COORDINATES INPUT TAKEN FROM ::PDB1BNA.ENT HEADER DEOXYRIBONUCLEIC ACID 26-JAN-81 1BNA 1BNA 3 COMPND /DNA$ (B, 1BNAD 1 COMPND 2 5(PRIME)-$D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3(PRIME)) 1BNAD 2 COMPND 3 (290 DEGREES K) 1BNAD 3 AUTHOR H.R.DREW,R.E.DICKERSON 1BNA 6 JRNL AUTH H.R.DREW,R.M.WING,T.TAKANO,C.BROKA,S.TANAKA, 1BNA 7 JRNL AUTH 2 K.ITAKURA,R.E.DICKERSON 1BNA 8 JRNL TITL STRUCTURE OF A B-/DNA$ DODECAMER. CONFORMATION AND 1BNA 9 JRNL TITL 2 DYNAMICS 1BNA 10 JRNL REF PROC.NAT.ACAD.SCI.USA V. 78 2179 1981 1BNAA 1 JRNL REFN ASTM PNASA6 US ISSN 0027-8424 040 1BNAA 2 The basepair Y-axis is along C6--C8 direction. Local Step Parameters: Tilt Roll Twist Dx Dy Dz --------------------------------------------------------------------- 1 C:G 24 -2.42 7.63 37.01 -0.38 0.26 3.19 2 G:C 23 0.46 -4.01 38.70 0.45 0.47 3.42 3 C:G 22 1.61 8.14 26.34 -0.32 0.66 3.74 4 G:C 21 -1.76 2.99 36.97 -0.07 0.04 3.17 5 A:T 20 -0.48 1.10 37.38 0.01 -0.40 3.25 6 A:T 19 1.74 -2.75 33.09 0.25 -0.62 3.20 7 T:A 18 2.25 0.62 35.54 -0.04 -0.31 3.23 8 T:A 17 0.86 -0.42 40.47 0.04 -0.10 3.01 9 C:G 16 -1.62 4.31 28.62 0.34 0.81 3.75 10 G:C 15 -2.56 -11.02 41.58 -1.16 0.65 3.42 11 C:G 14 0.76 -1.60 35.65 0.73 0.18 3.70 12 G:C 13 --------------------------------------------------------------------- Av. -0.11 0.45 35.58 -0.01 0.15 3.37 Std.Dev. 1.66 5.22 4.44 0.48 0.45 0.25 --------------------------------------------------------------------- Local Helical Parameters: Inclin. Tip Twist dx dy dz --------------------------------------------------------------------- 1 C:G 24 11.23 3.54 37.83 -0.63 0.27 3.19 2 G:C 23 -5.69 -0.65 38.90 1.25 -0.62 3.35 3 C:G 22 16.86 -3.29 27.59 -1.04 1.18 3.75 4 G:C 21 4.46 2.63 37.13 -0.35 -0.13 3.16 5 A:T 20 1.63 0.70 37.40 -0.77 -0.08 3.24 6 A:T 19 -4.61 -2.91 33.25 -0.61 -0.13 3.25 7 T:A 18 0.97 -3.50 35.61 -0.60 0.41 3.21 8 T:A 17 -0.57 -1.17 40.48 -0.10 0.04 3.01 9 C:G 16 8.37 3.14 28.98 0.49 -1.13 3.81 10 G:C 15 -14.17 3.27 43.03 2.16 1.37 3.20 11 C:G 14 -2.48 -1.18 35.70 0.56 -1.06 3.70 12 G:C 13 --------------------------------------------------------------------- Av. 1.45 0.05 35.99 0.03 0.01 3.35 Std.Dev. 8.21 2.61 4.39 0.94 0.76 0.26 --------------------------------------------------------------------- 