Calcium in PDB 5y2z: Crystal Structure of Human LGI1 Eptp-ADAM22 Complex

The structure of Crystal Structure of Human LGI1 Eptp-ADAM22 Complex, PDB code: 5y2z was solved by A.Yamagata, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.83 / 2.67
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	83.579, 83.608, 293.543, 86.40, 88.17, 59.95
R / Rfree (%)	24.4 / 27.9

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Human LGI1 Eptp-ADAM22 Complex (pdb code 5y2z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 24 binding sites of Calcium where determined in the Crystal Structure of Human LGI1 Eptp-ADAM22 Complex, PDB code: 5y2z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 24 in the Crystal Structure of Human LGI1 Eptp-ADAM22 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human LGI1 Eptp-ADAM22 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:27.2 occ:1.00 ND2 A:ASN436 2.3 37.0 1.0 OD2 A:ASP325 2.4 18.6 1.0 OE2 A:GLU242 2.4 35.6 1.0 OD1 A:ASP325 2.4 30.2 1.0 O A:HOH934 2.4 41.6 1.0 O A:CYS433 2.4 19.0 1.0 OD1 A:ASN436 2.4 47.0 1.0 CG A:ASN436 2.6 45.5 1.0 CG A:ASP325 2.7 18.5 1.0 O A:HOH921 2.8 20.1 1.0 CD A:GLU242 3.1 28.3 1.0 CG A:GLU242 3.4 24.7 1.0 C A:CYS433 3.6 32.2 1.0 OE1 A:GLU242 4.0 20.4 1.0 CB A:GLU242 4.1 24.0 1.0 CB A:ASN436 4.2 20.9 1.0 CB A:ASP325 4.3 18.3 1.0 CB A:CYS433 4.4 18.9 1.0 O A:TYR240 4.4 24.2 1.0 O A:ASN436 4.4 21.8 1.0 CA A:CYS433 4.5 19.1 1.0 N A:LEU434 4.6 25.0 1.0 CA A:LEU434 4.7 22.9 1.0 O A:HOH965 4.7 39.2 1.0 N A:ASN436 4.8 20.8 1.0 N A:GLU242 4.8 18.6 1.0 O A:HOH953 4.9 29.0 1.0 CA A:ASN436 4.9 21.2 1.0 SG A:CYS433 5.0 49.3 1.0

Calcium binding site 2 out of 24 in the Crystal Structure of Human LGI1 Eptp-ADAM22 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human LGI1 Eptp-ADAM22 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:47.0 occ:1.00 ND2 A:ASN449 2.3 51.1 1.0 O A:GLU446 2.4 57.5 1.0 OE1 A:GLU453 2.4 45.4 1.0 OE1 A:GLU456 2.4 39.4 1.0 OD2 A:ASP459 2.4 58.8 1.0 OD1 A:ASN449 2.4 53.0 1.0 O A:PHE451 2.4 35.7 1.0 CG A:ASN449 2.6 50.2 1.0 CD A:GLU456 3.3 43.8 1.0 C A:GLU446 3.3 54.3 1.0 CD A:GLU453 3.3 41.7 1.0 CG A:ASP459 3.4 53.8 1.0 OE2 A:GLU456 3.5 46.5 1.0 C A:PHE451 3.6 37.2 1.0 N A:GLU446 3.8 41.4 1.0 CG A:GLU453 3.8 38.6 1.0 CB A:ASN449 4.1 46.2 1.0 CA A:GLU446 4.1 50.3 1.0 N A:CYS447 4.1 54.9 1.0 N A:PHE451 4.1 43.7 1.0 CB A:ASP459 4.2 47.0 1.0 CB A:GLU453 4.2 37.9 1.0 CA A:PHE451 4.3 38.5 1.0 N A:GLU453 4.3 40.3 1.0 OE2 A:GLU453 4.3 44.5 1.0 OD1 A:ASP459 4.3 54.9 1.0 CA A:CYS447 4.3 56.5 1.0 CB A:PHE451 4.5 38.6 1.0 N A:ASN449 4.5 51.9 1.0 N A:GLY448 4.6 56.9 1.0 CG A:GLU456 4.6 46.6 1.0 N A:ILE452 4.6 36.6 1.0 CB A:GLU446 4.7 55.6 1.0 CA A:ASN449 4.8 45.5 1.0 C A:PRO445 4.9 42.2 1.0 CA A:ILE452 4.9 39.6 1.0 CA A:GLU453 4.9 40.2 1.0 C A:CYS447 4.9 58.7 1.0 N A:GLY450 5.0 43.1 1.0

