Table 4. Short hydrogen bonds in wild-type RGAE and RGAE D192N.
The estimated standard deviations on the distances were obtained from matrix inversion in SHELXL least-squares refinements. All ∠C—N⋯O, ∠C—O⋯N and ∠C—O⋯O are larger than 90°. The distances in square parentheses are included for comparison, but are not considered to be potential hydrogen bonds. The interactions highlighted in bold are illustrated in Figs. 2 ▶, 3 ▶ and 6 ▶.
| Donor–acceptor (or vice versa) | Distance in wild type (Å) | Distance in D192N (Å) | Relative accessibility† (%) | pKa‡ |
|---|---|---|---|---|
| Asp75 Oδ2—Asp87 Oδ2 | 2.47 (1) | 2.48 (2) | 1/6 | 4.1/10.2 |
| Glu202 O∊2—Glu206 O∊2 | 2.50 (2) | [5.48 (4)] | 27/25 | 2.6/8.7 |
| Tyr30 OH—Glu202 O∊2 | 2.63 (1) | [6.50 (2)] | 21/27 | 12.3/2.6 |
| Thr86 Oγ1—Gly76 O | 2.72 (1) | 2.62 (3) | 5/27 | —/— |
| Ser187 Oγ—Thr184 O | 2.69 (2) | 2.65 (2) | 64/38 | —/— |
| Ser44 Oγ—Arg85 O | 2.67 (1) | 2.69 (2) | 0/37 | —/— |
| Thr20 Oγ1—Gly17 O | 2.69 (2) | 2.71 (3) | 5/39 | —/— |
| Thr49 Oγ1—Ala45 O | 2.77 (1) | 2.73 (2) | 39/0 | —/— |
| Thr194 Oγ1—Asn136 Oδ1 | 2.87 (2) | 2.75 (2) | 18/38 | —/— |
| Ser218 Oγ—Glu165 O∊1 | 2.56 (2) | 2.56 (3) | 30/33 | —/3.3 |
| Thr10 Oγ1—Asp8 Oδ1 | 2.67 (1) | 2.62 (2) | 8/2 | —/4.6 |
| Ser98 Oγ—Asp82 Oδ2 | 2.64 (2) | 2.63 (3) | 15/20 | —/0.3 |
| Ser171 Oγ—Asp168 Oδ2 | 2.66 (1) | 2.69 (3) | 29/26 | —/2.4 |
| Ser131 Oγ—Glu70 O∊1 | 2.75 (1) | 2.74 (2) | 1/4 | —/3.6 |
| His195 Nδ1—Asp192 Oδ2 | 2.63 (2) | — | 20/40 | 5.1/1.7 |
| His195 Nδ1—Asn192 Oδ1 | — | [4.38 (2)]§ | 10/49 | 2.9/— |
| His169 Nδ1—Glu70 O∊1 | 2.61 (1) | 2.62 (2) | 0/3 | 4.6/3.6 |
| His193 Nδ1—Glu140 O∊1 | 2.66 (4) | 2.88 (4) | 41/60 | 7.2/4.0 |
| Arg53 N∊—Glu51 O∊1 | 2.78 (2) | 2.75 (2) | 30/41 | 11.8/3.5 |
| Arg46 NH1—Asp82 Oδ1 | 2.76 (2) | 2.80 (3) | 0/20 | 11.6/0.3 |
| Arg43 N∊—Glu51 O∊1 | 2.80 (2) | 2.78 (2) | 26/41 | 11.6/3.5 |
| Val3 N—Thr34 O | 2.77 (1) | 2.75 (2) | 0/61 | —/— |
| Glu115 N—Pro111 O | 2.79 (1) | 2.78 (2) | 14/0 | —/— |
| Arg85 N—Asn83 Oδ1 | 2.80 (2) | 2.80 (3) | 37/55 | —/— |
| Ser197 N—Tyr188 O | 2.83 (2) | 2.79 (2) | 15/9 | —/— |
| Ala201 N—Ser197 O | 2.84 (1) | 2.79 (2) | 0/15 | —/— |
| His195 Nδ1—Ser9 Oγ | — | 2.73 (2) | 10/0 | 2.9/— |
| His195 N∊2—Ser9 Oγ | [2.95 (2)] | — | 20/7 | 5.1/— |
| Lys124 Nζ—Ala58 O | 2.66 (2) | [4.64 (6)] | 43/12 | 9.8/— |
| His169 N∊2—Val204 O | 2.79 (1) | 2.73 (2) | 41/3 | 7.2/— |
Relative residue accessibility in wild-type RGAE compared with Ala-X-Ala, using a default probe size of 1.4 Å.
Listed pK a values are based on the wild-type structure.
Distance with side-chain configuration as in Fig. 2 ▶. The shortest distance between any two atoms in the two side chains is 3.36 Å.
Accessibility/pK a calculated for the RGAE D192N structure.