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Calcium in PDB 5y31: Crystal Structure of Human LGI1-ADAM22 Complex

Protein crystallography data

The structure of Crystal Structure of Human LGI1-ADAM22 Complex, PDB code: 5y31 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) 48.99 / 7.13
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.143, 124.324, 164.663, 90.00, 104.80, 90.00
R / Rfree (%) 26.5 / 31.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human LGI1-ADAM22 Complex (pdb code 5y31). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Human LGI1-ADAM22 Complex, PDB code: 5y31:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5y31

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Calcium binding site 1 out of 8 in the Crystal Structure of Human LGI1-ADAM22 Complex


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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-ADAM22 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:0.0
occ:1.00
 ND2 A:ASN436 2.3 0.7 1.0
OD2 A:ASP325 2.3 0.7 1.0
OE2 A:GLU242 2.4 0.5 1.0
OD1 A:ASP325 2.4 0.7 1.0
OD1 A:ASN436 2.4 0.1 1.0
O A:CYS433 2.4 0.4 1.0
CD A:GLU242 2.5 0.8 1.0
CG A:GLU242 2.6 0.7 1.0
CG A:ASN436 2.6 0.1 1.0
CG A:ASP325 2.7 0.1 1.0
OE1 A:GLU242 3.5 0.2 1.0
CB A:GLU242 3.6 0.8 1.0
C A:CYS433 3.7 0.7 1.0
CB A:ASN436 4.2 0.6 1.0
O A:TYR240 4.2 0.9 1.0
CB A:ASP325 4.2 0.9 1.0
O A:ASN436 4.2 1.0 1.0
N A:GLU242 4.4 0.3 1.0
N A:LEU434 4.5 0.6 1.0
CA A:LEU434 4.5 0.7 1.0
CB A:CYS433 4.6 0.1 1.0
CA A:CYS433 4.6 0.9 1.0
CA A:GLU242 4.7 0.2 1.0
N A:ASN436 4.7 0.2 1.0
CA A:ASN436 4.9 0.1 1.0
C A:LEU434 5.0 0.9 1.0
N A:ASP325 5.0 0.3 1.0

Calcium binding site 2 out of 8 in 5y31

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Calcium binding site 2 out of 8 in the Crystal Structure of Human LGI1-ADAM22 Complex


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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-ADAM22 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:0.3
occ:1.01
 ND2 A:ASN449 2.3 0.2 1.0
OE1 A:GLU456 2.4 0.2 1.0
OD2 A:ASP459 2.4 0.8 1.0
OE1 A:GLU453 2.4 0.4 1.0
O A:GLU446 2.4 0.1 1.0
OD1 A:ASN449 2.4 0.8 1.0
OE2 A:GLU456 2.4 0.7 1.0
O A:PHE451 2.4 0.1 1.0
CG A:ASN449 2.6 0.1 1.0
CD A:GLU456 2.7 0.4 1.0
C A:GLU446 3.2 0.2 1.0
CD A:GLU453 3.4 0.3 1.0
CG A:ASP459 3.5 0.5 1.0
C A:PHE451 3.6 0.0 1.0
N A:GLU446 3.8 0.9 1.0
CG A:GLU453 3.9 0.9 1.0
N A:CYS447 4.0 0.0 1.0
CA A:GLU446 4.1 0.1 1.0
N A:GLU453 4.1 0.5 1.0
CB A:GLU453 4.1 0.5 1.0
CB A:ASN449 4.1 0.8 1.0
CB A:ASP459 4.2 0.7 1.0
CG A:GLU456 4.2 0.3 1.0
CA A:CYS447 4.2 0.1 1.0
N A:PHE451 4.4 0.8 1.0
OE2 A:GLU453 4.4 0.8 1.0
OD1 A:ASP459 4.4 0.0 1.0
CA A:PHE451 4.4 0.6 1.0
N A:ILE452 4.6 0.1 1.0
N A:ASN449 4.6 0.8 1.0
N A:GLY448 4.7 0.5 1.0
CB A:PHE451 4.7 0.8 1.0
CA A:GLU453 4.8 0.4 1.0
CA A:ILE452 4.8 0.7 1.0
CB A:GLU446 4.8 0.1 1.0
C A:PRO445 4.8 0.2 1.0
C A:ILE452 4.9 0.6 1.0
CA A:ASN449 4.9 0.8 1.0
C A:CYS447 4.9 0.6 1.0

