Calcium in PDB 4gz8: Mouse Semaphorin 3A, Domains Sema-Psi-Ig

The structure of Mouse Semaphorin 3A, Domains Sema-Psi-Ig, PDB code: 4gz8 was solved by B.J.C.Janssen, T.Malinauskas, C.Siebold, E.Y.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.00 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.630, 126.170, 161.480, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 26.5

The binding sites of Calcium atom in the Mouse Semaphorin 3A, Domains Sema-Psi-Ig (pdb code 4gz8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Mouse Semaphorin 3A, Domains Sema-Psi-Ig, PDB code: 4gz8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Mouse Semaphorin 3A, Domains Sema-Psi-Ig


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mouse Semaphorin 3A, Domains Sema-Psi-Ig within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca807 b:28.4 occ:1.00 OD1 A:ASP310 2.4 35.9 1.0 OD2 A:ASP310 2.5 30.9 1.0 NE2 A:GLN433 2.6 28.2 1.0 CG A:ASP310 2.8 32.8 1.0 CD A:GLN433 3.3 28.6 1.0 OE1 A:GLN433 3.5 31.7 1.0 O A:MET492 4.1 41.3 1.0 CB A:ASP310 4.3 32.5 1.0 O A:ILE434 4.6 30.9 1.0 O A:VAL311 4.6 37.8 1.0 CG A:GLN433 4.6 28.2 1.0 N A:MET492 4.7 36.0 1.0 OE1 A:GLU493 4.7 61.2 1.0 CB A:GLN433 4.9 27.5 1.0

Calcium binding site 2 out of 5 in the Mouse Semaphorin 3A, Domains Sema-Psi-Ig


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mouse Semaphorin 3A, Domains Sema-Psi-Ig within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca808 b:42.9 occ:1.00 OE2 A:GLU122 2.4 41.7 1.0 OE1 A:GLU122 2.5 45.3 1.0 CD A:GLU122 2.8 43.1 1.0 CG A:GLU122 4.3 42.7 1.0 O A:PHE60 4.5 40.0 1.0 CD1 A:LEU61 4.5 34.2 1.0 O A:SER179 4.6 38.4 1.0 O A:LEU121 4.8 37.5 1.0

Calcium binding site 3 out of 5 in the Mouse Semaphorin 3A, Domains Sema-Psi-Ig


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mouse Semaphorin 3A, Domains Sema-Psi-Ig within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca809 b:68.3 occ:1.00 O A:SER54 2.9 33.9 1.0 OH A:TYR57 3.2 31.6 1.0 O A:LEU51 3.4 39.3 1.0 CE1 A:TYR57 3.8 31.6 1.0 C A:SER54 3.8 35.3 1.0 O A:ASN49 3.9 48.9 1.0 O A:THR506 3.9 30.3 1.0 CZ A:TYR57 4.0 31.3 1.0 O A:ALA507 4.1 30.1 1.0 CA A:SER55 4.2 37.0 1.0 N A:SER55 4.4 35.9 1.0 C A:LEU51 4.4 43.8 1.0 CB A:SER55 4.6 39.6 1.0 C A:GLY50 4.6 53.4 1.0 O A:GLY50 4.6 57.0 1.0 C A:ALA507 4.7 29.2 1.0 CA A:GLY50 4.8 55.0 1.0 CA A:ALA507 4.9 30.8 1.0 CA A:SER54 4.9 35.9 1.0 N A:SER54 4.9 37.9 1.0 N A:LEU51 5.0 49.2 1.0

Calcium binding site 4 out of 5 in the Mouse Semaphorin 3A, Domains Sema-Psi-Ig


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mouse Semaphorin 3A, Domains Sema-Psi-Ig within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:30.2 occ:1.00 OE1 B:GLN433 2.3 49.1 1.0 OD2 B:ASP310 2.5 30.7 1.0 OD1 B:ASP310 2.5 29.7 1.0 CG B:ASP310 2.8 31.2 1.0 CD B:GLN433 3.3 44.4 1.0 NE2 B:GLN433 3.7 43.7 1.0 O B:MET492 4.0 36.4 1.0 CB B:ASP310 4.4 31.7 1.0 N B:MET492 4.5 37.7 1.0 CG B:GLN433 4.6 40.8 1.0 O B:ILE434 4.6 33.0 1.0 OE1 B:GLU493 4.6 66.7 1.0 O B:VAL311 4.8 40.7 1.0 CB B:GLN433 4.8 38.6 1.0

Calcium binding site 5 out of 5 in the Mouse Semaphorin 3A, Domains Sema-Psi-Ig


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mouse Semaphorin 3A, Domains Sema-Psi-Ig within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:49.8 occ:1.00 OE1 B:GLU122 2.6 38.8 1.0 OE2 B:GLU122 2.6 40.2 1.0 CD B:GLU122 3.0 37.4 1.0 O B:SER179 4.3 38.7 1.0 CG B:GLU122 4.5 35.5 1.0 CD1 B:LEU61 4.8 30.4 1.0 O B:PHE60 4.9 31.7 1.0

B.J.C.Janssen, T.Malinauskas, G.A.Weir, M.Z.Cader, C.Siebold, E.Y.Jones. Neuropilins Lock Secreted Semaphorins Onto Plexins in A Ternary Signaling Complex. Nat.Struct.Mol.Biol. V. 19 1293 2012.
ISSN: ISSN 1545-9993
PubMed: 23104057
DOI: 10.1038/NSMB.2416