HEADER RNA 08-MAR-17 5NDH TITLE THE STRUCTURE OF THE G. VIOLACEUS GUANIDINE II RIBOSWITCH P2 STEM-LOOP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*(CBV) COMPND 3 P*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*GP*C)-3'); COMPND 4 CHAIN: A, B, C, D; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: GLOEOBACTER VIOLACEUS; SOURCE 4 ORGANISM_TAXID: 33072 KEYWDS GUANIDINE II RIBOSWITCH, STEM-LOOP, TETRA LOOP, DIMER, RNA EXPDTA X-RAY DIFFRACTION AUTHOR L.HUANG,J.WANG,D.M.J.LILLEY REVDAT 3 30-AUG-17 5NDH 1 REMARK REVDAT 2 05-JUL-17 5NDH 1 JRNL REVDAT 1 31-MAY-17 5NDH 0 JRNL AUTH L.HUANG,J.WANG,D.M.J.LILLEY JRNL TITL THE STRUCTURE OF THE GUANIDINE-II RIBOSWITCH. JRNL REF CELL CHEM BIOL V. 24 695 2017 JRNL REFN ESSN 2451-9456 JRNL PMID 28529131 JRNL DOI 10.1016/J.CHEMBIOL.2017.05.014 REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2219: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 49436 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 : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2455 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 50.1849 - 4.7422 1.00 2597 176 0.1514 0.1914 REMARK 3 2 4.7422 - 3.7644 1.00 2646 146 0.1493 0.1739 REMARK 3 3 3.7644 - 3.2887 1.00 2652 132 0.1534 0.1408 REMARK 3 4 3.2887 - 2.9880 0.99 2619 144 0.1831 0.1837 REMARK 3 5 2.9880 - 2.7739 1.00 2646 141 0.2205 0.2391 REMARK 3 6 2.7739 - 2.6104 1.00 2646 121 0.2406 0.2997 REMARK 3 7 2.6104 - 2.4796 1.00 2654 156 0.2431 0.2774 REMARK 3 8 2.4796 - 2.3717 1.00 2632 128 0.2557 0.2663 REMARK 3 9 2.3717 - 2.2804 1.00 2647 134 0.2583 0.2741 REMARK 3 10 2.2804 - 2.2017 1.00 2624 144 0.2772 0.3154 REMARK 3 11 2.2017 - 2.1329 1.00 2666 127 0.2852 0.2940 REMARK 3 12 2.1329 - 2.0719 0.99 2635 131 0.3094 0.3176 REMARK 3 13 2.0719 - 2.0173 0.99 2615 150 0.3264 0.3602 REMARK 3 14 2.0173 - 1.9681 0.99 2597 133 0.3656 0.3504 REMARK 3 15 1.9681 - 1.9234 0.98 2622 129 0.3739 0.3913 REMARK 3 16 1.9234 - 1.8824 0.96 2571 127 0.3807 0.4013 REMARK 3 17 1.8824 - 1.8448 0.95 2533 109 0.3989 0.4011 REMARK 3 18 1.8448 - 1.8100 0.90 2379 127 0.4185 0.3869 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.70 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 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 : 0.005 1556 REMARK 3 ANGLE : 2.055 2424 REMARK 3 CHIRALITY : 0.039 312 REMARK 3 PLANARITY : 0.006 68 REMARK 3 DIHEDRAL : 10.451 720 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.1912 46.1383 13.8955 REMARK 3 T TENSOR REMARK 3 T11: 0.3149 T22: 0.3374 REMARK 3 T33: 0.3695 T12: -0.0475 REMARK 3 T13: -0.0408 T23: 0.0451 REMARK 3 L TENSOR REMARK 3 L11: 0.5762 L22: 6.6858 REMARK 3 L33: 0.2316 L12: 0.7111 REMARK 3 L13: -0.2052 L23: 0.5638 REMARK 3 S TENSOR REMARK 3 S11: -0.0023 S12: -0.0131 S13: 0.1387 REMARK 3 S21: -0.2399 S22: -0.1042 S23: -0.3906 REMARK 3 S31: -0.0548 S32: -0.0322 S33: 0.1249 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.2622 5.1741 11.7150 REMARK 3 T TENSOR REMARK 3 T11: 0.3744 T22: 0.3082 REMARK 3 T33: 0.3352 T12: -0.0505 REMARK 3 T13: -0.0625 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: 4.1639 L22: 1.0494 REMARK 3 L33: 0.6855 L12: 0.3001 REMARK 3 L13: -0.3524 L23: 