Calcium binding site 3 out of 8 in 5y31

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Calcium binding site 3 out of 8 in the Crystal Structure of Human LGI1-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-ADAM22 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:0.8
occ:1.00
 OD1 A:ASP511 2.4 0.2 1.0
OE2 A:GLU514 2.4 0.5 1.0
OD2 A:ASP511 2.4 0.9 1.0
O A:ILE512 2.4 0.1 1.0
OD1 A:ASN526 2.4 0.3 1.0
O A:ILE527 2.4 0.1 1.0
CG A:ASP511 2.6 0.2 1.0
CD A:GLU514 3.4 0.5 1.0
C A:ILE512 3.5 0.8 1.0
CG A:ASN526 3.5 1.0 1.0
C A:ILE527 3.6 0.2 1.0
N A:ILE512 3.7 0.1 1.0
N A:ILE527 3.9 0.6 1.0
CG A:GLU514 4.0 0.4 1.0
CB A:ASP511 4.1 0.2 1.0
CA A:ILE512 4.1 0.6 1.0
ND2 A:ASN526 4.2 0.9 1.0
CA A:ILE527 4.4 0.3 1.0
OE1 A:GLU514 4.4 0.6 1.0
C A:ASN526 4.5 0.9 1.0
N A:ARG513 4.5 0.2 1.0
N A:HIS528 4.5 1.0 1.0
CA A:ASN526 4.5 0.5 1.0
C A:ASP511 4.6 0.8 1.0
CA A:ASP511 4.6 1.0 1.0
CB A:ASN526 4.6 0.2 1.0
CA A:HIS528 4.7 0.8 1.0
CB A:ILE512 4.7 0.8 1.0
CA A:ARG513 4.8 0.6 1.0
CB A:HIS528 4.9 0.6 1.0
C A:ARG513 4.9 0.1 1.0

Calcium binding site 4 out of 8 in 5y31

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Calcium binding site 4 out of 8 in the Crystal Structure of Human LGI1-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-ADAM22 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:0.4
occ:1.00
 OD2 B:ASP334 2.4 0.1 1.0
OD1 B:ASP381 2.4 0.2 1.0
OE1 B:GLU336 2.4 0.5 1.0
OD2 B:ASP381 2.4 0.5 1.0
OD1 B:ASP334 2.4 0.4 1.0
O B:VAL382 2.4 0.2 1.0
CG B:ASP334 2.6 0.4 1.0
CG B:ASP381 2.6 0.8 1.0
CD B:GLU336 3.5 0.4 1.0
C B:VAL382 3.5 0.1 1.0
N B:VAL382 3.6 0.7 1.0
CB B:ASP334 3.9 0.9 1.0
CB B:ASP381 4.0 0.8 1.0
OE2 B:GLU336 4.0 0.2 1.0
CA B:VAL382 4.2 0.5 1.0
CA B:ASP381 4.4 0.4 1.0
C B:ASP381 4.4 0.3 1.0
OE1 B:GLU383 4.6 0.3 1.0
CG B:GLU336 4.6 0.5 1.0
N B:GLU383 4.6 1.0 1.0
CB B:VAL382 4.9 0.2 1.0
CA B:GLU383 5.0 0.6 1.0
CB B:GLU336 5.0 0.1 1.0

Calcium binding site 5 out of 8 in 5y31

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Calcium binding site 5 out of 8 in the Crystal Structure of Human LGI1-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-ADAM22 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca801

b:0.1
occ:1.00
 ND2 C:ASN436 2.3 0.3 1.0
OD2 C:ASP325 2.3 0.4 1.0
OE2 C:GLU242 2.4 0.2 1.0
OD1 C:ASP325 2.4 0.3 1.0
OD1 C:ASN436 2.4 1.0 1.0
O C:CYS433 2.4 0.8 1.0
CG C:GLU242 2.6 0.3 1.0
CD C:GLU242 2.6 0.5 1.0
CG C:ASN436 2.7 0.9 1.0
CG C:ASP325 2.7 0.7 1.0
OE1 C:GLU242 3.6 0.8 1.0
CB C:GLU242 3.6 0.7 1.0
C C:CYS433 3.7 0.1 1.0
CB C:ASN436 4.2 0.3 1.0
O C:TYR240 4.2 0.3 1.0
CB C:ASP325 4.2 0.5 1.0
O C:ASN436 4.3 0.2 1.0
N C:GLU242 4.4 0.4 1.0
N C:LEU434 4.5 0.8 1.0
CB C:CYS433 4.6 0.4 1.0
CA C:LEU434 4.6 0.7 1.0
CA C:CYS433 4.6 0.4 1.0
CA C:GLU242 4.7 1.0 1.0
N C:ASN436 4.8 0.3 1.0
CA C:ASN436 4.9 0.6 1.0

