PDB Short entry for 106D HEADER DNA 22-DEC-94 106D TITLE SOLUTION STRUCTURES OF THE I-MOTIF TETRAMERS OF D(TCC), D(5MCCT) AND TITLE 2 D(T5MCC). NOVEL NOE CONNECTIONS BETWEEN AMINO PROTONS AND SUGAR TITLE 3 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 5 16-FEB-22 106D 1 REMARK LINK 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 D(TCC), JRNL TITL 2 D(5METHYLCCT) AND D(T5METHYLCC): NOVEL NOE CONNECTIONS JRNL TITL 3 BETWEEN AMINO PROTONS AND SUGAR 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 5MC STANDS FOR 5-METHYLCYTIDINE. THE REMARK 3 STRUCTURE IS FORMED OF FOUR EQUIVALENT 5MCCT STRANDS DESIGNATED REMARK 3 A, B, C, D. STRANDS A AND C, CONNECTED BY TWO HEMI-PROTONATED REMARK 3 BASE PAIRS (5MC1.5MC1+ AND C2.C2+), FORM A PARALLEL-STRANDED REMARK 3 DUPLEX. THE RELATION BETWEEN STRANDS B AND D IS THE SAME AS THAT REMARK 3 BETWEEN STRANDS A AND C. THE STRANDS OF EACH DUPLEX ARE RELATED REMARK 3 BY A LONGITUDINAL TWO-FOLD SYMMETRY AXIS. THE DUPLEXES HAVE THE REMARK 3 SAME LONGITUDINAL AXIS, AND THEY ARE ANTI-PARALLEL. THEIR HEMI- REMARK 3 PROTONATED C.C+ BASE PAIRS ARE INTERCALATED FACE-TO-FACE. THE REMARK 3 DUPLEXES CAN BE TRANSFORMED INTO ONE ANOTHER BY A 180 DEGREE REMARK 3 ROTATION AROUND A TWO-FOLD AXIS PERPENDICULAR TO THE REMARK 3 LONGITUDINAL AXIS, AND CONSEQUENTLY AROUND A THIRD AXIS REMARK 3 PERPENDICULAR TO THE FIRST TWO. THE H3 IMINO PROTONS OF THE HEMI- REMARK 3 PROTONATED 5MC1.5MC1+ PAIRS WERE NOT INCORPORATED IN THE REMARK 3 COMPUTATIONS. THOSE OF THE C2.C2+ PAIRS WERE ARBITRARILY LOCATED REMARK 3 ON THE C2 RESIDUES OF STRANDS A AND 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 100 THE DEPOSITION ID IS D_1000170015. 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 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 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