106D - Header Asymmetric Unit

HEADER DNA 22-DEC-94 106D

TITLE SOLUTION STRUCTURES OF THE I-MOTIF TETRAMERS OF D(TCC), TITLE 2 D(5MCCT) AND D(T5MCC). NOVEL NOE CONNECTIONS BETWEEN AMINO TITLE 3 PROTONS AND SUGAR PROTONS

COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*MCYP*CP*T)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES

KEYWDS DNA

EXPDTA SOLUTION NMR

NUMMDL 8

AUTHOR J.-L.LEROY,M.GUERON

REVDAT 4 07-APR-09 106D 1 REMARK REVDAT 3 24-FEB-09 106D 1 VERSN REVDAT 2 01-APR-03 106D 1 JRNL REVDAT 1 07-FEB-95 106D 0

JRNL AUTH J.L.LEROY,M.GUERON JRNL TITL SOLUTION STRUCTURES OF THE I-MOTIF TETRAMERS OF JRNL TITL 2 D(TCC), D(5METHYLCCT) AND D(T5METHYLCC): NOVEL NOE JRNL TITL 3 CONNECTIONS BETWEEN AMINO PROTONS AND SUGAR JRNL TITL 4 PROTONS. JRNL REF STRUCTURE V. 3 101 1995 JRNL REFN ISSN 0969-2126 JRNL PMID 7743125 JRNL DOI 10.1016/S0969-2126(01)00138-1

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 5MC STANDS FOR 5-METHYLCYTIDINE. REMARK 3 THE STRUCTURE IS FORMED OF FOUR EQUIVALENT 5MCCT STRANDS REMARK 3 DESIGNATED A, B, C, D. STRANDS A AND C, CONNECTED BY TWO HEMI- REMARK 3 PROTONATED BASE PAIRS (5MC1.5MC1+ AND C2.C2+), FORM A PARALLEL REMARK 3 -STRANDED DUPLEX. THE RELATION BETWEEN STRANDS B AND D IS THE REMARK 3 SAME AS THAT BETWEEN STRANDS A AND C. THE STRANDS OF EACH REMARK 3 DUPLEX ARE RELATED BY A LONGITUDINAL TWO-FOLD SYMMETRY AXIS. REMARK 3 THE DUPLEXES HAVE THE SAME LONGITUDINAL AXIS, AND THEY ARE REMARK 3 ANTI-PARALLEL. THEIR HEMI-PROTONATED C.C+ BASE PAIRS ARE REMARK 3 INTERCALATED FACE-TO-FACE. THE DUPLEXES CAN BE TRANSFORMED REMARK 3 INTO ONE ANOTHER BY A 180 DEGREE ROTATION AROUND A TWO-FOLD REMARK 3 AXIS PERPENDICULAR TO THE LONGITUDINAL AXIS, AND CONSEQUENTLY REMARK 3 AROUND A THIRD AXIS PERPENDICULAR TO THE FIRST TWO. THE H3 REMARK 3 IMINO PROTONS OF THE HEMI-PROTONATED 5MC1.5MC1+ PAIRS WERE NOT REMARK 3 INCORPORATED IN THE COMPUTATIONS. THOSE OF THE C2.C2+ PAIRS REMARK 3 WERE ARBITRARILY LOCATED ON THE C2 RESIDUES OF STRANDS A AND REMARK 3 B, RESPECTIVELY.

REMARK 4 REMARK 4 106D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 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 2 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DC A 2 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC B 5 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC C 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT C 9 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC D 11 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT D 12 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DC A 2 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DC B 5 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DC B 5 C2 - N3 - C4 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DC B 5 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC C 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT C 9 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC D 11 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT D 12 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DC A 2 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DC B 5 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DC C 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DT C 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DC D 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DT D 12 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DC A 2 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 DC B 5 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 DC B 5 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 DC C 8 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 DT C 9 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 4 DC D 11 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DT D 12 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 5 DC A 2 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 5 DC A 2 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 DT A 3 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 5 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 5 DC B 5 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 5 DC C 8 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 5 DT C 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 5 DC D 11 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 81 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL

DBREF 106D A 1 3 PDB 106D 106D 1 3 DBREF 106D B 4 6 PDB 106D 106D 4 6 DBREF 106D C 7 9 PDB 106D 106D 7 9 DBREF 106D D 10 12 PDB 106D 106D 10 12

SEQRES 1 A 3 MCY DC DT SEQRES 1 B 3 MCY DC DT SEQRES 1 C 3 MCY DC DT SEQRES 1 D 3 MCY DC DT

MODRES 106D MCY A 1 DC 5-METHYL-2'-DEOXYCYTIDINE MODRES 106D MCY B 4 DC 5-METHYL-2'-DEOXYCYTIDINE MODRES 106D MCY C 7 DC 5-METHYL-2'-DEOXYCYTIDINE MODRES 106D MCY D 10 DC 5-METHYL-2'-DEOXYCYTIDINE

HET MCY A 1 31 HET MCY B 4 31 HET MCY C 7 31 HET MCY D 10 31

HETNAM MCY 5-METHYL-2'-DEOXYCYTIDINE

FORMUL 1 MCY 4(C10 H15 N3 O4)

LINK O3' MCY A 1 P DC A 2 1555 1555 1.61 LINK O3' MCY B 4 P DC B 5 1555 1555 1.61 LINK O3' MCY C 7 P DC C 8 1555 1555 1.61 LINK O3' MCY D 10 P DC D 11 1555 1555 1.61

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