Calcium in PDB 3i9g: Crystal Structure of the LT1009 (Sonepcizumab) Antibody Fab Fragment in Complex with Sphingosine-1-Phosphate

The structure of Crystal Structure of the LT1009 (Sonepcizumab) Antibody Fab Fragment in Complex with Sphingosine-1-Phosphate, PDB code: 3i9g was solved by T.Huxford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.052, 70.889, 138.719, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 21.9

The structure of Crystal Structure of the LT1009 (Sonepcizumab) Antibody Fab Fragment in Complex with Sphingosine-1-Phosphate also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Crystal Structure of the LT1009 (Sonepcizumab) Antibody Fab Fragment in Complex with Sphingosine-1-Phosphate (pdb code 3i9g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the LT1009 (Sonepcizumab) Antibody Fab Fragment in Complex with Sphingosine-1-Phosphate, PDB code: 3i9g:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the LT1009 (Sonepcizumab) Antibody Fab Fragment in Complex with Sphingosine-1-Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the LT1009 (Sonepcizumab) Antibody Fab Fragment in Complex with Sphingosine-1-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca301 b:30.1 occ:1.00 OD1 L:ASP30 2.1 15.2 1.0 O L:HOH501 2.2 20.0 1.0 OD1 L:ASP32 2.2 15.5 1.0 OD1 L:ASP31 2.2 21.4 1.0 O25 L:S1P401 2.3 20.2 1.0 O L:HOH504 2.3 23.5 1.0 CG L:ASP32 3.1 15.1 1.0 O23 L:S1P401 3.2 19.2 1.0 P22 L:S1P401 3.3 20.9 1.0 CG L:ASP30 3.3 15.6 1.0 CG L:ASP31 3.4 22.0 1.0 OD2 L:ASP32 3.5 16.2 1.0 CA L:CA302 3.8 31.4 1.0 OD2 L:ASP30 3.9 17.5 1.0 O L:HOH633 3.9 23.2 1.0 OD2 L:ASP31 3.9 22.7 1.0 N L:ASP31 4.1 18.3 1.0 N2 L:S1P401 4.2 20.1 1.0 OE2 L:GLU50 4.2 18.9 1.0 N L:ASP32 4.2 17.6 1.0 O1 L:S1P401 4.2 18.3 1.0 C1 L:S1P401 4.2 17.8 1.0 C L:ASP31 4.3 18.0 1.0 CB L:ASP32 4.4 15.1 1.0 CB L:ASP30 4.4 17.5 1.0 O24 L:S1P401 4.4 18.8 1.0 CA L:ASP31 4.5 18.4 1.0 CA L:ASP32 4.5 15.5 1.0 CB L:ASP31 4.5 18.8 1.0 C2 L:S1P401 4.8 19.5 1.0 CD L:GLU50 4.8 18.3 1.0 O L:ILE29 4.8 17.1 1.0 O L:ASP31 4.9 18.5 1.0 O L:HOH503 5.0 17.7 1.0 O L:HOH506 5.0 35.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the LT1009 (Sonepcizumab) Antibody Fab Fragment in Complex with Sphingosine-1-Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the LT1009 (Sonepcizumab) Antibody Fab Fragment in Complex with Sphingosine-1-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca302 b:31.4 occ:1.00 OD2 L:ASP32 2.1 16.2 1.0 OD2 L:ASP92 2.2 17.8 1.0 OD2 L:ASP30 2.2 17.5 1.0 O L:HOH502 2.2 17.3 1.0 O25 L:S1P401 2.2 20.2 1.0 O L:HOH503 2.3 17.7 1.0 CG L:ASP30 3.1 15.6 1.0 CG L:ASP32 3.2 15.1 1.0 OD1 L:ASP30 3.2 15.2 1.0 CG L:ASP92 3.3 17.3 1.0 P22 L:S1P401 3.4 20.9 1.0 O24 L:S1P401 3.5 18.8 1.0 OD1 L:ASP32 3.7 15.5 1.0 CB L:ASP92 3.8 18.1 1.0 CA L:CA301 3.8 30.1 1.0 N2 L:S1P401 3.8 20.1 1.0 CA L:ASP92 3.9 19.6 1.0 O1 L:S1P401 4.0 18.3 1.0 O L:ILE29 4.1 17.1 1.0 O L:ASP92 4.2 20.6 1.0 OD1 L:ASP92 4.4 16.4 1.0 CB L:ASP32 4.4 15.1 1.0 CB L:ASP30 4.5 17.5 1.0 C L:ASP92 4.5 19.5 1.0 C L:ILE29 4.6 17.9 1.0 O23 L:S1P401 4.7 19.2 1.0 C1 L:S1P401 4.9 17.8 1.0 C2 L:S1P401 4.9 19.5 1.0

J.M.Wojciak, N.Zhu, K.T.Schuerenberg, K.Moreno, W.S.Shestowsky, M.Hiraiwa, R.Sabbadini, T.Huxford. The Crystal Structure of Sphingosine-1-Phosphate in Complex with A Fab Fragment Reveals Metal Bridging of An Antibody and Its Antigen. Proc.Natl.Acad.Sci.Usa V. 106 17717 2009.
ISSN: ISSN 0027-8424
PubMed: 19815502
DOI: 10.1073/PNAS.0906153106