HEADER DNA 18-AUG-13 2MCC TITLE STRUCTURAL STUDIES ON DINUCLEAR RUTHENIUM(II) COMPLEXES THAT BIND TITLE 2 DIASTEREOSELECTIVELY TO AN ANTI-PARALLEL FOLDED HUMAN TELOMERE TITLE 3 SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN_TELOMERE_QUADRUPLEX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: STANDARD CHEMISTRY, HPLC PURIFIED KEYWDS DNA, QUADRUPLEX, COMPLEX, RUTHENIUM EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR M.P.WILLIAMSON,T.WILSON,J.A.THOMAS,V.FELIX,P.J.COSTA REVDAT 3 22-JAN-14 2MCC 1 JRNL REVDAT 2 16-OCT-13 2MCC 1 JRNL REVDAT 1 02-OCT-13 2MCC 0 JRNL AUTH T.WILSON,P.J.COSTA,V.FELIX,M.P.WILLIAMSON,J.A.THOMAS JRNL TITL STRUCTURAL STUDIES ON DINUCLEAR RUTHENIUM(II) COMPLEXES THAT JRNL TITL 2 BIND DIASTEREOSELECTIVELY TO AN ANTIPARALLEL FOLDED HUMAN JRNL TITL 3 TELOMERE SEQUENCE. JRNL REF J.MED.CHEM. V. 56 8674 2013 JRNL REFN ISSN 0022-2623 JRNL PMID 24088028 JRNL DOI 10.1021/JM401119B REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH 2.14 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MCC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-13. REMARK 100 THE RCSB ID CODE IS RCSB103469. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM HUMAN TELOMERE REMARK 210 QUADRUPLEX, 0.3 MM LL-(RU[BIPY]2) REMARK 210 TPPZ4+, 50 MM SODIUM CHLORIDE, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY; 2D 1H-31P HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR_NIH 2.14 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 H21 DG A 4 N7 DG A 8 1.44 REMARK 500 N7 DG A 16 H22 DG A 20 1.51 REMARK 500 O3' DG A 10 H73 DT A 11 1.51 REMARK 500 H1 DG A 2 O6 DG A 10 1.53 REMARK 500 H21 DG A 2 O6 DG A 10 1.55 REMARK 500 H4' DG A 9 O5' DG A 10 1.57 REMARK 500 H2'' DA A 7 OP2 DG A 8 1.58 REMARK 500 N7 DG A 3 H21 DG A 9 1.59 REMARK 500 N7 DG A 4 H21 DG A 16 1.59 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 2 DG A 3 N7 DG A 3 C8 -0.036 REMARK 500 2 DG A 4 N3 DG A 4 C4 -0.070 REMARK 500 2 DG A 4 C8 DG A 4 N9 -0.048 REMARK 500 2 DG A 4 C2 DG A 4 N2 -0.126 REMARK 500 2 DG A 8 O4' DG A 8 C4' 0.070 REMARK 500 2 DG A 8 C2 DG A 8 N3 0.057 REMARK 500 2 DG A 8 C5 DG A 8 N7 -0.088 REMARK 500 2 DG A 8 N7 DG A 8 C8 -0.057 REMARK 500 2 DG A 8 C8 DG A 8 N9 -0.051 REMARK 500 2 DG A 8 N9 DG A 8 C4 0.098 REMARK 500 3 DG A 3 C8 DG A 3 N9 -0.049 REMARK 500 3 DG A 8 P DG A 8 O5' 0.068 REMARK 500 3 DG A 8 N7 DG A 8 C8 -0.039 REMARK 500 3 DG A 20 C5 DG A 20 N7 0.041 REMARK 500 4 DT A 5 C5' DT A 5 C4' 0.046 REMARK 500 4 DT A 6 C5 DT A 6 C7 0.058 REMARK 500 4 DG A 8 C2 DG A 8 N3 0.053 REMARK 500 4 DG A 8 N7 DG A 8 C8 -0.047 REMARK 500 4 DG A 8 C8 DG A 8 N9 -0.050 REMARK 500 4 DG A 8 N9 DG A 8 C4 0.054 REMARK 500 5 DG A 4 C8 DG A 4 N9 -0.044 REMARK 500 5 DT A 6 C5 DT A 6 C7 0.037 REMARK 500 5 DG A 8 N7 DG A 8 C8 -0.039 REMARK 500 5 DG A 8 C8 DG A 8 N9 -0.058 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. = 2.4 DEGREES REMARK 500 1 DA A 1 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 7 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 7 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 8 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 9 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 DG A 9 C5 - N7 - C8 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 9 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DG A 10 C1' - O4' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 9.7 DEGREES REMARK 500 1 DG A 10 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 10 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 10 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DT A 11 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 12 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 13 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA A 13 