HEADER DNA 15-MAR-23 8OFC TITLE STRUCTURE OF AN I-MOTIF DOMAIN WITH THE CYTOSINE ANALOG 1,3-DIAZA-2- TITLE 2 OXOPHENOXACIONE (TC) AT NEUTRAL PH COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*(YCO)P*GP*TP*TP*CP*(DNR) COMPND 3 P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*CP*(DNR)P*GP*T)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS I-MOTIF, FLUORESCENT, NON-CANONICAL DNA, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR B.MIR,I.SERRANO-CHACON,M.TERRAZAS,A.GANDIOSO,M.GARAVIS,M.OROZCO, AUTHOR 2 N.ESCAJA,C.GONZALEZ REVDAT 3 24-APR-24 8OFC 1 JRNL REVDAT 2 06-MAR-24 8OFC 1 JRNL REVDAT 1 07-FEB-24 8OFC 0 JRNL AUTH B.MIR,I.SERRANO-CHACON,P.MEDINA,V.MACALUSO,M.TERRAZAS, JRNL AUTH 2 A.GANDIOSO,M.GARAVIS,M.OROZCO,N.ESCAJA,C.GONZALEZ JRNL TITL SITE-SPECIFIC INCORPORATION OF A FLUORESCENT NUCLEOBASE JRNL TITL 2 ANALOG ENHANCES I-MOTIF STABILITY AND ALLOWS MONITORING OF JRNL TITL 3 I-MOTIF FOLDING INSIDE CELLS. JRNL REF NUCLEIC ACIDS RES. V. 52 3375 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38366792 JRNL DOI 10.1093/NAR/GKAE106 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8OFC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1292129184. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 298 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 10; 10 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 500 UM DNA (5' REMARK 210 -D(*CP*(YCO)P*GP*TP*TP*CP*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP* REMARK 210 TP*CP*(DNR)P*GP*T)-3'), 10 MM SODIUM PHOSPHATE, 0.5 V/V DSS, 90% REMARK 210 H2O/10% D2O; 500 UM DNA (5'-D(*CP*(YCO)P*GP*TP*TP*CP*(DNR)P*GP* REMARK 210 TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*CP*(DNR)P*GP*T)-3'), 10 MM SODIUM REMARK 210 PHOSPHATE, 0.5 V/V DSS, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, CYANA, MOLMOL REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 15 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 HO5' DC A 1 OP1 YCO A 2 1.35 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 1 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DC A 1 N1 - C2 - O2 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 DC A 1 N3 - C2 - O2 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC A 6 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DT A 11 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 13 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DC A 14 N1 - C2 - O2 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DC A 14 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DC A 14 N3 - C4 - N4 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DC A 15 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 15 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 16 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 9.1 DEGREES REMARK 500 1 DT A 18 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC A 19 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 21 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT A 22 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DT A 22 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DC A 1 N1 - C2 - O2 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 6 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT A 9 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 2 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT A 11 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DT A 12 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DT A 13 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DC A 14 N1 - C2 - O2 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DC A 14 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DC A 14 N3 - C4 - N4 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DC A 15 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DC A 15 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 DG A 16 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DT A 17 O4' - C1' - N1 ANGL. DEV. = 9.7 DEGREES REMARK 500 2 DT A 18 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DC A 19 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 245 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 DT A 9 0.07 SIDE CHAIN REMARK 500 1 DC A 14 0.06 SIDE CHAIN REMARK 500 1 DT A 17 0.18 SIDE CHAIN REMARK 500 1 DG A 21 0.07 SIDE CHAIN REMARK 500 2 DG A 8 0.07 SIDE CHAIN REMARK 500 2 DT A 17 0.17 SIDE CHAIN REMARK 500 2 DG A 21 0.06 SIDE CHAIN REMARK 500 3 DC A 1 0.09 SIDE CHAIN REMARK 500 3 DG A 8 0.06 