**************************************************************************** 3DNA v2.3-2017feb08, created and maintained by Xiang-Jun Lu (PhD) **************************************************************************** 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: 1I0T.pdb Date and time: Mon Apr 30 19:35:10 2018 Number of base-pairs: 6 Number of atoms: 240 **************************************************************************** HEADER DNA 29-JAN-01 1I0T TITLE 0.6 A STRUCTURE OF Z-DNA CGCGCG **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.021) ....>A:...1_:[.DC]C-----G[.DG]:..12_:B<.... (0.023) | 2 (0.021) ....>A:...2_:[.DG]G-----C[.DC]:..11_:B<.... (0.016) | 3 (0.017) ....>A:...3_:[.DC]C-----G[.DG]:..10_:B<.... (0.016) | 4 (0.018) ....>A:...4_:[.DG]G-----C[.DC]:...9_:B<.... (0.012) | 5 (0.031) ....>A:...5_:[.DC]C-----G[.DG]:...8_:B<.... (0.028) | 6 (0.026) ....>A:...6_:[.DG]G-----C[.DC]:...7_:B<.... (0.007) | **************************************************************************** Detailed H-bond information: atom-name pair and length [ O N] 1 C-----G [3] O2 - N2 2.87 N3 - N1 2.93 N4 - O6 2.87 2 G-----C [3] O6 - N4 2.84 N1 - N3 2.90 N2 - O2 2.87 3 C-----G [3] O2 - N2 2.94 N3 - N1 2.91 N4 - O6 2.88 4 G-----C [3] O6 - N4 2.84 N1 - N3 2.89 N2 - O2 2.85 5 C-----G [3] O2 - N2 2.81 N3 - N1 2.88 N4 - O6 2.87 6 G-----C [3] O6 - N4 2.89 N1 - N3 2.90 N2 - O2 2.85 **************************************************************************** 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 CG/CG 0.00( 0.00) 3.16( 0.80) 0.00( 0.00) 0.00( 0.00) 3.16( 0.80) 2 GC/GC 2.31( 0.09) 0.00( 0.00) 0.00( 0.00) 4.83( 2.00) 7.14( 2.09) 3 CG/CG 0.00( 0.00) 3.55( 0.97) 0.00( 0.00) 0.00( 0.00) 3.55( 0.97) 4 GC/GC 6.15( 2.94) 0.00( 0.00) 0.00( 0.00) 3.10( 0.28) 9.25( 3.21) 5 CG/CG 0.00( 0.00) 3.48( 0.95) 0.00( 0.00) 0.00( 0.00) 3.48( 0.95) **************************************************************************** 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 10.002 11.866 32.834 0.009 0.072 -0.997 2 G-C 15.366 11.343 29.166 -0.037 0.052 -0.998 3 C-G 14.765 11.822 25.994 -0.016 -0.065 -0.998 4 G-C 18.463 15.788 22.128 -0.014 -0.032 -0.999 5 C-G 18.982 14.518 18.892 -0.002 -0.045 -0.999 6 G-C 16.952 19.397 14.860 0.014 -0.082 -0.997 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 C-G -0.20 -0.13 0.06 1.81 -3.20 2.76 2 G-C 0.26 -0.17 0.13 -2.76 3.83 1.81 3 C-G -0.29 -0.15 0.03 2.81 6.27 2.78 4 G-C 0.29 -0.18 0.04 -4.97 3.46 2.40 5 C-G -0.18 -0.18 -0.05 5.49 -7.91 1.10 6 G-C 0.22 -0.16 0.06 -3.91 2.66 1.75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.02 -0.16 0.05 -0.25 0.85 2.10 s.d. 0.27 0.02 0.06 4.21 5.32 0.66 **************************************************************************** Local base-pair step parameters step Shift Slide Rise Tilt Roll Twist 1 CG/CG 0.27 5.46 3.55 2.35 -1.57 -9.21 2 GC/GC 0.65 -0.30 3.18 1.33 -6.72 -54.64 3 CG/CG -0.43 5.58 3.61 -1.58 1.08 -7.15 4 GC/GC -0.70 -1.05 3.28 0.61 -0.76 -51.54 5 CG/CG 0.10 5.52 3.70 2.34 -0.13 -6.77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.02 3.04 3.47 1.01 -1.62 -25.86 s.d. 0.55 3.40 0.22 1.62 3.01 24.90 **************************************************************************** Local base-pair helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 CG/CG -28.65 7.36 4.22 9.52 14.22 -9.63 2 GC/GC 0.71 0.78 3.11 7.29 1.44 -55.04 3 CG/CG -46.78 -8.57 2.59 -8.47 -12.37 -7.40 4 GC/GC 1.26 -0.77 3.27 0.87 0.70 -51.55 5 CG/CG -43.65 10.54 3.57 1.05 19.09 -7.16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -23.42 1.87 3.35 2.05 4.62 -26.16 s.d. 23.31 7.46 0.60 7.00 12.41 24.82 **************************************************************************** The 'simple' base-pair and step parameters were introduced into 3DNA as of v2.3-2016jan01. This list of 'simple' parameters is reported by default, but can be turned off by specifying 'analyze -simple=false'. The simple parameters are 'intuitive' for non-Watson-Crick base pairs and associated base-pair steps, where the above corresponding 3DNA parameters may appear cryptic. Note that the following sets of simple parameters are for structural description only, not to be fed into the 'rebuild' program. Overall, they complement the rigorous characterization of base-pair geometry, as exemplified by the original 3DNA analyze/rebuild programs. In short, the 'simple' base-pair parameters employ the RC8--YC6 (default, or RN9--YN1) vector as the (long) y-axis of the pair. As before, the z-axis is the average of two base normals, taking consideration of the M-N vs M+N base-pair classification. In essence, the 'simple' parameters make geometrical sense through the introduction of an ad hoc base-pair reference frame in each case. See x3dna.org for more details. The same idea applies to the 'simple' inter-base-pair step parameters, which use consecutive C1'--C1' vectors. Here, 'angle' refers to the inter-base angle of each pair, with values in the range of [0, 90] degrees corresponding to the net non-planarity, i.e., sqrt(buckle^2 + propeller^2). This structure contains 0 non-Watson-Crick (with leading *) base pair(s) ---------------------------------------------------------------------------- Simple base-pair parameters based on RC8--YC6 vectors bp Shear Stretch Stagger Buckle Propeller Opening angle 1 C-G -0.20 -0.13 0.06 1.77 -3.23 2.76 3.7 2 G-C 0.26 -0.16 0.13 -2.83 3.78 1.81 4.7 3 C-G -0.30 -0.15 0.03 2.97 6.19 2.77 6.9 4 G-C 0.30 -0.17 0.04 -5.05 3.33 2.40 6.1 5 C-G -0.18 -0.18 -0.05 5.40 -7.98 1.09 9.6 6 G-C 0.22 -0.15 0.06 -3.94 2.61 1.75 4.7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.02 -0.16 0.05 -0.28 0.79 2.10 s.d. 0.27 0.02 0.06 4.24 5.31 0.66 ---------------------------------------------------------------------------- Simple base-pair step parameters based on consecutive C1'-C1' vectors step Shift Slide Rise Tilt Roll Twist 1 CG/CG 0.24 5.46 3.55 2.36 -1.56 -11.48 2 GC/GC 0.66 -0.30 3.18 1.35 -6.72 -52.01 3 CG/CG -0.46 5.58 3.61 -1.58 1.07 -9.95 4 GC/GC -0.70 -1.06 3.28 0.61 -0.75 -48.94 5 CG/CG 0.10 5.52 3.70 2.34 -0.13 -8.58 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.03 3.04 3.47 1.02 -1.62 -26.19 s.d. 0.54 3.41 0.22 1.63 3.01 22.22 **************************************************************************** Structure classification: This is a left-handed Z-form 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 51.9 48.7 10.9 9.0 9.9 2 G-C 51.9 54.4 10.7 9.0 9.9 3 C-G 53.6 48.8 10.8 9.0 9.9 4 G-C 50.0 52.3 10.8 9.0 9.9 5 C-G 54.5 50.5 10.7 8.9 9.8 6 G-C 49.1 54.6 10.8 9.0 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 CG/CG 5.22 5.52 -2.75 -23.58 5.88 -1.65 2 GC/GC 4.44 7.42 -1.24 5.07 7.51 -0.39 3 CG/CG 5.17 5.49 -3.01 -41.70 4.99 -3.63 4 GC/GC 3.91 7.90 