1 Molecule has been reoriented along best linear axis obtained from C1' atoms. Molecule rotated along( -0.9476 0.3194 0.0000) by 163.325 Deg. and translated by 0.418-22.538A along X and Y directions. GLOBAL Helical Parameters: Inclin. Tip Twist dx dy dz --------------------------------------------------------------------- 1 C:G 24 10.95 0.18 37.62 0.40 -0.23 3.19 2 G:C 23 8.95 1.07 39.03 -0.25 -0.62 3.47 3 C:G 22 6.81 -8.43 26.52 -0.39 -0.43 3.74 4 G:C 21 5.66 -3.26 36.91 -1.17 0.19 3.16 5 A:T 20 1.87 -2.79 37.33 -1.12 0.76 3.25 6 A:T 19 -0.31 -2.22 33.14 -0.70 0.90 3.21 7 T:A 18 -0.62 -4.69 35.61 -0.22 0.56 3.22 8 T:A 17 -1.02 -3.54 40.47 -0.20 0.42 3.00 9 C:G 16 -2.45 -2.68 28.67 -0.01 0.49 3.70 10 G:C 15 -3.93 3.24 41.76 0.83 1.35 3.34 11 C:G 14 -6.67 -3.71 35.93 0.77 1.79 3.67 12 G:C 13 -7.37 -0.79 2.42 1.44 --------------------------------------------------------------------- Av. 0.99 -2.30 35.73 0.03 0.55 3.36 Std.Dev. 5.72 2.87 4.46 0.94 0.72 0.24 --------------------------------------------------------------------- Intra base-pair Parameters: PROP. BUCKLE OPENING GLYCOSIDIC C8..C6 C1..C1 --------------------------------------------------------------------- 1 C:G 24 -14.31 -2.08 21.67 46.36 56.98 9.78 10.71 2 G:C 23 -10.86 4.41 23.04 51.06 51.54 9.77 10.77 3 C:G 22 -3.90 6.96 18.52 52.29 55.55 9.78 10.58 4 G:C 21 -10.75 -8.94 17.31 53.40 55.54 9.57 10.35 5 A:T 20 -16.21 -5.57 14.93 55.93 53.06 9.76 10.44 6 A:T 19 -18.16 -3.49 11.00 55.74 57.10 9.94 10.46 7 T:A 18 -17.68 -1.26 7.74 59.99 57.01 9.85 10.23 8 T:A 17 -17.71 0.96 14.79 55.17 54.33 9.79 10.49 9 C:G 16 -17.30 10.23 18.21 53.47 53.82 9.75 10.59 10 G:C 15 -5.28 -1.74 15.45 58.37 53.96 9.77 10.44 11 C:G 14 -18.10 3.95 24.95 51.16 49.17 9.76 10.81 12 G:C 13 1.65 -6.67 22.06 50.25 53.26 9.93 10.89 --------------------------------------------------------------------- Av. -12.38 -0.27 17.47 53.60 54.28 9.79 10.56 Std.Dev. 6.39 5.51 4.85 3.58 2.28 0.09 0.19 --------------------------------------------------------------------- 1 LOCAL HELIX ORIGINS LOCAL HELIX AXES -0.655 0.933 -33.808 0.0483 -0.0335 0.9983 1.479 0.214 -30.449 -0.0648 0.2461 0.9671 -1.627 0.640 -27.085 0.1855 -0.0577 0.9810 0.541 0.697 -23.325 0.0096 0.1042 0.9945 0.670 