Calcium binding site 3 out of 24 in the Crystal Structure of Human LGI1 Eptp-ADAM22 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human LGI1 Eptp-ADAM22 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:29.7 occ:1.00 O A:HOH926 2.2 42.1 1.0 OD1 A:ASP511 2.4 33.6 1.0 OE2 A:GLU514 2.4 46.2 1.0 OD2 A:ASP511 2.4 30.5 1.0 O A:ILE512 2.4 38.8 1.0 O A:ILE527 2.4 33.9 1.0 OD1 A:ASN526 2.4 21.4 1.0 O A:HOH911 2.6 14.0 1.0 CG A:ASP511 2.7 27.3 1.0 CD A:GLU514 3.4 41.6 1.0 C A:ILE512 3.5 36.1 1.0 CG A:ASN526 3.5 29.9 1.0 C A:ILE527 3.6 30.2 1.0 N A:ILE512 3.8 29.9 1.0 N A:ILE527 3.8 26.4 1.0 CG A:GLU514 4.0 37.2 1.0 CB A:ASP511 4.1 27.1 1.0 CA A:ILE512 4.2 33.0 1.0 ND2 A:ASN526 4.2 31.2 1.0 CA A:ILE527 4.4 25.8 1.0 O A:HOH917 4.4 45.9 1.0 C A:ASN526 4.4 30.5 1.0 OE1 A:GLU514 4.4 45.0 1.0 CA A:ASN526 4.5 32.2 1.0 N A:HIS528 4.5 29.4 1.0 N A:ARG513 4.5 43.0 1.0 CB A:ASN526 4.6 32.1 1.0 C A:ASP511 4.6 30.9 1.0 CA A:HIS528 4.7 22.0 1.0 CA A:ASP511 4.7 30.9 1.0 CA A:ARG513 4.8 40.2 1.0 CB A:ILE512 4.8 23.8 1.0 CB A:HIS528 4.9 21.8 1.0 C A:ARG513 4.9 33.8 1.0

Calcium binding site 4 out of 24 in the Crystal Structure of Human LGI1 Eptp-ADAM22 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human LGI1 Eptp-ADAM22 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:27.7 occ:1.00 ND2 C:ASN436 2.3 36.7 1.0 O C:HOH914 2.3 39.7 1.0 OE2 C:GLU242 2.4 29.3 1.0 OD2 C:ASP325 2.4 25.0 1.0 OD1 C:ASP325 2.4 30.5 1.0 O C:CYS433 2.4 18.2 1.0 OD1 C:ASN436 2.4 45.2 1.0 O C:HOH941 2.4 36.2 1.0 CG C:ASN436 2.7 33.2 1.0 CG C:ASP325 2.7 24.4 1.0 CD C:GLU242 3.1 29.8 1.0 CG C:GLU242 3.4 26.1 1.0 C C:CYS433 3.6 18.3 1.0 OE1 C:GLU242 4.1 30.9 1.0 CB C:GLU242 4.1 17.7 1.0 CB C:ASN436 4.2 23.9 1.0 CB C:ASP325 4.3 21.7 1.0 O C:ASN436 4.4 31.6 1.0 CB C:CYS433 4.4 23.0 1.0 O C:TYR240 4.4 21.8 1.0 CA C:CYS433 4.4 18.9 1.0 N C:LEU434 4.6 19.0 1.0 CA C:LEU434 4.7 18.8 1.0 N C:ASN436 4.8 32.5 1.0 N C:GLU242 4.8 16.8 1.0 CA C:ASN436 4.9 29.6 1.0

