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. 2005 Jun 10;33(10):3424–3434. doi: 10.1093/nar/gki663

Figure 2.

Figure 2

Comparison of the DNA parameters between human and X.laevis NCPs. (A) B-factors of phosphates, metal binding sites, r.m.s.d. values and twist base-pair-step parameter of the 146 bp DNA compared between human and X.laevis NCPs. The base pair numbers (−72 to 73) and SHL (−7 to 7) labels are the same as those in the earlier structures (11,12). The primary bound-phosphate groups are indicated above the base sequence by the pointers showing the strand direction (dark, 3′→5′; light, 5′→3′) and the interacting histone motif (L1, loop1; L2, loop 2; A1, α1). B-factors (Å2) are plotted for the 5′ phosphate group of each base (brown for the I chain and forest green for the J chain). Mn2+ binding sites are indicated above the base sequence by the yellow and light blue arrows (solid, binding the DNA major groove; broken, binding the DNA minor groove) in the structures of human and X.laevis NCPs (PDB code 1KX3) (11), respectively. The r.m.s.d. values below the base sequence were calculated by the superposition of 18 or 19 bp between two NCPs. The twist base-pair-step parameters were plotted as open circles and closed squares for the human (yellow line) and X.laevis (light blue line) nucleosomal DNA, respectively. The pink, orange and green ellipsoids of the twist parameters represent the corresponding regions illustrated by those in Figures 3A and B and Figure 4A. (B–D) The simplified stereo model of the DNA duplexes in the regions surrounded by the ellipsoids in (A). The differences in helical twist are shown by the superposition between human (yellow) and X.laevis (light blue; PDB code 1KX3) (11) NCPs, based on the histone octamers alone. Numbers presented for each base pair are the same as those in Figure 2A.