Calcium binding site 6 out of 8 in 5y31

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Calcium binding site 6 out of 8 in the Crystal Structure of Human LGI1-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-ADAM22 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca802

b:0.5
occ:1.01
 ND2 C:ASN449 2.3 0.4 1.0
OE1 C:GLU456 2.4 0.2 1.0
O C:GLU446 2.4 0.9 1.0
OE1 C:GLU453 2.4 0.8 1.0
OD2 C:ASP459 2.4 0.7 1.0
OD1 C:ASN449 2.4 0.3 1.0
O C:PHE451 2.4 0.9 1.0
OE2 C:GLU456 2.4 0.8 1.0
CG C:ASN449 2.6 0.4 1.0
CD C:GLU456 2.7 0.3 1.0
C C:GLU446 3.3 0.6 1.0
CD C:GLU453 3.4 0.7 1.0
CG C:ASP459 3.5 0.2 1.0
C C:PHE451 3.6 0.1 1.0
N C:GLU446 3.8 0.7 1.0
CG C:GLU453 3.9 0.2 1.0
N C:CYS447 4.0 0.1 1.0
CA C:GLU446 4.1 0.9 1.0
CB C:GLU453 4.1 0.5 1.0
N C:GLU453 4.1 0.5 1.0
CB C:ASN449 4.1 0.4 1.0
CA C:CYS447 4.2 0.8 1.0
CG C:GLU456 4.2 0.1 1.0
CB C:ASP459 4.2 0.2 1.0
N C:PHE451 4.4 0.7 1.0
OE2 C:GLU453 4.4 0.7 1.0
OD1 C:ASP459 4.4 0.2 1.0
CA C:PHE451 4.4 0.5 1.0
N C:ILE452 4.6 0.8 1.0
N C:ASN449 4.7 0.9 1.0
CB C:PHE451 4.7 0.0 1.0
N C:GLY448 4.7 0.6 1.0
CA C:GLU453 4.8 0.1 1.0
CA C:ILE452 4.8 0.1 1.0
CB C:GLU446 4.8 0.8 1.0
C C:PRO445 4.9 0.4 1.0
C C:ILE452 4.9 0.1 1.0
CA C:ASN449 5.0 0.6 1.0
C C:CYS447 5.0 0.3 1.0

Calcium binding site 7 out of 8 in 5y31

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Calcium binding site 7 out of 8 in the Crystal Structure of Human LGI1-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-ADAM22 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca803

b:0.3
occ:1.00
 OD1 C:ASP511 2.4 0.6 1.0
OE2 C:GLU514 2.4 0.7 1.0
OD2 C:ASP511 2.4 0.4 1.0
O C:ILE512 2.4 0.5 1.0
OD1 C:ASN526 2.4 0.0 1.0
O C:ILE527 2.4 0.1 1.0
CG C:ASP511 2.6 0.8 1.0
CD C:GLU514 3.4 0.5 1.0
C C:ILE512 3.5 0.6 1.0
CG C:ASN526 3.5 0.9 1.0
C C:ILE527 3.5 0.0 1.0
N C:ILE512 3.7 0.9 1.0
N C:ILE527 3.9 0.4 1.0
CG C:GLU514 4.0 0.1 1.0
CB C:ASP511 4.1 0.9 1.0
CA C:ILE512 4.1 0.6 1.0
ND2 C:ASN526 4.3 0.9 1.0
CA C:ILE527 4.4 0.2 1.0
OE1 C:GLU514 4.4 0.5 1.0
C C:ASN526 4.5 0.4 1.0
N C:HIS528 4.5 0.7 1.0
N C:ARG513 4.5 0.9 1.0
CA C:ASN526 4.5 0.8 1.0
C C:ASP511 4.6 0.3 1.0
CA C:ASP511 4.6 0.1 1.0
CA C:HIS528 4.6 0.5 1.0
CB C:ASN526 4.6 0.5 1.0
CB C:ILE512 4.7 1.0 1.0
CA C:ARG513 4.8 0.2 1.0
CB C:HIS528 4.8 0.7 1.0
C C:ARG513 4.9 0.2 1.0

Calcium binding site 8 out of 8 in 5y31

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Calcium binding site 8 out of 8 in the Crystal Structure of Human LGI1-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-ADAM22 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:0.2
occ:1.00
 OE1 D:GLU336 2.4 0.4 1.0
OD2 D:ASP334 2.4 0.0 1.0
OD1 D:ASP381 2.4 0.8 1.0
OD2 D:ASP381 2.4 0.9 1.0
OD1 D:ASP334 2.4 0.5 1.0
O D:VAL382 2.4 0.5 1.0
CG D:ASP334 2.5 0.7 1.0
CG D:ASP381 2.6 0.3 1.0
CD D:GLU336 3.5 0.8 1.0
C D:VAL382 3.5 0.4 1.0
N D:VAL382 3.6 0.9 1.0
CB D:ASP334 3.9 0.8 1.0
OE2 D:GLU336 4.0 0.5 1.0
CB D:ASP381 4.0 0.4 1.0
CA D:VAL382 4.2 0.9 1.0
CA D:ASP381 4.4 1.0 1.0
C D:ASP381 4.4 0.3 1.0
OE1 D:GLU383 4.5 0.8 1.0
CG D:GLU336 4.6 0.5 1.0
N D:GLU383 4.6 0.1 1.0
CB D:VAL382 4.9 1.0 1.0
CA D:GLU383 4.9 0.7 1.0
O D:ILE335 5.0 0.3 1.0
CB D:GLU336 5.0 0.1 1.0

Reference:

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
Page generated: Mon Jul 15 15:16:13 2024

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