Table 2. Root mean square deviation values for Ca overlays.
Structure | RMSD (Å) | Structure | RMSD (Å) | Structure | RMSD (Å) |
---|---|---|---|---|---|
1XU7_a | 2.139 | 2RBE_c | 0.341 | 3D4N_c | 2.463 |
1.624 | 0.355 | 0.404 | |||
| |||||
1XU7_b | 1.925 | 2RBE_d | 0.915 | 3D4N_d | 2.452 |
0.364 | 0.505 | 0.416 | |||
| |||||
1XU7_c | 1.944 | 3BYZ_a | 0.543 | 3D5Q_a | 2.051 |
0.345 | 0.452 | 0.329 | |||
| |||||
1XU7_d | 1.928 | 3BYZ_b | 0.528 | 3D5Q_b | 1.906 |
0.304 | 0.443 | 0.376 | |||
| |||||
1XU9_a | 2.227 | 3BYZ_c | 0.366 | 3D5Q_c | 0.974 |
1.621 | 0.328 | 0.302 | |||
| |||||
1XU9_b | 2.519 | 3BYZ_d | 0.877 | 3D5Q_d | 1.940 |
0.414 | 0.440 | 0.426 | |||
| |||||
1XU9_c | 2.524 | 3BZU_a | 0.865 | 3EY4_a | 0.654 |
0.439 | 0.456 | 0.553 | |||
| |||||
1XU9_d | 2.487 | 3BZU_b | 1.436 | 3EY4_b | 0.483 |
0.332 | 0.343 | 0.484 | |||
| |||||
2BEL_a | 1.176 | 3BZU_c | 0.663 | 3EY4_c | 0.383 |
0.797 | 0.269 | 0.458 | |||
| |||||
2BEL_b | 3.045 | 3BZU_d | 0.620 | 3EY4_d | 0.909 |
0.815/0.816 | 0.387 | 0.509 | |||
| |||||
2BEL_c | 4.390 | 3CH6_a | 0.837 | 3FCO_a | 1.646 |
0.444 | 0.223 | 0.585 | |||
| |||||
2BEL_d | 2.997 | 3CH6_b | 3.906 | 3FCO_b | 1.609/1.608 |
0.633 | 0.218 | 0.462/0.461 | |||
| |||||
2IRW_a | 0.820 | 3CH6_d | 3.873 | 3FRJ_a | 1.969 |
0.241 | 0.186 | 0.566 | |||
| |||||
2IRW_b | 0.822 | 3CH6_e | 0.857 | 3FRJ_b | 2.480 |
0.237 | 0.231 | 0.714 | |||
| |||||
2IRW_c | 0.404 | 3CZR_a | 2.490 | 3H6K_a | 0.817 |
0.259 | 0.612 | 0.441 | |||
| |||||
2IRW_d | 0.791 | 3CZR_b | 2.005 | 3H6K_b | 0.740 |
0.262 | 1.003 | 0.256 | |||
| |||||
2IRW_e | 0.387 | 3D3E_a | 1.975 | 3H6K_c | 0.729 |
0.279 | 0.891 | 0.451 | |||
| |||||
2IRW_f | 0.820 | 3D3E_b | 1.975 | 3H6K_d | 0.561 |
0.309 | 0.457 | 0.360 | |||
| |||||
2IRW_g | 0.837 | 3D3E_c | 2.021 | 3HFG_a | 0.673 |
0.257 | 0.743 | 0.538 | |||
| |||||
2IRW_h | 0.831 | 3D3E_d | 2.014 | 3HFG_b | 1.465 |
0.250 | 0.748 | 0.333 | |||
| |||||
2RBE_a | 0.669 | 3D4N_a | 1.936 | 3HFG_c | 0.594 |
0.587 | 0.408 | 0.414 | |||
| |||||
2RBE_b | 0.380 | 3D4N_b | 2.472 | 3HFG_d | 0.561 |
0.353 | 0.304 | 0.373 |
For each protein molecule (indicated by the lowercase letter) in each crystal structure of human 11β-HSD1, the Cα atoms were superimposed on those of 2ILT_a and the RMSD was calculated using the Sybyl software [101]. 2ILT_a was used as the reference structure simply because it is the only structure of 11β-HSD1 with only one protein chain in the structure. The numbers in normal type are for the whole protein and the numbers in bold are for the residues around the substrate and cofactor binding sites (T40-G47, T64-S67, G91-F98, N119-L126, K138-V142, V168-K187 and L215-M233). Note that for the whole protein 3FCO_b has three Cα atoms with alternate conformations, giving rise to different values for the RMSD. The 2BEL_b, 3CZR_a and 3CZR_b structures have, respectively, two, three and one Cα atoms with alternate conformations, but in these structures the differences, at least to four significant figures, make no difference to the RMSD when superimposed on 2ILT_a. For the binding-site residues, the 2BEL_b structure has different RMSD values for the two conformations. RMSD: Root mean square deviation.