HEADER RNA 02-MAR-17 5V1L TITLE STRUCTURE OF S-GNA DODECAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*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 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS GLYCOL NUCLEIC ACID, GNA, RNA, RNA X-RAY STRUCTURE, NUCLEASE KEYWDS 2 STABILITY, MODIFIED RNA EXPDTA X-RAY DIFFRACTION AUTHOR P.S.PALLAN,M.EGLI REVDAT 4 22-JUN-22 5V1L 1 REMARK SEQRES LINK REVDAT 3 16-AUG-17 5V1L 1 REMARK REVDAT 2 12-JUL-17 5V1L 1 JRNL REVDAT 1 14-JUN-17 5V1L 0 JRNL AUTH M.K.SCHLEGEL,D.J.FOSTER,A.V.KEL'IN,I.ZLATEV,A.BISBE, JRNL AUTH 2 M.JAYARAMAN,J.G.LACKEY,K.G.RAJEEV,K.CHARISSE,J.HARP, JRNL AUTH 3 P.S.PALLAN,M.A.MAIER,M.EGLI,M.MANOHARAN JRNL TITL CHIRALITY DEPENDENT POTENCY ENHANCEMENT AND STRUCTURAL JRNL TITL 2 IMPACT OF GLYCOL NUCLEIC ACID MODIFICATION ON SIRNA. JRNL REF J. AM. CHEM. SOC. V. 139 8537 2017 JRNL REFN ESSN 1520-5126 JRNL PMID 28570818 JRNL DOI 10.1021/JACS.7B02694 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 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) : 0.133 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 38614 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 : 1008 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 334 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) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL 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 5V1L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000226710. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-10 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 : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9787 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40705 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 27.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.3400 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: OLIGONUCLEOTIDE (0.6 MM), SODIUM REMARK 280 CACODYLATE (20 MM, PH 6.0), LITHIUM CHLORIDE (20 MM), STRONTIUM REMARK 280 CHLORIDE (40 MM), MAGNESIUM CHLORIDE (10 MM), SPERMINE REMARK 280 TETRAHYDROCHLORIDE (6 MM), AND 2-METHYL-2,4-PENTANEDIOL (MPD; 5% REMARK 280 (V/V), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 17.47550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.11950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 17.47550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.11950 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: 2600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -112.0 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: 2530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -151.0 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 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 362 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 369 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 671 LIES ON A SPECIAL POSITION. 