Calcium in PDB 5l73: Mam Domain of Human Neuropilin-1

The structure of Mam Domain of Human Neuropilin-1, PDB code: 5l73 was solved by T.Yelland, S.Djordjevic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.33 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.172, 59.558, 136.654, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.8

The binding sites of Calcium atom in the Mam Domain of Human Neuropilin-1 (pdb code 5l73). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Mam Domain of Human Neuropilin-1, PDB code: 5l73:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Mam Domain of Human Neuropilin-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mam Domain of Human Neuropilin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:9.7 occ:1.00 O A:ASN691 2.2 9.5 1.0 OE2 A:GLU651 2.2 12.7 1.0 O A:HOH1033 2.3 8.8 1.0 OD2 A:ASP685 2.4 10.7 1.0 OD2 A:ASP796 2.4 8.1 1.0 OD1 A:ASP796 2.5 8.0 1.0 O A:GLU651 2.5 9.0 1.0 CG A:ASP796 2.8 8.4 1.0 C A:ASN691 3.4 10.3 1.0 CG A:ASP685 3.4 11.8 1.0 CD A:GLU651 3.4 12.6 1.0 C A:GLU651 3.5 10.3 1.0 N A:ASN691 3.7 12.0 1.0 CA A:GLU651 3.9 11.0 1.0 CB A:GLU651 4.0 11.4 1.0 CB A:ASP685 4.0 12.2 1.0 CA A:ASN691 4.2 11.3 1.0 OE1 A:GLU651 4.2 13.8 1.0 O A:HOH1047 4.3 26.2 1.0 CG A:GLU651 4.3 12.0 1.0 CB A:ASP796 4.3 8.3 1.0 OD1 A:ASP685 4.3 11.8 1.0 O A:HOH1070 4.3 20.3 1.0 C A:GLY690 4.4 13.5 1.0 N A:PHE692 4.4 9.9 1.0 O A:HOH1035 4.6 24.2 1.0 CA A:GLY690 4.6 14.7 1.0 CA A:PHE692 4.6 9.4 1.0 N A:PHE652 4.7 9.8 1.0 O6 A:BCN903 4.7 14.8 1.0 O A:GLY653 4.8 12.0 1.0 N A:ASP797 4.8 10.8 1.0 CB A:ASN691 4.9 11.4 1.0 CB A:PHE692 4.9 9.6 1.0

Calcium binding site 2 out of 4 in the Mam Domain of Human Neuropilin-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mam Domain of Human Neuropilin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:11.1 occ:1.00 O22 A:BCN903 2.3 17.3 1.0 O A:HOH1035 2.3 24.2 1.0 O A:HOH1065 2.3 18.3 1.0 OD1 A:ASP685 2.4 11.8 1.0 O4 A:BCN903 2.4 22.3 1.0 O6 A:BCN903 2.4 14.8 1.0 N1 A:BCN903 2.7 17.0 1.0 C4 A:BCN903 3.2 20.0 1.0 C2 A:BCN903 3.2 18.3 1.0 C5 A:BCN903 3.4 16.0 1.0 C6 A:BCN903 3.4 15.3 1.0 C1 A:BCN903 3.4 17.5 1.0 CG A:ASP685 3.5 11.8 1.0 C3 A:BCN903 3.5 18.7 1.0 O A:HOH1047 4.0 26.2 1.0 OD2 A:ASP685 4.1 10.7 1.0 O21 A:BCN903 4.4 19.1 1.0 CB A:THR687 4.4 20.5 1.0 OD2 A:ASP796 4.4 8.1 1.0 CA A:ASP685 4.4 13.0 1.0 CB A:ASP685 4.5 12.2 1.0 N A:GLY688 4.6 23.2 1.0 C A:ASP685 4.7 14.0 1.0 N A:THR687 4.7 19.7 1.0 OE1 A:GLU651 4.8 13.8 1.0 OE2 B:GLU765 4.8 23.8 1.0 OG1 A:THR687 4.9 19.8 1.0 OE1 B:GLU765 4.9 25.2 1.0 CA A:THR687 5.0 20.6 1.0

