HEADER DNA 31-JAN-18 5Z8F TITLE SOLUTION STRUCTURE FOR THE UNIQUE DIMERIC 4:2 COMPLEX OF A TITLE 2 PLATINUM(II)-BASED TRIPOD BOUND TO A HYBRID-1 HUMAN TELOMERIC G- TITLE 3 QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: G-QUADRUPLEX DNA (26-MER); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS G-QUADRUPLEX COMPLEX, DIMERIC G-QUADRUPLEX, HUMAN TELOMERIC G- KEYWDS 2 QUADRUPLEX, PLATINUM(II) COMPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR W.T.LIU,Y.F.ZHONG,L.Y.LIU,W.J.ZENG,F.Y.WANG,D.Z.YANG,Z.W.MAO REVDAT 3 15-MAY-24 5Z8F 1 REMARK REVDAT 2 14-JUN-23 5Z8F 1 REMARK REVDAT 1 19-SEP-18 5Z8F 0 JRNL AUTH W.LIU,Y.F.ZHONG,L.Y.LIU,C.T.SHEN,W.ZENG,F.WANG,D.YANG, JRNL AUTH 2 Z.W.MAO JRNL TITL SOLUTION STRUCTURES OF MULTIPLE G-QUADRUPLEX COMPLEXES JRNL TITL 2 INDUCED BY A PLATINUM(II)-BASED TRIPOD REVEAL DYNAMIC JRNL TITL 3 BINDING JRNL REF NAT COMMUN V. 9 3496 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30158518 JRNL DOI 10.1038/S41467-018-05810-4 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR, DISCOVER, SPARKY REMARK 3 AUTHORS : BRUNGER (X-PLOR), ACCELRYS SOFTWARE INC. REMARK 3 (DISCOVER), GODDARD (SPARKY) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5Z8F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300006644. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 288; 278 REMARK 210 PH : 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 95; 95; 95 REMARK 210 PRESSURE : AMBIENT MBAR; AMBIENT MBAR; REMARK 210 AMBIENT MBAR REMARK 210 SAMPLE CONTENTS : 1 MM 15N THYMINE G-QUADRUPLEX REMARK 210 DNA (26-MER), 3 MM PT-TRIPOD, 25 REMARK 210 MM POTASSIUM PHOSPHATE, 70 MM REMARK 210 POTASSIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O; 1 MM G-QUADRUPLEX DNA (26- REMARK 210 MER), 3 MM PT-TRIPOD, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 70 MM REMARK 210 POTASSIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, TOPSPIN REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: DIMERIC 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 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 1 DT A 7 C5 DT A 7 C7 0.052 REMARK 500 1 DT A 8 C5 DT A 8 C7 0.053 REMARK 500 1 DT A 13 C5 DT A 13 C7 0.050 REMARK 500 1 DT A 14 C5 DT A 14 C7 0.052 REMARK 500 1 DT A 19 C5 DT A 19 C7 0.053 REMARK 500 1 DT A 20 C5 DT A 20 C7 0.052 REMARK 500 1 DT B 7 C5 DT B 7 C7 0.051 REMARK 500 1 DT B 8 C5 DT B 8 C7 0.052 REMARK 500 1 DT B 13 C5 DT B 13 C7 0.052 REMARK 500 1 DT B 14 C5 DT B 14 C7 0.053 REMARK 500 1 DT B 19 C5 DT B 19 C7 0.053 REMARK 500 1 DT B 20 C5 DT B 20 C7 0.052 REMARK 500 2 DT A 7 C5 DT A 7 C7 0.053 REMARK 500 2 DT A 8 C5 DT A 8 C7 0.053 REMARK 500 2 DT A 13 C5 DT A 13 C7 0.050 REMARK 500 2 DT A 14 C5 DT A 14 C7 0.052 REMARK 500 2 DT A 19 C5 DT A 19 C7 0.053 REMARK 500 2 DT A 20 C5 DT A 20 C7 0.052 REMARK 500 2 DT B 7 C5 DT B 7 C7 0.053 REMARK 500 2 DT B 8 C5 DT B 8 C7 0.051 REMARK 500 2 DT B 13 C5 DT B 13 C7 0.052 REMARK 500 2 DT B 14 C5 DT B 14 C7 0.052 REMARK 500 2 DT B 19 C5 DT B 19 C7 0.054 REMARK 500 2 DT B 20 C5 DT B 20 C7 0.051 REMARK 500 3 DT A 7 C5 DT A 7 C7 0.053 REMARK 500 3 DT A 8 C5 DT A 8 C7 0.052 REMARK 500 3 DT A 13 C5 DT A 13 C7 0.050 REMARK 500 3 DT A 14 C5 DT A 14 C7 0.053 REMARK 500 3 DT A 19 C5 DT A 19 C7 0.052 REMARK 500 3 DT A 20 C5 DT A 20 C7 0.053 REMARK 500 3 DT B 7 C5 DT B 7 C7 0.052 REMARK 500 3 DT B 8 C5 DT B 8 C7 0.051 REMARK 500 3 DT B 13 C5 DT B 13 C7 0.052 REMARK 500 3 DT B 14 C5 DT B 14 C7 0.052 REMARK 500 3 DT B 19 C5 DT B 19 C7 0.054 REMARK 500 3 DT B 20 C5 DT B 20 C7 0.052 REMARK 500 4 DT A 7 C5 DT A 7 C7 0.052 REMARK 500 4 DT A 8 C5 DT A 8 C7 0.053 REMARK 500 4 DT A 13 C5 DT A 13 C7 0.051 REMARK 500 4 DT A 14 C5 DT A 14 C7 0.053 REMARK 500 4 DA A 15 C5' DA A 15 C4' 0.044 REMARK 500 4 DT A 19 C5 DT A 19 C7 0.054 REMARK 500 4 DT A 20 C5 DT A 20 C7 0.051 REMARK 500 4 DT B 7 C5 DT B 7 C7 0.052 REMARK 500 4 DT B 8 C5 DT B 8 C7 0.052 REMARK 500 4 DT B 13 C5 DT B 13 C7 0.052 REMARK 500 4 DT B 14 C5 DT B 14 C7 0.052 REMARK 500 4 DT B 19 C5 DT B 19 C7 0.053 REMARK 500 4 DT B 20 C5 DT B 20 C7 0.052 REMARK 500 5 DT A 7 C5 DT A 7 C7 0.052 REMARK 500 REMARK 500 THIS ENTRY HAS 121 BOND DEVIATIONS. 