0.614 -20.159 -0.0252 0.0557 0.9981 0.479 0.922 -16.931 -0.0297 -0.0699 0.9971 0.379 0.158 -13.689 -0.0212 0.0275 0.9994 -0.311 0.242 -10.516 -0.0379 -0.0183 0.9991 -1.695 -0.126 -7.591 -0.2054 -0.0560 0.9771 0.365 -1.271 -3.604 0.1719 0.0460 0.9840 -1.705 -2.277 -0.643 -0.0019 -0.0855 0.9963 BASE/B.P. CENTERS BASE/B.P. NORMALS -0.235 0.394 -33.755 0.0857 0.1571 0.9839 0.158 0.649 -30.570 -0.0363 0.1233 0.9917 -0.051 0.578 -27.097 0.0309 0.1731 0.9844 0.515 1.072 -23.359 -0.0954 0.0879 0.9916 0.324 1.311 -20.200 -0.0473 0.0344 0.9983 -0.110 1.138 -16.954 -0.0272 0.0296 0.9992 -0.227 0.554 -13.743 -0.0820 0.0113 0.9966 -0.412 0.215 -10.523 -0.0525 -0.0330 0.9981 -0.485 0.100 -7.519 -0.0480 -0.0369 0.9982 -1.521 0.439 -3.819 -0.1073 0.0289 0.9938 -1.612 -1.090 -0.484 -0.0443 -0.1899 0.9808 -2.334 -1.576 3.187 0.0227 -0.1521 0.9881 1 ANGLE BETWEEN SUCCESSIVE LOCAL HELIX AXES: 1. 0.00 17.44 8.05 8.21 6.63 4.94 5.30 5.02 14.69 8.47 4.14 2. 17.44 0.00 22.71 9.32 11.30 18.38 12.94 15.39 19.20 17.86 19.51 3. 8.05 22.71 0.00 13.75 13.77 12.41 12.87 13.07 22.54 5.99 10.90 4. 8.21 9.32 13.75 0.00 3.43 10.25 4.75 7.54 15.45 9.91 10.91 5. 6.63 11.30 13.77 3.43 0.00 7.21 1.64 4.31 12.24 11.35 8.21 6. 4.94 18.38 12.41 10.25 7.21 0.00 5.60 3.00 10.18 13.38 1.83 7. 5.30 12.94 12.87 4.75 1.64 5.60 0.00 2.79 11.68 11.16 6.57 8. 5.02 15.39 13.07 7.54 4.31 3.00 2.79 0.00 9.93 12.63 4.37 9. 14.69 19.20 22.54 15.45 12.24 10.18 11.68 9.93 0.00 22.54 11.86 10. 8.47 17.86 5.99 9.91 11.35 13.38 11.16 12.63 22.54 0.00 12.53 11. 4.14 19.51 10.90 10.91 8.21 1.83 6.57 4.37 11.86 12.53 0.00 ANGLE BETWEEN SUCCESSIVE BASE/BASE-PAIR NORMALS: 1. 0.00 7.27 3.27 11.14 10.42 9.81 12.78 13.52 13.56 13.32 21.35 18.16 2. 7.27 0.00 4.81 3.95 5.15 5.41 6.94 9.02 9.22 6.77 18.03 16.19 3. 3.27 4.81 0.00 8.75 9.17 8.92 11.34 12.79 12.91 11.48 21.36 18.72 4. 11.14 3.95 8.75 0.00 4.14 5.16 4.46 7.36 7.66 3.45 16.25 15.37 5. 10.42 5.15 9.17 4.14 0.00 1.19 2.39 3.87 4.09 3.46 12.92 11.45 6. 9.81 5.41 8.92 5.16 1.19 0.00 3.31 3.87 4.00 4.60 12.68 10.83 7. 12.78 6.94 11.34 4.46 2.39 3.31 0.00 3.05 3.38 1.77 11.78 11.15 8. 13.52 9.02 12.79 7.36 3.87 3.87 3.05 0.00 0.34 4.74 9.06 8.10 9. 13.56 9.22 12.91 7.66 4.09 4.00 3.38 0.34 0.00 5.08 8.83 7.77 10. 