Calcium binding site 5 out of 24 in the Crystal Structure of Human LGI1 Eptp-ADAM22 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human LGI1 Eptp-ADAM22 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca802 b:45.0 occ:1.00 ND2 C:ASN449 2.3 60.2 1.0 O C:GLU446 2.3 53.1 1.0 OE1 C:GLU453 2.4 47.7 1.0 OD2 C:ASP459 2.4 61.6 1.0 OE1 C:GLU456 2.4 42.7 1.0 OE2 C:GLU456 2.4 37.4 1.0 OD1 C:ASN449 2.4 52.7 1.0 O C:PHE451 2.4 50.4 1.0 CG C:ASN449 2.6 51.4 1.0 CD C:GLU456 2.7 53.0 1.0 C C:GLU446 3.2 54.0 1.0 CD C:GLU453 3.3 41.3 1.0 CG C:ASP459 3.4 55.3 1.0 C C:PHE451 3.6 41.9 1.0 CG C:GLU453 3.8 32.5 1.0 N C:GLU446 3.9 47.4 1.0 N C:CYS447 4.0 53.4 1.0 CB C:GLU453 4.1 37.8 1.0 CB C:ASN449 4.1 40.4 1.0 N C:GLU453 4.1 45.0 1.0 CA C:GLU446 4.1 53.9 1.0 CB C:ASP459 4.1 45.8 1.0 CA C:CYS447 4.1 53.5 1.0 CG C:GLU456 4.2 53.5 1.0 OD1 C:ASP459 4.3 55.3 1.0 OE2 C:GLU453 4.3 46.3 1.0 N C:PHE451 4.4 42.6 1.0 CA C:PHE451 4.4 37.8 1.0 N C:ASN449 4.5 44.3 1.0 N C:GLY448 4.5 57.4 1.0 N C:ILE452 4.6 40.2 1.0 CB C:PHE451 4.7 34.9 1.0 CA C:GLU453 4.8 46.1 1.0 CA C:ILE452 4.8 41.4 1.0 C C:CYS447 4.8 58.6 1.0 CA C:ASN449 4.9 38.4 1.0 C C:ILE452 4.9 40.2 1.0 CB C:GLU446 4.9 55.8 1.0 C C:PRO445 4.9 45.3 1.0

Calcium binding site 6 out of 24 in the Crystal Structure of Human LGI1 Eptp-ADAM22 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human LGI1 Eptp-ADAM22 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca803 b:26.4 occ:1.00 OE2 C:GLU514 2.3 54.3 1.0 O C:ILE512 2.4 25.4 1.0 OD1 C:ASP511 2.4 35.2 1.0 OD2 C:ASP511 2.4 37.4 1.0 OD1 C:ASN526 2.4 42.0 1.0 O C:ILE527 2.4 44.3 1.0 CG C:GLU514 2.6 52.0 1.0 CG C:ASP511 2.7 36.0 1.0 CD C:GLU514 2.8 53.8 1.0 CG C:ASN526 3.5 34.8 1.0 C C:ILE512 3.6 42.4 1.0 C C:ILE527 3.6 35.8 1.0 N C:ILE527 3.8 27.0 1.0 N C:ILE512 4.0 36.9 1.0 OE1 C:GLU514 4.0 56.7 1.0 CB C:GLU514 4.2 38.2 1.0 CB C:ASP511 4.3 24.7 1.0 ND2 C:ASN526 4.3 32.7 1.0 CA C:ASN526 4.3 30.8 1.0 C C:ASN526 4.4 28.6 1.0 CA C:ILE527 4.4 31.3 1.0 CA C:ILE512 4.4 33.9 1.0 N C:GLU514 4.5 26.6 1.0 CB C:ASN526 4.5 33.9 1.0 C C:ARG513 4.5 36.0 1.0 N C:ARG513 4.5 44.2 1.0 CA C:ARG513 4.6 40.4 1.0 N C:HIS528 4.7 30.0 1.0 CD C:ARG504 4.7 26.0 1.0 C C:ASP511 4.9 40.5 1.0 CB C:ILE512 4.9 29.3 1.0 CA C:GLU514 4.9 26.6 1.0 O C:ARG504 4.9 36.0 1.0 O C:ARG513 5.0 42.1 1.0 CA C:ASP511 5.0 46.9 1.0

