Table 1.
Mn2+ sites in the nucleosome core particle
| Site | Location, bp | Sequence, 5′ to 3′ | Bond dist., Å | Nr. H2O ligands | Mean dist. to H2O, Å | Anom. signal, σ | Occupancy | B- factor, Å2 | Mode of binding | Roll, ° | Shift, Å | Slide, Å | Slide at 5′ TG, Å | 5′N7-3′O6 Dist., Å |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1-GG | 61 | AGGT | 2.6/2.5 N | 5/4 | 2.5/2.5 | 6.2/4.8 | 1.0/0.9 | 59/62 | 3-bond | 14.0 | −0.52 | −0.70 | — | 4.05 |
| 2-GG | 48 | TGGT | 2.4/2.5 N | 4/4 | 2.4/2.5 | 4.7/5.3 | 1.0/1.0 | 59/75 | 3-bond | 8.2 | −0.16 | −0.29 | 1.76 | 3.88 |
| 3-GG | −3 | TGGA | 2.5/2.4 N | 2/5 | 2.5/2.4 | 4.9/8.8 | 0.6/1.0 | 49/45 | 3-bond | 11.5 | −0.29 | −0.23 | 0.90 | 3.92 |
| 4-GG | −35 | TGGA | 2.4/2.6 N | 4/3 | 2.5/2.5 | 5.5/3.0 | 1.0/1.0 | 69/69 | 4-bond | 5.6 | 1.04 | 0.10 | 1.55 | 3.31 |
| 2.6/2.4 O | ||||||||||||||
| 5-GC | 27 | AGCA | 2.4/2.5 N | 5/3 | 2.3/2.6 | 7.6/6.2 | 1.0/0.7 | 52/64 | 3-bond | −5.6 | −1.01 | 0.15 | — | — |
| 6-GC | 5 | AGCT | 2.4/2.5 O | 4/3 | 2.5/2.3 | 3.2/4.4 | 0.7/0.6 | 67/45 | 4-bond | −10.1 | −1.18 | 0.20 | — | — |
| 7-sg | 13 | ATG | 6 | 2.3 | 6.7 | 0.7 | 35 | Minor grv. | ||||||
| 8-xGG | −16 | AGGC | Vacant | −10.8 | −0.96 | 0.71 | — | 4.40 | ||||||
| 9-xGG | 24 | TGGA | Vacant | −2.0 | 1.46 | −0.13 | 0.21 | 4.05 | ||||||
| 10-xGG | 64 | TGGA | Vacant | 6.2 | 0.48 | 0.12 | 0.17 | 4.02 | ||||||
| 11-xGC | 58\−59 | TGCA\TGCA | Vacant | 3.9 | −0.18\+0.18 | −0.47 | 0.72\1.63 | — | ||||||
| 12-xGC | 14\−15 | TGCC\GGCA | Vacant | −13.0 | −1.33\+1.33 | −0.08 | 0.18\— | — |
Unique Mn2+ binding sites. All sites are in the DNA major groove except for 7-sg in the minor (small) groove. GG and GC denote the type of base pair step binding the ion. x denotes a potential, but vacant Mn2+ site.
Distance in base pairs from the site of the central base pair (bp 0) on the molecular pseudo-dyad axis (15). Both chains run from base pair −73 at the 5′ terminus to +73 at the 3′ terminus. The 147-bp DNA is 2-fold sequence symmetric about bp 0. \ indicates the superposition of two GC sites.
Underlined nucleotide bases indicate the dinucleotide step defining Mn2+ binding sites in the major groove.
Bond distance from metal center to either the N7 or O6 liganded DNA atom. The two values correspond to the two halves of the DNA superhelix.
Parameter values are the average for two base pair steps, one from the identical sequence in each half of the DNA superhelix. DNA geometrical parameters are defined in ref. 39.