Calcium in PDB 5i2l: Structure of Ef-Hand Containing Protein

The structure of Structure of Ef-Hand Containing Protein, PDB code: 5i2l was solved by K.R.Park, M.S.Kwon, J.Y.An, J.G.Lee, H.S.Youn, Y.Lee, J.Y.Kang, T.G.Kim, J.J.Lim, J.S.Park, S.H.Lee, W.K.Song, H.Cheong, C.Jun, S.H.Eom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.75 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.325, 50.670, 53.381, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 20.7

The binding sites of Calcium atom in the Structure of Ef-Hand Containing Protein (pdb code 5i2l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Ef-Hand Containing Protein, PDB code: 5i2l:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Ef-Hand Containing Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Ef-Hand Containing Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:16.5 occ:1.00 O A:HOH387 2.5 18.8 1.0 O A:HOH332 2.5 21.3 1.0 OD1 A:ASP109 2.5 14.6 1.0 O A:PHE111 2.5 12.6 1.0 OD1 A:ASP105 2.6 20.9 1.0 OE1 A:GLU116 2.6 15.5 1.0 OE2 A:GLU116 2.7 16.2 1.0 CD A:GLU116 3.0 16.9 1.0 CG A:ASP109 3.4 20.4 1.0 CG A:ASP105 3.5 19.1 1.0 C A:PHE111 3.6 20.2 1.0 OD2 A:ASP109 3.7 19.6 1.0 N A:GLY107 4.2 28.9 1.0 OD2 A:ASP105 4.2 18.9 1.0 N A:PHE111 4.2 14.4 1.0 CA A:ASP105 4.3 14.9 1.0 CB A:ASP105 4.3 14.5 1.0 O A:HOH359 4.3 29.9 1.0 CA A:PHE111 4.4 11.7 1.0 CA A:GLY107 4.4 21.7 1.0 CA A:ILE112 4.5 5.5 1.0 N A:ASP109 4.5 18.5 1.0 N A:ILE112 4.5 10.8 1.0 CG A:GLU116 4.5 13.6 1.0 C A:ASP105 4.5 18.2 1.0 CB A:PHE111 4.6 15.9 1.0 OD2 A:ASP113 4.6 23.3 1.0 CB A:ASP109 4.6 23.9 1.0 N A:ASP113 4.6 9.9 1.0 N A:ARG108 4.7 19.8 1.0 N A:ALA106 4.7 22.7 1.0 C A:GLY107 4.8 25.6 1.0 O A:HOH389 4.8 40.6 1.0 CG A:ASP113 4.9 21.5 1.0 O A:ASP105 5.0 21.3 1.0 CA A:ASP109 5.0 23.3 1.0

Calcium binding site 2 out of 2 in the Structure of Ef-Hand Containing Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Ef-Hand Containing Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:14.7 occ:1.00 OD1 A:ASP143 2.6 15.8 1.0 OD1 A:ASP145 2.6 13.4 1.0 OD1 A:ASP141 2.6 13.0 1.0 O A:HOH319 2.6 20.2 1.0 OE1 A:GLU152 2.6 15.0 1.0 O A:LYS147 2.6 9.8 1.0 OE2 A:GLU152 2.7 12.8 1.0 CD A:GLU152 3.0 18.0 1.0 CG A:ASP145 3.4 17.3 1.0 CG A:ASP143 3.6 24.7 1.0 CG A:ASP141 3.7 13.1 1.0 C A:LYS147 3.7 16.7 1.0 OD2 A:ASP145 3.7 16.2 1.0 OD2 A:ASP143 4.0 19.5 1.0 N A:ASP145 4.3 12.1 1.0 N A:LYS147 4.3 13.8 1.0 CA A:ASP141 4.4 14.7 1.0 N A:ASP143 4.4 15.4 1.0 CG A:GLU152 4.4 8.9 1.0 CA A:LEU148 4.4 11.1 1.0 OD2 A:ASP141 4.4 16.6 1.0 N A:SER149 4.4 10.9 1.0 O A:HOH326 4.5 27.1 1.0 CB A:ASP141 4.5 8.9 1.0 N A:LEU148 4.5 11.4 1.0 CB A:ASP145 4.6 17.4 1.0 N A:PHE144 4.6 13.0 1.0 C A:ASP141 4.7 16.6 1.0 CA A:LYS147 4.7 11.5 1.0 C A:ASP143 4.7 13.2 1.0 CB A:ASP143 4.8 17.1 1.0 CA A:ASP145 4.8 13.5 1.0 CA A:ASP143 4.8 14.4 1.0 N A:GLU142 4.8 14.8 1.0 N A:SER146 4.8 13.0 1.0 CG A:LYS147 4.8 11.8 1.0 C A:LEU148 4.9 9.1 1.0 O A:HOH312 5.0 21.5 1.0 C A:ASP145 5.0 15.9 1.0

K.R.Park, M.S.Kwon, J.Y.An, J.G.Lee, H.S.Youn, Y.Lee, J.Y.Kang, T.G.Kim, J.J.Lim, J.S.Park, S.H.Lee, W.K.Song, H.K.Cheong, C.D.Jun, S.H.Eom. Structural Implications of Ca(2+)-Dependent Actin-Bundling Function of Human EFHD2/Swiprosin-1. Sci Rep V. 6 39095 2016.
ISSN: ESSN 2045-2322
PubMed: 27974828
DOI: 10.1038/SREP39095