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 14 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DG A 14 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DG A 15 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 15 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DG A 16 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DG A 16 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DG A 16 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 16 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 18 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA A 19 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 19 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 20 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DG A 20 C5 - N7 - C8 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG A 20 N7 - C8 - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DG A 20 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 DG A 21 C1' - O4' - C4' ANGL. DEV. = -6.7 DEGREES REMARK 500 1 DG A 21 O4' - C1' - N9 ANGL. DEV. = 9.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 295 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 2 0.06 SIDE CHAIN REMARK 500 1 DG A 3 0.05 SIDE CHAIN REMARK 500 1 DG A 8 0.08 SIDE CHAIN REMARK 500 1 DG A 10 0.07 SIDE CHAIN REMARK 500 1 DG A 14 0.08 SIDE CHAIN REMARK 500 1 DG A 15 0.07 SIDE CHAIN REMARK 500 1 DG A 16 0.05 SIDE CHAIN REMARK 500 1 DG A 20 0.08 SIDE CHAIN REMARK 500 1 DG A 21 0.05 SIDE CHAIN REMARK 500 1 DG A 22 0.08 SIDE CHAIN REMARK 500 2 DG A 2 0.06 SIDE CHAIN REMARK 500 2 DG A 4 0.08 SIDE CHAIN REMARK 500 2 DT A 6 0.08 SIDE CHAIN REMARK 500 2 DA A 7 0.13 SIDE CHAIN REMARK 500 2 DG A 8 0.09 SIDE CHAIN REMARK 500 2 DG A 9 0.07 SIDE CHAIN REMARK 500 2 DG A 10 0.06 SIDE CHAIN REMARK 500 2 DG A 14 0.09 SIDE CHAIN REMARK 500 2 DG A 15 0.08 SIDE CHAIN REMARK 500 2 DG A 16 0.07 SIDE CHAIN REMARK 500 2 DG A 20 0.08 SIDE CHAIN REMARK 500 2 DG A 21 0.05 SIDE CHAIN REMARK 500 2 DG A 22 0.07 SIDE CHAIN REMARK 500 3 DG A 2 0.06 SIDE CHAIN REMARK 500 3 DG A 3 0.06 SIDE CHAIN REMARK 500 3 DG A 8 0.08 SIDE CHAIN REMARK 500 3 DG A 10 0.06 SIDE CHAIN REMARK 500 3 DG A 14 0.09 SIDE CHAIN REMARK 500 3 DG A 15 0.07 SIDE CHAIN REMARK 500 3 DG A 16 0.05 SIDE CHAIN REMARK 500 3 DG A 20 0.09 SIDE CHAIN REMARK 500 3 DG A 21 0.05 SIDE CHAIN REMARK 500 3 DG A 22 0.08 SIDE CHAIN REMARK 500 4 DG A 2 0.06 SIDE CHAIN REMARK 500 4 DT A 6 0.10 SIDE CHAIN REMARK 500 4 DA A 7 0.10 SIDE CHAIN REMARK 500 4 DG A 8 0.08 SIDE CHAIN REMARK 500 4 DG A 9 0.06 SIDE CHAIN REMARK 500 4 DG A 10 0.06 SIDE CHAIN REMARK 500 4 DG A 14 0.10 SIDE CHAIN REMARK 500 4 DG A 15 0.07 SIDE CHAIN REMARK 500 4 DG A 16 0.08 SIDE CHAIN REMARK 500 4 DG A 20 0.09 SIDE CHAIN REMARK 500 4 DG A 21 0.05 SIDE CHAIN REMARK 500 4 DG A 22 0.07 SIDE CHAIN REMARK 500 5 DG A 2 0.06 SIDE CHAIN REMARK 500 5 DT A 6 0.12 SIDE CHAIN REMARK 500 5 DA A 7 0.15 SIDE CHAIN REMARK 500 5 DG A 8 0.08 SIDE CHAIN REMARK 500 5 DG A 9 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 57 PLANE DEVIATIONS. 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 RUL A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19435 RELATED DB: BMRB REMARK 900 RELATED ID: 2MCO RELATED DB: PDB DBREF 2MCC A 1 22 PDB 2MCC 2MCC 1 22 SEQRES 1 A 22 DA DG DG DG DT DT DA DG DG DG DT DT DA SEQRES 2 A 22 DG DG DG DT DT DA DG DG DG HET RUL A 101 124 HETNAM RUL TETRAKIS(2,2'-BIPYRIDINE-KAPPA~2~N~1~,N~1'~)(MU- HETNAM 2 RUL TETRAPYRIDO[3,2-A:2',3'-C:3'',2''-H:2''',3'''- HETNAM 3 RUL J]PHENAZINE-1KAPPA~2~N~4~,N~5~:2KAPPA~2~N~13~,N~14~) HETNAM 4 RUL DIRUTHENIUM(4+) FORMUL 2 RUL C64 H44 N14 RU2 4+ SITE 1 AC1 5 DG A 4 DT A 5 DA A 7 DG A 8 SITE 2 AC1 5 DG A 20 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 273 0 1 0 0 0 2 6 0 0 0 2 END