HEADER    DNA                                     24-JUL-99   1C34              
TITLE     SOLUTION STRUCTURE OF A QUADRUPLEX FORMING DNA AND ITS INTERMIDIATE   
CAVEAT     1C34    SEVEN RIBOSE CARBONS HAVE INCORRECT CHIRALITY                
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-   
COMPND   3 3');                                                                 
COMPND   4 CHAIN: A;                                                            
COMPND   5 ENGINEERED: YES;                                                     
COMPND   6 OTHER_DETAILS: THROMBIN BINDING APTAMER INTERMIDIATE                 
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES                                                       
KEYWDS    APTAMER, THROMBIN BINDING, POTASSIUM, METAL BINDING SITES,            
KEYWDS   2 QUADRUPLEX, INTERMEDIATE, DNA                                        
EXPDTA    SOLUTION NMR                                                          
NUMMDL    11                                                                    
AUTHOR    P.H.BOLTON,V.M.MARATHIAS,K.WANG                                       
REVDAT   6   22-MAY-24 1C34    1       REMARK                                   
REVDAT   5   16-FEB-22 1C34    1       REMARK                                   
REVDAT   4   24-FEB-09 1C34    1       VERSN                                    
REVDAT   3   16-MAY-00 1C34    1       CAVEAT JRNL   EXPDTA                     
REVDAT   2   29-DEC-99 1C34    1       JRNL                                     
REVDAT   1   18-AUG-99 1C34    0                                                
JRNL        AUTH   V.M.MARATHIAS,P.H.BOLTON                                     
JRNL        TITL   STRUCTURES OF THE POTASSIUM-SATURATED, 2:1, AND              
JRNL        TITL 2 INTERMEDIATE, 1:1, FORMS OF A QUADRUPLEX DNA.                
JRNL        REF    NUCLEIC ACIDS RES.            V.  28  1969 2000              
JRNL        REFN                   ISSN 0305-1048                               
JRNL        PMID   10756199                                                     
JRNL        DOI    10.1093/NAR/28.9.1969                                        
REMARK   1                                                                      
REMARK   1 REFERENCE 1                                                          
REMARK   1  AUTH   P.H.BOLTON,V.M.MARATHIAS,K.WANG                              
REMARK   1  TITL   DETERMINATION OF THE NUMBER AND LOCATION OF THE MANGANESE    
REMARK   1  TITL 2 BINDING SITES OF DNA QUADRUPLEXES IN SOLUTION BY EPR AND NMR 
REMARK   1  TITL 3 IN THE PRESENCE AND ABSENCE OF THROMBIN                      
REMARK   1  REF    J.MOL.BIOL.                   V. 260   378 1996              
REMARK   1  REFN                   ISSN 0022-2836                               
REMARK   1  DOI    10.1006/JMBI.1996.0408                                       
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : VNMR 6.1B, FELIX 970, X-PLOR 3.1                     
REMARK   3   AUTHORS     : VARIAN (VNMR), MSI (FELIX), BRUNGER (X-PLOR)         
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1C34 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-99.                  
REMARK 100 THE DEPOSITION ID IS D_1000009397.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 288; 278                           
REMARK 210  PH                             : 7.0; 7.0                           
REMARK 210  IONIC STRENGTH                 : 140 MM NACL,; 140 MM NACL,         
REMARK 210  PRESSURE                       : 1 ATM; 1 ATM                       
REMARK 210  SAMPLE CONTENTS                : 140 MM NACL, 1.4 MM KCL, 20 MM     
REMARK 210                                   TRISD11 PH=7.0; 140 MM NACL, 1.4   
REMARK 210                                   MM KCL, 20 MM TRISD11 PH=7.0       
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D NOESY; PE-COSY; ROESY; BASD     
REMARK 210                                   -TOCSY                             
REMARK 210  SPECTROMETER FIELD STRENGTH    : 500 MHZ; 400 MHZ                   
REMARK 210  SPECTROMETER MODEL             : INOVA; UNITYPLUS                   
REMARK 210  SPECTROMETER MANUFACTURER      : VARIAN                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : VNMR 6.1B, FELIX 970, X-PLOR 3.1   
REMARK 210   METHOD USED                   : STRUCTURE REFINEMENT OF THE DNA    
REMARK 210                                   WAS PREFORMED USING COMPLETE       
REMARK 210                                   RELAXATION MATRIX, RESTRAINED      
REMARK 210                                   MOLECULAR DYNAMICS.                
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 11                                 
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 11                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : 80 TO 100PS STRUCTURES FROM        
REMARK 210                                   DYNAMICS                           
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL                
REMARK 210                                                                      
REMARK 210 REMARK: THIS STRUCTURE IS THE INTERMEDIATE FORM OF THE 15MER         
REMARK 210  QUADRUPLEX WITH ONLY 1 POTASSSIUM PER DNA MOLECULE.                 
