Calcium in PDB 4gz9: Mouse Neuropilin-1, Extracellular Domains 1-4 (A1A2B1B2)

The structure of Mouse Neuropilin-1, Extracellular Domains 1-4 (A1A2B1B2), PDB code: 4gz9 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)	81.00 / 2.70
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	245.359, 245.359, 47.930, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 22.3

The binding sites of Calcium atom in the Mouse Neuropilin-1, Extracellular Domains 1-4 (A1A2B1B2) (pdb code 4gz9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Mouse Neuropilin-1, Extracellular Domains 1-4 (A1A2B1B2), PDB code: 4gz9:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Mouse Neuropilin-1, Extracellular Domains 1-4 (A1A2B1B2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mouse Neuropilin-1, Extracellular Domains 1-4 (A1A2B1B2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:73.6 occ:1.00 O A:ILE253 2.2 77.4 1.0 O A:ALA252 2.2 78.0 1.0 OD2 A:ASP209 2.3 70.8 1.0 OD1 A:ASP250 2.3 72.4 1.0 OE1 A:GLU195 2.4 75.7 1.0 O A:HOH728 2.4 71.9 1.0 OD1 A:ASP209 2.6 71.0 1.0 CG A:ASP209 2.7 71.0 1.0 C A:ILE253 3.3 80.5 1.0 C A:ALA252 3.4 80.2 1.0 CG A:ASP250 3.6 72.1 1.0 CD A:GLU195 3.6 78.2 1.0 O A:ASP250 3.9 71.1 1.0 N A:ASP250 4.0 65.8 1.0 CA A:ILE253 4.1 83.7 1.0 N A:ILE253 4.2 83.9 1.0 CB A:ASP209 4.2 68.4 1.0 CB A:GLU195 4.2 76.7 1.0 OD2 A:ASP250 4.3 74.6 1.0 OE2 A:GLU195 4.4 81.6 1.0 C A:ASP250 4.4 71.3 1.0 N A:ALA254 4.4 83.0 1.0 OD1 A:ASN169 4.5 77.7 1.0 CB A:ILE253 4.5 84.2 1.0 N A:ALA252 4.5 78.7 1.0 CG A:GLU195 4.5 78.4 1.0 CA A:ASP250 4.5 68.4 1.0 CA A:ALA252 4.6 81.6 1.0 CB A:ASP250 4.6 69.8 1.0 CA A:ALA254 4.7 80.6 1.0 OH A:TYR167 4.7 70.1 1.0 CE1 A:TYR167 4.7 70.4 1.0 CB A:THR249 4.8 63.5 1.0 C A:THR249 4.9 64.2 1.0 N A:ASP209 4.9 72.2 1.0

Calcium binding site 2 out of 2 in the Mouse Neuropilin-1, Extracellular Domains 1-4 (A1A2B1B2)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mouse Neuropilin-1, Extracellular Domains 1-4 (A1A2B1B2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:0.2 occ:1.00 O A:THR129 2.3 0.1 1.0 OD2 A:ASP85 2.3 99.3 1.0 O A:HOH729 2.3 98.3 1.0 OD1 A:ASP126 2.4 0.5 1.0 O A:GLU128 2.4 0.6 1.0 OE1 A:GLU78 2.4 0.0 1.0 C A:GLU128 3.0 0.2 1.0 CG A:ASP85 3.1 98.0 1.0 OD1 A:ASP85 3.2 99.5 1.0 C A:THR129 3.3 0.5 1.0 N A:THR129 3.5 0.3 1.0 CG A:ASP126 3.6 0.2 1.0 CD A:GLU78 3.6 0.9 1.0 CA A:THR129 3.8 0.0 1.0 N A:GLU128 4.0 0.0 1.0 CA A:GLU128 4.0 0.1 1.0 O A:ASP126 4.2 0.3 1.0 OD2 A:ASP126 4.2 0.4 1.0 ND1 A:HIS130 4.4 92.9 1.0 C A:ASP126 4.4 0.6 1.0 N A:ASP126 4.4 99.0 1.0 OE2 A:GLU78 4.5 0.4 1.0 N A:HIS130 4.5 95.8 1.0 CB A:THR129 4.5 0.1 1.0 CG A:GLU78 4.5 0.2 1.0 OH A:TYR48 4.5 82.3 1.0 CB A:ASP85 4.5 95.7 1.0 CE1 A:TYR48 4.6 80.8 1.0 CE1 A:HIS130 4.6 96.5 1.0 CB A:GLU78 4.7 0.2 1.0 CB A:GLU128 4.7 0.9 1.0 C A:TYR127 4.7 0.4 1.0 CB A:ASP126 4.7 1.0 1.0 CA A:ASP126 4.7 0.3 1.0 CA A:HIS130 4.9 91.3 1.0 N A: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