Calcium in PDB 3d34: Structure of the F-Spondin Domain of Mindin

The structure of Structure of the F-Spondin Domain of Mindin, PDB code: 3d34 was solved by Y.Li, R.A.Mariuzza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.600, 68.027, 110.130, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.5

The structure of Structure of the F-Spondin Domain of Mindin also contains other interesting chemical elements:

Nickel

(Ni)

6 atoms

The binding sites of Calcium atom in the Structure of the F-Spondin Domain of Mindin (pdb code 3d34). 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 the F-Spondin Domain of Mindin, PDB code: 3d34:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of the F-Spondin Domain of Mindin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the F-Spondin Domain of Mindin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca228 b:12.1 occ:1.00 O A:ASP166 2.3 14.0 1.0 OD2 A:ASP162 2.4 14.0 1.0 OD1 A:ASP162 2.5 12.8 1.0 O A:HOH318 2.5 14.6 1.0 O A:HOH319 2.5 14.0 1.0 OD1 A:ASP134 2.6 11.0 1.0 O A:HOH242 2.6 9.3 1.0 OD2 A:ASP134 2.6 11.6 1.0 CG A:ASP162 2.8 13.8 1.0 CG A:ASP134 2.9 13.2 1.0 C A:ASP166 3.5 13.5 1.0 N A:ASP166 4.1 12.1 1.0 NE1 A:TRP135 4.2 13.1 1.0 N A:GLY164 4.2 12.4 1.0 CB A:ASP162 4.3 12.6 1.0 N A:SER167 4.3 13.5 1.0 CA A:SER167 4.3 13.4 1.0 CA A:ASP166 4.4 12.8 1.0 CA A:GLY164 4.4 13.6 1.0 O A:HOH328 4.4 32.1 1.0 CB A:ASP134 4.5 12.0 1.0 N A:THR165 4.6 11.5 1.0 CD1 A:TRP135 4.6 13.0 1.0 OG1 A:THR178 4.6 17.4 1.0 O A:HOH272 4.8 22.4 1.0 C A:GLY164 4.8 14.3 1.0 O A:HOH290 4.9 22.2 1.0 O A:HOH262 4.9 22.8 1.0 N A:ALA163 4.9 12.3 1.0 CA A:ASP162 5.0 13.2 1.0 C A:SER167 5.0 13.5 1.0 CB A:ASP166 5.0 13.0 1.0 O A:GLY168 5.0 14.1 1.0

Calcium binding site 2 out of 2 in the Structure of the F-Spondin Domain of Mindin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the F-Spondin Domain of Mindin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca226 b:13.7 occ:1.00 O B:ASP166 2.4 15.7 1.0 OD2 B:ASP162 2.4 15.2 1.0 O B:HOH364 2.5 14.6 1.0 OD1 B:ASP162 2.5 14.4 1.0 OD2 B:ASP134 2.5 12.8 1.0 OD1 B:ASP134 2.5 11.8 1.0 O B:HOH361 2.5 13.9 1.0 O B:HOH431 2.6 16.4 1.0 CG B:ASP162 2.8 13.9 1.0 CG B:ASP134 2.8 14.1 1.0 C B:ASP166 3.5 17.3 1.0 NE1 B:TRP135 4.0 11.2 1.0 N B:ASP166 4.1 17.7 1.0 N B:GLY164 4.2 15.6 1.0 CB B:ASP162 4.2 14.2 1.0 CB B:ASP134 4.4 12.2 1.0 CA B:ASP166 4.4 17.4 1.0 CA B:GLY164 4.4 15.7 1.0 N B:SER167 4.4 17.1 1.0 CA B:SER167 4.5 17.8 1.0 CD1 B:TRP135 4.5 11.1 1.0 N B:THR165 4.6 17.2 1.0 O B:HOH366 4.6 16.5 1.0 O B:HOH436 4.6 28.4 1.0 OG1 B:THR178 4.7 21.4 1.0 C B:GLY164 4.8 17.8 1.0 CA B:ASP162 4.9 12.1 1.0 N B:ALA163 5.0 12.8 1.0 O B:GLY168 5.0 17.2 1.0 CB B:ASP166 5.0 17.7 1.0

Y.Li, C.Cao, W.Jia, L.Yu, M.Mo, Q.Wang, Y.Huang, J.M.Lim, M.Ishihara, L.Wells, P.Azadi, H.Robinson, Y.W.He, L.Zhang, R.A.Mariuzza. Structure of the F-Spondin Domain of Mindin, An Integrin Ligand and Pattern Recognition Molecule. Embo J. V. 28 286 2009.
ISSN: ISSN 0261-4189
PubMed: 19153605
DOI: 10.1038/EMBOJ.2008.288