PDB Short entry for 3EY3 HEADER DNA 17-OCT-08 3EY3 TITLE A CONFORMATIONAL TRANSITION IN THE STRUCTURE OF A 2'-THIOMETHYL- TITLE 2 MODIFIED DNA VISUALIZED AT HIGH RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3'; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED MODIFIED DNA (OLIGONUCLEOTIDE) KEYWDS MODIFIED DNA DUPLEX, 2'-THIOMETHYL URIDINE, MODIFIED SUGAR, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.EGLI,P.S.PALLAN REVDAT 5 06-SEP-23 3EY3 1 REMARK LINK REVDAT 4 25-OCT-17 3EY3 1 REMARK REVDAT 3 26-MAY-09 3EY3 1 REMARK REVDAT 2 05-MAY-09 3EY3 1 JRNL REVDAT 1 28-APR-09 3EY3 0 JRNL AUTH P.S.PALLAN,T.P.PRAKASH,F.LI,R.L.EOFF,M.MANOHARAN,M.EGLI JRNL TITL A CONFORMATIONAL TRANSITION IN THE STRUCTURE OF A JRNL TITL 2 2'-THIOMETHYL-MODIFIED DNA VISUALIZED AT HIGH RESOLUTION. JRNL REF CHEM.COMMUN.(CAMB.) V. 15 2017 2009 JRNL REFN ISSN 1359-7345 JRNL PMID 19333476 JRNL DOI 10.1039/B822781K 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) : 6.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 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) : 0.147 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) : 4317 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL 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 : 980 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 349 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) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.028 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 : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3EY3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000049911. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 120 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) : 0.9200 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43276 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 6.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.1000 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) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.920 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: MODIFIED DNA DUPLEX ALONE FROM PDB 3EY1 (GENERATED REMARK 200 BY USING THE ROTATION MATRIX -1.0 0.0 0.0; 0.0 1.0 0.0; 0.0 0.0 - REMARK 200 1.0) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% MPD, 20 MM NA CACODYLATE PH 7.0, 6 REMARK 280 MM SPERMINE TETRA-HCL, 20 MM LICL, 40 MM SRCL2., VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K 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 20.03700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.35600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.60900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.35600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.03700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.60900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 DC A 101 O4' - C1' - N1 ANGL. DEV. = -5.8 DEGREES REMARK 500 DG A 104 C3' - O3' - P ANGL. DEV. = 9.8 DEGREES REMARK 500 DC A 109 O4' - C1' - N1 ANGL. DEV. = -4.2 DEGREES REMARK 500 DC A 111 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA B 205 O4' - C1' - N9 ANGL. DEV. = -4.2 DEGREES REMARK 500 DA B 206 