**************************************************************************** 3DNA v2.0 [June 8, 2008] (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: 3exj.pdb Date and time: Thu Apr 5 09:57:21 2018 Number of base-pairs: 11 Number of atoms: 4093 **************************************************************************** HEADER TRANSCRIPTION/DNA 16-OCT-08 3EXJ TITLE CRYSTAL STRUCTURE OF A P53 CORE TETRAMER BOUND TO DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: MOUSE P53 CORE DOMAIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(P*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DCP*DA)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: P53 CONSENSUS SEQUENCE; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(*DTP*DTP*DGP*DAP*DGP*DCP*DAP*DTP*DGP*DCP*DTP*DC)-3'; COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: P53 CONSENSUS SEQUENCE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, ACETYLATION, ACTIVATOR, ANTI-ONCOGENE, KEYWDS 2 APOPTOSIS, CELL CYCLE, COVALENT PROTEIN-RNA LINKAGE, CYTOPLASM, KEYWDS 3 DISEASE MUTATION, DNA-BINDING, ENDOPLASMIC RETICULUM, METAL-BINDING, KEYWDS 4 METHYLATION, NUCLEUS, PHOSPHOPROTEIN, TRANSCRIPTION, TRANSCRIPTION KEYWDS 5 REGULATION, UBL CONJUGATION, ZINC, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.A.MALECKA REVDAT 3 25-OCT-17 3EXJ 1 REMARK REVDAT 2 03-FEB-09 3EXJ 1 JRNL REVDAT 1 16-DEC-08 3EXJ 0 JRNL AUTH K.A.MALECKA,W.C.HO,R.MARMORSTEIN JRNL TITL CRYSTAL STRUCTURE OF A P53 CORE TETRAMER BOUND TO DNA. JRNL REF ONCOGENE V. 28 325 2009 JRNL REFN ISSN 0950-9232 JRNL PMID 18978813 JRNL DOI 10.1038/ONC.2008.400 HELIX 1 1 GLN A 101 GLY A 105 5 5 HELIX 2 2 THR A 115 VAL A 119 5 5 HELIX 3 3 CYS A 173 ARG A 178 1 6 HELIX 4 4 CYS A 274 LYS A 288 1 15 HELIX 5 5 GLN B 101 GLY B 105 5 5 HELIX 6 6 THR B 115 VAL B 119 5 5 HELIX 7 7 CYS B 173 ARG B 178 1 6 HELIX 8 8 CYS B 274 ARG B 287 1 14 SHEET 1 A 4 HIS A 107 PHE A 110 0 SHEET 2 A 4 CYS A 138 TRP A 143 -1 O GLN A 141 N GLY A 109 SHEET 3 A 4 THR A 227 TYR A 233 -1 O THR A 227 N LEU A 142 SHEET 4 A 4 ILE A 192 GLU A 195 -1 N GLU A 195 O HIS A 230 SHEET 1 B 7 CYS A 121 SER A 124 0 SHEET 2 B 7 LYS A 129 CYS A 132 -1 O PHE A 131 N THR A 122 SHEET 3 B 7 LEU A 261 VAL A 271 1 O GLU A 268 N LEU A 130 SHEET 4 B 7 ILE A 248 GLU A 255 -1 N LEU A 254 O LEU A 262 SHEET 5 B 7 ARG A 153 TYR A 160 -1 N ARG A 153 O GLU A 255 SHEET 6 B 7 HIS A 211 PRO A 216 -1 O VAL A 215 N VAL A 154 SHEET 7 B 7 GLU A 201 GLU A 204 -1 N LEU A 203 O SER A 212 SHEET 1 C 4 HIS B 107 PHE B 110 0 SHEET 2 C 4 CYS B 138 TRP B 143 -1 O GLN B 141 N GLY B 109 SHEET 3 C 4 THR B 227 TYR B 233 -1 O TYR B 231 N CYS B 138 SHEET 4 C 4 ILE B 192 GLU B 195 -1 N GLU B 195 O HIS B 230 SHEET 1 D 7 CYS B 121 SER B 124 0 SHEET 