Calcium binding site 3 out of 4 in the Mam Domain of Human Neuropilin-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mam Domain of Human Neuropilin-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:11.6 occ:1.00 OE2 B:GLU651 2.2 18.2 1.0 O B:ASN691 2.3 15.2 1.0 O B:HOH1014 2.3 15.2 1.0 OD2 B:ASP685 2.5 15.2 1.0 OD1 B:ASP796 2.5 14.2 1.0 O B:GLU651 2.5 13.5 1.0 OD2 B:ASP796 2.5 15.7 1.0 CG B:ASP796 2.8 14.6 1.0 CG B:ASP685 3.4 15.4 1.0 C B:ASN691 3.5 15.9 1.0 CD B:GLU651 3.5 18.9 1.0 C B:GLU651 3.5 15.2 1.0 CA B:GLU651 3.9 17.3 1.0 CB B:GLU651 4.0 17.5 1.0 CB B:ASP685 4.1 15.1 1.0 OD1 B:ASP685 4.2 15.0 1.0 N B:ASN691 4.2 17.2 1.0 CA B:ASN691 4.2 16.3 1.0 OE1 B:GLU651 4.3 20.6 1.0 CG B:GLU651 4.3 18.2 1.0 CB B:ASP796 4.4 14.2 1.0 CB B:ASN691 4.4 16.5 1.0 N B:PHE692 4.5 14.9 1.0 O B:HOH1019 4.5 14.5 1.0 O B:GLY688 4.6 21.0 1.0 CA B:PHE692 4.7 14.8 1.0 N B:PHE652 4.7 14.9 1.0 O6 B:BCN903 4.8 15.4 1.0 N B:ASP797 4.8 16.2 1.0 O B:GLY653 4.8 21.6 1.0 CA B:GLY688 4.9 21.0 1.0

Calcium binding site 4 out of 4 in the Mam Domain of Human Neuropilin-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mam Domain of Human Neuropilin-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:13.3 occ:1.00 O4 B:BCN903 2.1 18.3 1.0 O B:HOH1019 2.2 14.5 1.0 OD1 B:ASP685 2.2 15.0 1.0 OG1 B:THR687 2.3 17.6 1.0 O21 B:BCN903 2.4 15.0 1.0 O6 B:BCN903 2.4 15.4 1.0 N1 B:BCN903 2.7 15.8 1.0 C4 B:BCN903 3.2 16.5 1.0 C2 B:BCN903 3.3 15.6 1.0 CG B:ASP685 3.4 15.4 1.0 C3 B:BCN903 3.4 16.8 1.0 C6 B:BCN903 3.5 15.5 1.0 C1 B:BCN903 3.5 16.3 1.0 C5 B:BCN903 3.5 15.9 1.0 CB B:THR687 3.5 17.7 1.0 N B:THR687 3.9 17.8 1.0 CG2 B:THR687 4.0 17.4 1.0 OD2 B:ASP685 4.1 15.2 1.0 CA B:THR687 4.2 17.9 1.0 O B:HOH1017 4.2 33.0 1.0 N B:GLY688 4.3 20.6 1.0 CB B:ASP685 4.3 15.1 1.0 OD2 B:ASP796 4.3 15.7 1.0 CA B:ASP685 4.4 15.1 1.0 O22 B:BCN903 4.4 16.5 1.0 C B:THR687 4.6 20.3 1.0 OD2 B:ASP797 4.6 26.2 1.0 C B:ASP685 4.6 14.8 1.0 N B:HIS686 4.7 14.8 1.0 OE1 B:GLU651 4.8 20.6 1.0 OE2 B:GLU651 5.0 18.2 1.0

T.Yelland, S.Djordjevic. Crystal Structure of the Neuropilin-1 Mam Domain: Completing the Neuropilin-1 Ectodomain Picture. Structure V. 24 2008 2016.
ISSN: ISSN 0969-2126
PubMed: 27720589
DOI: 10.1016/J.STR.2016.08.017