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES REMARK 500 DC B 209 O4' - C1' - N1 ANGL. DEV. = -6.0 DEGREES REMARK 500 DC B 211 O4' - C1' - N1 ANGL. DEV. = -6.7 DEGREES REMARK 500 DC C 301 O4' - C1' - N1 ANGL. DEV. = -6.9 DEGREES REMARK 500 DA C 305 N1 - C2 - N3 ANGL. DEV. = -3.4 DEGREES REMARK 500 DA C 305 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 DA C 306 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 DA C 306 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES REMARK 500 DC C 309 O4' - C1' - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 DC C 311 N1 - C1' - C2' ANGL. DEV. = 10.5 DEGREES REMARK 500 DC C 311 O4' - C1' - N1 ANGL. DEV. = -12.1 DEGREES REMARK 500 DC D 401 O4' - C1' - N1 ANGL. DEV. = -6.7 DEGREES REMARK 500 DA D 405 O4' - C1' - N9 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA D 405 N1 - C6 - N6 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC D 409 O4' - C1' - N1 ANGL. DEV. = -6.0 DEGREES REMARK 500 DG D 410 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG D 410 C5 - C6 - O6 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC D 411 O4' - C1' - N1 ANGL. DEV. = -5.3 DEGREES REMARK 500 DG D 412 O4' - C1' - N9 ANGL. DEV. = 6.8 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 SR A 504 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 612 O REMARK 620 2 HOH A 615 O 76.5 REMARK 620 3 HOH A 616 O 78.7 72.9 REMARK 620 4 HOH A 617 O 92.2 140.9 68.2 REMARK 620 5 HOH B 610 O 145.3 132.3 123.6 75.6 REMARK 620 6 HOH B 611 O 145.1 73.3 76.0 100.2 69.5 REMARK 620 7 HOH B 613 O 73.3 134.9 130.8 73.3 72.1 141.5 REMARK 620 8 HOH B 614 O 97.2 71.1 143.7 148.0 79.4 89.3 80.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR A 506 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 623 O REMARK 620 2 HOH A 710 O 74.1 REMARK 620 3 HOH A 719 O 87.7 84.5 REMARK 620 4 HOH A 870 O 74.7 139.3 68.9 REMARK 620 5 HOH A 877 O 132.3 61.0 73.5 132.2 REMARK 620 6 HOH A 930 O 137.8 146.0 104.7 72.8 89.8 REMARK 620 7 HOH A 931 O 75.7 124.1 139.5 71.1 143.1 68.8 REMARK 620 8 HOH B 878 O 102.5 69.7 147.9 143.1 77.3 88.1 72.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR B 501 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA B 205 OP1 REMARK 620 2 HOH B 601 O 145.4 REMARK 620 3 HOH B 602 O 146.7 66.9 REMARK 620 4 HOH B 603 O 73.9 138.8 72.8 REMARK 620 5 HOH B 604 O 77.9 68.5 128.8 139.0 REMARK 620 6 HOH B 879 O 85.9 91.3 85.4 77.1 71.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR C 503 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 605 O REMARK 620 2 HOH C 606 O 91.8 REMARK 620 3 HOH C 609 O 74.2 74.1 REMARK 620 4 HOH C 665 O 143.5 98.3 75.2 REMARK 620 5 HOH C 728 O 68.6 77.1 131.5 147.9 REMARK 620 6 HOH D 607 O 99.2 144.0 141.9 92.9 75.3 REMARK 620 7 HOH D 608 O 76.5 147.1 73.2 76.1 124.2 68.8 REMARK 620 8 HOH D 727 O 141.8 76.1 133.3 74.6 73.4 74.1 130.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR C 507 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 642 O REMARK 620 2 HOH C 720 O 86.7 REMARK 620 3 HOH C 805 O 76.8 77.6 REMARK 620 4 HOH C 874 O 152.8 116.8 119.4 REMARK 620 5 HOH C 876 O 66.8 135.8 125.3 86.2 REMARK 620 6 HOH C 929 O 153.1 74.7 80.2 53.4 139.