Calcium in PDB 9kzc: Cryo-Em Structure of the LGI1 Lrr-LGI1 Eptp-ADAM22 Ecd Complex

The binding sites of Calcium atom in the Cryo-Em Structure of the LGI1 Lrr-LGI1 Eptp-ADAM22 Ecd Complex (pdb code 9kzc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of the LGI1 Lrr-LGI1 Eptp-ADAM22 Ecd Complex, PDB code: 9kzc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of the LGI1 Lrr-LGI1 Eptp-ADAM22 Ecd Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of the LGI1 Lrr-LGI1 Eptp-ADAM22 Ecd Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:24.1 occ:1.00 O A:CYS433 2.4 25.0 1.0 OD1 A:ASP325 2.4 20.9 1.0 OD1 A:ASN436 2.5 30.4 1.0 OD2 A:ASP325 2.9 20.9 1.0 CG A:ASP325 3.0 20.9 1.0 ND2 A:ASN436 3.1 30.4 1.0 CG A:ASN436 3.2 30.4 1.0 OE1 A:GLU242 3.5 22.4 1.0 CD A:GLU242 3.5 22.4 1.0 C A:CYS433 3.6 25.0 1.0 CG A:GLU242 3.9 22.4 1.0 OE2 A:GLU242 3.9 22.4 1.0 CB A:CYS433 4.3 25.0 1.0 O A:TYR240 4.4 27.2 1.0 SG A:CYS433 4.4 25.0 1.0 CB A:GLU242 4.4 22.4 1.0 CA A:CYS433 4.4 25.0 1.0 CB A:ASP325 4.5 20.9 1.0 N A:LEU434 4.5 23.7 1.0 CA A:LEU434 4.6 23.7 1.0 CB A:ASN436 4.6 30.4 1.0 O A:ASN436 4.7 30.4 1.0 N A:GLU242 4.9 22.4 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of the LGI1 Lrr-LGI1 Eptp-ADAM22 Ecd Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of the LGI1 Lrr-LGI1 Eptp-ADAM22 Ecd Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:102.1 occ:1.00 OD1 A:ASN449 2.5 98.0 1.0 OE1 A:GLU456 2.5 112.3 1.0 ND2 A:ASN449 2.7 98.0 1.0 O A:PHE451 2.7 78.7 1.0 CG A:ASN449 3.0 98.0 1.0 OE2 A:GLU456 3.1 112.3 1.0 OD2 A:ASP459 3.2 108.6 1.0 CD A:GLU456 3.2 112.3 1.0 O A:GLU446 3.3 103.7 1.0 C A:PHE451 3.9 78.7 1.0 N A:GLU446 3.9 103.7 1.0 CG A:GLU453 4.2 99.1 1.0 CD A:GLU453 4.2 99.1 1.0 CG A:ASP459 4.2 108.6 1.0 C A:GLU446 4.3 103.7 1.0 CA A:PRO445 4.4 100.2 1.0 OE1 A:GLU453 4.4 99.1 1.0 CB A:PRO445 4.4 100.2 1.0 N A:PHE451 4.4 78.7 1.0 CB A:ASN449 4.4 98.0 1.0 CB A:GLU453 4.5 99.1 1.0 N A:GLU453 4.5 99.1 1.0 OE2 A:GLU453 4.6 99.1 1.0 CA A:PHE451 4.6 78.7 1.0 C A:PRO445 4.7 100.2 1.0 CG A:GLU456 4.7 112.3 1.0 CA A:GLU446 4.7 103.7 1.0 CB A:PHE451 4.8 78.7 1.0 N A:ILE452 4.9 93.0 1.0 OD1 A:ASP459 5.0 108.6 1.0 N A:GLY450 5.0 89.6 1.0 CB A:ASP459 5.0 108.6 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of the LGI1 Lrr-LGI1 Eptp-ADAM22 Ecd Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of the LGI1 Lrr-LGI1 Eptp-ADAM22 Ecd Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:49.9 occ:1.00 OD1 A:ASP511 2.4 56.4 1.0 OE1 A:GLU514 2.4 65.9 1.0 O A:ILE512 2.5 60.5 1.0 OD1 A:ASN526 2.5 49.0 1.0 OE2 A:GLU514 2.5 65.9 1.0 CD A:GLU514 2.8 65.9 1.0 OD2 A:ASP511 2.8 56.4 1.0 CG A:ASP511 2.9 56.4 1.0 O A:ILE527 3.3 55.6 1.0 CG A:ASN526 3.5 49.0 1.0 C A:ILE512 3.6 60.5 1.0 N A:ILE512 3.9 60.5 1.0 ND2 A:ASN526 4.2 49.0 1.0 CG A:GLU514 4.3 65.9 1.0 CB A:ASP511 4.3 56.4 1.0 CA A:ILE512 4.3 60.5 1.0 N A:ILE527 4.4 55.6 1.0 C A:ILE527 4.4 55.6 1.0 CA A:ASN526 4.5 49.0 1.0 CD A:ARG504 4.5 60.0 1.0 N A:ARG513 4.5 66.7 1.0 CB A:ASN526 4.6 49.0 1.0 CA A:ARG513 4.7 66.7 1.0 N A:GLU514 4.7 65.9 1.0 C A:ASN526 4.7 49.0 1.0 C A:ASP511 4.7 56.4 1.0 CG A:ARG504 4.7 60.0 1.0 O A:ARG504 4.7 60.0 1.0 C A:ARG513 4.8 66.7 1.0 CA A:ASP511 4.8 56.4 1.0 CB A:GLU514 4.9 65.9 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of the LGI1 Lrr-LGI1 Eptp-ADAM22 Ecd Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of the LGI1 Lrr-LGI1 Eptp-ADAM22 Ecd Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:28.5 occ:1.00 OD2 B:ASP334 2.5 11.0 1.0 O B:VAL382 2.7 9.2 1.0 OE1 B:GLU336 3.1 11.3 1.0 OD1 B:ASP381 3.3 10.1 1.0 CG B:ASP334 3.5 11.0 1.0 OD2 B:ASP381 3.7 10.1 1.0 OE1 B:GLU383 3.8 9.6 1.0 C B:VAL382 3.8 9.2 1.0 OD1 B:ASP334 3.8 11.0 1.0 CG B:ASP381 3.8 10.1 1.0 NZ B:LYS436 3.9 9.1 1.0 CD B:GLU336 4.0 11.3 1.0 N B:VAL382 4.4 9.2 1.0 CA B:GLU383 4.5 9.6 1.0 N B:GLU383 4.6 9.6 1.0 OE2 B:GLU336 4.6 11.3 1.0 CB B:GLU336 4.7 11.3 1.0 CA B:VAL382 4.7 9.2 1.0 CB B:ASP334 4.8 11.0 1.0 CB B:GLU383 4.9 9.6 1.0 O B:VAL435 4.9 8.5 1.0 CG B:GLU336 5.0 11.3 1.0 CD B:GLU383 5.0 9.6 1.0

T.Yamagachi, K.Okatsu, M.Kubota, A.Mitsumori, A.Yamagata, Y.Fukata, M.Fukata, M.Shibata, S.Fukai. Structural Insights Into Heterohexameric Assembly of Epilepsy-Related Ligand-Receptor Complex LGI1-ADAM22. Elife 2025.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.105918.2