0.3086 REMARK 3 S TENSOR REMARK 3 S11: -0.0139 S12: -0.1853 S13: 0.1503 REMARK 3 S21: 0.1400 S22: -0.0287 S23: -0.0986 REMARK 3 S31: -0.0280 S32: 0.0371 S33: -0.0038 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.6230 25.5320 3.0236 REMARK 3 T TENSOR REMARK 3 T11: 0.3901 T22: 0.2802 REMARK 3 T33: 0.2507 T12: -0.0491 REMARK 3 T13: -0.0063 T23: 0.0459 REMARK 3 L TENSOR REMARK 3 L11: 1.3433 L22: 2.9869 REMARK 3 L33: 2.7038 L12: -0.1284 REMARK 3 L13: -0.0552 L23: 1.3653 REMARK 3 S TENSOR REMARK 3 S11: 0.1026 S12: -0.0357 S13: 0.0380 REMARK 3 S21: -0.3138 S22: 0.0018 S23: 0.0423 REMARK 3 S31: -0.1226 S32: -0.1911 S33: -0.1637 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.1431 2.1838 22.3261 REMARK 3 T TENSOR REMARK 3 T11: 0.3491 T22: 0.4058 REMARK 3 T33: 0.2960 T12: -0.0710 REMARK 3 T13: -0.0578 T23: 0.0139 REMARK 3 L TENSOR REMARK 3 L11: 2.2800 L22: 1.3227 REMARK 3 L33: 3.8447 L12: -0.2884 REMARK 3 L13: -1.1488 L23: -0.4821 REMARK 3 S TENSOR REMARK 3 S11: 0.0079 S12: -0.2186 S13: -0.1423 REMARK 3 S21: -0.0753 S22: 0.1252 S23: 0.0106 REMARK 3 S31: -0.0057 S32: 0.1700 S33: -0.1160 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 5NDH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200003925. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92011 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49436 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 50.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 1.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M MAGNESIUM SULFATE, 0.05 M REMARK 280 SODIUM CACODYLATE PH 6.0, 1.8 M LITHIUM SULFATE MONOHYDRATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 24.36350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.43100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.91250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.43100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.36350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.91250 REMARK 290 SMTRY3 4 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 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, C 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 O3' G A 1 O3P CBV A 2 0.40 REMARK 500 O3' G B 1 O2P CBV B 2 0.41 REMARK 500 HO3' CBV B 2 P G B 3 0.80 REMARK 500 HO3' CBV C 2 P G C 3 0.80 REMARK 500 HO3' CBV D 2 P G D 3 0.81 REMARK 500 HO3' CBV A 2 P G A 3 0.84 REMARK 500 O3P CBV C 2 O HOH C 201 1.90 REMARK 500 O HOH B 208 O HOH B 216 2.15 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 103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 15 O2' REMARK 620 2 HOH A 218 O 170.7 REMARK 620 3 HOH A 216 O 83.9 87.1 REMARK 620 4 G B 4 O2' 115.4 73.7 145.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C C 8 O2' REMARK 620 2 C C 8 O2 71.6 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 GAI 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 MG A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GAI B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GAI C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GAI D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide G B 1 and CBV B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide CBV B 2 and G B 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide G C 1 and CBV C 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide CBV C 2 and G C 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide G D 1 and CBV D 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide CBV D 2 and G D 3 DBREF 5NDH A 1 16 PDB 5NDH 5NDH 1 16 DBREF 5NDH B 1 16 PDB 5NDH 5NDH 1 16 DBREF 5NDH C 1 16 PDB 5NDH 5NDH 1 16 DBREF 5NDH D 1 16 PDB 5NDH 5NDH 1 16 SEQRES 1 A 16 G CBV G G G G A C G A C C C SEQRES 2 A 16 C G C SEQRES 1 B 16 G CBV G G G G A C G A C C C SEQRES 2 B 16 C G C SEQRES 1 C 16 G CBV G G G G A C G A C C C SEQRES 2 C 16 C G C SEQRES 1 D 16 G CBV G G G G A C G A C C C SEQRES 2 D 16 C G C HET CBV A 2 33 HET CBV B 2 33 HET CBV C 2 33 HET CBV D 2 33 HET GAI A 101 9 HET NA A 102 1 HET MG A 103 1 HET GAI B 101 9 HET NA B 102 1 HET NA B 103 1 HET GAI C 101 9 HET NA C 102 1 HET GAI D 101 9 HET SO4 D 102 5 HET SO4 D 103 5 HETNAM CBV 5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM GAI GUANIDINE HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION FORMUL 1 CBV 4(C9 H13 BR N3 O8 P) FORMUL 5 GAI 4(C H5 N3) FORMUL 6 NA 4(NA 1+) FORMUL 7 MG MG 2+ FORMUL 14 SO4 2(O4 S 2-) FORMUL 16 HOH *81(H2 O) LINK O3' G A 1 P CBV A 2 1555 1555 1.62 LINK O3' CBV A 2 P G A 3 1555 1555 1.61 LINK O2' G A 15 MG MG A 103 1555 1555 2.70 LINK O3' G B 1 P CBV B 2 1555 1555 1.63 LINK O3' CBV B 2 P G B 3 1555 1555 1.61 LINK O6 G B 3 NA NA B 102 1555 1555 2.86 LINK O3' G C 1 P CBV C 2 1555 1555 1.61 LINK O3' CBV C 2 P G C 3 1555 1555 1.61 LINK O2' C C 8 NA NA C 102 1555 1555 3.05 LINK O2 C C 8 NA NA C 102 1555 1555 3.14 LINK O3' G D 1 P CBV D 2 1555 1555 1.61 LINK O3' CBV D 2 P G D 3 1555 1555 1.60 LINK NA NA A 102 O HOH C 220 1555 1555 2.57 LINK MG MG A 103 O HOH A 218 1555 1555 2.47 LINK MG MG A 103 O HOH A 216 1555 1555 2.06 LINK O2' G B 4 MG MG A 103 1555 1545 2.99 SITE 1 AC1 4 G A 6 A A 7 C A 8 G A 9 SITE 1 AC2 2 C A 8 HOH C 220 SITE 1 AC3 5 G A 15 C A 16 HOH A 216 HOH A 218 SITE 2 AC3 5 G B 4 SITE 1 AC4 4 G B 6 A B 7 C B 8 G B 9 SITE 1 AC5 3 CBV B 2 G B 3 G B 4 SITE 1 AC6 1 G B 1 SITE 1 AC7 4 G C 6 A C 7 C C 8 G C 9 SITE 1 AC8 2 C A 11 C C 8 SITE 1 AC9 4 G D 6 A D 7 C D 8 G D 9 SITE 1 AD1 6 A B 10 G C 4 G C 5 A D 10 SITE 2 AD1 6 HOH D 202 HOH D 218 SITE 1 AD2 4 G D 4 C D 13 C D 14 HOH D 205 SITE 1 AD3 8 G B 3 G B 15 C B 16 NA B 102 SITE 2 AD3 8 NA B 103 HOH B 213 G C 1 C C 16 SITE 1 AD4 10 G A 15 HOH A 206 HOH A 207 G B 1 SITE 2 AD4 10 G B 4 C B 14 G B 15 C B 16 SITE 3 AD4 10 NA B 102 HOH B 213 SITE 1 AD5 8 G B 1 C B 16 G C 3 G C 15 SITE 2 AD5 8 C C 16 HOH C 201 HOH C 207 HOH C 213 SITE 1 AD6 9 A B 10 G C 1 G C 4 C C 14 SITE 2 AD6 9 G C 15 C C 16 HOH C 201 HOH C 212 SITE 3 AD6 9 HOH C 213 SITE 1 AD7 7 G A 1 C A 16 HOH A 211 G D 3 SITE 2 AD7 7 G D 15 C D 16 HOH D 222 SITE 1 AD8 7 A A 10 G D 1 G D 4 C D 14 SITE 2 AD8 7 G D 15 HOH D 208 HOH D 222 CRYST1 48.727 57.825 100.862 90.00 90.00 90.00 P 21 21 21 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 0.020523 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017293 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009915 0.00000 MASTER 378 0 15 0 0 0 27 6 0 0 0 8 END