0.35 5.04 7.90 0.45 5 CG/CG 5.53 5.35 -2.53 -38.37 5.39 -2.26 **************************************************************************** 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 CG/CG --- --- --- --- 2 GC/GC --- --- --- --- 3 CG/CG 11.9 --- 20.6 --- 4 GC/GC --- --- --- --- 5 CG/CG --- --- --- --- **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 3.60(0.11) Helix: 0.0284 0.0123 -0.9995 HETATM 9998 XS X X 999 15.062 14.565 33.054 HETATM 9999 XE X X 999 15.572 14.785 15.091 Average and standard deviation of helix radius: P: 6.87(1.51), O4': 6.03(2.24), C1': 5.53(2.79) 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 4.51 2.08 -11.55 3.59 2 G-C 1.03 3.04 -52.17 3.65 3 C-G 2.62 2.43 -9.91 3.59 4 G-C 2.68 1.80 -49.07 3.63 5 C-G 1.57 3.54 -8.61 3.52 6 G-C 3.79 3.57 --- --- **************************************************************************** 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 --- --- 55.3 139.9 -93.8 77.5 -145.3 2 G 64.5 -175.7 175.8 100.1 -109.3 -74.2 63.6 3 C -145.8 -137.9 57.4 148.8 -89.9 77.4 -161.6 4 G 70.6 -172.5 178.3 90.5 -125.7 -33.5 55.0 5 C -162.9 -148.5 50.7 131.7 -94.1 64.9 -157.4 6 G 82.8 174.4 -177.2 148.0 --- --- 71.7 Strand II base alpha beta gamma delta epsilon zeta chi 1 G 84.5 -173.7 -172.8 149.9 --- --- 72.6 2 C -156.5 -130.7 53.1 143.8 -92.4 62.2 -160.2 3 G 66.5 179.0 -178.9 98.4 -128.8 -57.5 61.2 4 C 159.8 149.9 51.5 143.1 -94.0 71.9 -148.8 5 G 70.2 -171.1 -178.9 94.5 -165.4 69.7 56.7 6 C --- --- -71.4 150.1 -92.6 71.2 -158.2 **************************************************************************** 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: the amplitude of pucker P: the phase angle of pseudorotation Strand I base v0 v1 v2 v3 v4 tm P Puckering 1 C -28.3 35.5 -30.2 14.4 9.0 35.6 147.8 C2'-endo 2 G -6.0 -9.0 19.1 -23.1 18.3 22.8 33.1 C3'-endo 3 C -20.1 34.9 -35.8 24.7 -2.7 36.9 165.9 C2'-endo 4 G -12.4 -6.7 21.4 -29.0 25.6 29.0 42.4 C4'-exo 5 C -32.0 36.0 -26.2 8.4 14.9 35.7 137.3 C1'-exo 6 G -19.2 34.7 -36.6 26.4 -4.0 37.4 168.2 C2'-endo Strand II base v0 v1 v2 v3 v4 tm P Puckering 1 G -22.2 38.3 -40.4 29.0 -3.7 41.4 167.4 C2'-endo 2 C -27.3 38.4 -35.0 20.4 4.7 38.6 155.1 C2'-endo 3 G -1.9 -12.4 20.9 -22.8 15.3 22.8 23.1 C3'-endo 4 C -26.2 37.6 -34.4 20.6 3.6 37.6 156.1 C2'-endo 5 G -6.7 -9.9 21.3 -25.8 20.6 25.5 33.4 C3'-endo 6 C -22.1 36.3 -36.5 24.8 -1.5 38.0 164.1 C2'-endo **************************************************************************** Same strand P--P and C1'--C1' virtual bond distances Strand I Strand II step P--P C1'--C1' step P--P C1'--C1' 1 C/G --- 6.29 1 G/C 5.93 6.15 2 G/C 6.42 6.95 2 C/G 6.51 6.19 3 C/G 6.30 6.17 3 G/C 6.69 6.41 4 G/C 6.46 6.43 4 C/G 7.06 6.89 5 C/G 5.61 6.30 5 G/C --- 6.18 **************************************************************************** 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 CG/CG 27.94 29.36 29.20 22.80 26.41 26.61 2 GC/GC 9.50 7.45 6.87 8.66 6.02 5.49 3 CG/CG 40.79 44.24 44.50 44.82 46.87 46.78 4 GC/GC 9.25 6.36 5.86 9.59 7.65 7.11 5 CG/CG 42.47 44.63 44.34 37.84 41.39 41.73 **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step step Px Py Pz Hx Hy Hz 1 CG/CG 11.13 40.35 24.63 0.10 -0.21 -0.97 2 GC/GC 14.65 10.74 27.53 0.09 0.01 -1.00 3 CG/CG -13.85 49.44 31.48 -0.27 -0.03 -0.96 4 GC/GC 19.95 15.67 20.50 0.00 -0.03 -1.00 5 CG/CG -16.71 -8.26 3.82 0.30 0.07 -0.95