK K K E 307 O6 G H 5 1555 1555 2.80 LINK K K E 308 O6 G F 5 1555 1555 3.10 LINK K K E 308 O4 U F 6 1555 1555 2.86 LINK K K E 308 O6 G G 5 1555 1555 3.00 LINK K K E 308 O4 U G 6 1555 1555 2.85 LINK K K E 308 O6 G H 5 1555 1555 2.98 LINK K K E 308 O4 U H 6 1555 1555 2.86 LINK O2' U F 6 K K F 313 1555 1555 2.91 LINK O3' U F 6 K K F 313 1555 1555 3.16 LINK O HOH F 18 K K F 313 1555 1555 2.68 LINK O HOH F 186 K K F 313 1555 1555 3.08 LINK K K F 313 O HOH H 81 1555 1555 2.93 LINK O2' U H 6 K K H 309 1555 1555 3.13 LINK O3' U H 6 K K H 309 1555 1555 2.99 LINK O HOH H 27 K K H 309 1555 1555 2.70 LINK O HOH H 40 K K H 309 1555 1555 2.90 SITE 1 AC1 9 G A 5 U A 6 K A 302 G B 5 SITE 2 AC1 9 U B 6 G C 5 U C 6 G D 5 SITE 3 AC1 9 U D 6 SITE 1 AC2 10 G A 4 G A 5 K A 301 K A 303 SITE 2 AC2 10 G B 4 G B 5 G C 4 G C 5 SITE 3 AC2 10 G D 4 G D 5 SITE 1 AC3 10 I A 3 G A 4 K A 302 K A 304 SITE 2 AC3 10 I B 3 G B 4 I C 3 G C 4 SITE 3 AC3 10 I D 3 G D 4 SITE 1 AC4 9 G A 2 I A 3 K A 303 G B 2 SITE 2 AC4 9 I B 3 G C 2 I C 3 G D 2 SITE 3 AC4 9 I D 3 SITE 1 AC5 9 G E 2 I E 3 K E 306 G F 2 SITE 2 AC5 9 I F 3 G G 2 I G 3 G H 2 SITE 3 AC5 9 I H 3 SITE 1 AC6 10 I E 3 G E 4 K E 305 K E 307 SITE 2 AC6 10 I F 3 G F 4 I G 3 G G 4 SITE 3 AC6 10 I H 3 G H 4 SITE 1 AC7 10 G E 4 G E 5 K E 306 K E 308 SITE 2 AC7 10 G F 4 G F 5 G G 4 G G 5 SITE 3 AC7 10 G H 4 G H 5 SITE 1 AC8 9 G E 5 U E 6 K E 307 G F 5 SITE 2 AC8 9 U F 6 G G 5 U G 6 G H 5 SITE 3 AC8 9 U H 6 SITE 1 AC9 4 HOH E 46 U H 6 HOH H 27 HOH H 40 SITE 1 BC1 3 HOH A 315 U D 6 HOH D 322 SITE 1 BC2 4 U F 6 HOH F 18 HOH F 186 HOH H 81 SITE 1 BC3 4 U B 6 HOH B 63 HOH B 132 HOH B 175 CRYST1 29.060 52.738 37.344 90.00 102.98 90.00 P 1 21 1 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 0.034412 0.000000 0.007932 0.00000 SCALE2 0.000000 0.018962 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027480 0.00000