13.32 6.77 11.48 3.45 3.46 4.60 1.77 4.74 5.08 0.00 13.09 12.80 11. 21.35 18.03 21.36 16.25 12.92 12.68 11.78 9.06 8.83 13.09 0.00 4.43 12. 18.16 16.19 18.72 15.37 11.45 10.83 11.15 8.10 7.77 12.80 4.43 0.00 1PHOSPHATE ATOMIC COORDINATES & P--P DISTANCES R PHI Z DELP DELZ P--P Strand : 1 P 1. 8.68 -83.76 -31.13 37.44 3.43 6.64 P 2. 9.01 -46.32 -27.70 35.33 3.33 6.47 P 3. 9.27 -10.99 -24.37 36.30 3.15 6.83 P 4. 10.05 25.31 -21.22 36.72 2.26 6.88 P 5. 10.54 62.03 -18.96 34.52 2.99 6.90 P 6. 10.40 96.55 -15.97 31.16 3.10 6.29 P 7. 9.90 127.71 -12.87 36.58 3.03 6.87 P 8. 9.73 164.28 -9.85 37.23 2.15 6.70 P 9. 10.13 -158.49 -7.70 25.25 4.81 6.55 P10. 10.22 -133.24 -2.89 38.15 1.71 7.05 P11. 10.66 -95.09 -1.18 Strand : 2 P 1. 7.19 68.48 2.58 -43.26 -3.58 6.62 P 2. 7.84 25.22 -1.00 -33.93 -4.48 6.46 P 3. 8.08 -8.70 -5.48 -42.49 -3.67 7.12 P 4. 8.70 -51.19 -9.15 -41.46 -2.46 6.77 P 5. 9.10 -92.65 -11.60 -36.90 -3.52 6.71 P 6. 8.93 -129.55 -15.13 -37.92 -3.32 6.70 P 7. 8.99 -167.47 -18.45 -37.16 -3.28 6.70 P 8. 9.32 155.37 -21.73 -28.38 -3.91 6.17 P 9. 9.98 127.00 -25.64 -27.89 -4.56 6.60 P10. 9.80 99.11 -30.20 -32.76 -3.79 6.67 P11. 9.67 66.35 -34.00 INTER-CHAIN P--P DISTANCES STRAND 2 --> STRAND 1 P 1. 37.07 33.00 27.61 22.52 19.58 17.41 17.32 18.27 18.81 18.50 17.96 P 2. 33.23 28.47 22.91 18.57 17.60 17.32 18.20 18.97 19.06 18.14 16.78 P 3. 28.98 24.01 18.93 16.44 17.53 18.17 18.83 18.65 18.01 16.69 15.26 P 4. 24.78 20.34 16.72 16.78 19.03 19.50 19.12 17.57 16.15 14.93 14.53 P 5. 21.83 19.05 17.38 18.85 20.53 19.75 17.75 14.74 12.90 12.99 15.08 P 6. 19.29 18.48 18.10 19.58 19.92 17.82 14.65 11.31 11.06 14.25 18.78 P 7. 17.77 18.28 18.27 18.96 17.88 14.89 11.58 9.99 12.77 18.00 23.36 P 8. 17.75 18.70 18.30 17.57 14.86 11.49 9.77 11.98 17.01 22.92 28.24 P 9. 18.95 19.16 17.72 15.25 11.19 8.90 10.92 15.99 21.69 27.35 32.04 P10. 17.96 17.84 16.43 13.95 11.05 12.32 16.60 22.04 27.50 32.70 36.77 P11. 