2 D 7 LYS B 129 CYS B 132 -1 O PHE B 131 N THR B 122 SHEET 3 D 7 LEU B 261 VAL B 271 1 O GLU B 268 N LEU B 130 SHEET 4 D 7 ILE B 248 GLU B 255 -1 N LEU B 254 O LEU B 262 SHEET 5 D 7 ARG B 153 TYR B 160 -1 N MET B 157 O ILE B 251 SHEET 6 D 7 HIS B 211 PRO B 216 -1 O VAL B 215 N VAL B 154 SHEET 7 D 7 GLU B 201 GLU B 204 -1 N LEU B 203 O SER B 212 **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.007) ....>C:..13_:[.DG]G-----C[.DC]:..12_:D<.... (0.003) | 2 (0.004) ....>C:..14_:[.DA]A-----T[.DT]:..11_:D<.... (0.005) | 3 (0.007) ....>C:..15_:[.DG]G-----C[.DC]:..10_:D<.... (0.004) | 4 (0.004) ....>C:..16_:[.DC]C-----G[.DG]:...9_:D<.... (0.008) | 5 (0.013) ....>C:..17_:[.DA]A-----T[.DT]:...8_:D<.... (0.006) | 6 (0.004) ....>C:..18_:[.DT]T-----A[.DA]:...7_:D<.... (0.014) | 7 (0.006) ....>C:..19_:[.DG]G-----C[.DC]:...6_:D<.... (0.004) | 8 (0.007) ....>C:..20_:[.DC]C-----G[.DG]:...5_:D<.... (0.008) | 9 (0.005) ....>C:..21_:[.DT]T-----A[.DA]:...4_:D<.... (0.003) | 10 (0.003) ....>C:..22_:[.DC]C-----G[.DG]:...3_:D<.... (0.002) | 11 (0.008) ....>C:..23_:[.DA]A-----T[.DT]:...2_:D<.... (0.002) | **************************************************************************** Detailed H-bond information: atom-name pair and length [ O N] 1 G-----C [3] O6 - N4 2.94 N1 - N3 2.97 N2 - O2 2.90 2 A-----T [2] N6 - O4 2.92 N1 - N3 2.72 3 G-----C [3] O6 - N4 2.97 N1 - N3 2.95 N2 - O2 2.85 4 C-----G [3] O2 - N2 2.84 N3 - N1 2.98 N4 - O6 3.03 5 A-----T [2] N6 - O4 3.33 N1 - N3 2.51 6 T-----A [2] N3 - N1 2.53 O4 - N6 3.25 7 G-----C [3] O6 - N4 2.90 N1 - N3 2.93 N2 - O2 2.86 8 C-----G [3] O2 - N2 2.83 N3 - N1 2.99 N4 - O6 3.04 9 T-----A [2] N3 - N1 2.83 O4 - N6 2.94 10 C-----G [3] O2 - N2 2.90 N3 - N1 2.99 N4 - O6 2.97 11 A-----T [2] N6 - O4 2.88 N1 - N3 2.94 **************************************************************************** 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 GA/TC 4.54( 1.53) 0.00( 0.00) 0.00( 0.00) 5.61( 0.93) 10.15( 2.46) 2 AG/CT 6.32( 4.69) 0.00( 0.00) 0.00( 0.00) 3.89( 0.00) 10.21( 4.69) 3 GC/GC 4.62( 2.24) 0.00( 0.00) 0.00( 0.00) 2.80( 0.91) 7.42( 3.14) 4 CA/TG 4.01( 0.59) 0.00( 0.00) 0.00( 0.00) 0.02( 0.00) 4.03( 0.59) 5 AT/AT 6.07( 2.26) 0.00( 0.00) 0.00( 0.00) 6.02( 2.07) 12.09( 4.33) 6 TG/CA 0.02( 0.00) 0.00( 0.00) 0.00( 0.00) 4.23( 0.67) 4.25( 0.67) 7 GC/GC 3.47( 1.29) 0.00( 0.00) 0.00( 0.00) 4.70( 2.21) 8.17( 3.50) 8 CT/AG 3.85( 0.00) 0.00( 0.00) 0.00( 0.00) 6.02( 4.45) 9.87( 4.45) 9 TC/GA 4.51( 0.50) 0.00( 0.00) 0.00( 0.00) 3.99( 0.97) 8.50( 1.47) 10 CA/TG 3.79( 0.03) 0.00( 0.00) 0.00( 0.00) 3.09( 0.00) 6.89( 0.03) **************************************************************************** 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 G-C 0.27 32.94 2.70 -0.69 0.09 