HEADER DNA 22-NOV-20 7DJU OBSLTE 03-APR-24 7DJU TITLE NMR SOLUTION STRUCTURE OF THE 1:1 COMPLEX OF A PLATINUM(II) COMPOUND TITLE 2 BOUND TO 5'-END OF MYC1234 G-QUADRUPLEX REVEALS THE MECHANISM OF TITLE 3 CONFORMATIONAL SWITCH AND DYNAMIC BINDING OF G-QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYC1234 G-QUADRUPLEX DNA (5'- COMPND 3 D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS G-QUADRUPLEX, C-MYC, DNA-LIGAND COMPLEX, BINDING DYNAMICS, STRUCTURAL KEYWDS 2 CHANGE, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR W.LIU,Z.W.MAO REVDAT 3 03-APR-24 7DJU 1 OBSLTE JRNL REVDAT 2 21-DEC-22 7DJU 1 JRNL REVDAT 1 12-JAN-22 7DJU 0 JRNL AUTH W.LIU,B.C.ZHU,L.Y.LIU,X.Y.XIA,Z.W.MAO JRNL TITL RETRACTED: G-QUADRUPLEX STRUCTURAL TRANSITION DRIVEN BY A JRNL TITL 2 PLATINUM COMPOUND JRNL REF NUCLEIC ACIDS RES. V. 50 7816 2022 JRNL REFN ESSN 1362-4962 JRNL DOI 10.1093/NAR/GKAC572 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, DISCOVERY STUDIO REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), ACCELRYS (DISCOVERY STUDIO) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7DJU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 5 REMARK 5 PAPER RETRACTED REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1300019541. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.15; 288.15; 278.15 REMARK 210 PH : 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 100; 100; 100 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM MYC1234 G-QUADRUPLEX, 1.0 REMARK 210 MM PT-PHEN COMPOUND, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 75 MM REMARK 210 POTASSIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O; 1.0 MM MYC1234 G-QUADRUPLEX, REMARK 210 1.0 MM PT-PHEN COMPOUND, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 75 MM REMARK 210 POTASSIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 2D COSY 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 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 H22 DG A 5 N7 DG A 9 1.58 REMARK 500 REMARK 500 REMARK: NULL 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 1 C5 DT A 1 C7 0.052 REMARK 500 1 DT A 1 O3' DA A 2 P -0.103 REMARK 500 1 DA A 2 P DA A 2 O5' -0.071 REMARK 500 1 DG A 4 C5' DG A 4 C4' 0.059 REMARK 500 1 DA A 6 C2' DA A 6 C1' 0.103 REMARK 500 1 DA A 6 O3' DG A 7 P 0.096 REMARK 500 1 DG A 7 C5' DG A 7 C4' 0.049 REMARK 500 1 DT A 10 C5 DT A 10 C7 0.053 REMARK 500 1 DG A 14 C2' DG A 14 C1' 0.061 REMARK 500 1 DG A 14 C5 DG A 14 N7 -0.050 REMARK 500 1 DA A 15 C5' DA A 15 C4' 0.071 REMARK 500 1 DG A 16 C5' DG A 16 C4' 0.071 REMARK 500 1 DG A 17 C5' DG A 17 C4' 0.053 REMARK 500 1 DT A 19 C5 DT A 19 C7 0.051 REMARK 500 2 DT A 1 C5 DT A 1 C7 0.052 REMARK 500 2 DG A 3 P DG A 3 O5' -0.068 REMARK 500 2 DA A 6 P DA A 6 O5' -0.066 REMARK 500 2 DG A 7 O3' DG A 8 P -0.073 REMARK 500 2 DT A 10 C5 DT A 10 C7 0.053 REMARK 500 2 DG A 12 C5' DG A 12 C4' 0.072 REMARK 500 2 DA A 15 C5' DA A 15 C4' 0.061 REMARK 500 2 DG A 17 P DG A 17 O5' 0.091 REMARK 500 2 DG A 17 C5' DG A 17 C4' 0.109 REMARK 500 2 DG A 17 C4' DG A 17 C3' 0.063 REMARK 500 2 DT A 19 C5 DT A 19 C7 0.051 REMARK 500 3 DT A 1 C5 DT A 1 C7 0.053 REMARK 500 3 DA A 2 O3' DG A 3 P -0.079 REMARK 500 3 DG A 4 C5' DG A 4 C4' 0.077 REMARK 500 3 DG A 5 C5' DG A 5 C4' 0.054 REMARK 500 3 DA A 6 C5' DA A 6 C4' 0.065 REMARK 500 3 DG A 9 C5' DG A 9 C4' 0.046 REMARK 500 3 DT A 10 C5 DT A 10 C7 0.052 REMARK 500 3 DG A 14 C5' DG A 14 C4' 0.043 REMARK 500 3 DA A 15 C5' DA A 15 C4' 0.075 REMARK 500 3 DG A 17 C5' DG A 17 C4' 0.053 REMARK 500 3 DG A 18 C2' DG A 18 C1' -0.064 REMARK 500 3 DT A 19 C5 DT A 19 C7 0.051 REMARK 500 4 DT A 1 C5' DT A 1 C4' 0.059 REMARK 500 4 DT A 1 C5 DT A 1 C7 0.053 REMARK 500 4 DA A 2 O3' DG A 3 P -0.081 REMARK 500 4 DG A 4 C5' DG A 4 C4' 0.071 REMARK 500 4 DG A 5 C4' DG A 5 C3' 0.068 REMARK 500 4 DA A 6 C5' DA A 6 C4' 0.049 REMARK 500 4 DG A 9 C5' DG A 9 C4' 0.053 REMARK 500 4 DT A 10 C5 DT A 10 C7 0.053 REMARK 500 4 DG A 12 C5' DG A 12 C4' 0.065 REMARK 500 4 DG A 14 C5' DG A 14 C4' 0.042 REMARK 500 4 DA A 15 C5' DA A 15 C4' 0.058 REMARK 500 4 DG A 16 C5' DG A 16 C4' 0.065 REMARK 500 4 DG A 17 C5' DG A 17 C4' 0.067 REMARK 500 REMARK 500 THIS ENTRY HAS 222 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 DT A 1 O4' - C1' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DA A 2 O3' - P - O5' ANGL. DEV. = 13.6 