Table 2.
Amino acid ligands for Ca2+ in X-ray structures and modeled LG domains.
| LG domain and PDB | D–E loop | F–G loop | J–K loop | Species and NCBI accession codes |
|---|---|---|---|---|
| Laminin α1 LG4 2JD4 (Mg2+) | NQMD2771YAT | FMFDL2788GKGR | GKaATT2838LD2840VERK | Mus musculus P19137 |
| Laminin α2 LG4 5IK5 (Ca2+) | NHAD2808FATV | FSYDL2825GSGD | KKADI2874LD2876VV | Mus musculus Q60675 |
| Laminin α2 LG5 1QU0 (Ca2+) | QKMD2982GMG | MFHVDN2999GAG | SASTS3053AD3055TNDP | Mus musculus Q60675 |
| Laminin α3 LG4 model on 2JD4 | – | FALGT3050D3051GKKLR | LPGNS3098T3099ISIR | Homo sapiens Q16787 |
| Laminin α5 LG3 model on 2JD4 | RASPD3169GLCQ | – | PPPE3233LQ3235PQP | Homo sapiens O15230 |
| Laminin α5 LG4 model on 2JD4 | VAQM3405E3406GLGT | – | HQGAE3460HPQP | Homo sapiens O15230 |
| Agrin LG3 1PZ7,1PZ8 (Ca2+) 1PZ9 (Ca2+ -free) |
GLERSD1953YIALA | MMYDL1970GSKP | LGATQ2020LD2022TD | Gallus gallus P31696 |
| Perlecan LG3 3SH5 (Ca2+) 3SH4 (Ca2+-free) |
GVEVGEAGQGKD4258FISL | VFRYQL4275GSGEAR | PGPN4323VA4325VN4327AKGS | Homo sapiens P98160 |
| Neurexin 1α LG2 2H0B (Ca2+) | GKSAD329YVN | SLVINL346GGSGAF | EDYTM414LGSDD | Bos taurus XP_010808206 |
| Neurexin 1β LG1 2R1D (Ca2+) | SGLGD137YLE | VKFNV154GTDD | GRQLTI236FN238SQAT | Rattus norvegicus Q63373 |
| Slit-1 LG1 model on 2JD4 |
GDND1210HIAV | VSYDP1227GSYP | GKHYT1278LNSEA | Homo sapiens O75093 |
| Slit-2 LG1 model on 1QU0 and 2JD4 |
GDKD1204HIA | ASYDT1221GSHP | NLSKQ1270ST1272LN1274F | Homo sapiens O94813 |
| Slit-3 LG1 model on 2JD4 |
KGDND1209PLA | VYDS1226L1227SSPP | QKQPA1277VGIN | Homo sapiens NP_001258875 |
a
K is reported as a N in the NCBI sequence: a mutation introduced to eliminate N-glycosylation. Amino acids in bold and italics provide side chain (carboxyl, amide or hydroxyl) or backbone carbonyl Ca2+ liganding groups in the observed or modeled Ca2+ binding sites. The highly conserved glycine residue that follows the Ca2+ liganding group in the F-G loop of many LG domains is underlined.