Calcium in PDB 4gza: Complex of Mouse Plexin A2 - Semaphorin 3A - Neuropilin-1

The structure of Complex of Mouse Plexin A2 - Semaphorin 3A - Neuropilin-1, PDB code: 4gza 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)	125.51 / 7.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	191.632, 293.604, 252.176, 90.00, 106.38, 90.00
R / Rfree (%)	28.5 / 28.5

The binding sites of Calcium atom in the Complex of Mouse Plexin A2 - Semaphorin 3A - Neuropilin-1 (pdb code 4gza). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Complex of Mouse Plexin A2 - Semaphorin 3A - Neuropilin-1, PDB code: 4gza:

Calcium binding site 1 out of 1 in the Complex of Mouse Plexin A2 - Semaphorin 3A - Neuropilin-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Mouse Plexin A2 - Semaphorin 3A - Neuropilin-1 within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca601 b:0.5 occ:1.00 O H:THR129 2.3 0.5 1.0 OD2 H:ASP85 2.3 0.5 1.0 OD1 H:ASP126 2.4 0.5 1.0 O H:GLU128 2.4 0.5 1.0 OE1 H:GLU78 2.4 0.5 1.0 C H:GLU128 3.0 0.5 1.0 CG H:ASP85 3.1 0.5 1.0 OD1 H:ASP85 3.2 0.5 1.0 C H:THR129 3.3 0.5 1.0 N H:THR129 3.5 0.5 1.0 CG H:ASP126 3.6 0.5 1.0 CD H:GLU78 3.6 0.5 1.0 CA H:THR129 3.8 0.5 1.0 N H:GLU128 4.0 0.5 1.0 CA H:GLU128 4.0 0.5 1.0 O H:ASP126 4.2 0.5 1.0 OD2 H:ASP126 4.2 0.5 1.0 ND1 H:HIS130 4.4 0.5 1.0 C H:ASP126 4.4 0.5 1.0 N H:ASP126 4.4 0.5 1.0 OE2 H:GLU78 4.5 0.5 1.0 N H:HIS130 4.5 0.5 1.0 CB H:THR129 4.5 0.5 1.0 CG H:GLU78 4.5 0.5 1.0 OH H:TYR48 4.5 0.5 1.0 CB H:ASP85 4.5 0.5 1.0 CE1 H:TYR48 4.6 0.5 1.0 CE1 H:HIS130 4.6 0.5 1.0 CB H:GLU78 4.7 0.5 1.0 CB H:GLU128 4.7 0.5 1.0 C H:TYR127 4.7 0.5 1.0 CB H:ASP126 4.7 0.5 1.0 CA H:ASP126 4.7 0.5 1.0 CA H:HIS130 4.9 0.5 1.0 N H:TYR127 5.0 0.5 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