0.72 2 A-T -1.30 33.70 5.02 -0.57 -0.06 0.82 3 G-C -2.43 33.56 8.29 -0.57 -0.08 0.82 4 C-G -3.90 33.15 11.31 -0.57 -0.13 0.81 5 A-T -5.77 34.29 14.68 -0.49 -0.11 0.86 6 T-A -6.62 34.22 17.09 -0.48 0.10 0.87 7 G-C -8.56 33.12 20.65 -0.56 0.14 0.82 8 C-G -10.26 33.78 23.63 -0.59 0.07 0.80 9 T-A -11.33 34.19 26.90 -0.51 0.04 0.86 10 C-G -12.90 33.69 29.49 -0.55 0.05 0.83 11 A-T -13.91 33.72 32.63 -0.59 -0.06 0.81 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 G-C -0.11 -0.06 0.03 -5.42 -9.42 -1.28 2 A-T 0.03 -0.23 0.18 11.77 -17.76 1.53 3 G-C -0.13 -0.06 0.14 9.63 -9.30 0.59 4 C-G 0.27 -0.03 -0.31 6.89 -10.30 2.16 5 A-T 0.10 -0.22 -0.18 -10.73 -6.99 20.67 6 T-A -0.09 -0.20 -0.28 20.83 -7.76 17.84 7 G-C -0.23 -0.11 -0.25 -3.71 -10.46 0.04 8 C-G 0.09 0.01 0.33 -12.01 -7.88 1.25 9 T-A -0.05 -0.14 0.48 -12.06 -13.03 -1.66 10 C-G 0.14 -0.04 0.18 -2.42 -7.76 -0.99 11 A-T 0.09 -0.05 -0.22 9.64 -3.31 -2.87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.01 -0.10 0.01 1.13 -9.45 3.39 s.d. 0.14 0.08 0.27 11.16 3.68 8.01 **************************************************************************** Local base-pair step parameters step Shift Slide Rise Tilt Roll Twist 1 GA/TC -0.42 0.62 2.80 -2.24 12.24 32.85 2 AG/CT 0.85 0.39 3.33 1.31 0.09 34.67 3 GC/GC 0.48 -0.21 3.34 2.80 -0.64 39.26 4 CA/TG 1.46 0.68 3.68 3.98 3.51 40.30 5 AT/AT -0.06 -0.42 2.53 1.08 12.52 25.39 6 TG/CA -1.44 0.69 3.88 -3.94 4.91 40.17 7 GC/GC -0.24 -0.40 3.47 -4.47 0.54 39.23 8 CT/AG -0.93 0.10 3.34 -3.34 -4.95 34.97 9 TC/GA 0.52 0.38 3.00 2.87 0.88 39.69 10 CA/TG 0.01 0.96 3.16 2.90 6.65 30.10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.02 0.28 3.25 0.10 3.57 35.66 s.d. 0.85 0.49 0.40 3.24 5.63 5.05 **************************************************************************** Local base-pair helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 GA/TC -0.61 0.39 2.87 20.73 3.80 35.07 2 AG/CT 0.65 -1.22 3.36 0.14 -2.20 34.70 3 GC/GC -0.23 -0.38 3.37 -0.96 -4.16 39.36 4 CA/TG 0.53 -1.59 3.84 5.07 -5.74 40.64 5 AT/AT -3.03 0.30 2.09 26.51 -2.29 28.29 6 TG/CA 0.33 1.54 4.05 7.10 5.69 40.64 7 GC/GC -0.66 -0.20 3.47 0.80 6.63 39.47 8 CT/AG 0.92 1.02 3.36 -8.17 5.50 35.46 9 TC/GA 0.47 -0.46 3.03 1.30 -4.21 39.80 10 CA/TG 0.51 0.54 3.28 12.58 -5.49 30.94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.11 -0.01 3.27 6.51 -0.25 36.44 s.d. 1.16 0.96 0.54 10.61 5.04 4.31 **************************************************************************** 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 G-C 53.3 53.1 10.8 9.1 10.0 2 A-T 53.0 56.4 10.4 8.7 9.7 3 G-C 55.1 55.5 10.7 9.0 9.9 4 C-G 57.2 53.9 10.7 9.0 10.0 5 A-T 70.1 66.1 9.2 8.1 9.5 6 T-A 64.4 70.1 9.3 8.1 9.5 7 G-C 53.0 55.9 10.7 9.0 9.9 8 C-G 55.8 56.2 10.7 