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 1 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DA A 2 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 6 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 6 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 9 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 9 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DG A 10 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 10 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 11 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG A 12 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 12 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DT A 13 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DT A 14 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DA A 15 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 15 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 16 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 16 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DG A 17 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG A 17 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 17 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 18 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 18 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DT A 19 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 20 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 21 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA A 21 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 21 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 22 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1272 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 DG A 12 0.05 SIDE CHAIN REMARK 500 2 DG A 12 0.05 SIDE CHAIN REMARK 500 3 DG A 12 0.05 SIDE CHAIN REMARK 500 5 DG A 12 0.05 SIDE CHAIN REMARK 500 6 DG A 12 0.06 SIDE CHAIN REMARK 500 7 DG A 12 0.06 SIDE CHAIN REMARK 500 8 DG A 12 0.06 SIDE CHAIN REMARK 500 9 DG A 12 0.05 SIDE CHAIN REMARK 500 10 DG A 12 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9F0 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9F0 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9F0 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9F0 B 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36160 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE FOR THE UNIQUE DIMERIC 4:2 COMPLEX OF A REMARK 900 PLATINUM(II)-BASED TRIPOD BOUND TO A HYBRID-1 HUMAN TELOMERIC G- REMARK 900 QUADRUPLEX DBREF 5Z8F A 1 26 PDB 5Z8F 5Z8F 1 26 DBREF 5Z8F B 1 26 PDB 5Z8F 5Z8F 1 26 SEQRES 1 A 26 DA DA DA DG DG DG DT DT DA DG DG DG DT SEQRES 2 A 26 DT DA DG DG DG DT DT DA DG DG DG DA DA SEQRES 1 B 26 DA DA DA DG DG DG DT DT DA DG DG DG DT SEQRES 2 B 26 DT DA DG DG DG DT DT DA DG DG DG DA DA HET 9F0 A 101 124 HET 9F0 A 102 124 HET 9F0 B 101 124 HET 9F0 B 102 124 HETNAM 9F0 4-[1-(2,5,8-TRIAZONIA-1$L^4-PLATINABICYCLO[3.3.0]OCTAN- HETNAM 2 9F0 1-YL)PYRIDIN-1-IUM-4-YL]-N,N-BIS[4-[1-(2,5,8- HETNAM 3 9F0 TRIAZONIA-1$L^4-PLATINABICYCLO[3.3.0]OCTAN-1-YL) HETNAM 4 9F0 PYRIDIN-1-IUM-4-YL]PHENYL]ANILINE FORMUL 3 9F0 4(C45 H63 N13 PT3 12+) SITE 1 AC1 5 DG A 4 DT A 8 DG A 10 DT A 19 SITE 2 AC1 5 DG A 22 SITE 1 AC2 6 DG A 6 DT A 13 DT A 14 DG A 16 SITE 2 AC2 6 DG A 24 DA A 25 SITE 1 AC3 6 DT B 8 DA B 9 DG B 10 DT B 19 SITE 2 AC3 6 DG B 22 DG B 23 SITE 1 AC4 6 DG B 6 DT B 13 DT B 14 DG B 16 SITE 2 AC4 6 DG B 24 DA B 25 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