Calcium in PDB 9mym: Fertilization IZUMO1 Protein Ectodomain

The structure of Fertilization IZUMO1 Protein Ectodomain, PDB code: 9mym was solved by S.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.58 / 1.84
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	103.454, 103.454, 139.297, 90, 90, 90
R / Rfree (%)	17 / 19.1

The structure of Fertilization IZUMO1 Protein Ectodomain also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Fertilization IZUMO1 Protein Ectodomain (pdb code 9mym). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Fertilization IZUMO1 Protein Ectodomain, PDB code: 9mym:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Fertilization IZUMO1 Protein Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fertilization IZUMO1 Protein Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1508 b:33.1 occ:0.50 O A:HOH1878 2.4 27.6 0.5 O A:HOH1760 2.4 42.4 0.5 O A:HOH1718 2.4 34.4 1.0 O A:HOH1808 2.5 29.8 1.0 OD1 A:ASN81 3.2 42.0 0.7 O A:HOH1688 4.1 31.5 1.0 CG A:ASN81 4.3 35.4 0.7 O A:HOH1703 4.6 55.4 1.0 O A:HOH1637 4.8 30.5 1.0 CB A:GLU80 4.8 23.3 1.0 OE1 A:GLU84 4.9 33.2 1.0 O A:HOH1771 4.9 28.0 1.0 ND2 A:ASN81 5.0 38.4 0.7

Calcium binding site 2 out of 2 in the Fertilization IZUMO1 Protein Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fertilization IZUMO1 Protein Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1509 b:96.0 occ:0.49 O A:HOH1641 2.0 34.0 0.2 OE1 A:GLU105 2.5 33.0 1.0 O A:HOH1796 2.6 37.8 0.2 OE2 A:GLU105 2.9 46.6 1.0 CD A:GLU105 3.0 41.9 1.0 CG A:GLU105 4.3 33.2 1.0 O A:HOH1612 4.3 35.3 1.0 CB A:GLU105 4.4 23.5 1.0

Y.Lu, M.Ikawa, S.Tang. Allosteric Inhibition of the IZUMO1-Juno Fertilization Complex By the Naturally Occurring Antisperm Antibody OBF13. Proc.Natl.Acad.Sci.Usa V. 122 52122 2025.
ISSN: ESSN 1091-6490
PubMed: 40042902
DOI: 10.1073/PNAS.2425952122