9.0 10.0 9 T-A 55.2 53.4 10.6 8.9 9.8 10 C-G 54.2 52.6 10.8 9.1 10.0 11 A-T 54.9 52.1 10.7 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 GA/TC -3.03 8.92 -1.44 -3.58 8.89 1.64 B 2 AG/CT -2.64 8.69 -0.42 -2.03 8.69 -0.40 B 3 GC/GC -2.90 8.67 0.07 -3.15 8.67 -0.06 B 4 CA/TG -3.46 8.18 -0.17 -2.93 8.17 0.49 B 5 AT/AT -5.47 7.83 -1.67 -8.40 7.78 1.90 6 TG/CA -3.32 8.24 -0.19 -2.95 8.21 0.74 B 7 GC/GC -2.97 8.70 0.23 -3.62 8.69 0.35 B 8 CT/AG -2.72 8.76 -0.11 -1.88 8.67 -1.31 B 9 TC/GA -2.83 8.71 -0.41 -2.33 8.71 -0.23 B 10 CA/TG -2.58 8.98 -0.75 -2.09 8.93 1.15 B **************************************************************************** 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 GA/TC --- --- --- --- 2 AG/CT --- --- --- --- 3 GC/GC 9.7 --- 19.5 --- 4 CA/TG 11.0 10.6 18.2 18.1 5 AT/AT 12.6 12.2 16.4 16.2 6 TG/CA 10.9 10.5 18.1 17.8 7 GC/GC 9.4 9.2 18.8 18.8 8 CT/AG 10.9 --- 15.9 --- 9 TC/GA --- --- --- --- 10 CA/TG --- --- --- --- **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 3.39(0.51) Helix: -0.541 0.022 0.841 HETATM 9998 XS X X 999 2.021 33.999 3.058 HETATM 9999 XE X X 999 -16.431 34.756 31.755 Average and standard deviation of helix radius: P: 9.15(1.43), O4': 6.53(1.18), C1': 6.07(1.23) 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 G-C 2.66 6.73 32.74 4.05 2 A-T 3.89 0.97 35.62 3.15 3 G-C 3.48 4.69 36.95 2.92 4 C-G 3.70 2.05 41.15 2.97 5 A-T 3.43 1.22 27.48 4.47 6 T-A 3.47 0.65 40.80 2.98 7 G-C 3.84 0.91 37.27 2.91 8 C-G 3.44 2.66 35.85 3.13 9 T-A 3.67 -1.34 39.04 3.51 10 C-G 2.65 0.24 30.57 4.02 11 A-T 2.15 3.04 --- --- **************************************************************************** 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 G --- -113.6 175.3 152.8 -166.3 -122.2 -99.9 2 A 37.4 174.4 -59.9 156.0 162.4 -81.6 -89.0 3 G -62.3 -163.6 43.4 150.3 162.6 -116.8 -81.7 4 C -40.2 174.7 49.9 151.1 172.2 -102.2 -98.6 5 A -57.7 -171.2 51.4 155.0 -157.7 -108.5 -97.0 6 T 6.1 -160.4 -56.7 158.1 -165.4 -149.0 -73.5 7 G -69.2 149.5 66.9 148.9 178.8 -100.3 -115.2 8 C -53.7 -161.7 36.7 148.5 172.1 -114.9 -105.2 9 T -42.1 -175.3 42.9 149.3 177.0 -98.6 -101.4 10 C -50.2 -164.5 30.1 150.3 -176.7 -121.8 -79.2 11 A -50.2 177.1 42.4 157.0 --- --- -74.6 Strand II base alpha beta gamma delta epsilon zeta chi 1 C 43.4 151.6 -54.5 158.6 --- --- -65.5 2 T -45.2 -176.1 48.7 151.7 -168.4 -121.8 -98.1 3 C -54.1 -163.2 37.7 150.0 170.4 -118.5 -99.6 4 G -60.0 146.2 59.9 149.3 -179.5 -105.0 -115.0 5 T 18.8 -176.2 -59.2 158.9 -163.7 -157.2 -76.9 6 A -57.0 -179.4 53.8 154.4 -155.3 -119.5 -104.2 7 C -40.2 173.9 46.5 150.7 175.2 -106.4 -99.1 8 G -49.9 -172.3 44.5 150.6 169.5 -121.9 -84.6 9 A -78.0 -156.1 43.8 150.3 165.8 -97.1 -87.4 10 G -141.8 94.4 154.6 151.6 -171.9 -88.4 -132.9 11 T 35.6 -174.9 -66.8 151.7 -163.8 -68.5 -102.4 **************************************************************************** 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 G -6.5 26.0 -34.4 31.4 -15.8 34.8 187.9 C3'-exo 2 A -1.3 21.6 -32.3 32.0 -19.4 33.6 196.0 C3'-exo 3 G -12.8 31.5 -37.1 30.7 -11.3 37.1 178.8 C2'-endo 4 C -14.8 32.7 -37.2 29.8 -9.5 37.3 175.9 C2'-endo 5 A -13.0 31.5 -37.0 30.7 -11.2 37.1 178.7 C2'-endo 6 T -8.3 27.8 -35.5 31.6 -14.7 35.7 185.3 C3'-exo 7 G -14.4 31.9 -36.6 29.1 -9.3 36.7 175.9 C2'-endo 8 C -10.4 29.1 -35.8 30.5 -12.8 35.8 182.0 C3'-exo 9 T -12.5 30.6 -36.3 29.9 -11.1 36.3 178.9 C2'-endo 10 C -12.7 30.8 -36.3 29.8 -10.8 36.3 178.5 C2'-endo 11 A -14.1 32.4 -37.4 30.3 -10.3 37.4 177.1 C2'-endo Strand II base v0 v1 v2 v3 v4 tm P Puckering 1 C -7.6 26.8 -34.6 31.0 -14.8 34.8 186.1 C3'-exo 2 T -12.3 30.5 -36.3 30.1 -11.4 36.3 179.3 C2'-endo 3 C -11.4 30.0 -36.1 30.4 -12.0 36.2 180.5 C3'-exo 4 G -14.3 32.0 -36.8 29.4 -9.6 36.9 176.4 C2'-endo 5 T -8.8 28.3 -35.7 31.6 -14.4 35.8 184.6 C3'-exo 6 A -14.9 33.0 -37.4 30.0 -9.6 37.5 175.9 C2'-endo 7 C -16.0 33.7 -37.5 29.5 -8.6 37.7 174.3 C2'-endo 8 G -14.1 32.4 -37.3 30.3 -10.3 37.3 177.0 C2'-endo 9 A -9.6 28.1 -35.0 30.1 -13.0 35.0 182.9 C3'-exo 10 G -7.3 26.3 -34.2 30.6 -14.8 34.4 186.4 C3'-exo 11 T -5.8 24.7 -33.1 30.3 -15.5 33.4 188.5 C3'-exo **************************************************************************** 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 G/A 7.2 5.3 1 C/T 6.7 5.2 2 A/G 6.9 4.5 2 T/C 6.6 5.2 3 G/C 6.8 4.7 3 C/G 7.2 5.3 4 C/A 6.9 4.9 4 G/T 6.6 5.0 5 A/T 6.7 5.4 5 T/A 6.8 5.4 6 T/G 6.6 5.1 6 A/C 6.9 4.8 7 G/C 7.2 5.2 7 C/G 6.8 4.9 8 C/T 6.6 5.1 8 G/A 6.5 4.6 9 T/C 6.7 5.0 9 A/G 7.3 5.4 10 C/A 6.4 5.1 10 G/T 6.6 4.9 **************************************************************************** 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 GA/TC 9.8 7.0 6.2 9.4 6.2 5.6 2 AG/CT 8.0 4.8 4.5 9.9 7.0 6.7 3 GC/GC 8.8 6.1 5.7 9.6 6.9 6.4 4 CA/TG 7.2 4.6 4.1 10.2 7.6 7.1 5 AT/AT 11.7 8.5 7.9 11.2 8.2 7.5 6 TG/CA 10.1 7.7 7.0 7.4 4.7 4.3 7 GC/GC 9.3 6.6 6.1 9.5 6.8 6.4 8 CT/AG 9.7 6.6 6.4 8.0 4.8 4.6 9 TC/GA 8.7 5.5 5.2 9.4 6.8 6.1 10 CA/TG 9.5 6.6 6.1 8.8 6.0 5.1 **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step step Px Py Pz Hx Hy Hz 1 GA/TC -0.57 32.66 4.04 -0.41 0.27 0.87 2 AG/CT -2.08 34.93 6.64 -0.54 -0.08 0.84 3 GC/GC -3.10 33.76 9.88 -0.51 -0.10 0.85 4 CA/TG -6.10 34.11 12.16 -0.55 0.00 0.84 5 AT/AT -5.97 37.19 16.04 -0.82 0.03 0.57 6 TG/CA -6.46 34.21 19.65 -0.56 -0.02 0.83 7 GC/GC -9.97 33.45 21.82 -0.49 0.06 0.87 8 CT/AG -10.25 35.18 25.29 -0.51 0.21 0.84 9 TC/GA -11.61 34.09 28.52 -0.55 -0.02 0.84 10 CA/TG -13.93 34.16 30.89 -0.38 -0.09 0.92