Calcium binding site 7 out of 24 in the Crystal Structure of Human LGI1 Eptp-ADAM22 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human LGI1 Eptp-ADAM22 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca801 b:28.6 occ:1.00 ND2 E:ASN436 2.3 30.1 1.0 OE2 E:GLU242 2.4 39.8 1.0 OD2 E:ASP325 2.4 17.1 1.0 OD1 E:ASP325 2.4 18.4 1.0 OD1 E:ASN436 2.4 45.9 1.0 O E:HOH935 2.4 26.4 1.0 O E:CYS433 2.4 19.4 1.0 CD E:GLU242 2.5 31.3 1.0 O E:HOH936 2.5 14.1 1.0 CG E:GLU242 2.5 23.2 1.0 CG E:ASN436 2.7 32.9 1.0 CG E:ASP325 2.7 18.9 1.0 OE1 E:GLU242 3.5 29.5 1.0 CB E:GLU242 3.6 22.4 1.0 C E:CYS433 3.7 20.9 1.0 CB E:ASN436 4.2 23.3 1.0 O E:TYR240 4.2 25.9 1.0 CB E:ASP325 4.2 25.7 1.0 O E:ASN436 4.3 30.4 1.0 N E:GLU242 4.4 15.7 1.0 CB E:CYS433 4.5 18.7 1.0 N E:LEU434 4.6 25.4 1.0 CA E:CYS433 4.6 18.6 1.0 CA E:GLU242 4.6 18.5 1.0 CA E:LEU434 4.7 29.2 1.0 N E:ASN436 4.8 29.8 1.0 CA E:ASN436 4.9 27.0 1.0 O E:HOH959 5.0 41.4 1.0

Calcium binding site 8 out of 24 in the Crystal Structure of Human LGI1 Eptp-ADAM22 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human LGI1 Eptp-ADAM22 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca802 b:41.5 occ:1.00 ND2 E:ASN449 2.3 48.0 1.0 OE2 E:GLU456 2.3 37.9 1.0 OE1 E:GLU456 2.3 37.0 1.0 O E:GLU446 2.3 45.8 1.0 OD2 E:ASP459 2.4 58.4 1.0 OE1 E:GLU453 2.4 49.0 1.0 OD1 E:ASN449 2.4 45.4 1.0 O E:PHE451 2.4 36.6 1.0 CD E:GLU456 2.6 40.9 1.0 C E:GLU446 2.6 46.0 1.0 CG E:ASN449 2.6 47.0 1.0 N E:CYS447 3.3 46.5 1.0 N E:GLU446 3.4 47.8 1.0 CD E:GLU453 3.4 45.4 1.0 CG E:ASP459 3.4 54.2 1.0 CA E:GLU446 3.5 47.5 1.0 CA E:CYS447 3.7 52.9 1.0 C E:PHE451 3.7 37.8 1.0 CG E:GLU453 4.0 40.4 1.0 CG E:GLU456 4.1 46.4 1.0 CB E:ASN449 4.1 50.4 1.0 CB E:ASP459 4.2 46.6 1.0 CB E:GLU453 4.3 39.9 1.0 N E:GLU453 4.3 38.3 1.0 OD1 E:ASP459 4.3 56.3 1.0 OE2 E:GLU453 4.4 48.5 1.0 N E:GLY448 4.4 53.4 1.0 CB E:GLU446 4.5 54.7 1.0 C E:CYS447 4.5 54.3 1.0 C E:PRO445 4.5 42.5 1.0 N E:ASN449 4.6 53.8 1.0 N E:PHE451 4.6 51.7 1.0 CA E:PHE451 4.6 42.3 1.0 N E:ILE452 4.7 36.9 1.0 CB E:CYS447 4.9 55.5 1.0 CB E:PHE451 4.9 40.0 1.0 CA E:ASN449 4.9 49.3 1.0 SG E:CYS477 4.9 51.7 1.0 CA E:GLU453 5.0 40.2 1.0 CA E:ILE452 5.0 37.8 1.0