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 A 101 C2' C A 101 O2' 0.116 REMARK 500 U A 107 C2' U A 107 O2' -0.174 REMARK 500 C B 201 C2' C B 201 O2' 0.070 REMARK 500 U B 207 C2' U B 207 O2' -0.081 REMARK 500 C B 211 C2' C B 211 O2' 0.070 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 U A 107 O5' - P - OP2 ANGL. DEV. = -7.1 DEGREES REMARK 500 U A 107 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 G A 112 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 C B 201 C6 - N1 - C2 ANGL. DEV. = 2.6 DEGREES REMARK 500 G B 202 C3' - C2' - C1' ANGL. DEV. = -4.5 DEGREES REMARK 500 C B 203 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 C B 203 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 A B 206 N1 - C2 - N3 ANGL. DEV. = -3.4 DEGREES REMARK 500 A B 206 N1 - C6 - N6 ANGL. DEV. = 5.7 DEGREES REMARK 500 U B 207 C4 - C5 - C6 ANGL. DEV. = 4.0 DEGREES REMARK 500 U B 207 C5 - C6 - N1 ANGL. DEV. = -3.9 DEGREES REMARK 500 A B 209 OP1 - P - OP2 ANGL. DEV. = 9.1 DEGREES REMARK 500 A B 209 O5' - P - OP2 ANGL. DEV. = -6.3 DEGREES REMARK 500 A B 209 O5' - C5' - C4' ANGL. DEV. = -6.8 DEGREES REMARK 500 C B 211 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 C C 303 N1 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 C C 303 N3 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 G C 304 C2 - N3 - C4 ANGL. DEV. = 3.5 DEGREES REMARK 500 G C 304 C5 - N7 - C8 ANGL. DEV. = 4.1 DEGREES REMARK 500 G C 304 N7 - C8 - N9 ANGL. DEV. = -4.0 DEGREES REMARK 500 A C 305 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 A C 305 N7 - C8 - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 A C 305 C8 - N9 - C4 ANGL. DEV. = 2.9 DEGREES REMARK 500 A C 306 C3' - C2' - C1' ANGL. DEV. = -4.6 DEGREES REMARK 500 C C 311 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 C D 401 C2 - N3 - C4 ANGL. DEV. = 3.6 DEGREES REMARK 500 G D 404 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 G D 404 C4 - C5 - N7 ANGL. DEV. = -2.4 DEGREES REMARK 500 U D 407 C3' - O3' - P ANGL. DEV. = 11.3 DEGREES REMARK 500 U D 407 C3' - O3' - P ANGL. DEV. = -8.9 DEGREES REMARK 500 A D 409 C1' - O4' - C4' ANGL. DEV. = -5.6 DEGREES REMARK 500 G D 410 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 C D 411 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 C D 411 N1 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 C D 411 N3 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 380 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH B 465 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH C 594 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH C 595 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH D 694 DISTANCE = 5.84 ANGSTROMS 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 201 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 104 O6 REMARK 620 2 HOH A 350 O 117.3 REMARK 620 3 HOH A 352 O 72.9 71.4 REMARK 620 4 HOH A 354 O 69.5 125.8 59.4 REMARK 620 5 HOH A 357 O 144.2 74.1 80.4 76.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR B 302 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 344 O REMARK 620 2 G B 204 O6 106.3 REMARK 620 3 HOH B 434 O 151.0 78.6 REMARK 620 4 HOH B 457 O 96.5 156.3 78.3 REMARK 620 5 HOH B 462 O 98.8 114.3 54.8 54.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR B 301 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 204 O6 REMARK 620 2 HOH B 433 O 126.2 REMARK 620 3 HOH B 434 O 81.6 75.8 REMARK 620 4 HOH B 447 O 70.8 74.2 112.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR C 403 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G C 302 O2' REMARK 620 2 G C 302 N3 95.7 REMARK 620 3 HOH C 573 O 102.5 125.