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   OP1   DG A    11     H3    DT A    12              1.37            
REMARK 500   H1    DG A    10     O6    DG A    15              1.43            
REMARK 500   O6    DG A     1     H1    DG A    15              1.48            
REMARK 500   H22   DG A     8     O4    DT A     9              1.52            
REMARK 500   H1    DG A     1     O6    DG A     6              1.54            
REMARK 500   H3    DT A     7     N3    DG A    11              1.57            
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   3   C6     DT A   3   N1     -0.043                       
REMARK 500  1  DG A   5   C5'    DG A   5   C4'     0.042                       
REMARK 500  1  DT A   9   C5     DT A   9   C7      0.040                       
REMARK 500  2  DT A   4   C5     DT A   4   C7      0.055                       
REMARK 500  3  DG A   1   C5'    DG A   1   C4'     0.044                       
REMARK 500  3  DT A  12   C5     DT A  12   C7      0.040                       
REMARK 500  4  DT A   3   N3     DT A   3   C4     -0.067                       
REMARK 500  4  DT A   3   C4     DT A   3   C5     -0.057                       
REMARK 500  4  DT A   3   C6     DT A   3   N1     -0.069                       
REMARK 500  4  DT A   3   C2     DT A   3   O2     -0.057                       
REMARK 500  4  DT A   4   C5     DT A   4   C7      0.044                       
REMARK 500  4  DT A   9   N1     DT A   9   C2      0.052                       
REMARK 500  4  DT A  13   C5     DT A  13   C7      0.044                       
REMARK 500  5  DT A   3   C4     DT A   3   C5     -0.077                       
REMARK 500  5  DG A  15   C2'    DG A  15   C1'     0.072                       
REMARK 500  6  DT A   4   C5     DT A   4   C7      0.050                       
REMARK 500  6  DT A   9   C5     DT A   9   C7      0.042                       
REMARK 500  6  DT A  12   C5     DT A  12   C7      0.040                       
REMARK 500  6  DT A  13   C5     DT A  13   C7      0.046                       
REMARK 500  6  DG A  15   C2'    DG A  15   C1'     0.065                       
REMARK 500  7  DG A   2   O3'    DT A   3   P      -0.101                       
REMARK 500  7  DT A   3   C5     DT A   3   C7      0.047                       
REMARK 500  7  DT A   4   C5     DT A   4   C7      0.043                       
REMARK 500  7  DT A   9   C5     DT A   9   C7      0.047                       
REMARK 500  7  DT A  12   C3'    DT A  12   C2'     0.073                       
REMARK 500  7  DT A  13   C5     DT A  13   C7      0.040                       
REMARK 500  8  DT A   3   C5     DT A   3   C7      0.037                       
REMARK 500  8  DT A  13   C5     DT A  13   C7      0.043                       
REMARK 500  8  DG A  15   C2'    DG A  15   C1'     0.061                       
REMARK 500  9  DT A   4   C5     DT A   4   C7      0.036                       
REMARK 500  9  DT A  12   C3'    DT A  12   C2'     0.079                       
REMARK 500 10  DT A   3   N3     DT A   3   C4     -0.051                       
REMARK 500 10  DT A   3   C4     DT A   3   C5     -0.064                       
REMARK 500 10  DT A   3   C6     DT A   3   N1     -0.048                       
REMARK 500 10  DT A  13   C5     DT A  13   C7      0.039                       
REMARK 500 11  DG A   1   C5'    DG A   1   C4'     0.046                       
REMARK 500 11  DG A   2   C5'    DG A   2   C4'     0.046                       
REMARK 500 11  DT A   7   C5     DT A   7   C7      0.044                       
REMARK 500 11  DT A  13   C5     DT A  13   C7      0.039                       
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  DG A   1   C4' -  C3' -  C2' ANGL. DEV. =  -5.5 DEGREES          
REMARK 500  1  DG A   1   O4' -  C1' -  N9  ANGL. DEV. =   5.5 DEGREES          
REMARK 500  1  DG A   2   C5' -  C4' -  O4' ANGL. DEV. =   6.9 DEGREES          
REMARK 500  1  DG A   2   O4' -  C1' -  C2' ANGL. DEV. =  -8.8 DEGREES          
REMARK 500  1  DG A   2   O4' -  C1' -  N9  ANGL. DEV. =   7.9 DEGREES          