Calcium binding site 9 out of 24 in the Crystal Structure of Human LGI1 Eptp-ADAM22 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Human LGI1 Eptp-ADAM22 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca803 b:32.5 occ:1.00 O E:HOH922 2.1 47.2 1.0 OD1 E:ASP511 2.4 36.5 1.0 OE2 E:GLU514 2.4 29.7 1.0 OD2 E:ASP511 2.4 24.6 1.0 O E:ILE527 2.4 31.1 1.0 OD1 E:ASN526 2.4 35.3 1.0 O E:ILE512 2.4 36.7 1.0 CG E:ASP511 2.7 37.4 1.0 O E:HOH906 2.9 56.1 1.0 C E:ILE512 3.5 35.2 1.0 C E:ILE527 3.5 25.0 1.0 CD E:GLU514 3.5 38.0 1.0 CG E:ASN526 3.6 26.6 1.0 N E:ILE512 3.7 30.9 1.0 O E:HOH952 3.8 29.0 1.0 N E:ILE527 3.8 28.2 1.0 CB E:ASP511 4.1 26.0 1.0 CA E:ILE512 4.1 32.0 1.0 CG E:GLU514 4.2 37.9 1.0 CA E:ILE527 4.3 26.6 1.0 C E:ASN526 4.3 25.9 1.0 ND2 E:ASN526 4.3 21.1 1.0 CA E:ASN526 4.4 29.2 1.0 OE1 E:GLU514 4.5 46.7 1.0 N E:HIS528 4.5 26.7 1.0 N E:ARG513 4.6 41.8 1.0 C E:ASP511 4.6 28.0 1.0 CB E:ASN526 4.6 30.6 1.0 CA E:HIS528 4.6 27.1 1.0 CA E:ASP511 4.6 27.1 1.0 CB E:ILE512 4.7 29.0 1.0 CB E:HIS528 4.8 28.5 1.0 CA E:ARG513 4.9 39.0 1.0 C E:ARG513 5.0 37.3 1.0 O E:HOH953 5.0 39.0 1.0

Calcium binding site 10 out of 24 in the Crystal Structure of Human LGI1 Eptp-ADAM22 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Human LGI1 Eptp-ADAM22 Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca801 b:26.4 occ:1.00 ND2 G:ASN436 2.3 35.1 1.0 OE2 G:GLU242 2.4 28.6 1.0 OD2 G:ASP325 2.4 20.4 1.0 OD1 G:ASP325 2.4 23.0 1.0 OD1 G:ASN436 2.4 37.5 1.0 O G:CYS433 2.4 25.1 1.0 CD G:GLU242 2.5 29.0 1.0 O G:HOH922 2.5 42.9 1.0 CG G:GLU242 2.6 23.6 1.0 CG G:ASN436 2.7 31.1 1.0 CG G:ASP325 2.7 20.6 1.0 OE1 G:GLU242 3.4 32.5 1.0 CB G:GLU242 3.6 21.1 1.0 C G:CYS433 3.7 20.7 1.0 CB G:ASN436 4.2 27.5 1.0 O G:TYR240 4.2 28.5 1.0 CB G:ASP325 4.2 27.4 1.0 O G:ASN436 4.2 37.1 1.0 N G:GLU242 4.4 18.2 1.0 CB G:CYS433 4.6 24.5 1.0 N G:LEU434 4.6 21.1 1.0 CA G:CYS433 4.6 24.4 1.0 CA G:LEU434 4.6 25.0 1.0 CA G:GLU242 4.7 19.1 1.0 N G:ASN436 4.8 34.3 1.0 CA G:ASN436 4.9 32.7 1.0 C G:ASN436 5.0 34.5 1.0

A.Yamagata, Y.Miyazaki, N.Yokoi, H.Shigematsu, Y.Sato, S.Goto-Ito, A.Maeda, T.Goto, M.Sanbo, M.Hirabayashi, M.Shirouzu, Y.Fukata, M.Fukata, S.Fukai. Structural Basis of Epilepsy-Related Ligand-Receptor Complex LGI1-ADAM22. Nat Commun V. 9 1546 2018.
ISSN: ESSN 2041-1723
PubMed: 29670100
DOI: 10.1038/S41467-018-03947-W