Atomistry » Calcium » PDB 5xu9-5yhr » 5y31
Atomistry »
  Calcium »
    PDB 5xu9-5yhr »
      5y31 »

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

Go back to Calcium Binding Sites List in 5y31
Calcium binding site 1 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 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

Go back to Calcium Binding Sites List in 5y31
Calcium binding site 2 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 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

Go back to Calcium Binding Sites List in 5y31
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

Go back to Calcium Binding Sites List in 5y31
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

Go back to Calcium Binding Sites List in 5y31
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

Go back to Calcium Binding Sites List in 5y31
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

Go back to Calcium Binding Sites List in 5y31
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

Go back to Calcium Binding Sites List in 5y31
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy