**************************************************************************** 3DNA v2.0 [August 2007] (by Dr. Xiang-Jun Lu; 3dna.lu@gmail.com) **************************************************************************** 1. The list of the parameters given below correspond to the 5' to 3' direction of strand I and 3' to 5' direction of strand II. 2. All angular parameters, except for the phase angle of sugar pseudo- rotation, are measured in degrees in the range of [-180, +180], and all displacements are measured in Angstrom units. **************************************************************************** File name: 2R5Y_B.pdb Date and time: Fri Apr 10 00:02:44 2009 Number of base-pairs: 19 Number of atoms: 2066 **************************************************************************** HEADER TRANSCRIPTION/DNA 04-SEP-07 XXXX TITLE STRUCTURE OF SCR/EXD COMPLEX BOUND TO A CONSENSUS HOX-EXD TITLE 2 SITE COMPND HOMEOTIC PROTEIN SEX COMBS REDUCED/HOMEOBOX PROTEIN COMPND 2 EXTRADENTICLE/DNA COMPLEX KEYWDS HOMEODOMAIN, HOMEOTIC PROTEINS, SPECIFICITY, DEVELOPMENTAL KEYWDS 2 PROTEIN, DNA-BINDING, HOMEOBOX, NUCLEUS, TRANSCRIPTION, KEYWDS 3 TRANSCRIPTION REGULATION, TRANSCRIPTION/DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.K.AGGARWAL, J.M.PASSNER, R.JAIN JRNL AUTH R.JOSHI, J.M.PASSNER, R.ROHS, R.JAIN, A.SOSINSKY, JRNL AUTH 2 M.A.CRICKMORE, V.JACOB, A.K.AGGARWAL, B.HONIG, JRNL AUTH 3 R.S.MANN JRNL TITL FUNCTIONAL SPECIFICITY OF A HOX PROTEIN MEDIATED JRNL TITL 2 BY THE RECOGNITION OF MINOR GROOVE STRUCTURE JRNL REF CELL(CAMBRIDGE,MASS.) V. 131 530 2007 JRNL REFN ASTM CELLB5 US ISSN 0092-8674 HELIX 1 1 TYR A 82 LYS A 86 5 5 HELIX 2 2 THR A 109 HIS A 121 1 13 HELIX 3 3 THR A 127 LEU A 138 1 12 HELIX 4 4 THR A 141 LYS A 158 1 18 HELIX 5 5 SER B 209 HIS B 223 1 15 HELIX 6 6 SER B 227 GLY B 239 1 13 HELIX 7 7 THR B 241 ASN B 259 1 19 **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.007) ...1>C:...2_:[.DC]C-----G[.DG]:..40_:D<...1 (0.004) | 2 (0.004) ...1>C:...3_:[.DT]T-----A[.DA]:..39_:D<...1 (0.012) | 3 (0.006) ...1>C:...4_:[.DC]C-----G[.DG]:..38_:D<...1 (0.008) | 4 (0.009) ...1>C:...5_:[.DT]T-----A[.DA]:..37_:D<...1 (0.021) | 5 (0.008) ...1>C:...6_:[.DA]A-----T[.DT]:..36_:D<...1 (0.004) | 6 (0.003) ...1>C:...7_:[.DT]T-----A[.DA]:..35_:D<...1 (0.005) | 7 (0.005) ...1>C:...8_:[.DG]G-----C[.DC]:..34_:D<...1 (0.004) | 8 (0.007) ...1>C:...9_:[.DA]A-----T[.DT]:..33_:D<...1 (0.007) | 9 (0.007) ...1>C:..10_:[.DT]T-----A[.DA]:..32_:D<...1 (0.006) | 10 (0.017) ...1>C:..11_:[.DT]T-----A[.DA]:..31_:D<...1 (0.012) | 11 (0.008) ...1>C:..12_:[.DT]T-----A[.DA]:..30_:D<...1 (0.011) | 12 (0.014) ...1>C:..13_:[.DA]A-----T[.DT]:..29_:D<...1 (0.012) | 13 (0.008) ...1>C:..14_:[.DT]T-----A[.DA]:..28_:D<...1 (0.007) | 14 (0.007) ...1>C:..15_:[.DG]G-----C[.DC]:..27_:D<...1 (0.006) | 15 (0.008) ...1>C:..16_:[.DG]G-----C[.DC]:..26_:D<...1 (0.009) | 16 (0.007) ...1>C:..17_:[.DG]G-----C[.DC]:..25_:D<...1 (0.009) | 17 (0.003) ...1>C:..18_:[.DC]C-----G[.DG]:..24_:D<...1 (0.012) | 18 (0.006) ...1>C:..19_:[.DT]T-----A[.DA]:..23_:D<...1 (0.011) | 19 (0.004) ...1>C:..20_:[.DG]G-----C[.DC]:..22_:D<...1 (0.004) | **************************************************************************** Detailed H-bond information: atom-name pair and length [ON] 1 C-----G [4] O2 - N2 2.80 N3 - N1 3.13 N3 - N2 2.90 N4 - O6 3.51 2 T-----A [2] N3 - N1 3.40 O4 - N6 3.60 3 C-----G [3] O2 - N2 2.77 N3 - N1 3.21 N4 - O6 3.56 4 T-----A [2] N3 - N1 2.97 O4 - N6 3.12 5 A-----T [2] N6 - O4 3.34 N1 - N3 3.16 6 T-----A [2] N3 - N1 2.85 O4 - N6 3.23 7 G-----C [3] O6 - N4 2.93 N1 - N3 2.98 N2 - O2 2.95 8 A-----T [2] N6 - O4 3.06 N1 - N3 2.89 9 T-----A [2] N3 - N1 2.94 O4 - N6 2.97 10 T-----A [2] N3 - N1 2.64 O4 - N6 2.72 11 T-----A [2] N3 - N1 2.63 O4 - N6 2.87 12 A-----T [2] N6 - O4 3.12 N1 - N3 2.88 13 T-----A [2] N3 - N1 2.92 O4 - N6 2.90 14 G-----C [3] O6 - N4 2.72 N1 - N3 2.66 N2 - O2 2.44 15 G-----C [3] O6 - N4 2.50 N1 - N3 2.57 N2 - O2 2.56 16 G-----C [3] O6 - N4 3.05 N1 - N3 3.01 N2 - O2 2.93 17 C-----G [2] O2 - N2 2.99 N3 - N2 3.40 18 T-----A [2] N3 - N1 3.71 O4 - N6 3.93 19 G-----C [3] O6 - N4 3.42 N1 - N3 2.98 N2 - O2 2.59 **************************************************************************** Overlap area in Angstrom^2 between polygons defined by atoms on successive bases. Polygons projected in the mean plane of the designed base-pair step. Values in parentheses measure the overlap of base ring atoms only. Those outside parentheses include exocyclic atoms on the ring. Intra- and inter-strand overlap is designated according to the following diagram: i2 3' 5' j2 /|\ | | | Strand I | | II | | | | | \|/ i1 5' 3' j1 step i1-i2 i1-j2 j1-i2 j1-j2 sum 1 CT/AG 4.90( 0.00) 0.00( 0.00) 0.00( 0.00) 4.59( 3.31) 9.49( 3.32) 2 TC/GA 4.64( 0.26) 0.00( 0.00) 0.00( 0.00) 1.58( 0.12) 6.23( 0.38) 3 CT/AG 3.63( 0.00) 0.00( 0.00) 0.00( 0.00) 6.72( 5.16) 10.35( 5.16) 4 TA/TA 4.58( 0.50) 0.00( 0.00) 0.00( 0.00) 0.22( 0.00) 4.80( 0.50) 5 AT/AT 5.58( 1.66) 0.00( 0.00) 0.00( 0.00) 5.92( 2.04) 11.50( 3.71) 6 TG/CA 0.89( 0.00) 0.00( 0.00) 0.00( 0.00) 2.12( 0.10) 3.01( 0.10) 7 GA/TC 5.36( 2.82) 0.00( 0.00) 0.00( 0.00) 1.02( 0.00) 6.37( 2.82) 8 AT/AT 5.12( 1.46) 0.00( 0.00) 0.00( 0.00) 6.56( 2.92) 11.68( 4.38) 9 TT/AA 4.98( 0.05) 0.00( 0.00) 0.00( 0.00) 3.29( 1.83) 8.27( 1.88) 10 TT/AA 5.53( 0.15) 0.00( 0.00) 0.00( 0.00) 5.30( 3.54) 10.83( 3.69) 11 TA/TA 1.74( 0.42) 0.00( 0.00) 0.50( 0.39) 0.11( 0.00) 2.36( 0.81) 12 AT/AT 3.65( 0.73) 0.00( 0.00) 0.00( 0.00) 7.14( 4.15) 10.80( 4.88) 13 TG/CA 2.33( 0.37) 0.00( 0.00) 0.00( 0.00) 2.43( 0.21) 4.76( 0.58) 14 GG/CC 3.99( 1.19) 0.00( 0.00) 0.00( 0.00) 4.67( 1.03) 8.66( 2.23) 15 GG/CC 5.14( 2.16) 0.00( 0.00) 0.00( 0.00) 3.05( 0.12) 8.19( 2.29) 16 GC/GC 4.04( 1.70) 0.00( 0.00) 0.00( 0.00) 2.40( 0.52) 6.43( 2.21) 17 CT/AG 4.45( 0.00) 0.00( 0.00) 0.00( 0.00) 5.75( 4.21) 10.21( 4.21) 18 TG/CA 1.82( 0.00) 0.00( 0.00) 0.00( 0.00) 1.92( 0.00) 3.74( 0.00) **************************************************************************** Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in the coordinate system of the given structure bp Ox Oy Oz Nx Ny Nz 1 C-G 58.11 -9.01 12.47 -0.11 0.99 0.08 2 T-A 57.81 -5.62 13.50 -0.17 0.98 0.07 3 C-G 56.38 -2.32 14.98 -0.07 1.00 0.03 4 T-A 57.55 0.73 14.68 -0.05 1.00 0.02 5 A-T 58.57 4.41 15.88 -0.05 0.99 -0.14 6 T-A 58.21 7.58 15.59 -0.06 1.00 -0.06 7 G-C 57.99 10.76 14.90 0.13 0.99 -0.02 8 A-T 59.06 14.04 15.46 0.15 0.99 0.08 9 T-A 59.59 17.11 16.43 0.16 0.99 0.04 10 T-A 60.25 20.57 16.61 0.14 0.99 0.02 11 T-A 60.65 23.60 16.62 0.14 0.98 -0.12 12 A-T 60.91 26.88 14.99 0.04 0.98 -0.20 13 T-A 62.12 29.74 13.61 -0.01 0.98 -0.20 14 G-C 61.79 32.95 13.26 -0.12 0.98 -0.14 15 G-C 61.66 36.09 12.38 -0.09 0.99 -0.08 16 G-C 61.41 39.70 12.39 -0.09 0.99 0.05 17 C-G 61.52 42.97 13.50 -0.03 1.00 0.07 18 T-A 60.41 46.20 13.39 -0.04 0.99 0.11 19 G-C 59.82 49.83 11.70 -0.06 0.98 0.20 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 C-G -0.78 0.17 -0.06 -4.38 -16.61 10.52 2 T-A -0.06 0.46 0.19 -10.38 -26.88 0.30 3 C-G -0.05 0.32 0.26 -9.82 -6.34 8.60 4 T-A 0.04 -0.00 0.24 1.87 -25.11 -1.41 5 A-T -0.15 0.21 0.03 -5.81 -9.81 2.07 6 T-A -0.04 -0.04 -0.14 -0.38 -10.15 7.73 7 G-C 0.24 -0.02 0.07 4.05 -9.20 -1.66 8 A-T 0.10 -0.04 -0.32 -3.76 -9.42 2.80 9 T-A 0.05 -0.05 -0.11 -0.02 -16.57 -1.24 10 T-A -0.32 -0.28 0.18 -10.75 -18.79 -0.84 11 T-A -0.04 -0.32 -0.28 -3.11 -14.00 4.94 12 A-T -0.25 -0.06 -0.10 -11.07 -7.71 3.52 13 T-A -0.41 -0.05 -0.09 -4.26 -5.33 -2.50 14 G-C 0.38 -0.31 0.14 0.61 -4.25 1.07 15 G-C 0.02 -0.45 0.23 6.57 -2.15 -2.70 16 G-C -0.12 -0.00 -0.15 -0.63 -13.68 1.04 17 C-G -0.46 0.93 0.51 -9.38 -4.73 16.47 18 T-A -0.42 0.80 0.35 -3.27 -9.64 3.10 19 G-C -0.94 -0.10 -0.01 -3.14 -17.97 10.75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.17 0.06 0.05 -3.53 -12.02 3.29 s.d. 0.33 0.36 0.22 5.13 6.90 5.31 **************************************************************************** Local base-pair step parameters step Shift Slide Rise Tilt Roll Twist 1 CT/AG -0.63 0.47 3.47 -2.00 3.08 40.66 2 TC/GA 1.01 1.31 3.52 2.44 -5.79 39.56 3 CT/AG -1.30 0.50 2.97 -0.02 -1.40 34.83 4 TA/TA 1.10 1.50 3.54 2.21 -8.77 44.65 5 AT/AT -0.04 -0.18 3.20 2.41 3.99 29.41 6 TG/CA -0.59 0.28 3.19 -4.30 10.36 37.04 7 GA/TC 0.56 -0.50 3.42 5.67 0.92 37.21 8 AT/AT -0.45 -0.65 3.17 -1.24 1.38 32.16 9 TT/AA -0.03 -0.15 3.52 -1.50 0.96 35.30 10 TT/AA -0.14 0.08 3.05 2.50 7.67 34.29 11 TA/TA 0.71 -0.80 3.51 -0.05 7.55 33.04 12 AT/AT -1.07 -0.88 3.10 -0.20 2.84 31.75 13 TG/CA 0.20 0.12 3.23 -0.60 7.23 34.01 14 GG/CC -0.55 -0.09 3.21 -3.07 1.79 31.60 15 GG/CC 0.08 0.08 3.62 1.00 7.50 35.68 16 GC/GC 0.91 -0.34 3.32 -2.31 3.34 34.21 17 CT/AG -1.07 0.08 3.24 2.46 -0.31 31.94 18 TG/CA 0.38 2.23 3.35 4.72 -2.84 42.83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.05 0.17 3.31 0.45 2.19 35.56 s.d. 0.74 0.81 0.19 2.68 4.95 4.12 **************************************************************************** Local base-pair helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 CT/AG 0.31 0.66 3.52 4.42 2.86 40.82 2 TC/GA 2.62 -1.18 3.36 -8.50 -3.58 40.04 3 CT/AG 1.02 2.17 2.95 -2.34 0.04 34.85 4 TA/TA 2.75 -1.21 3.26 -11.41 -2.87 45.51 5 AT/AT -1.16 0.58 3.14 7.81 -4.71 29.77 6 TG/CA -0.85 0.37 3.20 15.87 6.58 38.64 7 GA/TC -0.90 -0.10 3.45 1.43 -8.82 37.63 8 AT/AT -1.40 0.59 3.15 2.48 2.23 32.21 9 TT/AA -0.41 -0.20 3.51 1.59 2.47 35.35 10 TT/AA -0.94 0.58 2.98 12.79 -4.18 35.20 11 TA/TA -2.66 -1.23 3.25 13.07 0.09 33.87 12 AT/AT -2.09 1.92 3.02 5.18 0.37 31.87 13 TG/CA -0.89 -0.42 3.19 12.18 1.02 34.76 14 GG/CC -0.48 0.45 3.24 3.27 5.61 31.79 15 GG/CC -1.03 0.02 3.56 12.07 -1.62 36.45 16 GC/GC -1.10 -1.89 3.21 5.65 3.91 34.45 17 CT/AG 0.20 2.37 3.15 -0.57 -4.47 32.03 18 TG/CA 3.31 -0.06 3.23 -3.87 -6.43 43.17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.21 0.19 3.24 3.95 -0.64 36.02 s.d. 1.65 1.17 0.18 7.61 4.24 4.24 **************************************************************************** Structure classification: This is a right-handed nucleic acid structure **************************************************************************** lambda: virtual angle between C1'-YN1 or C1'-RN9 glycosidic bonds and the base-pair C1'-C1' line C1'-C1': distance between C1' atoms for each base-pair RN9-YN1: distance between RN9-YN1 atoms for each base-pair RC8-YC6: distance between RC8-YC6 atoms for each base-pair bp lambda(I) lambda(II) C1'-C1' RN9-YN1 RC8-YC6 1 C-G 54.9 63.1 10.5 9.0 10.2 2 T-A 54.9 53.8 11.1 9.4 10.4 3 C-G 58.3 59.7 10.7 9.2 10.3 4 T-A 53.4 52.5 10.8 9.0 10.0 5 A-T 55.3 57.5 10.8 9.2 10.2 6 T-A 