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR C 401 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G C 304 O6 REMARK 620 2 HOH C 508 O 59.1 REMARK 620 3 HOH C 536 O 76.0 57.0 REMARK 620 4 HOH C 538 O 115.2 130.8 73.9 REMARK 620 5 HOH C 567 O 70.6 129.0 105.3 64.4 REMARK 620 6 HOH C 572 O 129.8 146.9 148.7 78.1 74.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR C 402 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G C 304 O6 REMARK 620 2 HOH C 567 O 76.3 REMARK 620 3 HOH C 572 O 122.8 75.1 REMARK 620 4 HOH D 691 O 147.1 118.0 90.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR C 404 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 511 O REMARK 620 2 HOH C 517 O 83.4 REMARK 620 3 HOH C 520 O 62.8 65.5 REMARK 620 4 HOH C 524 O 131.7 92.1 71.6 REMARK 620 5 HOH C 560 O 71.6 145.0 81.2 87.0 REMARK 620 6 HOH C 575 O 125.2 149.7 132.8 76.2 63.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR D 501 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G D 404 O6 REMARK 620 2 HOH D 605 O 59.0 REMARK 620 3 HOH D 635 O 116.5 117.9 REMARK 620 4 HOH D 638 O 62.6 55.7 173.4 REMARK 620 5 HOH D 643 O 78.1 136.8 75.2 110.4 REMARK 620 6 HOH D 663 O 67.2 54.2 67.2 107.2 106.7 REMARK 620 7 HOH D 681 O 99.7 125.4 116.6 69.8 63.0 165.5 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 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SR B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SR B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SPM B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SR C 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SR C 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SR C 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SR C 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SR D 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide ZTH B 208 and A B REMARK 800 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide ZTH C 308 and A C REMARK 800 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide ZTH D 408 and A D REMARK 800 409 DBREF 5V1L A 101 112 PDB 5V1L 5V1L 101 112 DBREF 5V1L B 201 212 PDB 5V1L 5V1L 201 212 DBREF 5V1L C 301 312 PDB 5V1L 5V1L 301 312 DBREF 5V1L D 401 412 PDB 5V1L 5V1L 401 412 SEQRES 1 A 12 C G C G A A U ZTH A G C G SEQRES 1 B 12 C G C G A A U ZTH A G C G SEQRES 1 C 12 C G C G A A U ZTH A G C G SEQRES 1 D 12 C G C G A A U ZTH A G C G HET ZTH A 108 24 HET ZTH B 208 17 HET ZTH C 308 17 HET ZTH D 408 34 HET SR A 201 1 HET SR B 301 1 HET SR B 302 1 HET SPM B 303 14 HET SR C 401 1 HET SR C 402 1 HET SR C 403 1 HET SR C 404 1 HET SR D 501 1 HETNAM ZTH (S)-1'-(2',3'-DIHYDROXYPROPYL)-THYMINE HETNAM SR STRONTIUM ION HETNAM SPM SPERMINE FORMUL 1 ZTH 4(C8 H13 N2 O7 P) FORMUL 5 SR 8(SR 2+) FORMUL 8 SPM C10 H26 N4 FORMUL 14 HOH *334(H2 O) LINK O3'A U A 107 P AZTH A 108 1555 1555 1.61 LINK O3'B U A 107 P BZTH A 108 1555 1555 1.58 LINK O2GAZTH A 108 P A A A 109 1555 1555 1.51 LINK O2GBZTH A 108 P B A A 109 1555 1555 1.58 LINK O3' U B 207 P ZTH B 208 1555 1555 1.59 LINK O2G ZTH B 208 P A B 209 1555 1555 1.47 LINK O3' U C 307 P ZTH C 308 1555 1555 1.60 LINK O2G ZTH C 308 P A C 309 1555 1555 1.62 LINK O3' U D 407 P AZTH D 408 1555 1555 1.57 LINK O3' U D 407 P BZTH D 408 1555 1555 1.64 LINK O2GAZTH D 408 P A A D 409 1555 1555 1.57 LINK O2GBZTH D 408 P B A D 409 1555 1555 1.60 LINK O6 G A 104 SR SR A 201 1555 