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR D 505 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 618 O REMARK 620 2 HOH C 620 O 137.6 REMARK 620 3 HOH C 729 O 71.2 66.7 REMARK 620 4 HOH C 730 O 77.9 144.2 149.1 REMARK 620 5 HOH C 871 O 135.3 74.2 130.3 74.2 REMARK 620 6 HOH C 938 O 77.1 91.1 80.1 94.2 71.0 REMARK 620 7 HOH D 619 O 132.4 78.4 124.3 76.8 73.2 144.2 REMARK 620 8 HOH D 666 O 73.9 100.6 77.0 93.7 141.4 147.4 68.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR D 502 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 412 OP1 REMARK 620 2 HOH D 721 O 72.2 REMARK 620 3 HOH D 722 O 114.1 73.4 REMARK 620 4 HOH D 723 O 76.8 111.8 66.6 REMARK 620 5 HOH D 724 O 83.3 149.9 134.3 78.2 REMARK 620 6 HOH D 725 O 78.9 83.0 146.9 145.6 75.2 REMARK 620 7 HOH D 726 O 147.3 83.5 77.9 133.8 110.7 76.7 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 SR B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR D 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR C 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR D 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR C 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD D 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EY1 RELATED DB: PDB REMARK 900 RELATED ID: 3EY2 RELATED DB: PDB DBREF 3EY3 A 101 112 PDB 3EY3 3EY3 101 112 DBREF 3EY3 B 201 212 PDB 3EY3 3EY3 201 212 DBREF 3EY3 C 301 312 PDB 3EY3 3EY3 301 312 DBREF 3EY3 D 401 412 PDB 3EY3 3EY3 401 412 SEQRES 1 A 12 DC DG DC DG DA DA USM USM DC DG DC DG SEQRES 1 B 12 DC DG DC DG DA DA USM USM DC DG DC DG SEQRES 1 C 12 DC DG DC DG DA DA USM USM DC DG DC DG SEQRES 1 D 12 DC DG DC DG DA DA USM USM DC DG DC DG MODRES 3EY3 USM A 107 DU MODRES 3EY3 USM A 108 DU MODRES 3EY3 USM B 207 DU MODRES 3EY3 USM B 208 DU MODRES 3EY3 USM C 307 DU MODRES 3EY3 USM C 308 DU MODRES 3EY3 USM D 407 DU MODRES 3EY3 USM D 408 DU HET USM A 107 21 HET USM A 108 21 HET USM B 207 21 HET USM B 208 21 HET USM C 307 25 HET USM C 308 21 HET USM D 407 21 HET USM D 408 21 HET SR A 504 1 HET SR A 506 1 HET SR B 501 1 HET MPD B1002 8 HET SR C 503 1 HET SR C 507 1 HET SR D 502 1 HET SR D 505 1 HET MPD D1001 8 HETNAM USM 2'-S-METHYL-2'-THIOURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM SR STRONTIUM ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 1 USM 8(C10 H15 N2 O8 P S) FORMUL 5 SR 7(SR 2+) FORMUL 8 MPD 2(C6 H14 O2) FORMUL 14 HOH *349(H2 O) LINK O3' DA A 106 P USM A 107 1555 1555 1.58 LINK O3' USM A 107 P USM A 108 1555 1555 1.61 LINK O3' USM A 108 P DC A 109 1555 1555 1.59 LINK O3' DA B 206 P USM B 207 1555 1555 1.60 LINK O3' USM B 207 P USM B 208 1555 1555 1.60 LINK O3' USM B 208 P DC B 209 1555 1555 1.60 LINK O3'A DA C 306 P AUSM C 307 1555 1555 1.60 LINK O3'B DA C 306 P BUSM C 307 1555 1555 1.60 LINK O3' USM C 307 P USM C 308 1555 1555 1.62 LINK O3' USM C 308 P DC C 309 1555 1555 1.61 LINK O3' DA D 406 P USM D 407 1555 1555 1.61 LINK O3' USM D 407 P USM D 408 1555 1555 1.60 LINK O3' USM D 408 P DC D 409 1555 1555 1.63 LINK SR SR A 504 O HOH A 612 1555 1555 2.68 LINK SR SR A 504 O HOH A 615 1555 1555 2.69 LINK SR SR A 504 O HOH A 616 1555 1555 2.61 LINK SR SR A 504 O HOH A 617 1555 