59.1 58.5 10.3 8.8 9.9 7 G-C 55.4 51.9 10.8 9.1 10.0 8 A-T 55.0 56.1 10.6 8.9 9.9 9 T-A 54.8 53.2 10.7 9.0 9.9 10 T-A 53.7 55.5 10.4 8.7 9.7 11 T-A 56.7 54.6 10.2 8.6 9.6 12 A-T 55.6 57.9 10.5 8.8 9.9 13 T-A 50.1 56.6 10.8 9.0 9.9 14 G-C 56.0 51.8 10.5 8.8 9.7 15 G-C 53.0 52.5 10.5 8.7 9.6 16 G-C 54.3 54.9 10.8 9.1 10.0 17 C-G 60.0 64.7 10.9 9.5 10.8 18 T-A 54.6 57.8 11.4 9.7 10.8 19 G-C 54.7 64.4 10.3 8.8 9.9 **************************************************************************** Classification of each dinucleotide step in a right-handed nucleic acid structure: A-like; B-like; TA-like; intermediate of A and B, or other cases step Xp Yp Zp XpH YpH ZpH Form 1 CT/AG -3.07 8.99 -0.70 -2.76 9.02 -0.05 B 2 TC/GA -3.09 8.84 -0.79 -0.55 8.64 -2.03 B 3 CT/AG -3.29 8.99 -0.92 -2.31 8.94 -1.27 B 4 TA/TA -2.48 8.72 -0.61 0.07 8.46 -2.21 B 5 AT/AT -3.46 8.96 -0.46 -4.57 8.94 0.72 B 6 TG/CA -3.28 8.90 -0.49 -4.05 8.72 1.82 B 7 GA/TC -2.98 8.94 0.14 -3.79 8.93 0.37 B 8 AT/AT -3.42 8.94 -0.44 -4.76 8.95 -0.08 B 9 TT/AA -2.96 8.96 -0.33 -3.36 8.97 -0.09 B 10 TT/AA -3.61 8.81 -1.28 -4.46 8.88 0.61 B 11 TA/TA -3.63 8.78 0.07 -6.17 8.55 1.97 B 12 AT/AT -3.06 9.03 0.31 -5.07 8.97 1.10 B 13 TG/CA -2.85 9.15 -0.11 -3.70 8.99 1.74 B 14 GG/CC -3.07 9.02 -0.17 -3.47 9.02 0.29 B 15 GG/CC -2.67 9.02 0.32 -3.65 8.78 2.10 B 16 GC/GC -3.27 8.91 0.43 -4.35 8.83 1.30 B 17 CT/AG -3.51 9.22 -0.15 -3.29 9.22 -0.26 B 18 TG/CA -2.44 8.50 -0.46 0.65 8.45 -1.04 **************************************************************************** Minor and major groove widths: direct P-P distances and refined P-P distances which take into account the directions of the sugar-phosphate backbones (Subtract 5.8 Angstrom from the values to take account of the vdw radii of the phosphate groups, and for comparison with FreeHelix and Curves.) Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343. Minor Groove Major Groove P-P Refined P-P Refined 1 CT/AG --- --- --- --- 2 TC/GA --- --- --- --- 3 CT/AG 10.2 --- 16.8 --- 4 TA/TA 10.4 10.3 19.5 19.4 5 AT/AT 11.4 11.4 16.5 16.5 6 TG/CA 12.7 12.7 17.7 17.5 7 GA/TC 11.3 11.2 18.0 17.8 8 AT/AT 9.9 9.9 19.8 19.6 9 TT/AA 10.6 10.4 17.0 16.4 10 TT/AA 12.4 12.0 17.5 17.0 11 TA/TA 12.5 12.2 18.7 18.0 12 AT/AT 12.8 12.6 21.2 20.7 13 TG/CA 14.1 13.9 19.1 18.8 14 GG/CC 13.9 13.7 15.9 15.7 15 GG/CC 12.9 12.7 17.4 17.1 16 GC/GC 12.6 --- 16.2 --- 17 CT/AG --- --- --- --- 18 TG/CA --- --- --- --- **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 3.25(0.46) Helix: -0.008 1.000 -0.009 HETATM 9998 XS X X 999 59.854 -9.217 14.560 HETATM 9999 XE X X 999 59.374 49.157 14.035 Average and standard deviation of helix