Calcium in PDB 7m0r: Cryo-Em Structure of the SEMA3A/PLEXINA4/Neuropilin 1 Complex

The binding sites of Calcium atom in the Cryo-Em Structure of the SEMA3A/PLEXINA4/Neuropilin 1 Complex (pdb code 7m0r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of the SEMA3A/PLEXINA4/Neuropilin 1 Complex, PDB code: 7m0r:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of the SEMA3A/PLEXINA4/Neuropilin 1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of the SEMA3A/PLEXINA4/Neuropilin 1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca601 b:124.6 occ:1.00 O E:THR129 2.3 121.2 1.0 OD2 E:ASP85 2.3 117.0 1.0 OD1 E:ASP126 2.3 122.1 1.0 OE1 E:GLU78 2.4 119.7 1.0 OD2 E:ASP126 2.4 122.1 1.0 CG E:ASP126 2.7 122.1 1.0 C E:GLU128 3.3 122.3 1.0 C E:THR129 3.4 121.2 1.0 CG E:ASP85 3.4 117.0 1.0 CD E:GLU78 3.4 119.7 1.0 O E:GLU128 3.4 122.3 1.0 N E:THR129 3.5 121.2 1.0 CB E:GLU128 3.7 122.3 1.0 OD1 E:ASP85 3.8 117.0 1.0 CA E:GLU128 3.9 122.3 1.0 CA E:THR129 4.0 121.2 1.0 OG1 E:THR129 4.0 121.2 1.0 OE2 E:GLU78 4.1 119.7 1.0 CB E:ASP126 4.1 122.1 1.0 N E:GLU128 4.2 122.3 1.0 CB E:GLU78 4.2 119.7 1.0 NZ B:LYS343 4.2 118.3 1.0 CG E:GLU78 4.3 119.7 1.0 CB E:TYR84 4.4 119.8 1.0 N E:HIS130 4.5 122.3 1.0 CG E:GLU128 4.6 122.3 1.0 CB E:THR129 4.6 121.2 1.0 CB E:ASP85 4.7 117.0 1.0 CA E:HIS130 4.9 122.3 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of the SEMA3A/PLEXINA4/Neuropilin 1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of the SEMA3A/PLEXINA4/Neuropilin 1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca602 b:171.5 occ:1.00 O E:ILE253 2.1 154.9 1.0 OD1 E:ASP250 2.2 162.1 1.0 OD2 E:ASP209 2.3 168.6 1.0 OD1 E:ASP209 2.4 168.6 1.0 OE1 E:GLU195 2.4 162.2 1.0 OG1 E:THR249 2.4 172.8 1.0 CG E:ASP209 2.6 168.6 1.0 C E:ILE253 3.3 154.9 1.0 CG E:ASP250 3.4 162.1 1.0 N E:ASP250 3.5 162.1 1.0 CD E:GLU195 3.6 162.2 1.0 CB E:THR249 3.7 172.8 1.0 CE1 E:TYR167 3.8 172.6 1.0 O E:ASP250 4.0 162.1 1.0 OH E:TYR167 4.1 172.6 1.0 CB E:GLU195 4.1 162.2 1.0 CB E:ASP209 4.1 168.6 1.0 C E:THR249 4.2 172.8 1.0 CA E:THR249 4.2 172.8 1.0 N E:ALA254 4.2 167.8 1.0 CA E:ASP250 4.2 162.1 1.0 OD2 E:ASP250 4.2 162.1 1.0 N E:ILE253 4.2 154.9 1.0 CA E:ILE253 4.3 154.9 1.0 C E:ASP250 4.3 162.1 1.0 CA E:ALA254 4.3 167.8 1.0 CB E:ASP250 4.4 162.1 1.0 CZ E:TYR167 4.4 172.6 1.0 OE2 E:GLU195 4.5 162.2 1.0 CG E:GLU195 4.5 162.2 1.0 C E:ALA252 4.6 153.4 1.0 CB E:ILE253 4.7 154.9 1.0 CB E:ASN169 4.7 168.4 1.0 O E:ALA252 4.8 153.4 1.0 CD1 E:TYR167 4.8 172.6 1.0 CB E:ALA254 4.8 