REMARK 500  1  DT A   3   C3' -  C2' -  C1' ANGL. DEV. =  -6.4 DEGREES          
REMARK 500  1  DT A   3   O4' -  C1' -  N1  ANGL. DEV. =   3.4 DEGREES          
REMARK 500  1  DT A   3   N1  -  C2  -  N3  ANGL. DEV. =   4.0 DEGREES          
REMARK 500  1  DT A   3   C6  -  C5  -  C7  ANGL. DEV. =  -4.7 DEGREES          
REMARK 500  1  DT A   4   P   -  O5' -  C5' ANGL. DEV. =  11.3 DEGREES          
REMARK 500  1  DT A   4   C4' -  C3' -  C2' ANGL. DEV. =  -4.8 DEGREES          
REMARK 500  1  DT A   4   O4' -  C1' -  C2' ANGL. DEV. = -11.5 DEGREES          
REMARK 500  1  DT A   4   O4' -  C1' -  N1  ANGL. DEV. =   5.8 DEGREES          
REMARK 500  1  DT A   4   C4  -  C5  -  C6  ANGL. DEV. =   3.6 DEGREES          
REMARK 500  1  DT A   4   C6  -  C5  -  C7  ANGL. DEV. =  -6.2 DEGREES          
REMARK 500  1  DG A   5   C4' -  C3' -  C2' ANGL. DEV. =  -4.4 DEGREES          
REMARK 500  1  DG A   5   O4' -  C1' -  N9  ANGL. DEV. =   6.5 DEGREES          
REMARK 500  1  DG A   6   O4' -  C1' -  C2' ANGL. DEV. =  -9.1 DEGREES          
REMARK 500  1  DT A   7   C5' -  C4' -  O4' ANGL. DEV. =   9.0 DEGREES          
REMARK 500  1  DT A   7   O4' -  C1' -  C2' ANGL. DEV. =  -8.8 DEGREES          
REMARK 500  1  DT A   7   O4' -  C1' -  N1  ANGL. DEV. =   8.3 DEGREES          
REMARK 500  1  DG A   8   C4' -  C3' -  C2' ANGL. DEV. =  -4.2 DEGREES          
REMARK 500  1  DG A   8   O4' -  C1' -  C2' ANGL. DEV. =  -6.8 DEGREES          
REMARK 500  1  DT A   9   C4' -  C3' -  C2' ANGL. DEV. =  -4.7 DEGREES          
REMARK 500  1  DT A   9   O4' -  C1' -  C2' ANGL. DEV. =  -6.0 DEGREES          
REMARK 500  1  DT A   9   O4' -  C1' -  N1  ANGL. DEV. =  10.4 DEGREES          
REMARK 500  1  DT A   9   N3  -  C2  -  O2  ANGL. DEV. =  -4.9 DEGREES          
REMARK 500  1  DT A   9   C6  -  C5  -  C7  ANGL. DEV. =  -4.1 DEGREES          
REMARK 500  1  DT A   9   C3' -  O3' -  P   ANGL. DEV. =   8.1 DEGREES          
REMARK 500  1  DG A  10   O4' -  C1' -  C2' ANGL. DEV. =  -7.3 DEGREES          
REMARK 500  1  DG A  10   O4' -  C1' -  N9  ANGL. DEV. =   3.1 DEGREES          
REMARK 500  1  DG A  11   C4' -  C3' -  C2' ANGL. DEV. =  -4.7 DEGREES          
REMARK 500  1  DG A  11   O4' -  C1' -  C2' ANGL. DEV. =  -5.5 DEGREES          
REMARK 500  1  DG A  11   O4' -  C1' -  N9  ANGL. DEV. =   4.0 DEGREES          
REMARK 500  1  DT A  12   C3' -  C2' -  C1' ANGL. DEV. =  -7.2 DEGREES          
REMARK 500  1  DT A  12   O4' -  C1' -  N1  ANGL. DEV. =   4.0 DEGREES          
REMARK 500  1  DT A  12   N3  -  C2  -  O2  ANGL. DEV. =  -3.9 DEGREES          
REMARK 500  1  DT A  12   C6  -  C5  -  C7  ANGL. DEV. =  -4.0 DEGREES          
REMARK 500  1  DT A  13   O4' -  C1' -  C2' ANGL. DEV. =  -8.7 DEGREES          
REMARK 500  1  DT A  13   O4' -  C1' -  N1  ANGL. DEV. =   4.5 DEGREES          
REMARK 500  1  DT A  13   C6  -  C5  -  C7  ANGL. DEV. =  -4.1 DEGREES          
REMARK 500  1  DT A  13   C3' -  O3' -  P   ANGL. DEV. =   9.1 DEGREES          
REMARK 500  1  DG A  14   C4' -  C3' -  C2' ANGL. DEV. =  -6.9 DEGREES          
REMARK 500  1  DG A  14   O4' -  C1' -  C2' ANGL. DEV. =  -5.6 DEGREES          
REMARK 500  1  DG A  14   O4' -  C1' -  N9  ANGL. DEV. =   7.7 DEGREES          
REMARK 500  1  DG A  15   O4' -  C1' -  C2' ANGL. DEV. =  -7.7 DEGREES          
REMARK 500  1  DG A  15   O4' -  C1' -  N9  ANGL. DEV. =   5.9 DEGREES          
REMARK 500  2  DG A   1   C4' -  C3' -  C2' ANGL. DEV. =  -4.6 DEGREES          
REMARK 500  2  DG A   1   O4' -  C1' -  N9  ANGL. DEV. =   5.6 DEGREES          
REMARK 500  2  DG A   2   C4' -  C3' -  C2' ANGL. DEV. =  -5.4 DEGREES          
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     471 ANGLE DEVIATIONS.                             
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  1C34 A    1    15  PDB    1C34     1C34             1     15             
SEQRES   1 A   15   DG  DG  DT  DT  DG  DG  DT  DG  DT  DG  DG  DT  DT          
SEQRES   2 A   15   DG  DG                                                      
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