DEGREES REMARK 500 1 DA A 2 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DG A 3 OP1 - P - OP2 ANGL. DEV. = -12.3 DEGREES REMARK 500 1 DG A 3 C5' - C4' - O4' ANGL. DEV. = 9.6 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 3 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DG A 4 OP1 - P - OP2 ANGL. DEV. = -10.7 DEGREES REMARK 500 1 DG A 4 C5' - C4' - O4' ANGL. DEV. = 9.6 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.2 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. = -3.3 DEGREES REMARK 500 1 DG A 5 OP1 - P - OP2 ANGL. DEV. = -17.3 DEGREES REMARK 500 1 DG A 5 C5' - C4' - O4' ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DG A 5 C1' - O4' - C4' ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 5 O4' - C1' - N9 ANGL. DEV. = -7.7 DEGREES REMARK 500 1 DG A 5 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 5 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA A 6 O3' - P - O5' ANGL. DEV. = 11.9 DEGREES REMARK 500 1 DA A 6 C4' - C3' - C2' ANGL. DEV. = -10.9 DEGREES REMARK 500 1 DA A 6 C3' - C2' - C1' ANGL. DEV. = 7.2 DEGREES REMARK 500 1 DA A 6 O4' - C1' - C2' ANGL. DEV. = -7.5 DEGREES REMARK 500 1 DA A 6 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DA A 6 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DA A 6 C3' - O3' - P ANGL. DEV. = 10.6 DEGREES REMARK 500 1 DG A 7 O3' - P - O5' ANGL. DEV. = 13.8 DEGREES REMARK 500 1 DG A 7 O3' - P - OP1 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DG A 7 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 1 DG A 7 O4' - C4' - C3' ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG A 7 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DG A 7 C1' - O4' - C4' ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 7 O4' - C1' - C2' ANGL. DEV. = -11.2 DEGREES REMARK 500 1 DG A 7 N9 - C1' - C2' ANGL. DEV. = 9.1 DEGREES REMARK 500 1 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 7 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DG A 8 O3' - P - O5' ANGL. DEV. = 12.7 DEGREES REMARK 500 1 DG A 8 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 1 DG A 8 O4' - C4' - C3' ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 8 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 9 O3' - P - OP1 ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DG A 9 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 1 DG A 9 C1' - O4' - C4' ANGL. DEV. = -7.5 DEGREES REMARK 500 1 DG A 9 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG A 9 O4' - C1' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 12.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1916 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 4 DG A 9 0.05 SIDE CHAIN REMARK 500 5 DG A 9 0.05 SIDE CHAIN REMARK 500 11 DG A 9 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36398 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF THE 1:1 COMPLEX OF A PLATINUM(II) REMARK 900 COMPOUND BOUND TO 5'-END OF MYC1234 G-QUADRUPLEX REVEALS THE REMARK 900 MECHANISM OF CONFORMATIONAL SWITCH AND DYNAMIC BINDING OF G- REMARK 900 QUADRUPLEX DBREF 7DJU A 1 19 PDB 7DJU 7DJU 1 19 SEQRES 1 A 19 DT DA DG DG DG DA DG DG DG DT DA DG DG SEQRES 2 A 19 DG DA DG DG DG DT HET H9C A 101 45 HETNAM H9C BIS(1,10-PHENANTHROLINE)PLATINUM(II) FORMUL 2 H9C C24 H16 N4 PT 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 MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 621 622 634 649 CONECT 622 621 623 650 CONECT 623 622 624 651 CONECT 624 623 625 652 CONECT 625 624 626 634 CONECT 626 625 627 653 CONECT 627 626 628 654 CONECT 628 627 629 633 CONECT 629 628 630 655 CONECT 630 629 631 656 CONECT 631 630 632 657 CONECT 632 631 633 649 CONECT 633 628 632 634 CONECT 634 621 625 633 CONECT 635 636 648 649 CONECT 636 635 637 658 CONECT 637 636 638 659 CONECT 638 637 639 660 CONECT 639 638 640 648 CONECT 640 639 641 661 CONECT 641 640 642 662 CONECT 642 641 643 647 CONECT 643 642 644 663 CONECT 644 643 645 664 CONECT 645 644 646 665 CONECT 646 645 647 649 CONECT 647 642 646 648 CONECT 648 635 639 647 CONECT 649 621 632 635 646 CONECT 650 622 CONECT 651 623 CONECT 652 624 CONECT 653 626 CONECT 654 627 CONECT 655 629 CONECT 656 630 CONECT 657 631 CONECT 658 636 CONECT 659 637 CONECT 660 638 CONECT 661 640 CONECT 662 641 CONECT 663 643 CONECT 664 644 CONECT 665 645 MASTER 251 0 1 0 0 0 0 6 434 1 45 2 END