167.8 1.0 CG2 E:THR249 4.8 172.8 1.0 O E:TYR208 5.0 157.0 1.0 CG2 E:ILE253 5.0 154.9 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of the SEMA3A/PLEXINA4/Neuropilin 1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of the SEMA3A/PLEXINA4/Neuropilin 1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca601 b:125.6 occ:1.00 O F:THR129 2.3 121.1 1.0 OD2 F:ASP85 2.3 116.6 1.0 OD1 F:ASP126 2.3 121.7 1.0 OE1 F:GLU78 2.4 119.6 1.0 OD2 F:ASP126 2.4 121.7 1.0 CG F:ASP126 2.7 121.7 1.0 C F:GLU128 3.3 123.1 1.0 C F:THR129 3.4 121.1 1.0 CG F:ASP85 3.4 116.6 1.0 CD F:GLU78 3.4 119.6 1.0 O F:GLU128 3.4 123.1 1.0 N F:THR129 3.5 121.1 1.0 CB F:GLU128 3.7 123.1 1.0 OD1 F:ASP85 3.8 116.6 1.0 CA F:GLU128 3.9 123.1 1.0 CA F:THR129 4.0 121.1 1.0 OG1 F:THR129 4.0 121.1 1.0 OE2 F:GLU78 4.1 119.6 1.0 CB F:ASP126 4.1 121.7 1.0 N F:GLU128 4.2 123.1 1.0 CB F:GLU78 4.2 119.6 1.0 NZ A:LYS343 4.3 117.3 1.0 CG F:GLU78 4.3 119.6 1.0 CB F:TYR84 4.4 119.9 1.0 N F:HIS130 4.5 123.0 1.0 CG F:GLU128 4.6 123.1 1.0 CB F:THR129 4.6 121.1 1.0 CB F:ASP85 4.7 116.6 1.0 CA F:HIS130 4.9 123.0 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of the SEMA3A/PLEXINA4/Neuropilin 1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of the SEMA3A/PLEXINA4/Neuropilin 1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca602 b:175.2 occ:1.00 O F:ILE253 2.1 160.3 1.0 OD1 F:ASP250 2.2 167.7 1.0 OD2 F:ASP209 2.3 172.7 1.0 OD1 F:ASP209 2.4 172.7 1.0 OE1 F:GLU195 2.4 166.2 1.0 OG1 F:THR249 2.4 176.7 1.0 CG F:ASP209 2.6 172.7 1.0 C F:ILE253 3.3 160.3 1.0 CG F:ASP250 3.4 167.7 1.0 N F:ASP250 3.5 167.7 1.0 CD F:GLU195 3.6 166.2 1.0 CB F:THR249 3.7 176.7 1.0 CE1 F:TYR167 3.8 176.5 1.0 O F:ASP250 4.0 167.7 1.0 OH F:TYR167 4.1 176.5 1.0 CB F:GLU195 4.1 166.2 1.0 CB F:ASP209 4.1 172.7 1.0 C F:THR249 4.2 176.7 1.0 CA F:THR249 4.2 176.7 1.0 N F:ALA254 4.2 172.2 1.0 CA F:ASP250 4.2 167.7 1.0 OD2 F:ASP250 4.2 167.7 1.0 N F:ILE253 4.2 160.3 1.0 CA F:ILE253 4.3 160.3 1.0 C F:ASP250 4.3 167.7 1.0 CA F:ALA254 4.3 172.2 1.0 CB F:ASP250 4.4 167.7 1.0 CZ F:TYR167 4.4 176.5 1.0 OE2 F:GLU195 4.5 166.2 1.0 CG F:GLU195 4.5 166.2 1.0 C F:ALA252 4.6 159.0 1.0 CB F:ILE253 4.7 160.3 1.0 CB F:ASN169 4.7 172.3 1.0 O F:ALA252 4.8 159.0 1.0 CD1 F:TYR167 4.8 176.5 1.0 CB F:ALA254 4.8 172.2 1.0 CG2 F:THR249 4.8 176.7 1.0 O F:TYR208 5.0 161.5 1.0 CG2 F:ILE253 5.0 160.3 1.0

D.Lu, G.Shang, X.He, X.Bai, X.Zhang. Architecture of the SEMA3A/PLEXINA4/Neuropilin Tripartite Complex Nat Commun 2021.
ISSN: ESSN 2041-1723