Table 4.
Key amino-acid to base interactions distances (Å) at the primary kink sites of all CAP-DNA structures.
| Complex: half-complex | Crystal Form | Arg 180 | Glu 181 | Arg 185 | PDB ID Reference | ||
|---|---|---|---|---|---|---|---|
| 5G | 6C/6C′ | 7C′ | 7G | 8T′ | |||
| CAP-GC31: A | A | 2.9, 3.0, 2.7 | 3.3 | 3.7, 3.2 | 2.8 | 1CGP13 | |
| CAP-GC31: B | A | 3.3, 4.0, 3.8, 2.7 | 2.9 | 3.4 | 2.6 | 1CGP13 | |
| CAP-GCE31: A | A | 3.4, 2.5 | 2.7 | 2.8, 3.5 | 3.8, 3.7 | 1J5914 | |
| CAP-GCE31: B | A | 2.6, 3.4 | 3.5 | 3.9 | 3.5, 3.5 | 1J5914 | |
| CAP-ICAP30: A | A | 2.7, 3.1, 3.1 | 2.7 | 3.4, 2.9 | 2.9 | 1RUN15 | |
| CAP-ICAP30: B | A | 3.0, 2.5, 3.2 | 3.5, 3.0 | (4.7) | 3.4 | 1RUN15 | |
| [E181F]CAP-ICAP30: A | A | 3.6, 2.6, 2.8, 3.7 | 3.1* | 3.9, 3.3 | 3.6 | 1RUO15 | |
| [E181F]CAP-ICAP30: B | A | 2.6 | 3.2* | 3.2 | 3.7 | 1RUO15 | |
| CAP-[6C;17G]ICAP30: A | A | (7.3) | 4.0, 3.6 | 3.7 | 4.0, 3.4 | 1O3T28 | |
| CAP-[6C;17G]ICAP30: B | A | 3.6, 2.6, 2.4 | 2.8 (C) | 3.0, 3.4 | 3.5 | (5.1) | 1O3T28 |
| CAP-DNA46 | B | 3.5, 2.9 | 3.2 | 2.8 | 3.0, 2.6 | 2CGP30 | |
| CAP-ICAP38 | B | 3.0, 3.2, 2.9 | 3.3 | 3.2 | 2.7 | 1O3Q28 | |
| CAP-[6C;17G]ICAP38 | B | 2.8, 3.5, 2.8, 3.9 | 3.3 (C) | 2.8 | 2.9, 3.1 | 3.2 | 1O3R28 |
| [E181D]CAP-[6C;17G]ICAP38 | B | 3.8, 3.3 | 3.0+(C) | 3.5+ | 2.7, 3.7 | 3.0 | 1O3S36 |
| CAP-ICAP38: A | C | 3.6 3.2, 2.9 | 2.8 | 3.1 | 3.1 | 1ZRC | |
| CAP-ICAP38: B | C | 3.8, 2.9, 2.5 | 3.2 | 2.7, 3.5 | 3.5 | 1ZRC | |
| CAP-[6A;17T] ICAP38: A | C | 3.3, 2.6, 3.7 | 3.5 | 3.1, 3.3 | 3.5 | 1ZRD | |
| CAP-[6A;17T] ICAP38: B | C | 3.6, 2.8, 3.4 | 2.8 | 3.7, 3.7 | (4.2) | 1ZRD | |
| CAP-[6G;17C] ICAP38: A | C | 3.8, 3.0, 2.9 | 3.2 (C′) | 3.6 | 2.7 | 2.7, 3.9 | 1ZRE |
| CAP-[6G;17C]ICAP38: B | C | 3.4, 2.4, 2.8 | (4.6)(C′) | 3.9 | 2.6 | 3.6, 3.4 | 1ZRE |
| CAP-[6C;17G]ICAP38: A | C' | 3.9, 3.1, 2.8, 3.9 | 3.0 (C) | 3.2 | (6.5) | (5.6) | 1ZRF |
| CAP-[6C17;G] ICAP38: B | C' | 3.3, 2.8, 4.0 | 3.3 (C) | 2.8 | (8.8) | (7.6) | 1ZRF |
Key interaction distances at each primary kink site, with a 4.0 Å distance cutoff. Distances in parentheses are greater then 4.0 Å, but represent the nearest distance for that interaction. Unless noted, CAP is wild-type sequence and the DNA sequence at the primary kink site is 5′-T4G5T6G7A8-3′ / 5′-T′4C′5A′6C′7A′8-3′.
*
Aromatic hydrogen bond between Phe181 and Cyt 7′ 15.
+
Hydrogen bonding between Asp181 and Cyt 7′/Cyt 6 36.