Table 2. Interactiona of the bases of DNA with the cluster-forming residues.
| PDB | Cluster no. | Protein cluster compositionb | δASAavg (Å2)c | Interacting DNA based |
|---|---|---|---|---|
| 1awcA | 1 | Arg 376t | 25.22 | G 8(D) G 9(D) |
| Arg 379t | C 6(D),C 7(D),G 8(D) | |||
| Tyr 380p | A 10(D),A 11(D),C 32(E),T 33(E) | |||
| Tyr 382p | ||||
| Lys 389t | ||||
| Tyr 397h | ||||
| 1bc8C | 1 | Arg 61t | 25.12 | G 5(A) G 6(A) |
| Arg 64t | C 4(A) G 5(A),C 3(A) | |||
| Tyr 65p | G 6(A),A 7(A),A 8(A),C13(B),T14(B) | |||
| Tyr 67p | ||||
| Lys 74t | ||||
| Tyr 82h | ||||
| 1pueE | 1 | ARG 232t | 40.25 | G 8(A) G 9(A),A 10(A) |
| ARG 235t | G 7(A) G 8(A),G 6(A) | |||
| 1lmb3 | 1 | GLN 44p | 27.1 | T 3(1) A 4(1) |
| GLN 33p | ||||
| 1lmb4 | 1 | ASN 55− | 30.95 | G 13(1) G 14(1) |
| LYS 4− | G 13(1),G 14(1) | |||
| 1rpeL | 1 | GLN 28p | 17.87 | A 24(A) A 25(A) |
| GLN 17h | ||||
| ARG 10h | ||||
| 3croL | 1 | GLN 28p | 19.58 | T 3(B) A 4(B) |
| GLN 17h | ||||
| ARG 10h | ||||
| GLN 32− | A 4(B), C 5(B) | |||
| LYS 7p | ||||
| 1akhA | 1 | ASN 120t | 31.7 | G 25(C) A 26(C) |
| ARG 124m | T 24(C),G 25(C),A 26(C) | |||
| 1akhB | 1 | ARG 185t | 39.55 | T 5(C) G 6(C),T 7(C) |
| ASN 182t | T 37(C),A 38(C) | |||
| 1b72B | 1 | ASN 286t | 40.95 | G 8(D) A 9(D) |
| ARG 290m | T 7(D) G 8(D),A 9(D),T 33(E) | |||
| 1au7A | 1 | GLN 44t | 20.57 | T 459(C) A 460(C) |
| GLN 27t | ||||
| ARG 20t | ||||
| Isolated | ARG 49t | T 483(D) G 484(D) | ||
| 1ignAe | 1 | ARG 404 | 11.68 | G 30(D) G 31(D),G 32(D) |
| PHE 407 | ||||
| TYR 388 | ||||
| ARG 408 | G 31(D), G 32(D) | |||
| 2 | ARG 542 | 18.23 | T 22(D) G 23(D) | |
| ARG 546 | G 23(D) G 24(D), T 25(D) | |||
| PHE 545 | ||||
| PHE 526 | ||||
| Isolated | ASN 401 | A 7(C) C 8(C) | ||
| 1a3qA | 1 | ARG 52h | 27.6 | G606(D)G607(D),G608(D),C512(C),C513(C) |
| LYS 221h | G 607(D),G 608(D) | |||
| Isolated | ARG 54t | G 605(D) G 606(D) | ||
| 1a3qB | 1 | ARG 52h | 30.15 | G 506(C),G 507(C),C 612(D) |
| LYS 221h | G 507(C) G 508(C),T 611(D) | |||
| 2ramA | 1 | ARG 33h | 15.8 | G 6(D) A 7(D) |
| ARG 187t | ||||
| 1a73Ae | 1 | ARG 74 | 29.97 | A 17(D) G 18(D) |
| GLN 63 | G 16(D) A 17(D) | |||
| ASN 57 | A 15(D), G 16(D) | |||
| 6mhtA | 1 | ARG 240p | 16.7 | A 425(D) G 426(D) |
| ARG 228p | A 425(D) | |||
| TYR 242− | ||||
| 1a1gAf | 1 | ARG 124 | 27.43 | G 7(B) G 8 (B),C 9(B) |
| ASN 121 | G 8(B) C 9 (B) | |||
| ARG 146 | G 6(B) G 7 (B),C 55(C) | |||
| Isolated | ARG 174 | C 3(B) G 4 (B),T 5(B) | ||
| Isolated | ARG 180 | A 1(B) G 2 (B),C 3(B) | ||
| 1meyCf | 1 | ASN 19 | 35.45 | G 9(A) A 10 (A) |
| GLN 16 | A 10(A) A 11 (A) | |||
| 2 | LYS 22 | 27.85 | A 8(A) G 9 (A) | |
| GLN 44 | C 7(A) A 8 (A) | |||
| 3 | ARG 72 | 25.1 | A 4(A) G 5 (A) | |
| LYS 50 | G 5(A), G 6(A),T 7(B),G 8(B) | |||
| 1ubdCf | 1 | LYS 339 | 30.4 | G 32(B) G 33(B) |
| ARG 342 | T 31(B) G 32(B), C 8(A) | |||
| Isolated | ASN 369 | A 29(B) A 30(B) | ||
| Isolated | GLN 396 | A 27(B) A 28(B) | ||
| 1gd2Ee | 1 | ARG 82 | 38.6 | G −6(B) G −5(B),A 4(A) |
| ASN 86 | T 2(A) A 3(A) | |||
| GLN 85 | G −6(B) | |||
| 2 | ARG 94 | 33.96 | C −1(A) G 1(A) | |
| GLN 90 | T −3(B), T −4(B),G 1(A),T 2(A) | |||
| 1tc3C | 1 | ARG 236p | 24.65 | G 7(A) G 8(A) |
| ARG 240h | G 8(A), T 9(A) | |||
| 2nllB | 1 | ARG 328m | 16.78 | G 514(C) G 515(C),T 516(C),G523(D) |
| TYR 315y | ||||
| PHE 327t | ||||
| GLN 332p |
aThe reported cation–π/H-bond stair motif interactions of the protein residue (column 2) with the corresponding DNA bases (column 4) are given in bold face. The additional interactions detected by the present study are given in normal font. The other cation–π/H-bond stair motif interactions which belong to the same protein but do not form clusters are indicated as ‘isolated’ and are given in bold, italics.
bThe conservation information obtained from HOMSTRAD (26). The extent of conservation is given as superscript. t, totally conserved (>99% of list from the alignment); h, highly conserved(>90%); p, partially conserved(50–90%); m, conserved mutation; and dashes, non-conserved.
cδASAavg is the average loss of accessible surface area (Å2) upon complexation with DNA, averaged over all residues in a given cluster.
dNucleic acid base, the residue number, chain identifier (in parenthesis).
eSingle member family(26).
fMultispecific family of zinc fingers.