1555 2.54 LINK SR SR A 201 O HOH A 350 1555 1555 2.70 LINK SR SR A 201 O HOH A 352 1555 1555 2.83 LINK SR SR A 201 O HOH A 354 1555 1555 2.65 LINK SR SR A 201 O HOH A 357 1555 1555 2.64 LINK O HOH A 344 SR SR B 302 1555 1555 2.48 LINK O6 G B 204 SR SR B 301 1555 1555 2.50 LINK O6 G B 204 SR SR B 302 1555 1555 2.88 LINK SR SR B 301 O HOH B 433 1555 1555 2.42 LINK SR SR B 301 O HOH B 434 1555 1555 2.85 LINK SR SR B 301 O HOH B 447 1555 1555 2.72 LINK SR SR B 302 O HOH B 434 1555 1555 2.65 LINK SR SR B 302 O HOH B 457 1555 1555 2.44 LINK SR SR B 302 O HOH B 462 1555 1555 2.56 LINK O2' G C 302 SR SR C 403 1555 1555 2.69 LINK N3 G C 302 SR SR C 403 1555 1555 2.93 LINK O6 G C 304 SR SR C 401 1555 1555 2.63 LINK O6 G C 304 SR SR C 402 1555 1555 2.58 LINK SR SR C 401 O HOH C 508 1555 1555 2.75 LINK SR SR C 401 O HOH C 536 1555 1555 2.79 LINK SR SR C 401 O HOH C 538 1555 1555 2.78 LINK SR SR C 401 O HOH C 567 1555 1555 2.89 LINK SR SR C 401 O HOH C 572 1555 1555 2.78 LINK SR SR C 402 O HOH C 567 1555 1555 2.59 LINK SR SR C 402 O HOH C 572 1555 1555 2.98 LINK SR SR C 402 O HOH D 691 1555 1555 2.78 LINK SR SR C 403 O HOH C 573 1555 1555 2.72 LINK SR SR C 404 O HOH C 511 1555 1555 2.38 LINK SR SR C 404 O HOH C 517 1555 1555 2.85 LINK SR SR C 404 O HOH C 520 1555 1555 2.49 LINK SR SR C 404 O HOH C 524 1555 1555 2.74 LINK SR SR C 404 O HOH C 560 1555 1555 2.68 LINK SR SR C 404 O HOH C 575 1555 1555 2.57 LINK O6 G D 404 SR SR D 501 1555 1555 2.61 LINK SR SR D 501 O HOH D 605 1555 1555 2.40 LINK SR SR D 501 O HOH D 635 1555 1555 2.61 LINK SR SR D 501 O HOH D 638 1555 1555 2.73 LINK SR SR D 501 O HOH D 643 1555 1555 2.91 LINK SR SR D 501 O HOH D 663 1555 1555 2.82 LINK SR SR D 501 O HOH D 681 1555 1555 2.63 SITE 1 AC1 6 G A 104 HOH A 340 HOH A 350 HOH A 352 SITE 2 AC1 6 HOH A 354 HOH A 357 SITE 1 AC2 5 G B 204 SR B 302 HOH B 433 HOH B 434 SITE 2 AC2 5 HOH B 447 SITE 1 AC3 6 HOH A 344 G B 204 SR B 301 HOH B 434 SITE 2 AC3 6 HOH B 457 HOH B 462 SITE 1 AC4 10 C A 103 G A 104 G A 110 C A 111 SITE 2 AC4 10 HOH A 320 HOH A 327 G B 210 C B 211 SITE 3 AC4 10 HOH B 421 HOH B 429 SITE 1 AC5 7 G C 304 SR C 402 HOH C 508 HOH C 536 SITE 2 AC5 7 HOH C 538 HOH C 567 HOH C 572 SITE 1 AC6 6 G C 304 SR C 401 HOH C 567 HOH C 569 SITE 2 AC6 6 HOH C 572 HOH D 691 SITE 1 AC7 3 G C 302 C C 303 HOH C 573 SITE 1 AC8 6 HOH C 511 HOH C 517 HOH C 520 HOH C 524 SITE 2 AC8 6 HOH C 560 HOH C 575 SITE 1 AC9 7 G D 404 HOH D 605 HOH D 635 HOH D 638 SITE 2 AC9 7 HOH D 643 HOH D 663 HOH D 681 SITE 1 AD1 10 G A 104 A A 105 G A 110 U B 207 SITE 2 AD1 10 G B 210 HOH B 401 HOH B 405 HOH B 437 SITE 3 AD1 10 HOH B 440 HOH B 441 SITE 1 AD2 16 A B 206 U B 207 U C 307 G C 310 SITE 2 AD2 16 HOH C 503 HOH C 517 HOH C 528 HOH C 545 SITE 3 AD2 16 HOH C 552 HOH C 554 HOH C 555 HOH C 561 SITE 4 AD2 16 G D 404 A D 405 G D 410 HOH D 676 SITE 1 AD3 18 ZTH A 108 A A 109 HOH A 343 G C 304 SITE 2 AD3 18 A C 305 G C 310 HOH C 555 U D 407 SITE 3 AD3 18 G D 410 HOH D 602 HOH D 606 HOH D 608 SITE 4 AD3 18 HOH D 609 HOH D 610 HOH D 620 HOH D 632 SITE 5 AD3 18 HOH D 650 HOH D 655 CRYST1 34.951 46.239 82.928 90.00 100.09 90.00 C 1 2 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 0.028611 0.000000 0.005091 0.00000 SCALE2 0.000000 0.021627 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012248 0.00000