1555 2.63 LINK SR SR A 504 O HOH B 610 1555 1555 2.68 LINK SR SR A 504 O HOH B 611 1555 1555 2.63 LINK SR SR A 504 O HOH B 613 1555 1555 2.64 LINK SR SR A 504 O HOH B 614 1555 1555 2.56 LINK SR SR A 506 O HOH A 623 1555 1555 2.57 LINK SR SR A 506 O HOH A 710 1555 1555 2.63 LINK SR SR A 506 O HOH A 719 1555 1555 2.46 LINK SR SR A 506 O HOH A 870 1555 1555 2.50 LINK SR SR A 506 O HOH A 877 1555 1555 2.57 LINK SR SR A 506 O HOH A 930 1555 1555 2.30 LINK SR SR A 506 O HOH A 931 1555 1555 2.65 LINK SR SR A 506 O HOH B 878 1555 1555 2.76 LINK OP1 DA B 205 SR SR B 501 1555 1555 2.51 LINK SR SR B 501 O HOH B 601 1555 1555 2.59 LINK SR SR B 501 O HOH B 602 1555 1555 2.72 LINK SR SR B 501 O HOH B 603 1555 1555 2.66 LINK SR SR B 501 O HOH B 604 1555 1555 2.64 LINK SR SR B 501 O HOH B 879 1555 1555 2.60 LINK SR SR C 503 O HOH C 605 1555 1555 2.65 LINK SR SR C 503 O HOH C 606 1555 1555 2.62 LINK SR SR C 503 O HOH C 609 1555 1555 2.67 LINK SR SR C 503 O HOH C 665 1555 1555 2.59 LINK SR SR C 503 O HOH C 728 1555 1555 2.70 LINK SR SR C 503 O HOH D 607 1555 1555 2.57 LINK SR SR C 503 O HOH D 608 1555 1555 2.64 LINK SR SR C 503 O HOH D 727 1555 1555 2.66 LINK SR SR C 507 O HOH C 642 1555 1555 2.71 LINK SR SR C 507 O HOH C 720 1555 1555 2.53 LINK SR SR C 507 O HOH C 805 1555 1555 2.63 LINK SR SR C 507 O HOH C 874 1555 1555 2.36 LINK SR SR C 507 O HOH C 876 1555 1555 2.53 LINK SR SR C 507 O HOH C 929 1555 1555 2.67 LINK O HOH C 618 SR SR D 505 1555 1555 2.53 LINK O HOH C 620 SR SR D 505 1555 1555 2.61 LINK O HOH C 729 SR SR D 505 1555 1555 2.58 LINK O HOH C 730 SR SR D 505 1555 1555 2.64 LINK O HOH C 871 SR SR D 505 1555 1555 2.60 LINK O HOH C 938 SR SR D 505 1555 1555 2.62 LINK OP1 DG D 412 SR SR D 502 1555 1555 2.61 LINK SR SR D 502 O HOH D 721 1555 1555 2.53 LINK SR SR D 502 O HOH D 722 1555 1555 2.61 LINK SR SR D 502 O HOH D 723 1555 1555 2.63 LINK SR SR D 502 O HOH D 724 1555 1555 2.43 LINK SR SR D 502 O HOH D 725 1555 1555 2.70 LINK SR SR D 502 O HOH D 726 1555 1555 2.60 LINK SR SR D 505 O HOH D 619 1555 1555 2.68 LINK SR SR D 505 O HOH D 666 1555 1555 2.56 SITE 1 AC1 8 DA B 205 HOH B 601 HOH B 602 HOH B 603 SITE 2 AC1 8 HOH B 604 HOH B 629 HOH B 872 HOH B 879 SITE 1 AC2 8 DG D 412 HOH D 721 HOH D 722 HOH D 723 SITE 2 AC2 8 HOH D 724 HOH D 725 HOH D 726 HOH D 873 SITE 1 AC3 8 HOH C 605 HOH C 606 HOH C 609 HOH C 665 SITE 2 AC3 8 HOH C 728 HOH D 607 HOH D 608 HOH D 727 SITE 1 AC4 8 HOH A 612 HOH A 615 HOH A 616 HOH A 617 SITE 2 AC4 8 HOH B 610 HOH B 611 HOH B 613 HOH B 614 SITE 1 AC5 8 HOH C 618 HOH C 620 HOH C 729 HOH C 730 SITE 2 AC5 8 HOH C 871 HOH C 938 HOH D 619 HOH D 666 SITE 1 AC6 8 HOH A 623 HOH A 710 HOH A 719 HOH A 870 SITE 2 AC6 8 HOH A 877 HOH A 930 HOH A 931 HOH B 878 SITE 1 AC7 7 HOH C 642 HOH C 720 HOH C 805 HOH C 874 SITE 2 AC7 7 HOH C 875 HOH C 876 HOH C 929 SITE 1 AC8 7 DG B 212 HOH B 764 HOH C 677 DA D 406 SITE 2 AC8 7 USM D 407 HOH D 634 HOH D 708 SITE 1 AC9 4 HOH A 633 DA B 206 USM B 207 HOH B 643 CRYST1 40.074 43.218 88.712 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 0.024954 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023139 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011272 0.00000