Calcium in PDB 6pw7: X-Ray Crystal Structure of C. Elegans Stim Ef-Sam Domain

The structure of X-Ray Crystal Structure of C. Elegans Stim Ef-Sam Domain, PDB code: 6pw7 was solved by M.Enomoto, T.Nishikawa, S.I.Back, N.Ishiyama, L.Zheng, P.B.Stathopulos, M.Ikura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.80 / 1.89
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	111.543, 111.580, 70.704, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.6

The binding sites of Calcium atom in the X-Ray Crystal Structure of C. Elegans Stim Ef-Sam Domain (pdb code 6pw7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the X-Ray Crystal Structure of C. Elegans Stim Ef-Sam Domain, PDB code: 6pw7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the X-Ray Crystal Structure of C. Elegans Stim Ef-Sam Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Crystal Structure of C. Elegans Stim Ef-Sam Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:15.6 occ:1.00 O A:SER61 2.3 14.2 1.0 OD1 A:ASP55 2.3 17.0 1.0 OD1 A:ASP57 2.4 18.1 1.0 OE1 A:GLU66 2.4 15.4 1.0 O A:HOH347 2.4 20.6 1.0 OE2 A:GLU66 2.5 19.0 1.0 OG A:SER59 2.5 14.6 1.0 CD A:GLU66 2.8 19.4 1.0 CG A:ASP57 3.3 20.8 1.0 CG A:ASP55 3.5 18.8 1.0 C A:SER61 3.6 16.1 1.0 CB A:SER59 3.6 20.4 1.0 OD2 A:ASP57 3.7 22.7 1.0 N A:SER59 3.9 17.9 1.0 OD2 A:ASP55 4.2 20.7 1.0 CG A:GLU66 4.3 14.3 1.0 CA A:SER59 4.3 17.8 1.0 N A:SER61 4.3 15.0 1.0 N A:ASP57 4.3 23.7 1.0 CA A:ASP55 4.4 18.4 1.0 CA A:ILE62 4.4 12.9 1.0 OD2 A:ASP63 4.4 20.0 1.0 N A:ILE62 4.4 13.4 1.0 CB A:ASP55 4.5 16.8 1.0 C A:ASP55 4.5 21.4 1.0 CA A:SER61 4.5 15.4 1.0 CB A:ASP57 4.6 21.1 1.0 N A:ASP63 4.6 16.3 1.0 N A:HIS58 4.7 20.8 1.0 N A:ASP56 4.7 19.3 1.0 O B:HOH447 4.7 28.9 1.0 CA A:ASP57 4.8 18.4 1.0 O B:HOH327 4.8 26.0 1.0 N A:GLY60 4.8 18.2 1.0 C A:ASP57 4.9 20.0 1.0 C A:SER59 4.9 20.9 1.0 O B:HOH306 4.9 34.9 1.0 O A:HOH380 4.9 21.4 1.0 C A:ILE62 5.0 15.7 1.0 O A:ASP55 5.0 23.0 1.0

Calcium binding site 2 out of 2 in the X-Ray Crystal Structure of C. Elegans Stim Ef-Sam Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Crystal Structure of C. Elegans Stim Ef-Sam Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:15.8 occ:1.00 O B:SER61 2.3 15.2 1.0 OD1 B:ASP55 2.3 18.2 1.0 O B:HOH342 2.4 21.4 1.0 OD1 B:ASP57 2.4 22.6 1.0 OG B:SER59 2.5 16.5 1.0 OE1 B:GLU66 2.5 15.1 1.0 OE2 B:GLU66 2.5 20.6 1.0 CD B:GLU66 2.8 19.4 1.0 CG B:ASP57 3.4 22.4 1.0 C B:SER61 3.5 16.1 1.0 CG B:ASP55 3.5 19.9 1.0 CB B:SER59 3.6 19.1 1.0 OD2 B:ASP57 3.8 19.7 1.0 N B:SER59 4.0 17.7 1.0 OD2 B:ASP55 4.2 18.2 1.0 N B:SER61 4.3 16.8 1.0 CA B:SER59 4.3 17.6 1.0 CA B:ILE62 4.3 14.1 1.0 CG B:GLU66 4.4 17.3 1.0 N B:ILE62 4.4 14.2 1.0 OD2 B:ASP63 4.4 17.9 1.0 CA B:ASP55 4.4 18.8 1.0 N B:ASP57 4.4 22.4 1.0 CA B:SER61 4.5 16.0 1.0 CB B:ASP55 4.5 14.0 1.0 N B:ASP63 4.6 13.0 1.0 CB B:ASP57 4.6 22.9 1.0 C B:ASP55 4.6 21.7 1.0 N B:HIS58 4.7 20.9 1.0 N B:GLY60 4.8 19.6 1.0 C B:SER59 4.8 19.1 1.0 N B:ASP56 4.8 21.2 1.0 CA B:ASP57 4.8 20.9 1.0 C B:ASP57 4.9 22.6 1.0 C B:ILE62 4.9 13.9 1.0

M.Enomoto, T.Nishikawa, S.I.Back, N.Ishiyama, L.Zheng, P.B.Stathopulos, M.Ikura. Coordination of A Single Calcium Ion in the Ef-Hand Maintains the Off State of the Stromal Interaction Molecule Luminal Domain. J.Mol.Biol. 2019.
ISSN: ESSN 1089-8638
PubMed: 31626806
DOI: 10.1016/J.JMB.2019.10.003