radius: P: 9.62(1.37), O4': 6.78(1.38), C1': 6.23(1.32) Global parameters based on C1'-C1' vectors: disp.: displacement of the middle C1'-C1' point from the helix angle: inclination between C1'-C1' vector and helix (subtracted from 90) twist: helical twist angle between consecutive C1'-C1' vectors rise: helical rise by projection of the vector connecting consecutive C1'-C1' middle points onto the helical axis bp disp. angle twist rise 1 C-G 0.54 -12.30 37.48 3.50 2 T-A 0.39 -13.36 38.69 3.22 3 C-G 0.82 -1.17 35.23 3.53 4 T-A 1.89 -4.68 44.31 2.74 5 A-T 1.86 -1.09 29.35 3.59 6 T-A 3.42 -2.85 35.91 3.94 7 G-C 3.97 -4.25 36.68 2.85 8 A-T 3.66 3.26 32.98 3.04 9 T-A 4.31 4.76 36.82 2.75 10 T-A 4.75 4.39 34.20 3.58 11 T-A 5.23 4.99 34.25 2.92 12 A-T 4.22 10.10 32.87 2.99 13 T-A 5.01 9.45 30.58 3.51 14 G-C 4.88 9.40 33.90 3.36 15 G-C 4.89 5.61 36.53 3.36 16 G-C 4.17 2.20 35.97 2.94 17 C-G 2.46 6.02 31.89 3.40 18 T-A 1.77 5.62 45.26 3.17 19 G-C 1.79 0.76 --- --- **************************************************************************** Main chain and chi torsion angles: Note: alpha: O3'(i-1)-P-O5'-C5' beta: P-O5'-C5'-C4' gamma: O5'-C5'-C4'-C3' delta: C5'-C4'-C3'-O3' epsilon: C4'-C3'-O3'-P(i+1) zeta: C3'-O3'-P(i+1)-O5'(i+1) chi for pyrimidines(Y): O4'-C1'-N1-C2 chi for purines(R): O4'-C1'-N9-C4 Strand I base alpha beta gamma delta epsilon zeta chi 1 C -63.7 -176.5 43.8 139.9 -174.7 -162.8 -94.3 2 T -11.6 129.5 46.2 140.7 -142.9 -144.9 -113.8 3 C 110.4 -133.3 -164.5 141.9 -129.5 -153.4 -124.5 4 T -39.8 137.0 37.8 136.0 -147.6 -152.9 -103.3 5 A -28.9 126.3 48.0 131.5 -179.7 -110.1 -107.8 6 T -46.3 -176.4 36.8 144.3 -156.5 -131.3 -93.5 7 G -61.3 160.3 50.2 136.0 178.8 -106.9 -105.4 8 A -45.1 176.5 43.8 128.4 174.7 -97.6 -114.5 9 T -50.1 -173.5 42.6 137.2 -175.0 -116.8 -105.5 10 T -42.1 164.1 47.6 138.3 -159.9 -126.2 -116.1 11 T 135.4 -163.1 -178.1 136.8 -169.6 -83.4 -120.9 12 A -70.4 -176.6 41.2 125.5 178.2 -120.2 -111.7 13 T -46.0 -176.7 41.2 134.6 -169.2 -97.8 -111.3 14 G -55.8 175.4 42.3 137.3 -150.7 -142.0 -104.8 15 G -41.0 147.7 38.5 131.7 -154.9 -133.4 -109.3 16 G -39.7 149.1 41.5 135.5 177.3 -103.4 -110.7 17 C -61.3 -171.7 49.7 142.6 -159.4 -132.4 -109.8 18 T -48.8 157.8 47.8 138.4 -159.5 -153.6 -106.8 19 G -42.3 146.6 54.7 155.7 --- --- -99.9 Strand II base alpha beta gamma delta epsilon zeta chi 1 G 24.6 -147.1 -71.3 165.6 --- --- -98.1 2 A -41.9 124.1 45.2 145.2 -155.2 -113.2 -100.6 3 G 162.1 -177.0 171.6 141.4 -120.5 -178.1 -111.8 4 A -60.8 143.1 44.0 138.8 169.5 -88.0 -99.4 5 T -52.1 167.5 49.1 141.5 -104.9 161.4 -101.9 6 A 39.3 159.7 -49.3 152.5 176.1 -100.3 -89.3 7 C -43.6 149.0 44.2 133.9 -161.1 -125.4 -124.5 8 T -59.0 179.5 41.0 142.9 -155.4 -153.4 -99.4 9 A -46.2 151.9 54.3 132.4 -173.0 -100.3 -115.5 10 A -61.2 171.1 40.7 127.9 -167.1 -130.1 -96.7 11 A -50.0 -173.9 45.5 134.5 -160.9 -87.8 -115.5 12 T -49.9 177.2 43.0 121.2 179.5 -106.4 -113.0 13 A -47.0 171.3 43.2 134.8 179.0 -95.1 -101.6 14 C -41.6 176.2 23.5 131.9 -177.6 -115.3 -95.9 15 C -54.6 178.8 51.4 137.8 -165.3 -104.3 -113.7 16 C -39.4 178.4 35.1 131.9 -172.7 -98.7 -119.4 17 G -69.1 -165.4 49.2 134.1 172.5 -117.0 -99.5 18 A -51.7 137.5 52.2 145.5 166.1 -86.3 -95.0 19 C -68.9 176.5 39.9 138.0 -137.4 177.1 -83.4 **************************************************************************** Sugar conformational parameters: Note: v0: C4'-O4'-C1'-C2' v1: O4'-C1'-C2'-C3' v2: C1'-C2'-C3'-C4' v3: C2'-C3'-C4'-O4' v4: C3'-C4'-O4'-C1' tm: amplitude of pseudorotation of the sugar ring P: phase angle of pseudorotation of the sugar ring Strand I base v0 v1 v2 v3 v4 tm P Puckering 1 C -29.5 40.2 -35.0 18.9 6.5 39.7 152.0 C2'-endo 2 T -27.9 38.9 -34.8 19.5 5.1 38.7 153.9 C2'-endo 3 C -24.4 36.2 -33.7 20.2 2.5 36.4 157.5 C2'-endo 4 T -29.4 38.1 -32.2 15.9 8.3 37.6 148.8 C2'-endo 5 A -30.3 37.7 -30.6 13.7 10.2 37.1 145.6 C2'-endo 6 T -23.1 36.5 -35.4 23.1 -0.1 37.4 161.5 C2'-endo 7 G -23.3 33.7 -30.7 18.0 3.2 33.6 155.8 C2'-endo 8 A -26.6 33.1 -27.1 12.2 8.9 32.7 146.0 C2'-endo 9 T -25.0 35.3 -31.6 17.9 4.3 35.0 154.3 C2'-endo 10 T -30.8 41.0 -35.2 18.3 7.7 40.5 150.5 C2'-endo 11 T -23.0 33.9 -31.6 18.8 2.5 34.2 157.3 C2'-endo 12 A -33.9 38.3 -28.0 9.1 15.4 37.9 137.7 C1'-exo 13 T -20.6 31.8 -30.1 19.0 0.8 32.1 159.7 C2'-endo 14 G -26.5 37.8 -34.3 19.6 4.2 37.8 155.1 C2'-endo 15 G -25.9 35.2 -31.1 16.5 5.7 35.1 152.3 C2'-endo 16 G -26.2 35.4 -31.1 16.6 5.9 35.2 152.0 C2'-endo 17 C -21.0 33.7 -33.0 21.6 -0.5 34.6 162.2 C2'-endo 18 T -29.8 39.6 -34.0 17.6 7.4 39.0 150.5 C2'-endo 19 G -15.7 33.2 -37.2 29.0 -8.5 37.4 174.3 C2'-endo Strand II base v0 v1 v2 v3 v4 tm P Puckering 1 G 4.2 18.9 -33.1 36.5 -25.8 36.5 205.0 C3'-exo 2 A -23.3 37.2 -36.5 23.8 -0.6 38.3 162.2 C2'-endo 3 G -23.9 36.4 -34.8 21.7 1.1 37.1 159.7 C2'-endo 4 A -13.2 27.6 -30.8 23.6 -6.6 31.0 173.6 C2'-endo 5 T -33.1 43.1 -36.3 18.2 9.0 42.3 149.1 C2'-endo 6 A -5.1 22.6 -30.3 28.1 -14.6 30.7 189.1 C3'-exo 7 C -29.2 37.5 -31.5 15.3 8.5 37.1 148.3 C2'-endo 8 T -31.1 42.6 -37.4 20.6 6.3 42.1 152.7 C2'-endo 9 A -31.7 38.8 -30.9 13.4 11.4 38.1 144.3 C2'-endo 10 A -32.0 37.2 -28.3 10.5 13.5 36.8 140.4 C1'-exo 11 A -21.6 31.6 -29.1 17.3 2.6 31.7 156.8 C2'-endo 12 T -28.4 32.8 -24.3 8.3 12.7 32.3 138.7 C1'-exo 13 A -21.9 31.6 -29.0 16.9 3.0 31.8 156.1 C2'-endo 14 C -26.5 34.4 -29.1 14.2 