SIDE CHAIN REMARK 500 3 DT A 10 0.08 SIDE CHAIN REMARK 500 3 DT A 12 0.09 SIDE CHAIN REMARK 500 3 DT A 13 0.09 SIDE CHAIN REMARK 500 3 DC A 14 0.10 SIDE CHAIN REMARK 500 3 DG A 16 0.07 SIDE CHAIN REMARK 500 3 DT A 17 0.18 SIDE CHAIN REMARK 500 3 DG A 21 0.10 SIDE CHAIN REMARK 500 3 DT A 22 0.10 SIDE CHAIN REMARK 500 4 DC A 14 0.07 SIDE CHAIN REMARK 500 4 DT A 17 0.10 SIDE CHAIN REMARK 500 4 DC A 19 0.11 SIDE CHAIN REMARK 500 4 DG A 21 0.06 SIDE CHAIN REMARK 500 5 DC A 1 0.09 SIDE CHAIN REMARK 500 5 DG A 3 0.11 SIDE CHAIN REMARK 500 5 DG A 8 0.07 SIDE CHAIN REMARK 500 5 DC A 14 0.09 SIDE CHAIN REMARK 500 5 DT A 17 0.14 SIDE CHAIN REMARK 500 5 DG A 21 0.08 SIDE CHAIN REMARK 500 6 DG A 3 0.08 SIDE CHAIN REMARK 500 6 DG A 8 0.07 SIDE CHAIN REMARK 500 6 DT A 10 0.10 SIDE CHAIN REMARK 500 6 DT A 11 0.08 SIDE CHAIN REMARK 500 6 DT A 12 0.07 SIDE CHAIN REMARK 500 6 DT A 17 0.17 SIDE CHAIN REMARK 500 6 DC A 19 0.06 SIDE CHAIN REMARK 500 6 DG A 21 0.07 SIDE CHAIN REMARK 500 7 DG A 8 0.05 SIDE CHAIN REMARK 500 7 DT A 11 0.07 SIDE CHAIN REMARK 500 7 DC A 14 0.08 SIDE CHAIN REMARK 500 7 DT A 17 0.18 SIDE CHAIN REMARK 500 8 DC A 1 0.09 SIDE CHAIN REMARK 500 8 DG A 8 0.06 SIDE CHAIN REMARK 500 8 DT A 10 0.08 SIDE CHAIN REMARK 500 8 DT A 12 0.09 SIDE CHAIN REMARK 500 8 DT A 13 0.09 SIDE CHAIN REMARK 500 8 DC A 14 0.10 SIDE CHAIN REMARK 500 8 DG A 16 0.07 SIDE CHAIN REMARK 500 8 DT A 17 0.18 SIDE CHAIN REMARK 500 8 DG A 21 0.10 SIDE CHAIN REMARK 500 8 DT A 22 0.10 SIDE CHAIN REMARK 500 9 DT A 12 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 58 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34798 RELATED DB: BMRB REMARK 900 STRUCTURE OF AN I-MOTIF DOMAIN WITH TGE CYTOSINE ANALOG 1,3-DIAZA-2- REMARK 900 OXOPHENOXACIONE (TC) AT NEUTRAL PH DBREF 8OFC A 1 22 PDB 8OFC 8OFC 1 22 SEQRES 1 A 22 DC YCO DG DT DT DC DNR DG DT DT DT DT DT SEQRES 2 A 22 DC DC DG DT DT DC DNR DG DT HET YCO A 2 39 HET DNR A 7 31 HET DNR A 20 31 HETNAM YCO 3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 YCO PENTOFURANOSYL)-1H-PYRIMIDO[5,4-B][1,4]BENZOXAZIN- HETNAM 3 YCO 2(3H)-ONE HETNAM DNR 2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 YCO C15 H16 N3 O8 P FORMUL 1 DNR 2(C9 H15 N3 O7 P 1+) LINK O3' DC A 1 P YCO A 2 1555 1555 1.60 LINK O3' YCO A 2 P DG A 3 1555 1555 1.61 LINK O3' DC A 6 P DNR A 7 1555 1555 1.60 LINK O3' DNR A 7 P DG A 8 1555 1555 1.61 LINK O3' DC A 19 P DNR A 20 1555 1555 1.62 LINK O3' DNR A 20 P DG A 21 1555 1555 1.63 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL CONECT 6 29 CONECT 29 6 52 53 54 CONECT 30 31 36 40 CONECT 31 30 32 33 CONECT 32 31 CONECT 33 31 34 CONECT 34 33 35 37 CONECT 35 34 36 45 CONECT 36 30 35 56 CONECT 37 34 38 CONECT 38 37 39 44 CONECT 39 38 41 57 CONECT 40 30 46 50 58 CONECT 41 39 42 59 CONECT 42 41 43 60 CONECT 43 42 44 61 CONECT 44 38 43 45 CONECT 45 35 44 CONECT 46 40 47 62 63 CONECT 47 46 48 49 64 CONECT 48 47 68 CONECT 49 47 50 51 65 CONECT 50 40 49 CONECT 51 49 52 66 67 CONECT 52 29 51 CONECT 53 29 CONECT 54 29 CONECT 56 36 CONECT 57 39 CONECT 58 40 CONECT 59 41 CONECT 60 42 CONECT 61 43 CONECT 62 46 CONECT 63 46 CONECT 64 47 CONECT 65 49 CONECT 66 51 CONECT 67 51 CONECT 68 48 CONECT 173 195 CONECT 195 173 196 197 198 CONECT 196 195 CONECT 197 195 CONECT 198 195 199 CONECT 199 198 200 214 215 CONECT 200 199 201 212 216 CONECT 201 200 202 CONECT 202 201 203 211 217 CONECT 203 202 204 205 CONECT 204 203 210 218 CONECT 205 203 206 207 CONECT 206 205 CONECT 207 205 208 219 CONECT 208 207 209 210 CONECT 209 208 220 221 CONECT 210 204 208 222 CONECT 211 202 212 223 224 CONECT 212 200 211 213 225 CONECT 213 212 226 CONECT 214 199 CONECT 215 199 CONECT 216 200 CONECT 217 202 CONECT 218 204 CONECT 219 207 CONECT 220 209 CONECT 221 209 CONECT 222 210 CONECT 223 211 CONECT 224 211 CONECT 225 212 CONECT 226 213 CONECT 584 606 CONECT 606 584 607 608 609 CONECT 607 606 CONECT 608 606 CONECT 609 606 610 CONECT 610 609 611 625 626 CONECT 611 610 612 623 627 CONECT 612 611 613 CONECT 613 612 614 622 628 CONECT 614 613 615 616 CONECT 615 614 621 629 CONECT 616 614 617 618 CONECT 617 616 CONECT 618 616 619 630 CONECT 619 618 620 621 CONECT 620 619 631 632 CONECT 621 615 619 633 CONECT 622 613 623 634 635 CONECT 623 611 622 624 636 CONECT 624 623 637 CONECT 625 610 CONECT 626 610 CONECT 627 611 CONECT 628 613 CONECT 629 615 CONECT 630 618 CONECT 631 620 CONECT 632 620 CONECT 633 621 CONECT 634 622 CONECT 635 622 CONECT 636 623 CONECT 637 624 MASTER 222 0 3 0 0 0 0 6 444 1 106 2 END