18.06 16.11 13.65 10.92 10.55 15.20 20.85 26.26 31.14 35.42 38.46 1 BACKBONE AND GLYCOSIDIC TORSION ANGLES P-O5' O5'-C5' C5'-C4' C4'-C3' C3'-O3' O3'- P C1'-N ALPHA BETA GAMMA DELTA EPS ZETA CHI 0.0 0.0 174.2 156.8 -141.3 -143.9 -105.0 -65.6 169.8 40.1 128.1 174.2 -97.8 -110.5 -62.6 171.8 58.8 98.3 -176.7 -87.6 -135.1 -62.9 -179.9 57.2 155.7 -155.3 -152.5 -93.4 -43.0 142.8 52.4 119.6 179.9 -92.2 -126.3 -73.3 179.7 66.0 121.1 173.7 -88.5 -122.2 -56.6 -179.2 52.2 98.9 173.6 -85.9 -127.3 -59.2 173.4 64.1 108.9 170.6 -89.3 -125.7 -58.5 -179.5 60.5 128.7 -156.9 -94.0 -119.5 -67.3 169.1 47.2 142.9 -103.3 150.2 -89.6 -73.9 139.3 56.3 135.7 -161.8 -89.6 -125.1 -81.5 175.7 57.2 110.7 0.0 0.0 -112.0 0.0 0.0 55.9 136.7 -158.6 -124.9 -127.6 -51.3 163.9 49.0 121.9 177.7 -93.0 -116.4 -63.0 168.8 60.4 85.7 174.8 -85.5 -133.8 -69.2 171.1 73.2 135.9 174.1 -98.4 -114.8 -56.6 -169.5 53.8 146.6 176.9 -97.1 -106.4 -57.1 -173.6 47.7 130.2 174.4 -101.3 -108.3 -58.3 173.6 60.0 109.2 178.8 -88.3 -131.3 -58.6 179.5 55.3 122.4 178.5 -94.5 -120.5 -59.1 -175.4 45.0 110.3 -176.7 -86.5 -114.3 -66.8 179.1 50.2 149.7 -100.1 171.6 -88.4 -72.2 138.5 44.6 112.8 -174.4 -96.8 -125.3 -65.0 170.6 46.6 78.7 0.0 0.0 -135.2 Avg. -62.8 171.3 59.5 122.7 -169.0 -108.4 -117.2 S.D. 8.2 13.9 25.1 20.3 24.7 33.8 13.3 O4'-C1' C1'-C2' C2'-C3' C3'-C4' C4'-O4' AMPL PHASE CLASS -34.0 54.5 -52.4 33.7 0.0 55.3 161.2 2*ENDO -36.1 41.9 -31.7 10.8 16.1 41.7 139.5 1*EXO-2*ENDO -37.6 23.3 -1.9 -20.3 36.6 38.3 92.8 O*ENDO -26.7 46.3 -47.1 33.4 -4.4 48.5 166.3 2*ENDO -44.7 44.3 -28.9 3.4 25.8 46.3 128.6 1*EXO -48.1 47.5 -29.9 2.2 29.0 49.8 126.9 1*EXO -48.1 34.1 -9.3 -18.5 42.1 47.3 101.3 O*ENDO-1*EXO -50.1 42.8 -21.3 -7.4 36.2 49.2 115.6 O*ENDO-1*EXO -40.4 46.3 -35.7 12.9 17.1 46.4 140.4 1*EXO-2*ENDO -44.1 54.5 -44.1 20.4 14.1 53.4 145.8 1*EXO-2*ENDO -37.7 47.0 -39.7 18.6 11.7 47.0 147.5 1*EXO-2*ENDO -52.9 44.2 -20.9 -9.4 39.1 51.7 113.8 O*ENDO-1*EXO -31.3 42.9 -38.5 20.8 6.4 43.1 153.2 2*ENDO -43.4 42.7 -28.0 3.1 25.4 45.0 128.5 1*EXO -33.9 9.4 16.6 -37.0 44.6 43.8 67.7 4*EXO-O*ENDO -31.8 40.8 -35.3 17.3 9.0 41.0 149.3 1*EXO-2*ENDO -21.1 39.2 -41.6 30.1 -6.0 42.3 169.3 2*ENDO -33.7 43.1 -35.5 16.5 10.6 42.3 147.0 1*EXO-2*ENDO -48.0 42.0 -21.0 -6.6 34.5 47.5 116.3 O*ENDO-1*EXO -47.8 48.2 -31.8 4.7 27.1 49.9 129.6 1*EXO -43.6 36.8 -17.2 -8.0 32.7 42.9 113.6 O*ENDO-1*EXO -35.6 50.9 -46.7 27.9 4.3 51.0 156.3 2*ENDO -44.7 39.3 -20.0 -5.7 31.7 44.2 116.9 O*ENDO-1*EXO -12.8 -16.7 37.4 -46.3 37.4 45.5 34.7 3*ENDO-4*EXO Avg. -38.7 39.4 -26.0 4.0 21.7 46.4 127.6 S.D. 9.5 14.9 20.1 20.6 15.0 4.1 30.7