7.6 34.0 148.8 C2'-endo 15 C -19.5 32.5 -32.6 21.9 -1.6 33.9 164.1 C2'-endo 16 C -21.7 26.4 -20.8 8.8 8.1 25.9 143.4 C1'-exo 17 G -19.1 28.7 -27.0 16.4 1.7 29.1 158.3 C2'-endo 18 A -9.0 25.7 -31.8 27.2 -11.6 31.8 182.4 C3'-exo 19 C -26.5 34.6 -29.4 14.7 7.2 34.2 149.3 C2'-endo **************************************************************************** Same strand P--P and C1'--C1' virtual bond distances Strand I Strand II base P--P C1'--C1' base P--P C1'--C1' 1 C/T 6.7 4.8 1 G/A 6.8 5.1 2 T/C 6.7 5.1 2 A/G 7.1 5.0 3 C/T 7.2 5.1 3 G/A 6.9 4.8 4 T/A 6.6 4.5 4 A/T 6.6 5.4 5 A/T 6.9 5.1 5 T/A 6.5 4.4 6 T/G 6.4 5.1 6 A/C 6.8 5.4 7 G/A 7.0 4.9 7 C/T 6.6 5.1 8 A/T 6.8 5.0 8 T/A 7.0 5.0 9 T/T 6.7 4.9 9 A/A 6.6 4.8 10 T/T 6.9 5.4 10 A/A 6.6 4.8 11 T/A 7.6 5.0 11 A/T 6.7 5.3 12 A/T 6.6 5.5 12 T/A 6.7 4.7 13 T/G 6.6 4.9 13 A/C 6.4 4.8 14 G/G 6.7 5.0 14 C/C 6.8 4.9 15 G/G 6.7 4.9 15 C/C 6.5 5.2 16 G/C 6.8 5.1 16 C/G 6.7 5.0 17 C/T 6.6 5.2 17 G/A 7.0 4.7 18 T/G 6.8 5.2 18 A/C 6.4 5.4 **************************************************************************** Helix radius (radial displacement of P, O4', and C1' atoms in local helix frame of each dimer) Strand I Strand II step P O4' C1' P O4' C1' 1 CT/AG 9.8 7.1 6.6 9.1 5.7 5.2 2 TC/GA 7.4 4.6 4.1 9.9 7.1 6.6 3 CT/AG 11.3 8.3 7.7 7.2 4.0 3.5 4 TA/TA 7.4 4.2 4.0 9.6 6.6 6.4 5 AT/AT 10.4 7.5 7.0 9.6 6.6 6.0 6 TG/CA 9.8 7.2 6.4 9.5 6.7 6.0 7 GA/TC 9.7 6.6 6.2 9.7 7.1 6.5 8 AT/AT 10.6 7.6 7.1 9.7 6.6 6.2 9 TT/AA 9.4 6.3 5.8 9.7 6.7 6.1 10 TT/AA 10.4 7.5 6.8 9.5 6.3 5.6 11 TA/TA 10.2 7.3 6.7 11.0 8.9 8.2 12 AT/AT 11.8 9.3 8.7 8.9 6.2 5.6 13 TG/CA 9.5 6.6 5.8 10.0 7.3 6.5 14 GG/CC 9.9 7.0 6.3 9.4 6.1 5.7 15 GG/CC 9.6 7.0 6.3 9.4 7.0 6.3 16 GC/GC 8.4 6.0 5.4 11.5 8.9 8.2 17 CT/AG 12.1 8.9 8.4 7.5 4.6 4.1 18 TG/CA 8.4 5.6 5.3 8.6 5.6 5.5 **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step bp Px Py Pz Hx Hy Hz 1 CT/AG 58.57 -7.18 12.71 -0.15 0.98 0.16 2 TC/GA 59.49 -3.44 15.38 -0.17 0.98 -0.09 3 CT/AG 56.52 -0.84 12.58 -0.08 1.00 -0.01 4 TA/TA 59.70 2.84 13.07 -0.24 0.97 -0.06 5 AT/AT 58.32 6.10 16.98 0.10 0.99 -0.08 6 TG/CA 58.59 9.36 15.94 0.09 0.95 -0.31 7 GA/TC 59.33 12.16 15.03 0.28 0.96 -0.01 8 AT/AT 60.73 15.45 15.56 0.10 0.99 0.05 9 TT/AA 59.87 18.87 16.09 0.11 0.99 0.06 10 TT/AA 60.72 22.05 15.60 -0.08 1.00 -0.06 11 TA/TA 58.06 25.12 15.13 -0.04 1.00 0.01 12 AT/AT 59.71 28.09 12.26 0.01 0.99 -0.12 13 TG/CA 61.38 31.37 14.18 0.04 1.00 0.00 14 GG/CC 61.12 34.54 13.00 -0.01 0.99 -0.17 15 GG/CC 61.58 37.89 13.37 0.11 0.99 -0.01 16 GC/GC 63.52 41.38 12.61 -0.03 1.00 -0.05 17 CT/AG 60.11 44.37 15.55 0.03 0.99 0.12 18 TG/CA 57.21 48.02 13.58 0.07 0.98 0.18