Calcium in PDB 5f6t: Structure of Calexcitin-GD3+ Complex.

The structure of Structure of Calexcitin-GD3+ Complex., PDB code: 5f6t was solved by L.Chataigner, J.Guo, P.T.Erskine, A.R.Coker, S.P.Wood, J.B.Cooper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.35 / 2.20
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	77.020, 77.020, 29.260, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 30.4

The structure of Structure of Calexcitin-GD3+ Complex. also contains other interesting chemical elements:

Gadolinium

(Gd)

1 atom

The binding sites of Calcium atom in the Structure of Calexcitin-GD3+ Complex. (pdb code 5f6t). 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 Calexcitin-GD3+ Complex., PDB code: 5f6t:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Calexcitin-GD3+ Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Calexcitin-GD3+ Complex. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:52.2 occ:1.00 OE1 A:GLU85 2.3 70.1 1.0 OD1 A:ASN76 2.4 58.7 1.0 OD1 A:ASP74 2.4 46.5 1.0 O A:GLN80 2.4 59.9 1.0 OE2 A:GLU85 2.4 70.9 1.0 OD1 A:ASP78 2.4 56.1 1.0 CD A:GLU85 2.7 65.9 1.0 CG A:ASP78 3.2 63.7 1.0 CG A:ASN76 3.3 57.6 1.0 OD2 A:ASP78 3.4 67.0 1.0 ND2 A:ASN76 3.6 56.5 1.0 CG A:ASP74 3.6 49.5 1.0 C A:GLN80 3.6 65.8 1.0 CG A:GLU85 4.2 57.0 1.0 CA A:ASP74 4.3 50.5 1.0 CA A:VAL81 4.4 63.9 1.0 N A:ASN76 4.4 53.5 1.0 OD2 A:ASP74 4.4 49.4 1.0 N A:VAL81 4.4 67.8 1.0 CB A:ASP78 4.5 55.9 1.0 N A:GLU75 4.5 57.3 1.0 CB A:ASP74 4.5 48.4 1.0 N A:ASP78 4.6 63.2 1.0 CB A:ASN76 4.7 62.8 1.0 N A:THR82 4.7 62.8 1.0 C A:ASP74 4.7 58.3 1.0 N A:GLN80 4.7 59.5 1.0 CA A:GLN80 4.7 60.7 1.0 CG A:GLN80 4.8 60.1 1.0 CG2 A:THR82 4.8 69.2 1.0 CA A:ASN76 5.0 56.9 1.0

Calcium binding site 2 out of 2 in the Structure of Calexcitin-GD3+ Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Calexcitin-GD3+ Complex. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:64.0 occ:1.00 O A:ILE125 2.2 59.5 1.0 OD1 A:ASP123 2.3 85.6 1.0 OE2 A:GLU130 2.3 60.3 1.0 OD1 A:ASP119 2.4 65.8 1.0 OG A:SER121 2.4 62.5 1.0 OE1 A:GLU130 2.5 71.8 1.0 CD A:GLU130 2.7 76.0 1.0 CG A:ASP123 3.3 83.4 1.0 C A:ILE125 3.3 59.7 1.0 CB A:SER121 3.4 63.3 1.0 OD2 A:ASP123 3.5 85.0 1.0 CG A:ASP119 3.6 61.3 1.0 OD2 A:ASP127 3.7 67.2 1.0 N A:ILE125 4.1 59.4 1.0 CA A:ILE126 4.2 59.6 1.0 N A:ILE126 4.2 59.6 1.0 CA A:ILE125 4.2 60.3 1.0 CG A:GLU130 4.2 61.2 1.0 N A:ASP127 4.3 63.8 1.0 CA A:ASP119 4.3 54.8 1.0 N A:SER121 4.3 70.8 1.0 CA A:SER121 4.4 61.7 1.0 CB A:ASP119 4.4 54.3 1.0 N A:ASP123 4.4 60.8 1.0 OD2 A:ASP119 4.5 55.4 1.0 N A:GLY122 4.6 63.4 1.0 CG A:ASP127 4.6 68.0 1.0 CB A:ASP123 4.6 77.9 1.0 CB A:ILE125 4.6 66.9 1.0 C A:ASP119 4.8 55.2 1.0 C A:ILE126 4.8 62.1 1.0 C A:SER121 4.9 68.8 1.0 CA A:ASP123 4.9 62.1 1.0 N A:ASN124 5.0 64.7 1.0

L.Chataigner, J.Guo, P.T.Erskine, A.R.Coker, S.P.Wood, Z.Gombos, J.B.Cooper. Binding of Gd(3+) to the Neuronal Signalling Protein Calexcitin Identifies An Exchangeable Ca(2+)-Binding Site. Acta Crystallogr.,Sect.F V. 72 276 2016.
ISSN: ESSN 2053-230X
PubMed: 27050260
DOI: 10.1107/S2053230X16003526